[bug#58261] [PATCH 00/11] Add rdkit.

[bug#58261] [PATCH 00/11] Add rdkit.

[David Elsing]

Hello!

This patch series adds rdkit and its new dependencies.

Most optional components are enabled, except for the additional wrappers,
the "StructChecker" and the "compressed MolSuppliers".
All bundled software in External/ is unbundled and the included pickled data
(only used for a few tests) is removed.

freesasa is built as a shared library and the flex and bison files are generated.

For yaehmop-tightbind, I removed the transpiled Fortran->C files and built the
Fortran parts with GFortran instead.

gemmi included a patched version of sajson where numbers are kept as the
original strings, so I made a package variant and added a check for
sajson::TYPE_INTEGER in gemmi.
sajson also requires another small patch
(gnu/packages/patches/sajson-parse_flags-linking.patch) which I took from the
unmerged upstream pull request
https://github.com/chadaustin/sajson/pull/54/files, is that ok?

The packages were reproducible after two rounds (when setting the environment
variables as in python-build-system for rdkit), but I only built them on
x86_64 as emulation would take quite long.

David Elsing (11):
  gnu: Add fast-float.
  gnu: Add pocketfft.
  gnu: Add sajson.
  gnu: Add tinydir.
  gnu: Add optionparser.
  gnu: Add gemmi.
  gnu: Add freesasa.
  gnu: Add maeparser.
  gnu: Add coordgenlibs.
  gnu: Add yaehmop-tightbind.
  gnu: Add rdkit.

 gnu/packages/chemistry.scm                    | 531 ++++++++++++++++++
 gnu/packages/cpp.scm                          | 201 +++++++
 .../patches/gemmi-fix-sajson-types.patch      |  11 +
 .../rdkit-cmake-external-dependencies.patch   | 102 ++++
 .../sajson-for-gemmi-numbers-as-strings.patch | 195 +++++++
 .../patches/sajson-parse_flags-linking.patch  |  45 ++
 6 files changed, 1085 insertions(+)
 create mode 100644 gnu/packages/patches/gemmi-fix-sajson-types.patch
 create mode 100644 gnu/packages/patches/rdkit-cmake-external-dependencies.patch
 create mode 100644 gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch
 create mode 100644 gnu/packages/patches/sajson-parse_flags-linking.patch

-- 
2.37.0

[bug#58261] [PATCH 01/11] gnu: Add fast-float.

[David Elsing]

* gnu/packages/cpp.scm (fast-float): New variable.
---
 gnu/packages/cpp.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index d03e0bc7e1..e597dba40c 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -29,6 +29,7 @@
 ;;; Copyright © 2022 muradm <mail@muradm.net>
 ;;; Copyright © 2022 Attila Lendvai <attila@lendvai.name>
 ;;; Copyright © 2022 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2022 David Elsing <david.elsing@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1907,3 +1908,26 @@ (define-public cpp-mustache
 templated string type for compatibility with any STL-like string (std::string,
 std::wstring, etc).")
     (license license:boost1.0)))
+
+(define-public fast-float
+  (package
+    (name "fast-float")
+    (version "3.5.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/fastfloat/fast_float")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0z3rxxd0pwvw70dbnv63rm67biw829vdqf50y16isxm6g3sbrz8g"))))
+    (build-system cmake-build-system)
+    (arguments
+     ;; Tests require downloading a lot of additional data
+     (list #:tests? #f))
+    (home-page "https://github.com/fastfloat/fast_float")
+    (synopsis "Fast and exact implementation of the C++ from_chars functions")
+    (description "@code{fast_float} is a header-only C++ library which provides fast
+implementations of the from_chars functions for float and double types.")
+    (license (list license:asl2.0 license:expat)))) ; dual licensed
-- 
2.37.0

[bug#58261] [PATCH 01/11] gnu: Add fast-float.

[Liliana Marie Prikler via Guix-patches via]

Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
> * gnu/packages/cpp.scm (fast-float): New variable.
> ---
>  gnu/packages/cpp.scm | 24 ++++++++++++++++++++++++
>  1 file changed, 24 insertions(+)
> 
> diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
> index d03e0bc7e1..e597dba40c 100644
> --- a/gnu/packages/cpp.scm
> +++ b/gnu/packages/cpp.scm
> @@ -29,6 +29,7 @@
>  ;;; Copyright © 2022 muradm <mail@muradm.net>
>  ;;; Copyright © 2022 Attila Lendvai <attila@lendvai.name>
>  ;;; Copyright © 2022 Arun Isaac <arunisaac@systemreboot.net>
> +;;; Copyright © 2022 David Elsing <david.elsing@posteo.net>
>  ;;;
>  ;;; This file is part of GNU Guix.
>  ;;;
> @@ -1907,3 +1908,26 @@ (define-public cpp-mustache
>  templated string type for compatibility with any STL-like string
> (std::string,
>  std::wstring, etc).")
>      (license license:boost1.0)))
> +
> +(define-public fast-float
> +  (package
> +    (name "fast-float")
> +    (version "3.5.1")
> +    (source (origin
> +              (method git-fetch)
> +              (uri (git-reference
> +                    (url "https://github.com/fastfloat/fast_float")
> +                    (commit (string-append "v" version))))
> +              (file-name (git-file-name name version))
> +              (sha256
> +               (base32
> +               
> "0z3rxxd0pwvw70dbnv63rm67biw829vdqf50y16isxm6g3sbrz8g"))))
> +    (build-system cmake-build-system)
> +    (arguments
> +     ;; Tests require downloading a lot of additional data
> +     (list #:tests? #f))
I'm not quite sure how much you mean by "a lot" – it seems to be one
repo [1], but more importantly, you could try to disable the tests that
require external fetches.
> +    (home-page "https://github.com/fastfloat/fast_float")
> +    (synopsis "Fast and exact implementation of the C++ from_chars
> functions")
I'd call this a "Floating point number parser" or if you prefer the
verb form "Parse floating point numbers".
> +    (description "@code{fast_float} is a header-only C++ library
> which provides fast
> +implementations of the from_chars functions for float and double
> types.")
"@code{fast_float} is a header-only C++ library for parsing floating
point numbers from strings."  If you want to mention its speed, add
"Benchmarks show that it is several times faster than strtod."
> +    (license (list license:asl2.0 license:expat)))) ; dual licensed
Weird choice, but okay.

Cheers

[bug#58261] [PATCH 01/11] gnu: Add fast-float.

[David Elsing]

Liliana Marie Prikler <liliana.prikler@tugraz.at> writes:

> Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
>> * gnu/packages/cpp.scm (fast-float): New variable.
>> ---
>>  gnu/packages/cpp.scm | 24 ++++++++++++++++++++++++
>>  1 file changed, 24 insertions(+)
>> 
>> diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
>> index d03e0bc7e1..e597dba40c 100644
>> --- a/gnu/packages/cpp.scm
>> +++ b/gnu/packages/cpp.scm
>> @@ -29,6 +29,7 @@
>>  ;;; Copyright © 2022 muradm <mail@muradm.net>
>>  ;;; Copyright © 2022 Attila Lendvai <attila@lendvai.name>
>>  ;;; Copyright © 2022 Arun Isaac <arunisaac@systemreboot.net>
>> +;;; Copyright © 2022 David Elsing <david.elsing@posteo.net>
>>  ;;;
>>  ;;; This file is part of GNU Guix.
>>  ;;;
>> @@ -1907,3 +1908,26 @@ (define-public cpp-mustache
>>  templated string type for compatibility with any STL-like string
>> (std::string,
>>  std::wstring, etc).")
>>      (license license:boost1.0)))
>> +
>> +(define-public fast-float
>> +  (package
>> +    (name "fast-float")
>> +    (version "3.5.1")
>> +    (source (origin
>> +              (method git-fetch)
>> +              (uri (git-reference
>> +                    (url "https://github.com/fastfloat/fast_float")
>> +                    (commit (string-append "v" version))))
>> +              (file-name (git-file-name name version))
>> +              (sha256
>> +               (base32
>> +               
>> "0z3rxxd0pwvw70dbnv63rm67biw829vdqf50y16isxm6g3sbrz8g"))))
>> +    (build-system cmake-build-system)
>> +    (arguments
>> +     ;; Tests require downloading a lot of additional data
>> +     (list #:tests? #f))
> I'm not quite sure how much you mean by "a lot" – it seems to be one
> repo [1], but more importantly, you could try to disable the tests that
> require external fetches.
It's 262 MiB, so not too much. Oh sorry, I didn't notice that it was
just one test, but now I included the test data anyway.
>> +    (home-page "https://github.com/fastfloat/fast_float")
>> +    (synopsis "Fast and exact implementation of the C++ from_chars
>> functions")
> I'd call this a "Floating point number parser" or if you prefer the
> verb form "Parse floating point numbers".
>> +    (description "@code{fast_float} is a header-only C++ library
>> which provides fast
>> +implementations of the from_chars functions for float and double
>> types.")
> "@code{fast_float} is a header-only C++ library for parsing floating
> point numbers from strings."  If you want to mention its speed, add
> "Benchmarks show that it is several times faster than strtod."
Is it better now? I don't think it's necessary to mention speed.
>> +    (license (list license:asl2.0 license:expat)))) ; dual licensed
> Weird choice, but okay.
>
> Cheers

[bug#58261] [PATCH 02/11] gnu: Add pocketfft.

[David Elsing]

* gnu/packages/cpp.scm (pocketfft): New variable.
---
 gnu/packages/cpp.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index e597dba40c..65df317100 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -1931,3 +1931,29 @@ (define-public fast-float
     (description "@code{fast_float} is a header-only C++ library which provides fast
 implementations of the from_chars functions for float and double types.")
     (license (list license:asl2.0 license:expat)))) ; dual licensed
+
+(define-public pocketfft
+  (let ((commit "daa8bb18327bc5c7d22c69428c25cf5dc64167d3") (revision "0"))
+    (package
+      (name "pocketfft")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/mreineck/pocketfft")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1dbkkqkmkxgmz1qjpsqzic5ig3qw1pqndbb3dvjc7xq5f2rdzyq1"))))
+      (build-system copy-build-system)
+      (arguments
+       (list
+        #:install-plan
+        #~'(("pocketfft_hdronly.h" "include/"))))
+      (home-page "https://github.com/mreineck/pocketfft")
+      (synopsis "Heavily modified implementation of FFTPack in C++")
+      (description "This package contains the single-header PocketFFT library,
+which is an reimplementation of FFTPack with several advantages, such as
+multidimensional algorithms, different datatypes and vector instructions.")
+      (license license:bsd-3))))
-- 
2.37.0

[bug#58261] [PATCH 02/11] gnu: Add pocketfft.

[Liliana Marie Prikler]

Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
> * gnu/packages/cpp.scm (pocketfft): New variable.
> ---
>  gnu/packages/cpp.scm | 26 ++++++++++++++++++++++++++
>  1 file changed, 26 insertions(+)
> 
> diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
> index e597dba40c..65df317100 100644
> --- a/gnu/packages/cpp.scm
> +++ b/gnu/packages/cpp.scm
> @@ -1931,3 +1931,29 @@ (define-public fast-float
>      (description "@code{fast_float} is a header-only C++ library
> which provides fast
>  implementations of the from_chars functions for float and double
> types.")
>      (license (list license:asl2.0 license:expat)))) ; dual licensed
> +
> +(define-public pocketfft
> +  (let ((commit "daa8bb18327bc5c7d22c69428c25cf5dc64167d3")
> (revision "0"))
Split into two lines
> +    (package
> +      (name "pocketfft")
> +      (version (git-version "0.0.0" revision commit))
I'd simply use "0", but YMMV.
> +      (source (origin
> +                (method git-fetch)
> +                (uri (git-reference
> +                      (url "https://github.com/mreineck/pocketfft")
Note that there's also https://gitlab.mpcdf.mpg.de/mtr/pocketfft which
is C99-compliant.  
> +                      (commit commit)))
> +                (file-name (git-file-name name version))
> +                (sha256
> +                 (base32
> +                 
> "1dbkkqkmkxgmz1qjpsqzic5ig3qw1pqndbb3dvjc7xq5f2rdzyq1"))))
> +      (build-system copy-build-system)
> +      (arguments
> +       (list
> +        #:install-plan
> +        #~'(("pocketfft_hdronly.h" "include/"))))
> +      (home-page "https://github.com/mreineck/pocketfft")
> +      (synopsis "Heavily modified implementation of FFTPack in C++")
I'd write out "Fast Fourier Transformation" and perhaps one or two
other properties, e.g. "Header-only Fast Fourier Transformation
library".
> +      (description "This package contains the single-header
> PocketFFT library,
> +which is an reimplementation of FFTPack with several advantages,
> such as
> +multidimensional algorithms, different datatypes and vector
> instructions.")
"This package provides a single-header C++11 library for computing Fast
Fourier transformations.  It supports multidimensional arrays,
different floating point sizes and complex transformations."  As for
the vector instructions, we should convert the #ifndef
POCKETFFT_NO_VECTORS checks to #if POCKETFFT_NO_VECTORS and insert a
check that defines it to 1 if unset (for reproducibility of other
packages).
> +      (license license:bsd-3))))

Cheers

[bug#58261] [PATCH 02/11] gnu: Add pocketfft.

[David Elsing]

Liliana Marie Prikler <liliana.prikler@ist.tugraz.at> writes:

> Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
>> * gnu/packages/cpp.scm (pocketfft): New variable.
>> ---
>>  gnu/packages/cpp.scm | 26 ++++++++++++++++++++++++++
>>  1 file changed, 26 insertions(+)
>> 
>> diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
>> index e597dba40c..65df317100 100644
>> --- a/gnu/packages/cpp.scm
>> +++ b/gnu/packages/cpp.scm
>> @@ -1931,3 +1931,29 @@ (define-public fast-float
>>      (description "@code{fast_float} is a header-only C++ library
>> which provides fast
>>  implementations of the from_chars functions for float and double
>> types.")
>>      (license (list license:asl2.0 license:expat)))) ; dual licensed
>> +
>> +(define-public pocketfft
>> +  (let ((commit "daa8bb18327bc5c7d22c69428c25cf5dc64167d3")
>> (revision "0"))
> Split into two lines
>> +    (package
>> +      (name "pocketfft")
>> +      (version (git-version "0.0.0" revision commit))
> I'd simply use "0", but YMMV.
>> +      (source (origin
>> +                (method git-fetch)
>> +                (uri (git-reference
>> +                      (url "https://github.com/mreineck/pocketfft")
> Note that there's also https://gitlab.mpcdf.mpg.de/mtr/pocketfft which
> is C99-compliant.  
I renamed it to pocketfft-cpp, is that fine?
>> +                      (commit commit)))
>> +                (file-name (git-file-name name version))
>> +                (sha256
>> +                 (base32
>> +                 
>> "1dbkkqkmkxgmz1qjpsqzic5ig3qw1pqndbb3dvjc7xq5f2rdzyq1"))))
>> +      (build-system copy-build-system)
>> +      (arguments
>> +       (list
>> +        #:install-plan
>> +        #~'(("pocketfft_hdronly.h" "include/"))))
>> +      (home-page "https://github.com/mreineck/pocketfft")
>> +      (synopsis "Heavily modified implementation of FFTPack in C++")
> I'd write out "Fast Fourier Transformation" and perhaps one or two
> other properties, e.g. "Header-only Fast Fourier Transformation
> library".
>> +      (description "This package contains the single-header
>> PocketFFT library,
>> +which is an reimplementation of FFTPack with several advantages,
>> such as
>> +multidimensional algorithms, different datatypes and vector
>> instructions.")
> "This package provides a single-header C++11 library for computing Fast
> Fourier transformations.  It supports multidimensional arrays,
> different floating point sizes and complex transformations."  As for
> the vector instructions, we should convert the #ifndef
> POCKETFFT_NO_VECTORS checks to #if POCKETFFT_NO_VECTORS and insert a
> check that defines it to 1 if unset (for reproducibility of other
> packages).
Oh that's a good point! I assume you mean #if !(POCKETFFT_NO_VECTORS)?
>> +      (license license:bsd-3))))
>
> Cheers

[bug#58261] [PATCH 03/11] gnu: Add sajson.

[David Elsing]

* gnu/packages/cpp.scm (sajson): New variable.
---
 gnu/packages/cpp.scm                          | 63 +++++++++++++++++++
 .../patches/sajson-parse_flags-linking.patch  | 45 +++++++++++++
 2 files changed, 108 insertions(+)
 create mode 100644 gnu/packages/patches/sajson-parse_flags-linking.patch

diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index 65df317100..7bfa3d6cdf 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -57,6 +57,7 @@ (define-module (gnu packages cpp)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system python)
+  #:use-module (guix build-system scons)
   #:use-module (guix modules)
   #:use-module (guix gexp)
   #:use-module (gnu packages)
@@ -1957,3 +1958,65 @@ (define-public pocketfft
 which is an reimplementation of FFTPack with several advantages, such as
 multidimensional algorithms, different datatypes and vector instructions.")
       (license license:bsd-3))))
+
+(define-public sajson
+  (let ((commit "ec644013e34f9984a3cc9ba568cab97a391db9cd") (revision "0"))
+    (package
+      (name "sajson")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/chadaustin/sajson")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (patches
+                 (search-patches "sajson-parse_flags-linking.patch"))
+                (sha256
+                 (base32
+                  "0fjag27w7gvkc5pdhq3ad7yc09rabpzahndw1sgsg04ipznidmmq"))
+                (modules '((guix build utils)))
+                (snippet '(delete-file-recursively "third-party"))))
+      (build-system scons-build-system)
+      (arguments
+       (list
+        #:phases
+        #~(modify-phases %standard-phases
+            (add-after 'unpack 'disable-other-builds
+              (lambda _
+                (substitute* "SConstruct"
+                  (("for name, tools in builds:")
+                   "for name, tools in [('opt', [gcc, opt])]:"))
+                #t))
+            (add-after 'unpack 'use-external-unittest-cpp
+              (lambda* (#:key inputs #:allow-other-keys)
+                (substitute* "SConscript"
+                  (("unittestpp_env\\.Library") "_dummy = ")
+                  (("test_env = env.Clone\\(tools=\\[unittestpp, sajson\\]\\)")
+                   (string-append
+                    "test_env = env.Clone(tools=[sajson])\n"
+                    "test_env.Append(CPPPATH='"
+                    (search-input-directory inputs "/include/UnitTest++")
+                    "', LIBPATH='"
+                    (string-append #$(this-package-native-input "unittest-cpp")
+                                   "/lib")
+                    "', LIBS=['UnitTest++'])")))
+                #t))
+            (replace 'check
+              (lambda* (#:key tests? #:allow-other-keys)
+                (when tests?
+                  (invoke "build/opt/test")
+                  (invoke "build/opt/test_unsorted"))
+                #t))
+            (replace 'install
+              (lambda _
+                (let ((out (string-append #$output "/include")))
+                  (install-file "include/sajson.h" out)
+                  (install-file "include/sajson_ostream.h" out))
+                #t)))))
+      (native-inputs (list unittest-cpp))
+      (home-page "https://github.com/chadaustin/sajson")
+      (synopsis "Lightweight, extremely high-performance JSON parser for C++11")
+      (description "sajson is a high-performance, in-place JSON parser
+header-only library.")
+      (license license:expat))))
diff --git a/gnu/packages/patches/sajson-parse_flags-linking.patch b/gnu/packages/patches/sajson-parse_flags-linking.patch
new file mode 100644
index 0000000000..878706dc79
--- /dev/null
+++ b/gnu/packages/patches/sajson-parse_flags-linking.patch
@@ -0,0 +1,45 @@
+This patch is from the upstream pull request
+https://github.com/chadaustin/sajson/pull/54.
+It fixes linking with GCC.
+
+diff --git a/include/sajson.h b/include/sajson.h
+index 8b4e05a..1bd045b 100644
+--- a/include/sajson.h
++++ b/include/sajson.h
+@@ -138,12 +138,17 @@ constexpr inline size_t make_element(tag t, size_t value) {
+ // header. This trick courtesy of Rich Geldreich's Purple JSON parser.
+ template <typename unused = void>
+ struct globals_struct {
++    static const unsigned char parse_flags[256];
++};
++typedef globals_struct<> globals;
++
+ // clang-format off
+ 
+     // bit 0 (1) - set if: plain ASCII string character
+     // bit 1 (2) - set if: whitespace
+     // bit 4 (0x10) - set if: 0-9 e E .
+-    constexpr static const uint8_t parse_flags[256] = {
++    template <typename unused>
++    const unsigned char globals_struct<unused>::parse_flags[256] = {
+      // 0    1    2    3    4    5    6    7      8    9    A    B    C    D    E    F
+         0,   0,   0,   0,   0,   0,   0,   0,     0,   2,   2,   0,   0,   2,   0,   0, // 0
+         0,   0,   0,   0,   0,   0,   0,   0,     0,   0,   0,   0,   0,   0,   0,   0, // 1
+@@ -162,15 +167,13 @@ struct globals_struct {
+     };
+ 
+ // clang-format on
+-};
+-typedef globals_struct<> globals;
+ 
+-constexpr inline bool is_plain_string_character(char c) {
++inline bool is_plain_string_character(char c) {
+     // return c >= 0x20 && c <= 0x7f && c != 0x22 && c != 0x5c;
+     return (globals::parse_flags[static_cast<unsigned char>(c)] & 1) != 0;
+ }
+ 
+-constexpr inline bool is_whitespace(char c) {
++inline bool is_whitespace(char c) {
+     // return c == '\r' || c == '\n' || c == '\t' || c == ' ';
+     return (globals::parse_flags[static_cast<unsigned char>(c)] & 2) != 0;
+ }
-- 
2.37.0

[bug#58261] [PATCH 03/11] gnu: Add sajson.

[Liliana Marie Prikler]

Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
> * gnu/packages/cpp.scm (sajson): New variable.
> ---
>  gnu/packages/cpp.scm                          | 63
> +++++++++++++++++++
>  .../patches/sajson-parse_flags-linking.patch  | 45 +++++++++++++
>  2 files changed, 108 insertions(+)
>  create mode 100644 gnu/packages/patches/sajson-parse_flags-
> linking.patch
> 
> diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
> index 65df317100..7bfa3d6cdf 100644
> --- a/gnu/packages/cpp.scm
> +++ b/gnu/packages/cpp.scm
> @@ -57,6 +57,7 @@ (define-module (gnu packages cpp)
>    #:use-module (guix build-system gnu)
>    #:use-module (guix build-system meson)
>    #:use-module (guix build-system python)
> +  #:use-module (guix build-system scons)
>    #:use-module (guix modules)
>    #:use-module (guix gexp)
>    #:use-module (gnu packages)
> @@ -1957,3 +1958,65 @@ (define-public pocketfft
>  which is an reimplementation of FFTPack with several advantages,
> such as
>  multidimensional algorithms, different datatypes and vector
> instructions.")
>        (license license:bsd-3))))
> +
> +(define-public sajson
> +  (let ((commit "ec644013e34f9984a3cc9ba568cab97a391db9cd")
> (revision "0"))
> +    (package
> +      (name "sajson")
> +      (version (git-version "0.0.0" revision commit))
Note that the swift FFI is advertised as 1.0 and there has been a
blogpost claiming it to be 1.0 in 2013.
> +      (source (origin
> +                (method git-fetch)
> +                (uri (git-reference
> +                      (url "https://github.com/chadaustin/sajson")
> +                      (commit commit)))
> +                (file-name (git-file-name name version))
> +                (patches
> +                 (search-patches "sajson-parse_flags-
> linking.patch"))
> +                (sha256
> +                 (base32
> +                 
> "0fjag27w7gvkc5pdhq3ad7yc09rabpzahndw1sgsg04ipznidmmq"))
> +                (modules '((guix build utils)))
> +                (snippet '(delete-file-recursively "third-party"))))
> +      (build-system scons-build-system)
> +      (arguments
> +       (list
> +        #:phases
> +        #~(modify-phases %standard-phases
> +            (add-after 'unpack 'disable-other-builds
> +              (lambda _
> +                (substitute* "SConstruct"
> +                  (("for name, tools in builds:")
> +                   "for name, tools in [('opt', [gcc, opt])]:"))
> +                #t))
> +            (add-after 'unpack 'use-external-unittest-cpp
> +              (lambda* (#:key inputs #:allow-other-keys)
> +                (substitute* "SConscript"
> +                  (("unittestpp_env\\.Library") "_dummy = ")
> +                  (("test_env = env.Clone\\(tools=\\[unittestpp,
> sajson\\]\\)")
> +                   (string-append
> +                    "test_env = env.Clone(tools=[sajson])\n"
> +                    "test_env.Append(CPPPATH='"
> +                    (search-input-directory inputs
> "/include/UnitTest++")
> +                    "', LIBPATH='"
> +                    (string-append #$(this-package-native-input
> "unittest-cpp")
> +                                   "/lib")
> +                    "', LIBS=['UnitTest++'])")))
> +                #t))
> +            (replace 'check
> +              (lambda* (#:key tests? #:allow-other-keys)
> +                (when tests?
> +                  (invoke "build/opt/test")
> +                  (invoke "build/opt/test_unsorted"))
> +                #t))
> +            (replace 'install
> +              (lambda _
> +                (let ((out (string-append #$output "/include")))
> +                  (install-file "include/sajson.h" out)
> +                  (install-file "include/sajson_ostream.h" out))
> +                #t)))))
You don't need the trailing #ts
> +      (native-inputs (list unittest-cpp))
> +      (home-page "https://github.com/chadaustin/sajson")
> +      (synopsis "Lightweight, extremely high-performance JSON parser
> for C++11")
> +      (description "sajson is a high-performance, in-place JSON
> parser
> +header-only library.")
Cut down on the ads.
> +      (license license:expat))))
> diff --git a/gnu/packages/patches/sajson-parse_flags-linking.patch
> b/gnu/packages/patches/sajson-parse_flags-linking.patch
> new file mode 100644
> index 0000000000..878706dc79
> --- /dev/null
> +++ b/gnu/packages/patches/sajson-parse_flags-linking.patch
> @@ -0,0 +1,45 @@
> +This patch is from the upstream pull request
> +https://github.com/chadaustin/sajson/pull/54.
> +It fixes linking with GCC.
> +
> +diff --git a/include/sajson.h b/include/sajson.h
> +index 8b4e05a..1bd045b 100644
> +--- a/include/sajson.h
> ++++ b/include/sajson.h
> +@@ -138,12 +138,17 @@ constexpr inline size_t make_element(tag t,
> size_t value) {
> + // header. This trick courtesy of Rich Geldreich's Purple JSON
> parser.
> + template <typename unused = void>
> + struct globals_struct {
> ++    static const unsigned char parse_flags[256];
> ++};
> ++typedef globals_struct<> globals;
> ++
> + // clang-format off
> + 
> +     // bit 0 (1) - set if: plain ASCII string character
> +     // bit 1 (2) - set if: whitespace
> +     // bit 4 (0x10) - set if: 0-9 e E .
> +-    constexpr static const uint8_t parse_flags[256] = {
> ++    template <typename unused>
> ++    const unsigned char globals_struct<unused>::parse_flags[256] =
> {
> +      // 0    1    2    3    4    5    6    7      8    9    A   
> B    C    D    E    F
> +         0,   0,   0,   0,   0,   0,   0,   0,     0,   2,   2,  
> 0,   0,   2,   0,   0, // 0
> +         0,   0,   0,   0,   0,   0,   0,   0,     0,   0,   0,  
> 0,   0,   0,   0,   0, // 1
> +@@ -162,15 +167,13 @@ struct globals_struct {
> +     };
> + 
> + // clang-format on
> +-};
> +-typedef globals_struct<> globals;
> + 
> +-constexpr inline bool is_plain_string_character(char c) {
> ++inline bool is_plain_string_character(char c) {
> +     // return c >= 0x20 && c <= 0x7f && c != 0x22 && c != 0x5c;
> +     return (globals::parse_flags[static_cast<unsigned char>(c)] &
> 1) != 0;
> + }
> + 
> +-constexpr inline bool is_whitespace(char c) {
> ++inline bool is_whitespace(char c) {
> +     // return c == '\r' || c == '\n' || c == '\t' || c == ' ';
> +     return (globals::parse_flags[static_cast<unsigned char>(c)] &
> 2) != 0;
> + }
Since this fixes an error that occurs when building with GCC 10, the
patch name should reflect that, e.g. "sajson-build-with-gcc10" (whether
you include or do not include a dash between gcc and 10 doesn't seem to
matter).

Cheers

[bug#58261] [PATCH 03/11] gnu: Add sajson.

[David Elsing]

Liliana Marie Prikler <liliana.prikler@ist.tugraz.at> writes:

> Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
>> * gnu/packages/cpp.scm (sajson): New variable.
>> ---
>>  gnu/packages/cpp.scm                          | 63
>> +++++++++++++++++++
>>  .../patches/sajson-parse_flags-linking.patch  | 45 +++++++++++++
>>  2 files changed, 108 insertions(+)
>>  create mode 100644 gnu/packages/patches/sajson-parse_flags-
>> linking.patch
>> 
>> diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
>> index 65df317100..7bfa3d6cdf 100644
>> --- a/gnu/packages/cpp.scm
>> +++ b/gnu/packages/cpp.scm
>> @@ -57,6 +57,7 @@ (define-module (gnu packages cpp)
>>    #:use-module (guix build-system gnu)
>>    #:use-module (guix build-system meson)
>>    #:use-module (guix build-system python)
>> +  #:use-module (guix build-system scons)
>>    #:use-module (guix modules)
>>    #:use-module (guix gexp)
>>    #:use-module (gnu packages)
>> @@ -1957,3 +1958,65 @@ (define-public pocketfft
>>  which is an reimplementation of FFTPack with several advantages,
>> such as
>>  multidimensional algorithms, different datatypes and vector
>> instructions.")
>>        (license license:bsd-3))))
>> +
>> +(define-public sajson
>> +  (let ((commit "ec644013e34f9984a3cc9ba568cab97a391db9cd")
>> (revision "0"))
>> +    (package
>> +      (name "sajson")
>> +      (version (git-version "0.0.0" revision commit))
> Note that the swift FFI is advertised as 1.0 and there has been a
> blogpost claiming it to be 1.0 in 2013.
Ah ok, then I'll set it to 1.0.
>> +      (source (origin
>> +                (method git-fetch)
>> +                (uri (git-reference
>> +                      (url "https://github.com/chadaustin/sajson")
>> +                      (commit commit)))
>> +                (file-name (git-file-name name version))
>> +                (patches
>> +                 (search-patches "sajson-parse_flags-
>> linking.patch"))
>> +                (sha256
>> +                 (base32
>> +                 
>> "0fjag27w7gvkc5pdhq3ad7yc09rabpzahndw1sgsg04ipznidmmq"))
>> +                (modules '((guix build utils)))
>> +                (snippet '(delete-file-recursively "third-party"))))
>> +      (build-system scons-build-system)
>> +      (arguments
>> +       (list
>> +        #:phases
>> +        #~(modify-phases %standard-phases
>> +            (add-after 'unpack 'disable-other-builds
>> +              (lambda _
>> +                (substitute* "SConstruct"
>> +                  (("for name, tools in builds:")
>> +                   "for name, tools in [('opt', [gcc, opt])]:"))
>> +                #t))
>> +            (add-after 'unpack 'use-external-unittest-cpp
>> +              (lambda* (#:key inputs #:allow-other-keys)
>> +                (substitute* "SConscript"
>> +                  (("unittestpp_env\\.Library") "_dummy = ")
>> +                  (("test_env = env.Clone\\(tools=\\[unittestpp,
>> sajson\\]\\)")
>> +                   (string-append
>> +                    "test_env = env.Clone(tools=[sajson])\n"
>> +                    "test_env.Append(CPPPATH='"
>> +                    (search-input-directory inputs
>> "/include/UnitTest++")
>> +                    "', LIBPATH='"
>> +                    (string-append #$(this-package-native-input
>> "unittest-cpp")
>> +                                   "/lib")
>> +                    "', LIBS=['UnitTest++'])")))
>> +                #t))
>> +            (replace 'check
>> +              (lambda* (#:key tests? #:allow-other-keys)
>> +                (when tests?
>> +                  (invoke "build/opt/test")
>> +                  (invoke "build/opt/test_unsorted"))
>> +                #t))
>> +            (replace 'install
>> +              (lambda _
>> +                (let ((out (string-append #$output "/include")))
>> +                  (install-file "include/sajson.h" out)
>> +                  (install-file "include/sajson_ostream.h" out))
>> +                #t)))))
> You don't need the trailing #ts
Oh thanks, I think I read something outdated.
>> +      (native-inputs (list unittest-cpp))
>> +      (home-page "https://github.com/chadaustin/sajson")
>> +      (synopsis "Lightweight, extremely high-performance JSON parser
>> for C++11")
>> +      (description "sajson is a high-performance, in-place JSON
>> parser
>> +header-only library.")
> Cut down on the ads.
>> +      (license license:expat))))
>> diff --git a/gnu/packages/patches/sajson-parse_flags-linking.patch
>> b/gnu/packages/patches/sajson-parse_flags-linking.patch
>> new file mode 100644
>> index 0000000000..878706dc79
>> --- /dev/null
>> +++ b/gnu/packages/patches/sajson-parse_flags-linking.patch
>> @@ -0,0 +1,45 @@
>> +This patch is from the upstream pull request
>> +https://github.com/chadaustin/sajson/pull/54.
>> +It fixes linking with GCC.
>> +
>> +diff --git a/include/sajson.h b/include/sajson.h
>> +index 8b4e05a..1bd045b 100644
>> +--- a/include/sajson.h
>> ++++ b/include/sajson.h
>> +@@ -138,12 +138,17 @@ constexpr inline size_t make_element(tag t,
>> size_t value) {
>> + // header. This trick courtesy of Rich Geldreich's Purple JSON
>> parser.
>> + template <typename unused = void>
>> + struct globals_struct {
>> ++    static const unsigned char parse_flags[256];
>> ++};
>> ++typedef globals_struct<> globals;
>> ++
>> + // clang-format off
>> + 
>> +     // bit 0 (1) - set if: plain ASCII string character
>> +     // bit 1 (2) - set if: whitespace
>> +     // bit 4 (0x10) - set if: 0-9 e E .
>> +-    constexpr static const uint8_t parse_flags[256] = {
>> ++    template <typename unused>
>> ++    const unsigned char globals_struct<unused>::parse_flags[256] =
>> {
>> +      // 0    1    2    3    4    5    6    7      8    9    A   
>> B    C    D    E    F
>> +         0,   0,   0,   0,   0,   0,   0,   0,     0,   2,   2,  
>> 0,   0,   2,   0,   0, // 0
>> +         0,   0,   0,   0,   0,   0,   0,   0,     0,   0,   0,  
>> 0,   0,   0,   0,   0, // 1
>> +@@ -162,15 +167,13 @@ struct globals_struct {
>> +     };
>> + 
>> + // clang-format on
>> +-};
>> +-typedef globals_struct<> globals;
>> + 
>> +-constexpr inline bool is_plain_string_character(char c) {
>> ++inline bool is_plain_string_character(char c) {
>> +     // return c >= 0x20 && c <= 0x7f && c != 0x22 && c != 0x5c;
>> +     return (globals::parse_flags[static_cast<unsigned char>(c)] &
>> 1) != 0;
>> + }
>> + 
>> +-constexpr inline bool is_whitespace(char c) {
>> ++inline bool is_whitespace(char c) {
>> +     // return c == '\r' || c == '\n' || c == '\t' || c == ' ';
>> +     return (globals::parse_flags[static_cast<unsigned char>(c)] &
>> 2) != 0;
>> + }
> Since this fixes an error that occurs when building with GCC 10, the
> patch name should reflect that, e.g. "sajson-build-with-gcc10" (whether
> you include or do not include a dash between gcc and 10 doesn't seem to
> matter).
>
> Cheers

[bug#58261] [PATCH 04/11] gnu: Add tinydir.

[David Elsing]

* gnu/packages/cpp.scm (tinydir): New variable.
---
 gnu/packages/cpp.scm | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index 7bfa3d6cdf..4819f36052 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -2020,3 +2020,41 @@ (define-public sajson
       (description "sajson is a high-performance, in-place JSON parser
 header-only library.")
       (license license:expat))))
+
+(define-public tinydir
+  (package
+    (name "tinydir")
+    (version "1.2.5")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/cxong/tinydir")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1nprgdfx4i8wzc1idw6chan4fjfa75b5ll8kghdc0q2278pny259"))
+              (modules '((guix build utils)))
+              (snippet '(delete-file-recursively "tests/cbehave"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      ;; Tests require cbehave and rlutil
+      #:tests? #f
+      #:phases
+      ;; Build samples instead of tests
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'chdir
+            (lambda _ (chdir "samples") #t))
+          (add-after 'build 'chdir-back
+            (lambda _ (chdir "..") #t))
+          (replace 'install
+            (lambda _
+              (install-file "tinydir.h" (string-append #$output "/include"))
+              #t)))))
+    (home-page "https://github.com/cxong/tinydir")
+    (synopsis "Lightweight, portable and easy to integrate C directory and
+file reader")
+    (description "tinydir is a header-only C library to portably read files
+and directories.")
+    (license license:bsd-2)))
-- 
2.37.0

[bug#58261] [PATCH 04/11] gnu: Add tinydir.

[Liliana Marie Prikler]

Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
> * gnu/packages/cpp.scm (tinydir): New variable.
> ---
>  gnu/packages/cpp.scm | 38 ++++++++++++++++++++++++++++++++++++++
>  1 file changed, 38 insertions(+)
> 
> diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
> index 7bfa3d6cdf..4819f36052 100644
> --- a/gnu/packages/cpp.scm
> +++ b/gnu/packages/cpp.scm
> @@ -2020,3 +2020,41 @@ (define-public sajson
>        (description "sajson is a high-performance, in-place JSON
> parser
>  header-only library.")
>        (license license:expat))))
> +
> +(define-public tinydir
> +  (package
> +    (name "tinydir")
> +    (version "1.2.5")
> +    (source (origin
> +              (method git-fetch)
> +              (uri (git-reference
> +                    (url "https://github.com/cxong/tinydir")
> +                    (commit version)))
> +              (file-name (git-file-name name version))
> +              (sha256
> +               (base32
> +               
> "1nprgdfx4i8wzc1idw6chan4fjfa75b5ll8kghdc0q2278pny259"))
> +              (modules '((guix build utils)))
> +              (snippet '(delete-file-recursively "tests/cbehave"))))
> +    (build-system cmake-build-system)
> +    (arguments
> +     (list
> +      ;; Tests require cbehave and rlutil
> +      #:tests? #f
Then those should be packaged.
> +      #:phases
> +      ;; Build samples instead of tests
> +      #~(modify-phases %standard-phases
> +          (add-after 'unpack 'chdir
> +            (lambda _ (chdir "samples") #t))
> +          (add-after 'build 'chdir-back
> +            (lambda _ (chdir "..") #t))
We don't typically build samples.
> +          (replace 'install
> +            (lambda _
> +              (install-file "tinydir.h" (string-append #$output
> "/include"))
> +              #t)))))
> +    (home-page "https://github.com/cxong/tinydir")
> +    (synopsis "Lightweight, portable and easy to integrate C
> directory and
> +file reader")
> +    (description "tinydir is a header-only C library to portably
> read files
> +and directories.")
Cut down on the ads.
> +    (license license:bsd-2)))

Cheers

[bug#58261] [PATCH 04/11] gnu: Add tinydir.

[David Elsing]

Liliana Marie Prikler <liliana.prikler@ist.tugraz.at> writes:

> Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
>> * gnu/packages/cpp.scm (tinydir): New variable.
>> ---
>>  gnu/packages/cpp.scm | 38 ++++++++++++++++++++++++++++++++++++++
>>  1 file changed, 38 insertions(+)
>> 
>> diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
>> index 7bfa3d6cdf..4819f36052 100644
>> --- a/gnu/packages/cpp.scm
>> +++ b/gnu/packages/cpp.scm
>> @@ -2020,3 +2020,41 @@ (define-public sajson
>>        (description "sajson is a high-performance, in-place JSON
>> parser
>>  header-only library.")
>>        (license license:expat))))
>> +
>> +(define-public tinydir
>> +  (package
>> +    (name "tinydir")
>> +    (version "1.2.5")
>> +    (source (origin
>> +              (method git-fetch)
>> +              (uri (git-reference
>> +                    (url "https://github.com/cxong/tinydir")
>> +                    (commit version)))
>> +              (file-name (git-file-name name version))
>> +              (sha256
>> +               (base32
>> +               
>> "1nprgdfx4i8wzc1idw6chan4fjfa75b5ll8kghdc0q2278pny259"))
>> +              (modules '((guix build utils)))
>> +              (snippet '(delete-file-recursively "tests/cbehave"))))
>> +    (build-system cmake-build-system)
>> +    (arguments
>> +     (list
>> +      ;; Tests require cbehave and rlutil
>> +      #:tests? #f
> Then those should be packaged.
The problem is that the tests include a non-trivially modified
fork of cbehave, which uses an older (bundled) copy of rlutil for color
output. How should I deal with that?
>> +      #:phases
>> +      ;; Build samples instead of tests
>> +      #~(modify-phases %standard-phases
>> +          (add-after 'unpack 'chdir
>> +            (lambda _ (chdir "samples") #t))
>> +          (add-after 'build 'chdir-back
>> +            (lambda _ (chdir "..") #t))
> We don't typically build samples.
Ah ok :)
>> +          (replace 'install
>> +            (lambda _
>> +              (install-file "tinydir.h" (string-append #$output
>> "/include"))
>> +              #t)))))
>> +    (home-page "https://github.com/cxong/tinydir")
>> +    (synopsis "Lightweight, portable and easy to integrate C
>> directory and
>> +file reader")
>> +    (description "tinydir is a header-only C library to portably
>> read files
>> +and directories.")
> Cut down on the ads.
>> +    (license license:bsd-2)))
>
> Cheers

[bug#58261] [PATCH 04/11] gnu: Add tinydir.

[Liliana Marie Prikler]

Am Freitag, dem 07.10.2022 um 15:11 +0000 schrieb David Elsing:
> Liliana Marie Prikler <liliana.prikler@ist.tugraz.at> writes:
> 
> > Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
> > > * gnu/packages/cpp.scm (tinydir): New variable.
> > > ---
> > >  gnu/packages/cpp.scm | 38 ++++++++++++++++++++++++++++++++++++++
> > >  1 file changed, 38 insertions(+)
> > > 
> > > diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
> > > index 7bfa3d6cdf..4819f36052 100644
> > > --- a/gnu/packages/cpp.scm
> > > +++ b/gnu/packages/cpp.scm
> > > @@ -2020,3 +2020,41 @@ (define-public sajson
> > >        (description "sajson is a high-performance, in-place JSON
> > > parser
> > >  header-only library.")
> > >        (license license:expat))))
> > > +
> > > +(define-public tinydir
> > > +  (package
> > > +    (name "tinydir")
> > > +    (version "1.2.5")
> > > +    (source (origin
> > > +              (method git-fetch)
> > > +              (uri (git-reference
> > > +                    (url "https://github.com/cxong/tinydir")
> > > +                    (commit version)))
> > > +              (file-name (git-file-name name version))
> > > +              (sha256
> > > +               (base32
> > > +               
> > > "1nprgdfx4i8wzc1idw6chan4fjfa75b5ll8kghdc0q2278pny259"))
> > > +              (modules '((guix build utils)))
> > > +              (snippet '(delete-file-recursively
> > > "tests/cbehave"))))
> > > +    (build-system cmake-build-system)
> > > +    (arguments
> > > +     (list
> > > +      ;; Tests require cbehave and rlutil
> > > +      #:tests? #f
> > Then those should be packaged.
> The problem is that the tests include a non-trivially modified
> fork of cbehave, which uses an older (bundled) copy of rlutil for
> color output. How should I deal with that?
> > 
You could try to make the tests run with the upstream version and
disable those that don't.  Alternatively, you could package "for-
tinydir" variants of those packages, which inherit as much from
upstream as possible.

Cheers

[bug#58261] [PATCH 05/11] gnu: Add optionparser.

[David Elsing]

* gnu/packages/cpp.scm (optionparser): New variable.
---
 gnu/packages/cpp.scm | 50 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)

diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index 4819f36052..b30205109e 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -2058,3 +2058,53 @@ (define-public tinydir
     (description "tinydir is a header-only C library to portably read files
 and directories.")
     (license license:bsd-2)))
+
+(define-public optionparser
+  (package
+    (name "optionparser")
+    (version "1.7")
+    (source (origin
+              (method url-fetch)
+              (uri
+               (string-append "mirror://sourceforge/optionparser/optionparser-"
+                              version ".tar.gz"))
+              (sha256
+               (base32
+                "04gfxrdzwacaynb8scsz6rr7nh64n6yk6w9dh2qdhrxw4caqr0dk"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (delete 'configure)
+          (add-before 'build 'chdir
+            (lambda _ (chdir "src") #t))
+          (replace 'build
+            (lambda _
+              (invoke "make" "-j" (number->string (parallel-job-count))
+                      "example_arg" "testparse" "testprintusage" "testodr"
+                      "example")
+              #t))
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (if tests?
+                  (begin
+                    (invoke "./example_arg")
+                    (invoke "./testparse")
+                    (invoke "./testprintusage")
+                    (invoke "./testodr")
+                    (invoke "./example"))
+                  (format #t "test suite not run~%"))))
+          (replace 'install
+            (lambda _
+              (install-file "optionparser.h" (string-append #$output "/include"))
+              #t))
+          (add-after 'install 'chdir-back
+            (lambda _ (chdir "..") #t)))))
+    (home-page "https://optionparser.sourceforge.net/")
+    (synopsis "Header-only C++ library to parse command line options")
+    (description "The Lean Mean C++ Option Parser handles the program's
+command line arguments (argc, argv).  It supports the short and long option
+formats of getopt(), getopt_long() and getopt_long_only() but has a more
+convenient interface.")
+    (license license:expat)))
-- 
2.37.0

[bug#58261] [PATCH 05/11] gnu: Add optionparser.

[Liliana Marie Prikler]

Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
> * gnu/packages/cpp.scm (optionparser): New variable.
> ---
>  gnu/packages/cpp.scm | 50
> ++++++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 50 insertions(+)
> 
> diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
> index 4819f36052..b30205109e 100644
> --- a/gnu/packages/cpp.scm
> +++ b/gnu/packages/cpp.scm
> @@ -2058,3 +2058,53 @@ (define-public tinydir
>      (description "tinydir is a header-only C library to portably
> read files
>  and directories.")
>      (license license:bsd-2)))
> +
> +(define-public optionparser
> +  (package
> +    (name "optionparser")
> +    (version "1.7")
> +    (source (origin
> +              (method url-fetch)
> +              (uri
> +               (string-append
> "mirror://sourceforge/optionparser/optionparser-"
> +                              version ".tar.gz"))
The formattter doesn't know this, but I think in this case it might be
wiser to pull the "optionparser-" down a line on the same one with
version ".tar.gz"
> +              (sha256
> +               (base32
> +               
> "04gfxrdzwacaynb8scsz6rr7nh64n6yk6w9dh2qdhrxw4caqr0dk"))))
> +    (build-system gnu-build-system)
> +    (arguments
> +     (list
> +      #:phases
> +      #~(modify-phases %standard-phases
> +          (delete 'configure)
> +          (add-before 'build 'chdir
> +            (lambda _ (chdir "src") #t))
> +          (replace 'build
> +            (lambda _
> +              (invoke "make" "-j" (number->string (parallel-job-
> count))
> +                      "example_arg" "testparse" "testprintusage"
> "testodr"
> +                      "example")
#:make-flags exist.  Also, this is a bad way to hide that you're
missing doxygen. 
> +              #t))
> +          (replace 'check
> +            (lambda* (#:key tests? #:allow-other-keys)
> +              (if tests?
> +                  (begin
> +                    (invoke "./example_arg")
> +                    (invoke "./testparse")
> +                    (invoke "./testprintusage")
> +                    (invoke "./testodr")
> +                    (invoke "./example"))
> +                  (format #t "test suite not run~%"))))
> +          (replace 'install
> +            (lambda _
> +              (install-file "optionparser.h" (string-append #$output
> "/include"))
> +              #t))
> +          (add-after 'install 'chdir-back
> +            (lambda _ (chdir "..") #t)))))
I'm pretty sure this shouldn't be needed.
> +    (home-page "https://optionparser.sourceforge.net/")
> +    (synopsis "Header-only C++ library to parse command line
> options")
> +    (description "The Lean Mean C++ Option Parser handles the
> program's
> +command line arguments (argc, argv).  It supports the short and long
> option
> +formats of getopt(), getopt_long() and getopt_long_only() but has a
> more
> +convenient interface.")
As always, cut down on the ads :)
> +    (license license:expat)))

Cheers

[bug#58261] [PATCH 05/11] gnu: Add optionparser.

[David Elsing]

Liliana Marie Prikler <liliana.prikler@ist.tugraz.at> writes:

> Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
>> * gnu/packages/cpp.scm (optionparser): New variable.
>> ---
>>  gnu/packages/cpp.scm | 50
>> ++++++++++++++++++++++++++++++++++++++++++++
>>  1 file changed, 50 insertions(+)
>> 
>> diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
>> index 4819f36052..b30205109e 100644
>> --- a/gnu/packages/cpp.scm
>> +++ b/gnu/packages/cpp.scm
>> @@ -2058,3 +2058,53 @@ (define-public tinydir
>>      (description "tinydir is a header-only C library to portably
>> read files
>>  and directories.")
>>      (license license:bsd-2)))
>> +
>> +(define-public optionparser
>> +  (package
>> +    (name "optionparser")
>> +    (version "1.7")
>> +    (source (origin
>> +              (method url-fetch)
>> +              (uri
>> +               (string-append
>> "mirror://sourceforge/optionparser/optionparser-"
>> +                              version ".tar.gz"))
> The formattter doesn't know this, but I think in this case it might be
> wiser to pull the "optionparser-" down a line on the same one with
> version ".tar.gz"
Which formatter do you mean? Is it ok if I just use Emacs with the rules
in .dir-locals.el and guix lint? When I used guix style, lines sometimes
exceed 80 characters.
>> +              (sha256
>> +               (base32
>> +               
>> "04gfxrdzwacaynb8scsz6rr7nh64n6yk6w9dh2qdhrxw4caqr0dk"))))
>> +    (build-system gnu-build-system)
>> +    (arguments
>> +     (list
>> +      #:phases
>> +      #~(modify-phases %standard-phases
>> +          (delete 'configure)
>> +          (add-before 'build 'chdir
>> +            (lambda _ (chdir "src") #t))
>> +          (replace 'build
>> +            (lambda _
>> +              (invoke "make" "-j" (number->string (parallel-job-
>> count))
>> +                      "example_arg" "testparse" "testprintusage"
>> "testodr"
>> +                      "example")
> #:make-flags exist.  Also, this is a bad way to hide that you're
> missing doxygen.
Oops, I don't remember why I did that, it is easier to just build the
documentation...
>> +              #t))
>> +          (replace 'check
>> +            (lambda* (#:key tests? #:allow-other-keys)
>> +              (if tests?
>> +                  (begin
>> +                    (invoke "./example_arg")
>> +                    (invoke "./testparse")
>> +                    (invoke "./testprintusage")
>> +                    (invoke "./testodr")
>> +                    (invoke "./example"))
>> +                  (format #t "test suite not run~%"))))
>> +          (replace 'install
>> +            (lambda _
>> +              (install-file "optionparser.h" (string-append #$output
>> "/include"))
>> +              #t))
>> +          (add-after 'install 'chdir-back
>> +            (lambda _ (chdir "..") #t)))))
> I'm pretty sure this shouldn't be needed.
>> +    (home-page "https://optionparser.sourceforge.net/")
>> +    (synopsis "Header-only C++ library to parse command line
>> options")
>> +    (description "The Lean Mean C++ Option Parser handles the
>> program's
>> +command line arguments (argc, argv).  It supports the short and long
>> option
>> +formats of getopt(), getopt_long() and getopt_long_only() but has a
>> more
>> +convenient interface.")
> As always, cut down on the ads :)
>> +    (license license:expat)))
>
> Cheers

[bug#58261] [PATCH 06/11] gnu: Add gemmi.

[David Elsing]

* gnu/packages/chemistry.scm (gemmi): New variable.
---
 gnu/packages/chemistry.scm                    | 122 +++++++++++
 .../patches/gemmi-fix-sajson-types.patch      |  11 +
 .../sajson-for-gemmi-numbers-as-strings.patch | 195 ++++++++++++++++++
 3 files changed, 328 insertions(+)
 create mode 100644 gnu/packages/patches/gemmi-fix-sajson-types.patch
 create mode 100644 gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index c517610fe8..f8fd85814f 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -6,6 +6,7 @@
 ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
 ;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2022 David Elsing <david.elsing@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -23,6 +24,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages chemistry)
+  #:use-module (guix gexp)
   #:use-module (guix packages)
   #:use-module (guix utils)
   #:use-module ((guix licenses) #:prefix license:)
@@ -35,6 +37,7 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages cpp)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gl)
@@ -50,8 +53,10 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages qt)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages sphinx)
+  #:use-module (gnu packages stb)
   #:use-module (gnu packages xml)
   #:use-module (guix build-system cmake)
+  #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system python))
 
@@ -566,3 +571,120 @@ (define-public python-pymol
 used to prepare publication-quality figures, to share interactive results with
 your colleagues, or to generate pre-rendered animations.")
     (license license:bsd-3)))
+
+(define sajson-for-gemmi
+  (package/inherit sajson
+    (name "sajson-for-gemmi")
+    (source (origin
+              (inherit (package-source sajson))
+              (patches (cons
+                        (search-patch
+                         "sajson-for-gemmi-numbers-as-strings.patch")
+                        (origin-patches (package-source sajson))))))
+    (build-system copy-build-system)
+    (arguments
+     (list
+      #:install-plan
+      #~'(("include/sajson.h" "include/")
+          ("include/sajson_ostream.h" "include/"))))))
+
+(define-public gemmi
+  (package
+    (name "gemmi")
+    (version "0.5.7")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/project-gemmi/gemmi")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "00km5q726bslrw7xbfwb3f3mrsk19qbimfnl3hvr4wi1y3z8i18a"))
+              (patches
+               (search-patches "gemmi-fix-sajson-types.patch"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  (delete-file-recursively "include/gemmi/third_party")
+                  (delete-file-recursively "third_party")
+                  #t))))
+    (build-system cmake-build-system)
+    (native-inputs (list optionparser pybind11))
+    (propagated-inputs
+     (list fast-float
+           pocketfft
+           sajson-for-gemmi
+           stb-sprintf
+           pegtl
+           tinydir))
+    (inputs (list zlib python))
+    (outputs '("out" "bin" "python"))
+    (arguments
+     (list
+      #:configure-flags
+      #~(let* ((python-lib
+                (string-append
+                 #$output:python "/lib/python"
+                 #$(version-major+minor (package-version python))
+                 "/site-packages")))
+          (list "-DUSE_PYTHON=ON"
+                (string-append "-DPYTHON_INSTALL_DIR=" python-lib)))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-includes
+            (lambda _
+              (substitute* "include/gemmi/sprintf.hpp"
+                (("<stb/stb_sprintf.h>") "<stb_sprintf.h>"))
+              (substitute* "include/gemmi/dirwalk.hpp"
+                (("\"third_party/tinydir.h\"") "<tinydir.h>"))
+              (substitute* "include/gemmi/cif.hpp"
+                (("\"third_party/tao/pegtl.hpp\"") "<tao/pegtl.hpp>"))
+              (substitute* "include/gemmi/json.hpp"
+                (("\"third_party/sajson.h\"") "<sajson.h>"))
+              (substitute* "python/gemmi.cpp"
+                (("\"gemmi/third_party/tao/pegtl/parse_error.hpp\"")
+                 "<tao/pegtl/parse_error.hpp>"))
+              (substitute* '("include/gemmi/atof.hpp"
+                             "include/gemmi/numb.hpp")
+                (("\"third_party/fast_float.h\"")
+                 "<fast_float/fast_float.h>"))
+              (substitute* "include/gemmi/fourier.hpp"
+                (("\"third_party/pocketfft_hdronly.h\"")
+                 "<pocketfft_hdronly.h>"))
+              #t))
+          (add-after 'patch-includes 'patch-cif
+            (lambda _
+              (substitute* "include/gemmi/cif.hpp"
+                (((string-append
+                   "^.*using analyze_t = pegtl::analysis::generic"
+                   "<pegtl::analysis::rule_type::ANY>;.*$")) "")
+                (("TAOCPP_PEGTL_") "TAO_PEGTL_"))
+              #t))
+          (add-after 'unpack 'change-bin-prefix
+            (lambda _
+              (substitute* "CMakeLists.txt"
+                (("install\\(TARGETS program DESTINATION bin\\)")
+                 (string-append
+                  "install(TARGETS program DESTINATION "
+                  #$output:bin "/bin)")))
+              #t))
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (with-directory-excursion "../source"
+                  (setenv "PYTHONPATH" "../build")
+                  (invoke "python3" "-m" "unittest" "discover" "-v"
+                          "-s" "tests"))))))))
+    (home-page "https://gemmi.readthedocs.io/en/latest/")
+    (synopsis "Macromolecular crystallography library and utilities")
+    (description "GEMMI is a C++ library for macromolecular crystallography.
+It can be used for working with
+@enumerate
+@item macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files),
+@item refinement restraints (CIF files),
+@item reflection data (MTZ and mmCIF formats),
+@item data on a 3D grid (electron density maps, masks, MRC/CCP4 format)
+@item crystallographic symmetry.
+@end enumerate")
+    (license license:mpl2.0)))
diff --git a/gnu/packages/patches/gemmi-fix-sajson-types.patch b/gnu/packages/patches/gemmi-fix-sajson-types.patch
new file mode 100644
index 0000000000..9633ddac8b
--- /dev/null
+++ b/gnu/packages/patches/gemmi-fix-sajson-types.patch
@@ -0,0 +1,11 @@
+diff -ur a/include/gemmi/json.hpp b/include/gemmi/json.hpp
+--- a/include/gemmi/json.hpp
++++ b/include/gemmi/json.hpp
+@@ -38,6 +38,7 @@
+ 
+ inline std::string as_cif_value(const sajson::value& val) {
+   switch (val.get_type()) {
++    case sajson::TYPE_INTEGER:
+     case sajson::TYPE_DOUBLE:
+       return val.as_string();
+     case sajson::TYPE_NULL:
diff --git a/gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch b/gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch
new file mode 100644
index 0000000000..6f476b8583
--- /dev/null
+++ b/gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch
@@ -0,0 +1,195 @@
+Patch for gemmi: Keep numbers in JSON file as strings.
+
+Adapted from this commit of the bundled fork of sajson in gemmi:
+https://github.com/project-gemmi/gemmi/commit/fccbca4f6040364ba708613e1429c2251872240d
+
+diff -ur a/include/sajson.h b/include/sajson.h
+--- a/include/sajson.h
++++ b/include/sajson.h
+@@ -411,43 +411,6 @@
+ };
+ } // namespace internal
+ 
+-namespace integer_storage {
+-enum { word_length = 1 };
+-
+-inline int load(const size_t* location) {
+-    int value;
+-    memcpy(&value, location, sizeof(value));
+-    return value;
+-}
+-
+-inline void store(size_t* location, int value) {
+-    // NOTE: Most modern compilers optimize away this constant-size
+-    // memcpy into a single instruction. If any don't, and treat
+-    // punning through a union as legal, they can be special-cased.
+-    static_assert(
+-        sizeof(value) <= sizeof(*location),
+-        "size_t must not be smaller than int");
+-    memcpy(location, &value, sizeof(value));
+-}
+-} // namespace integer_storage
+-
+-namespace double_storage {
+-enum { word_length = sizeof(double) / sizeof(size_t) };
+-
+-inline double load(const size_t* location) {
+-    double value;
+-    memcpy(&value, location, sizeof(double));
+-    return value;
+-}
+-
+-inline void store(size_t* location, double value) {
+-    // NOTE: Most modern compilers optimize away this constant-size
+-    // memcpy into a single instruction. If any don't, and treat
+-    // punning through a union as legal, they can be special-cased.
+-    memcpy(location, &value, sizeof(double));
+-}
+-} // namespace double_storage
+-
+ /// Represents a JSON value.  First, call get_type() to check its type,
+ /// which determines which methods are available.
+ ///
+@@ -585,70 +548,10 @@
+         return length;
+     }
+ 
+-    /// If a numeric value was parsed as a 32-bit integer, returns it.
+-    /// Only legal if get_type() is TYPE_INTEGER.
+-    int get_integer_value() const {
+-        assert_tag(tag::integer);
+-        return integer_storage::load(payload);
+-    }
+-
+-    /// If a numeric value was parsed as a double, returns it.
+-    /// Only legal if get_type() is TYPE_DOUBLE.
+-    double get_double_value() const {
+-        assert_tag(tag::double_);
+-        return double_storage::load(payload);
+-    }
+-
+-    /// Returns a numeric value as a double-precision float.
+-    /// Only legal if get_type() is TYPE_INTEGER or TYPE_DOUBLE.
+-    double get_number_value() const {
+-        assert_tag_2(tag::integer, tag::double_);
+-        if (value_tag == tag::integer) {
+-            return get_integer_value();
+-        } else {
+-            return get_double_value();
+-        }
+-    }
+-
+-    /// Returns true and writes to the output argument if the numeric value
+-    /// fits in a 53-bit integer.  This is useful for timestamps and other
+-    /// situations where integral values with greater than 32-bit precision
+-    /// are used, as 64-bit values are not understood by all JSON
+-    /// implementations or languages.
+-    /// Returns false if the value is not an integer or not in range.
+-    /// Only legal if get_type() is TYPE_INTEGER or TYPE_DOUBLE.
+-    bool get_int53_value(int64_t* out) const {
+-        // Make sure the output variable is always defined to avoid any
+-        // possible situation like
+-        // https://gist.github.com/chadaustin/2c249cb850619ddec05b23ca42cf7a18
+-        *out = 0;
+-
+-        assert_tag_2(tag::integer, tag::double_);
+-        switch (value_tag) {
+-        case tag::integer:
+-            *out = get_integer_value();
+-            return true;
+-        case tag::double_: {
+-            double v = get_double_value();
+-            if (v < -(1LL << 53) || v > (1LL << 53)) {
+-                return false;
+-            }
+-            int64_t as_int = static_cast<int64_t>(v);
+-            if (as_int != v) {
+-                return false;
+-            }
+-            *out = as_int;
+-            return true;
+-        }
+-        default:
+-            return false;
+-        }
+-    }
+-
+     /// Returns the length of the string.
+     /// Only legal if get_type() is TYPE_STRING.
+     size_t get_string_length() const {
+-        assert_tag(tag::string);
++        assert_tag_3(tag::string, tag::integer, tag::double_);
+         return payload[1] - payload[0];
+     }
+ 
+@@ -659,7 +562,7 @@
+     /// embedded NULs.
+     /// Only legal if get_type() is TYPE_STRING.
+     const char* as_cstring() const {
+-        assert_tag(tag::string);
++        assert_tag_3(tag::string, tag::integer, tag::double_);
+         return text + payload[0];
+     }
+ 
+@@ -667,7 +570,7 @@
+     /// Returns a string's value as a std::string.
+     /// Only legal if get_type() is TYPE_STRING.
+     std::string as_string() const {
+-        assert_tag(tag::string);
++        assert_tag_3(tag::string, tag::integer, tag::double_);
+         return std::string(text + payload[0], text + payload[1]);
+     }
+ #endif
+@@ -690,6 +593,10 @@
+         assert(e1 == value_tag || e2 == value_tag);
+     }
+ 
++    void assert_tag_3(tag e1, tag e2, tag e3) const {
++        assert(e1 == value_tag || e2 == value_tag || e3 == value_tag);
++    }
++
+     void assert_in_bounds(size_t i) const { assert(i < get_length()); }
+ 
+     const tag value_tag;
+@@ -2059,6 +1966,8 @@
+     std::pair<char*, internal::tag> parse_number(char* p) {
+         using internal::tag;
+ 
++	size_t start = p - input.get_data();
++
+         // Assume 32-bit, two's complement integers.
+         static constexpr unsigned RISKY = INT_MAX / 10u;
+         unsigned max_digit_after_risky = INT_MAX % 10u;
+@@ -2235,23 +2144,18 @@
+                 u = 0u - u;
+             }
+         }
++
++        bool success;
++        size_t* out = allocator.reserve(2, &success);
++        if (SAJSON_UNLIKELY(!success)) {
++            return std::make_pair(oom(p, "number"), tag::null);
++        }
++        out[0] = start;
++        out[1] = p - input.get_data();
++
+         if (try_double) {
+-            bool success;
+-            size_t* out
+-                = allocator.reserve(double_storage::word_length, &success);
+-            if (SAJSON_UNLIKELY(!success)) {
+-                return std::make_pair(oom(p, "double"), tag::null);
+-            }
+-            double_storage::store(out, d);
+             return std::make_pair(p, tag::double_);
+         } else {
+-            bool success;
+-            size_t* out
+-                = allocator.reserve(integer_storage::word_length, &success);
+-            if (SAJSON_UNLIKELY(!success)) {
+-                return std::make_pair(oom(p, "integer"), tag::null);
+-            }
+-            integer_storage::store(out, static_cast<int>(u));
+             return std::make_pair(p, tag::integer);
+         }
+     }
-- 
2.37.0

[bug#58261] [PATCH 06/11] gnu: Add gemmi.

[Liliana Marie Prikler]

Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
> * gnu/packages/chemistry.scm (gemmi): New variable.
> ---
>  gnu/packages/chemistry.scm                    | 122 +++++++++++
>  .../patches/gemmi-fix-sajson-types.patch      |  11 +
>  .../sajson-for-gemmi-numbers-as-strings.patch | 195
> ++++++++++++++++++
>  3 files changed, 328 insertions(+)
>  create mode 100644 gnu/packages/patches/gemmi-fix-sajson-types.patch
>  create mode 100644 gnu/packages/patches/sajson-for-gemmi-numbers-as-
> strings.patch
> 
> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
> index c517610fe8..f8fd85814f 100644
> --- a/gnu/packages/chemistry.scm
> +++ b/gnu/packages/chemistry.scm
> @@ -6,6 +6,7 @@
>  ;;; Copyright © 2020 Björn Höfling
> <bjoern.hoefling@bjoernhoefling.de>
>  ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
>  ;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
> +;;; Copyright © 2022 David Elsing <david.elsing@posteo.net>
>  ;;;
>  ;;; This file is part of GNU Guix.
>  ;;;
> @@ -23,6 +24,7 @@
>  ;;; along with GNU Guix.  If not, see
> <http://www.gnu.org/licenses/>.
>  
>  (define-module (gnu packages chemistry)
> +  #:use-module (guix gexp)
>    #:use-module (guix packages)
>    #:use-module (guix utils)
>    #:use-module ((guix licenses) #:prefix license:)
> @@ -35,6 +37,7 @@ (define-module (gnu packages chemistry)
>    #:use-module (gnu packages boost)
>    #:use-module (gnu packages check)
>    #:use-module (gnu packages compression)
> +  #:use-module (gnu packages cpp)
>    #:use-module (gnu packages documentation)
>    #:use-module (gnu packages fontutils)
>    #:use-module (gnu packages gl)
> @@ -50,8 +53,10 @@ (define-module (gnu packages chemistry)
>    #:use-module (gnu packages qt)
>    #:use-module (gnu packages serialization)
>    #:use-module (gnu packages sphinx)
> +  #:use-module (gnu packages stb)
>    #:use-module (gnu packages xml)
>    #:use-module (guix build-system cmake)
> +  #:use-module (guix build-system copy)
>    #:use-module (guix build-system gnu)
>    #:use-module (guix build-system python))
>  
> @@ -566,3 +571,120 @@ (define-public python-pymol
>  used to prepare publication-quality figures, to share interactive
> results with
>  your colleagues, or to generate pre-rendered animations.")
>      (license license:bsd-3)))
> +
> +(define sajson-for-gemmi
> +  (package/inherit sajson
> +    (name "sajson-for-gemmi")
> +    (source (origin
> +              (inherit (package-source sajson))
> +              (patches (cons
> +                        (search-patch
> +                         "sajson-for-gemmi-numbers-as-
> strings.patch")
> +                        (origin-patches (package-source sajson))))))
> +    (build-system copy-build-system)
> +    (arguments
> +     (list
> +      #:install-plan
> +      #~'(("include/sajson.h" "include/")
> +          ("include/sajson_ostream.h" "include/"))))))
These are technically two packages; therefore two patches.
You should reuse as much as you can from sajson.  Since this patch is
likely to break tests, you might use an appropriately annotated
#:tests? #f to convey this information.

> +(define-public gemmi
> +  (package
> +    (name "gemmi")
> +    (version "0.5.7")
> +    (source (origin
> +              (method git-fetch)
> +              (uri (git-reference
> +                    (url "https://github.com/project-gemmi/gemmi")
> +                    (commit (string-append "v" version))))
> +              (file-name (git-file-name name version))
> +              (sha256
> +               (base32
> +               
> "00km5q726bslrw7xbfwb3f3mrsk19qbimfnl3hvr4wi1y3z8i18a"))
> +              (patches
> +               (search-patches "gemmi-fix-sajson-types.patch"))
> +              (modules '((guix build utils)))
> +              (snippet
> +               '(begin
> +                  (delete-file-recursively
> "include/gemmi/third_party")
> +                  (delete-file-recursively "third_party")
> +                  #t))))
> +    (build-system cmake-build-system)
> +    (native-inputs (list optionparser pybind11))
> +    (propagated-inputs
> +     (list fast-float
> +           pocketfft
> +           sajson-for-gemmi
> +           stb-sprintf
> +           pegtl
> +           tinydir))
Refrain from propagating inputs.
> +    (inputs (list zlib python))
> +    (outputs '("out" "bin" "python"))
> +    (arguments
The usual sequence is outputs, build-system, arguments, *inputs.
> +     (list
> +      #:configure-flags
> +      #~(let* ((python-lib
> +                (string-append
> +                 #$output:python "/lib/python"
> +                 #$(version-major+minor (package-version python))
> +                 "/site-packages")))
> +          (list "-DUSE_PYTHON=ON"
> +                (string-append "-DPYTHON_INSTALL_DIR=" python-lib)))
> +      #:phases
> +      #~(modify-phases %standard-phases
> +          (add-after 'unpack 'patch-includes
> +            (lambda _
> +              (substitute* "include/gemmi/sprintf.hpp"
> +                (("<stb/stb_sprintf.h>") "<stb_sprintf.h>"))
> +              (substitute* "include/gemmi/dirwalk.hpp"
> +                (("\"third_party/tinydir.h\"") "<tinydir.h>"))
> +              (substitute* "include/gemmi/cif.hpp"
> +                (("\"third_party/tao/pegtl.hpp\"")
> "<tao/pegtl.hpp>"))
> +              (substitute* "include/gemmi/json.hpp"
> +                (("\"third_party/sajson.h\"") "<sajson.h>"))
> +              (substitute* "python/gemmi.cpp"
> +                (("\"gemmi/third_party/tao/pegtl/parse_error.hpp\"")
> +                 "<tao/pegtl/parse_error.hpp>"))
> +              (substitute* '("include/gemmi/atof.hpp"
> +                             "include/gemmi/numb.hpp")
> +                (("\"third_party/fast_float.h\"")
> +                 "<fast_float/fast_float.h>"))
> +              (substitute* "include/gemmi/fourier.hpp"
> +                (("\"third_party/pocketfft_hdronly.h\"")
> +                 "<pocketfft_hdronly.h>"))
> +              #t))
> +          (add-after 'patch-includes 'patch-cif
> +            (lambda _
> +              (substitute* "include/gemmi/cif.hpp"
> +                (((string-append
> +                   "^.*using analyze_t = pegtl::analysis::generic"
> +                   "<pegtl::analysis::rule_type::ANY>;.*$")) "")
> +                (("TAOCPP_PEGTL_") "TAO_PEGTL_"))
> +              #t))
> +          (add-after 'unpack 'change-bin-prefix
> +            (lambda _
> +              (substitute* "CMakeLists.txt"
> +                (("install\\(TARGETS program DESTINATION bin\\)")
> +                 (string-append
> +                  "install(TARGETS program DESTINATION "
> +                  #$output:bin "/bin)")))
> +              #t))
> +          (replace 'check
> +            (lambda* (#:key tests? #:allow-other-keys)
> +              (when tests?
> +                (with-directory-excursion "../source"
> +                  (setenv "PYTHONPATH" "../build")
> +                  (invoke "python3" "-m" "unittest" "discover" "-v"
> +                          "-s" "tests"))))))))
> +    (home-page "https://gemmi.readthedocs.io/en/latest/")
> +    (synopsis "Macromolecular crystallography library and
> utilities")
> +    (description "GEMMI is a C++ library for macromolecular
> crystallography.
> +It can be used for working with
> +@enumerate
> +@item macromolecular models (content of PDB, PDBx/mmCIF and mmJSON
> files),
> +@item refinement restraints (CIF files),
> +@item reflection data (MTZ and mmCIF formats),
> +@item data on a 3D grid (electron density maps, masks, MRC/CCP4
> format)
> +@item crystallographic symmetry.
> +@end enumerate")
> +    (license license:mpl2.0)))
> diff --git a/gnu/packages/patches/gemmi-fix-sajson-types.patch
> b/gnu/packages/patches/gemmi-fix-sajson-types.patch
> new file mode 100644
> index 0000000000..9633ddac8b
> --- /dev/null
> +++ b/gnu/packages/patches/gemmi-fix-sajson-types.patch
> @@ -0,0 +1,11 @@
> +diff -ur a/include/gemmi/json.hpp b/include/gemmi/json.hpp
> +--- a/include/gemmi/json.hpp
> ++++ b/include/gemmi/json.hpp
> +@@ -38,6 +38,7 @@
> + 
> + inline std::string as_cif_value(const sajson::value& val) {
> +   switch (val.get_type()) {
> ++    case sajson::TYPE_INTEGER:
> +     case sajson::TYPE_DOUBLE:
> +       return val.as_string();
> +     case sajson::TYPE_NULL:
> diff --git a/gnu/packages/patches/sajson-for-gemmi-numbers-as-
> strings.patch b/gnu/packages/patches/sajson-for-gemmi-numbers-as-
> strings.patch
> new file mode 100644
> index 0000000000..6f476b8583
> --- /dev/null
> +++ b/gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch
> @@ -0,0 +1,195 @@
> +Patch for gemmi: Keep numbers in JSON file as strings.
> +
> +Adapted from this commit of the bundled fork of sajson in gemmi:
> +
> https://github.com/project-gemmi/gemmi/commit/fccbca4f6040364ba708613e
> 1429c2251872240d
> +
> +diff -ur a/include/sajson.h b/include/sajson.h
> +--- a/include/sajson.h
> ++++ b/include/sajson.h
> +@@ -411,43 +411,6 @@
> + };
> + } // namespace internal
> + 
> +-namespace integer_storage {
> +-enum { word_length = 1 };
> +-
> +-inline int load(const size_t* location) {
> +-    int value;
> +-    memcpy(&value, location, sizeof(value));
> +-    return value;
> +-}
> +-
> +-inline void store(size_t* location, int value) {
> +-    // NOTE: Most modern compilers optimize away this constant-size
> +-    // memcpy into a single instruction. If any don't, and treat
> +-    // punning through a union as legal, they can be special-cased.
> +-    static_assert(
> +-        sizeof(value) <= sizeof(*location),
> +-        "size_t must not be smaller than int");
> +-    memcpy(location, &value, sizeof(value));
> +-}
> +-} // namespace integer_storage
> +-
> +-namespace double_storage {
> +-enum { word_length = sizeof(double) / sizeof(size_t) };
> +-
> +-inline double load(const size_t* location) {
> +-    double value;
> +-    memcpy(&value, location, sizeof(double));
> +-    return value;
> +-}
> +-
> +-inline void store(size_t* location, double value) {
> +-    // NOTE: Most modern compilers optimize away this constant-size
> +-    // memcpy into a single instruction. If any don't, and treat
> +-    // punning through a union as legal, they can be special-cased.
> +-    memcpy(location, &value, sizeof(double));
> +-}
> +-} // namespace double_storage
> +-
> + /// Represents a JSON value.  First, call get_type() to check its
> type,
> + /// which determines which methods are available.
> + ///
> +@@ -585,70 +548,10 @@
> +         return length;
> +     }
> + 
> +-    /// If a numeric value was parsed as a 32-bit integer, returns
> it.
> +-    /// Only legal if get_type() is TYPE_INTEGER.
> +-    int get_integer_value() const {
> +-        assert_tag(tag::integer);
> +-        return integer_storage::load(payload);
> +-    }
> +-
> +-    /// If a numeric value was parsed as a double, returns it.
> +-    /// Only legal if get_type() is TYPE_DOUBLE.
> +-    double get_double_value() const {
> +-        assert_tag(tag::double_);
> +-        return double_storage::load(payload);
> +-    }
> +-
> +-    /// Returns a numeric value as a double-precision float.
> +-    /// Only legal if get_type() is TYPE_INTEGER or TYPE_DOUBLE.
> +-    double get_number_value() const {
> +-        assert_tag_2(tag::integer, tag::double_);
> +-        if (value_tag == tag::integer) {
> +-            return get_integer_value();
> +-        } else {
> +-            return get_double_value();
> +-        }
> +-    }
> +-
> +-    /// Returns true and writes to the output argument if the
> numeric value
> +-    /// fits in a 53-bit integer.  This is useful for timestamps
> and other
> +-    /// situations where integral values with greater than 32-bit
> precision
> +-    /// are used, as 64-bit values are not understood by all JSON
> +-    /// implementations or languages.
> +-    /// Returns false if the value is not an integer or not in
> range.
> +-    /// Only legal if get_type() is TYPE_INTEGER or TYPE_DOUBLE.
> +-    bool get_int53_value(int64_t* out) const {
> +-        // Make sure the output variable is always defined to avoid
> any
> +-        // possible situation like
> +-        //
> https://gist.github.com/chadaustin/2c249cb850619ddec05b23ca42cf7a18
> +-        *out = 0;
> +-
> +-        assert_tag_2(tag::integer, tag::double_);
> +-        switch (value_tag) {
> +-        case tag::integer:
> +-            *out = get_integer_value();
> +-            return true;
> +-        case tag::double_: {
> +-            double v = get_double_value();
> +-            if (v < -(1LL << 53) || v > (1LL << 53)) {
> +-                return false;
> +-            }
> +-            int64_t as_int = static_cast<int64_t>(v);
> +-            if (as_int != v) {
> +-                return false;
> +-            }
> +-            *out = as_int;
> +-            return true;
> +-        }
> +-        default:
> +-            return false;
> +-        }
> +-    }
> +-
> +     /// Returns the length of the string.
> +     /// Only legal if get_type() is TYPE_STRING.
> +     size_t get_string_length() const {
> +-        assert_tag(tag::string);
> ++        assert_tag_3(tag::string, tag::integer, tag::double_);
> +         return payload[1] - payload[0];
> +     }
> + 
> +@@ -659,7 +562,7 @@
> +     /// embedded NULs.
> +     /// Only legal if get_type() is TYPE_STRING.
> +     const char* as_cstring() const {
> +-        assert_tag(tag::string);
> ++        assert_tag_3(tag::string, tag::integer, tag::double_);
> +         return text + payload[0];
> +     }
> + 
> +@@ -667,7 +570,7 @@
> +     /// Returns a string's value as a std::string.
> +     /// Only legal if get_type() is TYPE_STRING.
> +     std::string as_string() const {
> +-        assert_tag(tag::string);
> ++        assert_tag_3(tag::string, tag::integer, tag::double_);
> +         return std::string(text + payload[0], text + payload[1]);
> +     }
> + #endif
> +@@ -690,6 +593,10 @@
> +         assert(e1 == value_tag || e2 == value_tag);
> +     }
> + 
> ++    void assert_tag_3(tag e1, tag e2, tag e3) const {
> ++        assert(e1 == value_tag || e2 == value_tag || e3 ==
> value_tag);
> ++    }
> ++
> +     void assert_in_bounds(size_t i) const { assert(i <
> get_length()); }
> + 
> +     const tag value_tag;
> +@@ -2059,6 +1966,8 @@
> +     std::pair<char*, internal::tag> parse_number(char* p) {
> +         using internal::tag;
> + 
> ++      size_t start = p - input.get_data();
> ++
> +         // Assume 32-bit, two's complement integers.
> +         static constexpr unsigned RISKY = INT_MAX / 10u;
> +         unsigned max_digit_after_risky = INT_MAX % 10u;
> +@@ -2235,23 +2144,18 @@
> +                 u = 0u - u;
> +             }
> +         }
> ++
> ++        bool success;
> ++        size_t* out = allocator.reserve(2, &success);
> ++        if (SAJSON_UNLIKELY(!success)) {
> ++            return std::make_pair(oom(p, "number"), tag::null);
> ++        }
> ++        out[0] = start;
> ++        out[1] = p - input.get_data();
> ++
> +         if (try_double) {
> +-            bool success;
> +-            size_t* out
> +-                = allocator.reserve(double_storage::word_length,
> &success);
> +-            if (SAJSON_UNLIKELY(!success)) {
> +-                return std::make_pair(oom(p, "double"), tag::null);
> +-            }
> +-            double_storage::store(out, d);
> +             return std::make_pair(p, tag::double_);
> +         } else {
> +-            bool success;
> +-            size_t* out
> +-                = allocator.reserve(integer_storage::word_length,
> &success);
> +-            if (SAJSON_UNLIKELY(!success)) {
> +-                return std::make_pair(oom(p, "integer"),
> tag::null);
> +-            }
> +-            integer_storage::store(out, static_cast<int>(u));
> +             return std::make_pair(p, tag::integer);
> +         }
> +     }
Cheers

[bug#58261] [PATCH 06/11] gnu: Add gemmi.

[David Elsing]

Liliana Marie Prikler <liliana.prikler@ist.tugraz.at> writes:

> Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
>> * gnu/packages/chemistry.scm (gemmi): New variable.
>> ---
>>  gnu/packages/chemistry.scm                    | 122 +++++++++++
>>  .../patches/gemmi-fix-sajson-types.patch      |  11 +
>>  .../sajson-for-gemmi-numbers-as-strings.patch | 195
>> ++++++++++++++++++
>>  3 files changed, 328 insertions(+)
>>  create mode 100644 gnu/packages/patches/gemmi-fix-sajson-types.patch
>>  create mode 100644 gnu/packages/patches/sajson-for-gemmi-numbers-as-
>> strings.patch
>> 
>> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
>> index c517610fe8..f8fd85814f 100644
>> --- a/gnu/packages/chemistry.scm
>> +++ b/gnu/packages/chemistry.scm
>> @@ -6,6 +6,7 @@
>>  ;;; Copyright © 2020 Björn Höfling
>> <bjoern.hoefling@bjoernhoefling.de>
>>  ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
>>  ;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
>> +;;; Copyright © 2022 David Elsing <david.elsing@posteo.net>
>>  ;;;
>>  ;;; This file is part of GNU Guix.
>>  ;;;
>> @@ -23,6 +24,7 @@
>>  ;;; along with GNU Guix.  If not, see
>> <http://www.gnu.org/licenses/>.
>>  
>>  (define-module (gnu packages chemistry)
>> +  #:use-module (guix gexp)
>>    #:use-module (guix packages)
>>    #:use-module (guix utils)
>>    #:use-module ((guix licenses) #:prefix license:)
>> @@ -35,6 +37,7 @@ (define-module (gnu packages chemistry)
>>    #:use-module (gnu packages boost)
>>    #:use-module (gnu packages check)
>>    #:use-module (gnu packages compression)
>> +  #:use-module (gnu packages cpp)
>>    #:use-module (gnu packages documentation)
>>    #:use-module (gnu packages fontutils)
>>    #:use-module (gnu packages gl)
>> @@ -50,8 +53,10 @@ (define-module (gnu packages chemistry)
>>    #:use-module (gnu packages qt)
>>    #:use-module (gnu packages serialization)
>>    #:use-module (gnu packages sphinx)
>> +  #:use-module (gnu packages stb)
>>    #:use-module (gnu packages xml)
>>    #:use-module (guix build-system cmake)
>> +  #:use-module (guix build-system copy)
>>    #:use-module (guix build-system gnu)
>>    #:use-module (guix build-system python))
>>  
>> @@ -566,3 +571,120 @@ (define-public python-pymol
>>  used to prepare publication-quality figures, to share interactive
>> results with
>>  your colleagues, or to generate pre-rendered animations.")
>>      (license license:bsd-3)))
>> +
>> +(define sajson-for-gemmi
>> +  (package/inherit sajson
>> +    (name "sajson-for-gemmi")
>> +    (source (origin
>> +              (inherit (package-source sajson))
>> +              (patches (cons
>> +                        (search-patch
>> +                         "sajson-for-gemmi-numbers-as-
>> strings.patch")
>> +                        (origin-patches (package-source sajson))))))
>> +    (build-system copy-build-system)
>> +    (arguments
>> +     (list
>> +      #:install-plan
>> +      #~'(("include/sajson.h" "include/")
>> +          ("include/sajson_ostream.h" "include/"))))))
> These are technically two packages; therefore two patches.
> You should reuse as much as you can from sajson.  Since this patch is
> likely to break tests, you might use an appropriately annotated
> #:tests? #f to convey this information.
>
You mean to copy the GCC10 patch?
Building the tests also fails, but the rest works. :)
Should I put it in a separate commit?
>> +(define-public gemmi
>> +  (package
>> +    (name "gemmi")
>> +    (version "0.5.7")
>> +    (source (origin
>> +              (method git-fetch)
>> +              (uri (git-reference
>> +                    (url "https://github.com/project-gemmi/gemmi")
>> +                    (commit (string-append "v" version))))
>> +              (file-name (git-file-name name version))
>> +              (sha256
>> +               (base32
>> +               
>> "00km5q726bslrw7xbfwb3f3mrsk19qbimfnl3hvr4wi1y3z8i18a"))
>> +              (patches
>> +               (search-patches "gemmi-fix-sajson-types.patch"))
>> +              (modules '((guix build utils)))
>> +              (snippet
>> +               '(begin
>> +                  (delete-file-recursively
>> "include/gemmi/third_party")
>> +                  (delete-file-recursively "third_party")
>> +                  #t))))
>> +    (build-system cmake-build-system)
>> +    (native-inputs (list optionparser pybind11))
>> +    (propagated-inputs
>> +     (list fast-float
>> +           pocketfft
>> +           sajson-for-gemmi
>> +           stb-sprintf
>> +           pegtl
>> +           tinydir))
> Refrain from propagating inputs.
Ah ok.
>> +    (inputs (list zlib python))
>> +    (outputs '("out" "bin" "python"))
>> +    (arguments
> The usual sequence is outputs, build-system, arguments, *inputs.
Is there also a usual sequence for the *inputs?
>> +     (list
>> +      #:configure-flags
>> +      #~(let* ((python-lib
>> +                (string-append
>> +                 #$output:python "/lib/python"
>> +                 #$(version-major+minor (package-version python))
>> +                 "/site-packages")))
>> +          (list "-DUSE_PYTHON=ON"
>> +                (string-append "-DPYTHON_INSTALL_DIR=" python-lib)))
>> +      #:phases
>> +      #~(modify-phases %standard-phases
>> +          (add-after 'unpack 'patch-includes
>> +            (lambda _
>> +              (substitute* "include/gemmi/sprintf.hpp"
>> +                (("<stb/stb_sprintf.h>") "<stb_sprintf.h>"))
>> +              (substitute* "include/gemmi/dirwalk.hpp"
>> +                (("\"third_party/tinydir.h\"") "<tinydir.h>"))
>> +              (substitute* "include/gemmi/cif.hpp"
>> +                (("\"third_party/tao/pegtl.hpp\"")
>> "<tao/pegtl.hpp>"))
>> +              (substitute* "include/gemmi/json.hpp"
>> +                (("\"third_party/sajson.h\"") "<sajson.h>"))
>> +              (substitute* "python/gemmi.cpp"
>> +                (("\"gemmi/third_party/tao/pegtl/parse_error.hpp\"")
>> +                 "<tao/pegtl/parse_error.hpp>"))
>> +              (substitute* '("include/gemmi/atof.hpp"
>> +                             "include/gemmi/numb.hpp")
>> +                (("\"third_party/fast_float.h\"")
>> +                 "<fast_float/fast_float.h>"))
>> +              (substitute* "include/gemmi/fourier.hpp"
>> +                (("\"third_party/pocketfft_hdronly.h\"")
>> +                 "<pocketfft_hdronly.h>"))
>> +              #t))
>> +          (add-after 'patch-includes 'patch-cif
>> +            (lambda _
>> +              (substitute* "include/gemmi/cif.hpp"
>> +                (((string-append
>> +                   "^.*using analyze_t = pegtl::analysis::generic"
>> +                   "<pegtl::analysis::rule_type::ANY>;.*$")) "")
>> +                (("TAOCPP_PEGTL_") "TAO_PEGTL_"))
>> +              #t))
>> +          (add-after 'unpack 'change-bin-prefix
>> +            (lambda _
>> +              (substitute* "CMakeLists.txt"
>> +                (("install\\(TARGETS program DESTINATION bin\\)")
>> +                 (string-append
>> +                  "install(TARGETS program DESTINATION "
>> +                  #$output:bin "/bin)")))
>> +              #t))
>> +          (replace 'check
>> +            (lambda* (#:key tests? #:allow-other-keys)
>> +              (when tests?
>> +                (with-directory-excursion "../source"
>> +                  (setenv "PYTHONPATH" "../build")
>> +                  (invoke "python3" "-m" "unittest" "discover" "-v"
>> +                          "-s" "tests"))))))))
>> +    (home-page "https://gemmi.readthedocs.io/en/latest/")
>> +    (synopsis "Macromolecular crystallography library and
>> utilities")
>> +    (description "GEMMI is a C++ library for macromolecular
>> crystallography.
>> +It can be used for working with
>> +@enumerate
>> +@item macromolecular models (content of PDB, PDBx/mmCIF and mmJSON
>> files),
>> +@item refinement restraints (CIF files),
>> +@item reflection data (MTZ and mmCIF formats),
>> +@item data on a 3D grid (electron density maps, masks, MRC/CCP4
>> format)
>> +@item crystallographic symmetry.
>> +@end enumerate")
>> +    (license license:mpl2.0)))
>> diff --git a/gnu/packages/patches/gemmi-fix-sajson-types.patch
>> b/gnu/packages/patches/gemmi-fix-sajson-types.patch
>> new file mode 100644
>> index 0000000000..9633ddac8b
>> --- /dev/null
>> +++ b/gnu/packages/patches/gemmi-fix-sajson-types.patch
>> @@ -0,0 +1,11 @@
>> +diff -ur a/include/gemmi/json.hpp b/include/gemmi/json.hpp
>> +--- a/include/gemmi/json.hpp
>> ++++ b/include/gemmi/json.hpp
>> +@@ -38,6 +38,7 @@
>> + 
>> + inline std::string as_cif_value(const sajson::value& val) {
>> +   switch (val.get_type()) {
>> ++    case sajson::TYPE_INTEGER:
>> +     case sajson::TYPE_DOUBLE:
>> +       return val.as_string();
>> +     case sajson::TYPE_NULL:
>> diff --git a/gnu/packages/patches/sajson-for-gemmi-numbers-as-
>> strings.patch b/gnu/packages/patches/sajson-for-gemmi-numbers-as-
>> strings.patch
>> new file mode 100644
>> index 0000000000..6f476b8583
>> --- /dev/null
>> +++ b/gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch
>> @@ -0,0 +1,195 @@
>> +Patch for gemmi: Keep numbers in JSON file as strings.
>> +
>> +Adapted from this commit of the bundled fork of sajson in gemmi:
>> +
>> https://github.com/project-gemmi/gemmi/commit/fccbca4f6040364ba708613e
>> 1429c2251872240d
>> +
>> +diff -ur a/include/sajson.h b/include/sajson.h
>> +--- a/include/sajson.h
>> ++++ b/include/sajson.h
>> +@@ -411,43 +411,6 @@
>> + };
>> + } // namespace internal
>> + 
>> +-namespace integer_storage {
>> +-enum { word_length = 1 };
>> +-
>> +-inline int load(const size_t* location) {
>> +-    int value;
>> +-    memcpy(&value, location, sizeof(value));
>> +-    return value;
>> +-}
>> +-
>> +-inline void store(size_t* location, int value) {
>> +-    // NOTE: Most modern compilers optimize away this constant-size
>> +-    // memcpy into a single instruction. If any don't, and treat
>> +-    // punning through a union as legal, they can be special-cased.
>> +-    static_assert(
>> +-        sizeof(value) <= sizeof(*location),
>> +-        "size_t must not be smaller than int");
>> +-    memcpy(location, &value, sizeof(value));
>> +-}
>> +-} // namespace integer_storage
>> +-
>> +-namespace double_storage {
>> +-enum { word_length = sizeof(double) / sizeof(size_t) };
>> +-
>> +-inline double load(const size_t* location) {
>> +-    double value;
>> +-    memcpy(&value, location, sizeof(double));
>> +-    return value;
>> +-}
>> +-
>> +-inline void store(size_t* location, double value) {
>> +-    // NOTE: Most modern compilers optimize away this constant-size
>> +-    // memcpy into a single instruction. If any don't, and treat
>> +-    // punning through a union as legal, they can be special-cased.
>> +-    memcpy(location, &value, sizeof(double));
>> +-}
>> +-} // namespace double_storage
>> +-
>> + /// Represents a JSON value.  First, call get_type() to check its
>> type,
>> + /// which determines which methods are available.
>> + ///
>> +@@ -585,70 +548,10 @@
>> +         return length;
>> +     }
>> + 
>> +-    /// If a numeric value was parsed as a 32-bit integer, returns
>> it.
>> +-    /// Only legal if get_type() is TYPE_INTEGER.
>> +-    int get_integer_value() const {
>> +-        assert_tag(tag::integer);
>> +-        return integer_storage::load(payload);
>> +-    }
>> +-
>> +-    /// If a numeric value was parsed as a double, returns it.
>> +-    /// Only legal if get_type() is TYPE_DOUBLE.
>> +-    double get_double_value() const {
>> +-        assert_tag(tag::double_);
>> +-        return double_storage::load(payload);
>> +-    }
>> +-
>> +-    /// Returns a numeric value as a double-precision float.
>> +-    /// Only legal if get_type() is TYPE_INTEGER or TYPE_DOUBLE.
>> +-    double get_number_value() const {
>> +-        assert_tag_2(tag::integer, tag::double_);
>> +-        if (value_tag == tag::integer) {
>> +-            return get_integer_value();
>> +-        } else {
>> +-            return get_double_value();
>> +-        }
>> +-    }
>> +-
>> +-    /// Returns true and writes to the output argument if the
>> numeric value
>> +-    /// fits in a 53-bit integer.  This is useful for timestamps
>> and other
>> +-    /// situations where integral values with greater than 32-bit
>> precision
>> +-    /// are used, as 64-bit values are not understood by all JSON
>> +-    /// implementations or languages.
>> +-    /// Returns false if the value is not an integer or not in
>> range.
>> +-    /// Only legal if get_type() is TYPE_INTEGER or TYPE_DOUBLE.
>> +-    bool get_int53_value(int64_t* out) const {
>> +-        // Make sure the output variable is always defined to avoid
>> any
>> +-        // possible situation like
>> +-        //
>> https://gist.github.com/chadaustin/2c249cb850619ddec05b23ca42cf7a18
>> +-        *out = 0;
>> +-
>> +-        assert_tag_2(tag::integer, tag::double_);
>> +-        switch (value_tag) {
>> +-        case tag::integer:
>> +-            *out = get_integer_value();
>> +-            return true;
>> +-        case tag::double_: {
>> +-            double v = get_double_value();
>> +-            if (v < -(1LL << 53) || v > (1LL << 53)) {
>> +-                return false;
>> +-            }
>> +-            int64_t as_int = static_cast<int64_t>(v);
>> +-            if (as_int != v) {
>> +-                return false;
>> +-            }
>> +-            *out = as_int;
>> +-            return true;
>> +-        }
>> +-        default:
>> +-            return false;
>> +-        }
>> +-    }
>> +-
>> +     /// Returns the length of the string.
>> +     /// Only legal if get_type() is TYPE_STRING.
>> +     size_t get_string_length() const {
>> +-        assert_tag(tag::string);
>> ++        assert_tag_3(tag::string, tag::integer, tag::double_);
>> +         return payload[1] - payload[0];
>> +     }
>> + 
>> +@@ -659,7 +562,7 @@
>> +     /// embedded NULs.
>> +     /// Only legal if get_type() is TYPE_STRING.
>> +     const char* as_cstring() const {
>> +-        assert_tag(tag::string);
>> ++        assert_tag_3(tag::string, tag::integer, tag::double_);
>> +         return text + payload[0];
>> +     }
>> + 
>> +@@ -667,7 +570,7 @@
>> +     /// Returns a string's value as a std::string.
>> +     /// Only legal if get_type() is TYPE_STRING.
>> +     std::string as_string() const {
>> +-        assert_tag(tag::string);
>> ++        assert_tag_3(tag::string, tag::integer, tag::double_);
>> +         return std::string(text + payload[0], text + payload[1]);
>> +     }
>> + #endif
>> +@@ -690,6 +593,10 @@
>> +         assert(e1 == value_tag || e2 == value_tag);
>> +     }
>> + 
>> ++    void assert_tag_3(tag e1, tag e2, tag e3) const {
>> ++        assert(e1 == value_tag || e2 == value_tag || e3 ==
>> value_tag);
>> ++    }
>> ++
>> +     void assert_in_bounds(size_t i) const { assert(i <
>> get_length()); }
>> + 
>> +     const tag value_tag;
>> +@@ -2059,6 +1966,8 @@
>> +     std::pair<char*, internal::tag> parse_number(char* p) {
>> +         using internal::tag;
>> + 
>> ++      size_t start = p - input.get_data();
>> ++
>> +         // Assume 32-bit, two's complement integers.
>> +         static constexpr unsigned RISKY = INT_MAX / 10u;
>> +         unsigned max_digit_after_risky = INT_MAX % 10u;
>> +@@ -2235,23 +2144,18 @@
>> +                 u = 0u - u;
>> +             }
>> +         }
>> ++
>> ++        bool success;
>> ++        size_t* out = allocator.reserve(2, &success);
>> ++        if (SAJSON_UNLIKELY(!success)) {
>> ++            return std::make_pair(oom(p, "number"), tag::null);
>> ++        }
>> ++        out[0] = start;
>> ++        out[1] = p - input.get_data();
>> ++
>> +         if (try_double) {
>> +-            bool success;
>> +-            size_t* out
>> +-                = allocator.reserve(double_storage::word_length,
>> &success);
>> +-            if (SAJSON_UNLIKELY(!success)) {
>> +-                return std::make_pair(oom(p, "double"), tag::null);
>> +-            }
>> +-            double_storage::store(out, d);
>> +             return std::make_pair(p, tag::double_);
>> +         } else {
>> +-            bool success;
>> +-            size_t* out
>> +-                = allocator.reserve(integer_storage::word_length,
>> &success);
>> +-            if (SAJSON_UNLIKELY(!success)) {
>> +-                return std::make_pair(oom(p, "integer"),
>> tag::null);
>> +-            }
>> +-            integer_storage::store(out, static_cast<int>(u));
>> +             return std::make_pair(p, tag::integer);
>> +         }
>> +     }
> Cheers

[bug#58261] [PATCH 06/11] gnu: Add gemmi.

[Liliana Marie Prikler]

Am Freitag, dem 07.10.2022 um 15:11 +0000 schrieb David Elsing:
> Liliana Marie Prikler <liliana.prikler@ist.tugraz.at> writes:
> 
> > Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
> > > * gnu/packages/chemistry.scm (gemmi): New variable.
> > > ---
> > >  gnu/packages/chemistry.scm                    | 122 +++++++++++
> > >  .../patches/gemmi-fix-sajson-types.patch      |  11 +
> > >  .../sajson-for-gemmi-numbers-as-strings.patch | 195
> > > ++++++++++++++++++
> > >  3 files changed, 328 insertions(+)
> > >  create mode 100644 gnu/packages/patches/gemmi-fix-sajson-
> > > types.patch
> > >  create mode 100644 gnu/packages/patches/sajson-for-gemmi-
> > > numbers-as-
> > > strings.patch
> > > 
> > > diff --git a/gnu/packages/chemistry.scm
> > > b/gnu/packages/chemistry.scm
> > > index c517610fe8..f8fd85814f 100644
> > > --- a/gnu/packages/chemistry.scm
> > > +++ b/gnu/packages/chemistry.scm
> > > @@ -6,6 +6,7 @@
> > >  ;;; Copyright © 2020 Björn Höfling
> > > <bjoern.hoefling@bjoernhoefling.de>
> > >  ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
> > >  ;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
> > > +;;; Copyright © 2022 David Elsing <david.elsing@posteo.net>
> > >  ;;;
> > >  ;;; This file is part of GNU Guix.
> > >  ;;;
> > > @@ -23,6 +24,7 @@
> > >  ;;; along with GNU Guix.  If not, see
> > > <http://www.gnu.org/licenses/>.
> > >  
> > >  (define-module (gnu packages chemistry)
> > > +  #:use-module (guix gexp)
> > >    #:use-module (guix packages)
> > >    #:use-module (guix utils)
> > >    #:use-module ((guix licenses) #:prefix license:)
> > > @@ -35,6 +37,7 @@ (define-module (gnu packages chemistry)
> > >    #:use-module (gnu packages boost)
> > >    #:use-module (gnu packages check)
> > >    #:use-module (gnu packages compression)
> > > +  #:use-module (gnu packages cpp)
> > >    #:use-module (gnu packages documentation)
> > >    #:use-module (gnu packages fontutils)
> > >    #:use-module (gnu packages gl)
> > > @@ -50,8 +53,10 @@ (define-module (gnu packages chemistry)
> > >    #:use-module (gnu packages qt)
> > >    #:use-module (gnu packages serialization)
> > >    #:use-module (gnu packages sphinx)
> > > +  #:use-module (gnu packages stb)
> > >    #:use-module (gnu packages xml)
> > >    #:use-module (guix build-system cmake)
> > > +  #:use-module (guix build-system copy)
> > >    #:use-module (guix build-system gnu)
> > >    #:use-module (guix build-system python))
> > >  
> > > @@ -566,3 +571,120 @@ (define-public python-pymol
> > >  used to prepare publication-quality figures, to share
> > > interactive
> > > results with
> > >  your colleagues, or to generate pre-rendered animations.")
> > >      (license license:bsd-3)))
> > > +
> > > +(define sajson-for-gemmi
> > > +  (package/inherit sajson
> > > +    (name "sajson-for-gemmi")
> > > +    (source (origin
> > > +              (inherit (package-source sajson))
> > > +              (patches (cons
> > > +                        (search-patch
> > > +                         "sajson-for-gemmi-numbers-as-
> > > strings.patch")
> > > +                        (origin-patches (package-source
> > > sajson))))))
> > > +    (build-system copy-build-system)
> > > +    (arguments
> > > +     (list
> > > +      #:install-plan
> > > +      #~'(("include/sajson.h" "include/")
> > > +          ("include/sajson_ostream.h" "include/"))))))
> > These are technically two packages; therefore two patches.
> > You should reuse as much as you can from sajson.  Since this patch
> > is
> > likely to break tests, you might use an appropriately annotated
> > #:tests? #f to convey this information.
> > 
> You mean to copy the GCC10 patch?
> Building the tests also fails, but the rest works. :)
> Should I put it in a separate commit?
One commit for sajson-for-gemmi, one commit for gemmi.
"Reuse as much as possible" particularly means reuse the build system,
but highlight that #:tests? need to be set to #f.  (Also, use
substitute-keyword-arguments to actually set it to #f.)

> > > +(define-public gemmi
> > > +  (package
> > > +    (name "gemmi")
> > > +    (version "0.5.7")
> > > +    (source (origin
> > > +              (method git-fetch)
> > > +              (uri (git-reference
> > > +                    (url
> > > "https://github.com/project-gemmi/gemmi")
> > > +                    (commit (string-append "v" version))))
> > > +              (file-name (git-file-name name version))
> > > +              (sha256
> > > +               (base32
> > > +               
> > > "00km5q726bslrw7xbfwb3f3mrsk19qbimfnl3hvr4wi1y3z8i18a"))
> > > +              (patches
> > > +               (search-patches "gemmi-fix-sajson-types.patch"))
> > > +              (modules '((guix build utils)))
> > > +              (snippet
> > > +               '(begin
> > > +                  (delete-file-recursively
> > > "include/gemmi/third_party")
> > > +                  (delete-file-recursively "third_party")
> > > +                  #t))))
> > > +    (build-system cmake-build-system)
> > > +    (native-inputs (list optionparser pybind11))
> > > +    (propagated-inputs
> > > +     (list fast-float
> > > +           pocketfft
> > > +           sajson-for-gemmi
> > > +           stb-sprintf
> > > +           pegtl
> > > +           tinydir))
> > Refrain from propagating inputs.
> Ah ok.
> > > +    (inputs (list zlib python))
> > > +    (outputs '("out" "bin" "python"))
> > > +    (arguments
> > The usual sequence is outputs, build-system, arguments, *inputs.
> Is there also a usual sequence for the *inputs?
IIRC it's plain, propagated, native.
> > 

Cheers

[bug#58261] [PATCH 07/11] gnu: Add freesasa.

[David Elsing]

* gnu/packages/chemistry.scm (freesasa): New variable.
---
 gnu/packages/chemistry.scm | 81 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 81 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index f8fd85814f..223a27a20d 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -34,11 +34,13 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages backup)
+  #:use-module (gnu packages bison)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cpp)
   #:use-module (gnu packages documentation)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages graphviz)
@@ -54,6 +56,7 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages sphinx)
   #:use-module (gnu packages stb)
+  #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system copy)
@@ -688,3 +691,81 @@ (define-public gemmi
 @item crystallographic symmetry.
 @end enumerate")
     (license license:mpl2.0)))
+
+(define-public freesasa
+  (package
+    (name "freesasa")
+    (version "2.1.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/mittinatten/freesasa")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "07wdnahf3g355ryaiqvfxd5f4rl54wv8jwxcbn0nia89fqysbv0f"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Remove C files generated by Flex and Bison
+                  (for-each delete-file
+                            '("src/parser.c" "src/parser.h"
+                              "src/lexer.c" "src/lexer.h"))
+                  #t))))
+    (build-system gnu-build-system)
+    (inputs
+     (list gemmi json-c libxml2))
+    (native-inputs
+     (list bison flex check autoconf automake pkg-config doxygen perl libtool))
+    (outputs '("out" "doc"))
+    (arguments
+     (list
+      #:configure-flags
+      #~(list "--enable-check"
+              "--enable-parser-generator"
+              "CXXFLAGS=-std=c++17"
+              "--enable-doxygen")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'remove-libc++-linking
+            (lambda _
+              (substitute* "src/Makefile.am"
+                (("-lc\\+\\+") ""))
+              #t))
+          (add-after 'unpack 'build-shared-library
+            (lambda _
+              (substitute* "src/Makefile.am"
+                (("lib_LIBRARIES") "lib_LTLIBRARIES")
+                (("libfreesasa\\.a") "libfreesasa.la")
+                (("freesasa_LDADD \\+= libfreesasa\\.la" prev)
+                 (string-append prev "\nlibfreesasa_la_LIBADD"
+                                " = -ljson-c ${libxml2_LIBS}\n"))
+                (("_a_SOURCES") "_la_SOURCES"))
+              (substitute* "configure.ac"
+                (("AC_PROG_INSTALL" inst)
+                 (string-append "AM_PROG_LIBTOOL\n" inst)))
+              (substitute* "tests/Makefile.am"
+                (("libfreesasa\\.a") "libfreesasa.la"))
+              #t))
+          (add-before 'build 'build-lexer-and-parser
+            (lambda _
+              (with-directory-excursion "src"
+                (invoke "make" "lexer.h")
+                (invoke "make" "parser.h"))
+              #t))
+          (add-after 'install 'install-doc
+            (lambda _
+              (copy-recursively
+               "doc/html"
+               (string-append #$output:doc "/share/doc/" #$name "-" #$version))
+              #t)))))
+    (home-page "https://freesasa.github.io/")
+    (synopsis "Library for calculating the solvent accessible surface area
+(SASA) of molecules")
+    (description "FreeSASA is a command line tool and C-library for
+calculating solvent accessible surface areas (SASA).  By default Lee &
+Richards' algorithm is used, but Shrake & Rupley's is also available.  Both can
+be parameterized to arbitrary precision, and for high resolution versions of
+the algorithms, the calculations give identical results.")
+    (license license:expat)))
-- 
2.37.0

[bug#58261] [PATCH 07/11] gnu: Add freesasa.

[Liliana Marie Prikler]

Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
> * gnu/packages/chemistry.scm (freesasa): New variable.
> ---
>  gnu/packages/chemistry.scm | 81
> ++++++++++++++++++++++++++++++++++++++
>  1 file changed, 81 insertions(+)
> 
> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
> index f8fd85814f..223a27a20d 100644
> --- a/gnu/packages/chemistry.scm
> +++ b/gnu/packages/chemistry.scm
> @@ -34,11 +34,13 @@ (define-module (gnu packages chemistry)
>    #:use-module (gnu packages algebra)
>    #:use-module (gnu packages autotools)
>    #:use-module (gnu packages backup)
> +  #:use-module (gnu packages bison)
>    #:use-module (gnu packages boost)
>    #:use-module (gnu packages check)
>    #:use-module (gnu packages compression)
>    #:use-module (gnu packages cpp)
>    #:use-module (gnu packages documentation)
> +  #:use-module (gnu packages flex)
>    #:use-module (gnu packages fontutils)
>    #:use-module (gnu packages gl)
>    #:use-module (gnu packages graphviz)
> @@ -54,6 +56,7 @@ (define-module (gnu packages chemistry)
>    #:use-module (gnu packages serialization)
>    #:use-module (gnu packages sphinx)
>    #:use-module (gnu packages stb)
> +  #:use-module (gnu packages web)
>    #:use-module (gnu packages xml)
>    #:use-module (guix build-system cmake)
>    #:use-module (guix build-system copy)
> @@ -688,3 +691,81 @@ (define-public gemmi
>  @item crystallographic symmetry.
>  @end enumerate")
>      (license license:mpl2.0)))
> +
> +(define-public freesasa
> +  (package
> +    (name "freesasa")
> +    (version "2.1.2")
> +    (source (origin
> +              (method git-fetch)
> +              (uri (git-reference
> +                    (url "https://github.com/mittinatten/freesasa")
> +                    (commit version)))
> +              (file-name (git-file-name name version))
> +              (sha256
> +               (base32
> +               
> "07wdnahf3g355ryaiqvfxd5f4rl54wv8jwxcbn0nia89fqysbv0f"))
> +              (modules '((guix build utils)))
> +              (snippet
> +               '(begin
> +                  ;; Remove C files generated by Flex and Bison
> +                  (for-each delete-file
> +                            '("src/parser.c" "src/parser.h"
> +                              "src/lexer.c" "src/lexer.h"))
> +                  #t))))
> +    (build-system gnu-build-system)
> +    (inputs
> +     (list gemmi json-c libxml2))
> +    (native-inputs
> +     (list bison flex check autoconf automake pkg-config doxygen
> perl libtool))
> +    (outputs '("out" "doc"))
> +    (arguments
> +     (list
> +      #:configure-flags
> +      #~(list "--enable-check"
> +              "--enable-parser-generator"
> +              "CXXFLAGS=-std=c++17"
> +              "--enable-doxygen")
> +      #:phases
> +      #~(modify-phases %standard-phases
> +          (add-after 'unpack 'remove-libc++-linking
> +            (lambda _
> +              (substitute* "src/Makefile.am"
> +                (("-lc\\+\\+") ""))
> +              #t))
Why?  If it's because you're building a shared library, do this in the
next phase.
> +          (add-after 'unpack 'build-shared-library
> +            (lambda _
> +              (substitute* "src/Makefile.am"
> +                (("lib_LIBRARIES") "lib_LTLIBRARIES")
> +                (("libfreesasa\\.a") "libfreesasa.la")
> +                (("freesasa_LDADD \\+= libfreesasa\\.la" prev)
> +                 (string-append prev "\nlibfreesasa_la_LIBADD"
> +                                " = -ljson-c ${libxml2_LIBS}\n"))
> +                (("_a_SOURCES") "_la_SOURCES"))
> +              (substitute* "configure.ac"
> +                (("AC_PROG_INSTALL" inst)
> +                 (string-append "AM_PROG_LIBTOOL\n" inst)))
> +              (substitute* "tests/Makefile.am"
> +                (("libfreesasa\\.a") "libfreesasa.la"))
> +              #t))
> +          (add-before 'build 'build-lexer-and-parser
> +            (lambda _
> +              (with-directory-excursion "src"
> +                (invoke "make" "lexer.h")
> +                (invoke "make" "parser.h"))
> +              #t))
You can do this in one make.
> +          (add-after 'install 'install-doc
> +            (lambda _
> +              (copy-recursively
> +               "doc/html"
> +               (string-append #$output:doc "/share/doc/" #$name "-"
> #$version))
> +              #t)))))
> +    (home-page "https://freesasa.github.io/")
> +    (synopsis "Library for calculating the solvent accessible
> surface area
> +(SASA) of molecules")
"Calculate the..."
> +    (description "FreeSASA is a command line tool and C-library for
> +calculating solvent accessible surface areas (SASA).  By default Lee
> &
Use @abbr.
> +Richards' algorithm is used, but Shrake & Rupley's is also
> available.  Both can
> +be parameterized to arbitrary precision, and for high resolution
> versions of
> +the algorithms, the calculations give identical results.")
> +    (license license:expat)))

Cheers

[bug#58261] [PATCH 07/11] gnu: Add freesasa.

[David Elsing]

Liliana Marie Prikler <liliana.prikler@ist.tugraz.at> writes:

> Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
>> * gnu/packages/chemistry.scm (freesasa): New variable.
>> ---
>>  gnu/packages/chemistry.scm | 81
>> ++++++++++++++++++++++++++++++++++++++
>>  1 file changed, 81 insertions(+)
>> 
>> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
>> index f8fd85814f..223a27a20d 100644
>> --- a/gnu/packages/chemistry.scm
>> +++ b/gnu/packages/chemistry.scm
>> @@ -34,11 +34,13 @@ (define-module (gnu packages chemistry)
>>    #:use-module (gnu packages algebra)
>>    #:use-module (gnu packages autotools)
>>    #:use-module (gnu packages backup)
>> +  #:use-module (gnu packages bison)
>>    #:use-module (gnu packages boost)
>>    #:use-module (gnu packages check)
>>    #:use-module (gnu packages compression)
>>    #:use-module (gnu packages cpp)
>>    #:use-module (gnu packages documentation)
>> +  #:use-module (gnu packages flex)
>>    #:use-module (gnu packages fontutils)
>>    #:use-module (gnu packages gl)
>>    #:use-module (gnu packages graphviz)
>> @@ -54,6 +56,7 @@ (define-module (gnu packages chemistry)
>>    #:use-module (gnu packages serialization)
>>    #:use-module (gnu packages sphinx)
>>    #:use-module (gnu packages stb)
>> +  #:use-module (gnu packages web)
>>    #:use-module (gnu packages xml)
>>    #:use-module (guix build-system cmake)
>>    #:use-module (guix build-system copy)
>> @@ -688,3 +691,81 @@ (define-public gemmi
>>  @item crystallographic symmetry.
>>  @end enumerate")
>>      (license license:mpl2.0)))
>> +
>> +(define-public freesasa
>> +  (package
>> +    (name "freesasa")
>> +    (version "2.1.2")
>> +    (source (origin
>> +              (method git-fetch)
>> +              (uri (git-reference
>> +                    (url "https://github.com/mittinatten/freesasa")
>> +                    (commit version)))
>> +              (file-name (git-file-name name version))
>> +              (sha256
>> +               (base32
>> +               
>> "07wdnahf3g355ryaiqvfxd5f4rl54wv8jwxcbn0nia89fqysbv0f"))
>> +              (modules '((guix build utils)))
>> +              (snippet
>> +               '(begin
>> +                  ;; Remove C files generated by Flex and Bison
>> +                  (for-each delete-file
>> +                            '("src/parser.c" "src/parser.h"
>> +                              "src/lexer.c" "src/lexer.h"))
>> +                  #t))))
>> +    (build-system gnu-build-system)
>> +    (inputs
>> +     (list gemmi json-c libxml2))
>> +    (native-inputs
>> +     (list bison flex check autoconf automake pkg-config doxygen
>> perl libtool))
>> +    (outputs '("out" "doc"))
>> +    (arguments
>> +     (list
>> +      #:configure-flags
>> +      #~(list "--enable-check"
>> +              "--enable-parser-generator"
>> +              "CXXFLAGS=-std=c++17"
>> +              "--enable-doxygen")
>> +      #:phases
>> +      #~(modify-phases %standard-phases
>> +          (add-after 'unpack 'remove-libc++-linking
>> +            (lambda _
>> +              (substitute* "src/Makefile.am"
>> +                (("-lc\\+\\+") ""))
>> +              #t))
> Why?  If it's because you're building a shared library, do this in the
> next phase.
This is libc++ from LLVM and the linking against the standard library is
automatic anyway, right?
>> +          (add-after 'unpack 'build-shared-library
>> +            (lambda _
>> +              (substitute* "src/Makefile.am"
>> +                (("lib_LIBRARIES") "lib_LTLIBRARIES")
>> +                (("libfreesasa\\.a") "libfreesasa.la")
>> +                (("freesasa_LDADD \\+= libfreesasa\\.la" prev)
>> +                 (string-append prev "\nlibfreesasa_la_LIBADD"
>> +                                " = -ljson-c ${libxml2_LIBS}\n"))
>> +                (("_a_SOURCES") "_la_SOURCES"))
>> +              (substitute* "configure.ac"
>> +                (("AC_PROG_INSTALL" inst)
>> +                 (string-append "AM_PROG_LIBTOOL\n" inst)))
>> +              (substitute* "tests/Makefile.am"
>> +                (("libfreesasa\\.a") "libfreesasa.la"))
>> +              #t))
>> +          (add-before 'build 'build-lexer-and-parser
>> +            (lambda _
>> +              (with-directory-excursion "src"
>> +                (invoke "make" "lexer.h")
>> +                (invoke "make" "parser.h"))
>> +              #t))
> You can do this in one make.
>> +          (add-after 'install 'install-doc
>> +            (lambda _
>> +              (copy-recursively
>> +               "doc/html"
>> +               (string-append #$output:doc "/share/doc/" #$name "-"
>> #$version))
>> +              #t)))))
>> +    (home-page "https://freesasa.github.io/")
>> +    (synopsis "Library for calculating the solvent accessible
>> surface area
>> +(SASA) of molecules")
> "Calculate the..."
>> +    (description "FreeSASA is a command line tool and C-library for
>> +calculating solvent accessible surface areas (SASA).  By default Lee
>> &
> Use @abbr.
I get the error "warning: invalid Texinfo markup", do you have an idea why?
>> +Richards' algorithm is used, but Shrake & Rupley's is also
>> available.  Both can
>> +be parameterized to arbitrary precision, and for high resolution
>> versions of
>> +the algorithms, the calculations give identical results.")
>> +    (license license:expat)))
>
> Cheers

[bug#58261] [PATCH 07/11] gnu: Add freesasa.

[Liliana Marie Prikler]

Am Freitag, dem 07.10.2022 um 15:12 +0000 schrieb David Elsing:
> Liliana Marie Prikler <liliana.prikler@ist.tugraz.at> writes:
> 
> > Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
> > > * gnu/packages/chemistry.scm (freesasa): New variable.
> > > ---
> > >  gnu/packages/chemistry.scm | 81
> > > ++++++++++++++++++++++++++++++++++++++
> > >  1 file changed, 81 insertions(+)
> > > 
> > > diff --git a/gnu/packages/chemistry.scm
> > > b/gnu/packages/chemistry.scm
> > > index f8fd85814f..223a27a20d 100644
> > > --- a/gnu/packages/chemistry.scm
> > > +++ b/gnu/packages/chemistry.scm
> > > @@ -34,11 +34,13 @@ (define-module (gnu packages chemistry)
> > >    #:use-module (gnu packages algebra)
> > >    #:use-module (gnu packages autotools)
> > >    #:use-module (gnu packages backup)
> > > +  #:use-module (gnu packages bison)
> > >    #:use-module (gnu packages boost)
> > >    #:use-module (gnu packages check)
> > >    #:use-module (gnu packages compression)
> > >    #:use-module (gnu packages cpp)
> > >    #:use-module (gnu packages documentation)
> > > +  #:use-module (gnu packages flex)
> > >    #:use-module (gnu packages fontutils)
> > >    #:use-module (gnu packages gl)
> > >    #:use-module (gnu packages graphviz)
> > > @@ -54,6 +56,7 @@ (define-module (gnu packages chemistry)
> > >    #:use-module (gnu packages serialization)
> > >    #:use-module (gnu packages sphinx)
> > >    #:use-module (gnu packages stb)
> > > +  #:use-module (gnu packages web)
> > >    #:use-module (gnu packages xml)
> > >    #:use-module (guix build-system cmake)
> > >    #:use-module (guix build-system copy)
> > > @@ -688,3 +691,81 @@ (define-public gemmi
> > >  @item crystallographic symmetry.
> > >  @end enumerate")
> > >      (license license:mpl2.0)))
> > > +
> > > +(define-public freesasa
> > > +  (package
> > > +    (name "freesasa")
> > > +    (version "2.1.2")
> > > +    (source (origin
> > > +              (method git-fetch)
> > > +              (uri (git-reference
> > > +                    (url
> > > "https://github.com/mittinatten/freesasa")
> > > +                    (commit version)))
> > > +              (file-name (git-file-name name version))
> > > +              (sha256
> > > +               (base32
> > > +               
> > > "07wdnahf3g355ryaiqvfxd5f4rl54wv8jwxcbn0nia89fqysbv0f"))
> > > +              (modules '((guix build utils)))
> > > +              (snippet
> > > +               '(begin
> > > +                  ;; Remove C files generated by Flex and Bison
> > > +                  (for-each delete-file
> > > +                            '("src/parser.c" "src/parser.h"
> > > +                              "src/lexer.c" "src/lexer.h"))
> > > +                  #t))))
> > > +    (build-system gnu-build-system)
> > > +    (inputs
> > > +     (list gemmi json-c libxml2))
> > > +    (native-inputs
> > > +     (list bison flex check autoconf automake pkg-config doxygen
> > > perl libtool))
> > > +    (outputs '("out" "doc"))
> > > +    (arguments
> > > +     (list
> > > +      #:configure-flags
> > > +      #~(list "--enable-check"
> > > +              "--enable-parser-generator"
> > > +              "CXXFLAGS=-std=c++17"
> > > +              "--enable-doxygen")
> > > +      #:phases
> > > +      #~(modify-phases %standard-phases
> > > +          (add-after 'unpack 'remove-libc++-linking
> > > +            (lambda _
> > > +              (substitute* "src/Makefile.am"
> > > +                (("-lc\\+\\+") ""))
> > > +              #t))
> > Why?  If it's because you're building a shared library, do this in
> > the
> > next phase.
> This is libc++ from LLVM and the linking against the standard library
> is
> automatic anyway, right?
> > > +          (add-after 'unpack 'build-shared-library
> > > +            (lambda _
> > > +              (substitute* "src/Makefile.am"
> > > +                (("lib_LIBRARIES") "lib_LTLIBRARIES")
> > > +                (("libfreesasa\\.a") "libfreesasa.la")
> > > +                (("freesasa_LDADD \\+= libfreesasa\\.la" prev)
> > > +                 (string-append prev "\nlibfreesasa_la_LIBADD"
> > > +                                " = -ljson-c
> > > ${libxml2_LIBS}\n"))
> > > +                (("_a_SOURCES") "_la_SOURCES"))
> > > +              (substitute* "configure.ac"
> > > +                (("AC_PROG_INSTALL" inst)
> > > +                 (string-append "AM_PROG_LIBTOOL\n" inst)))
> > > +              (substitute* "tests/Makefile.am"
> > > +                (("libfreesasa\\.a") "libfreesasa.la"))
> > > +              #t))
> > > +          (add-before 'build 'build-lexer-and-parser
> > > +            (lambda _
> > > +              (with-directory-excursion "src"
> > > +                (invoke "make" "lexer.h")
> > > +                (invoke "make" "parser.h"))
> > > +              #t))
> > You can do this in one make.
> > > +          (add-after 'install 'install-doc
> > > +            (lambda _
> > > +              (copy-recursively
> > > +               "doc/html"
> > > +               (string-append #$output:doc "/share/doc/" #$name
> > > "-"
> > > #$version))
> > > +              #t)))))
> > > +    (home-page "https://freesasa.github.io/")
> > > +    (synopsis "Library for calculating the solvent accessible
> > > surface area
> > > +(SASA) of molecules")
> > "Calculate the..."
> > > +    (description "FreeSASA is a command line tool and C-library
> > > for
> > > +calculating solvent accessible surface areas (SASA).  By default
> > > Lee
> > > &
> > Use @abbr.
> I get the error "warning: invalid Texinfo markup", do you have an
> idea why?
> > 
Typo'd?  @abbr{SASA, solvent accessible surface areas}

[bug#58261] [PATCH 08/11] gnu: Add maeparser.

[David Elsing]

* gnu/packages/chemistry.scm (maeparser): New variable.
---
 gnu/packages/chemistry.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 223a27a20d..4d8ce66230 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -769,3 +769,24 @@ (define-public freesasa
 be parameterized to arbitrary precision, and for high resolution versions of
 the algorithms, the calculations give identical results.")
     (license license:expat)))
+
+(define-public maeparser
+  (package
+    (name "maeparser")
+    (version "1.3.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/schrodinger/maeparser")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1yv4y5hn49fhylziigsg922bb244lb57p69r7vg9q899zd3l5b7l"))))
+    (build-system cmake-build-system)
+    (native-inputs (list boost))
+    (inputs (list zlib))
+    (home-page "https://github.com/schrodinger/maeparser")
+    (synopsis "Maestro file parser")
+    (description "maeparser is a parser for Schrodinger Maestro files.")
+    (license license:expat)))
-- 
2.37.0

[bug#58261] [PATCH 09/11] gnu: Add coordgenlibs.

[David Elsing]

* gnu/packages/chemistry.scm (coordgenlibs): New variable.
---
 gnu/packages/chemistry.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 4d8ce66230..cc26aa329a 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -790,3 +790,30 @@ (define-public maeparser
     (synopsis "Maestro file parser")
     (description "maeparser is a parser for Schrodinger Maestro files.")
     (license license:expat)))
+
+(define-public coordgenlibs
+  (package
+    (name "coordgenlibs")
+    (version "3.0.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/schrodinger/coordgenlibs/")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0d09x3v38i9y184bml020bq7xizdrdwng38qmdxlplzfhqkjdidv"))))
+    (build-system cmake-build-system)
+    (native-inputs (list boost))
+    (inputs (list maeparser))
+    (arguments
+     (list
+      #:configure-flags
+      #~(list "-DCOORDGEN_RIGOROUS_BUILD=OFF"
+              "-DCOORDGEN_USE_MAEPARSER=ON")))
+    (home-page "https://github.com/schrodinger/coordgenlibs/")
+    (synopsis "2D coordinate generation")
+    (description "@code{coordgenlibs} contains algorithms to generate 2D
+coordinates.  It has an emphasis on quality rather than speed.")
+    (license license:bsd-3)))
-- 
2.37.0

[bug#58261] [PATCH 10/11] gnu: Add yaehmop-tightbind.

[David Elsing]

* gnu/packages/chemistry.scm (yaehmop-tightbind): New variable.
---
 gnu/packages/chemistry.scm | 82 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 82 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index cc26aa329a..a39deff4bf 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -42,6 +42,7 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
+  #:use-module (gnu packages gcc)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages gv)
@@ -817,3 +818,84 @@ (define-public coordgenlibs
     (description "@code{coordgenlibs} contains algorithms to generate 2D
 coordinates.  It has an emphasis on quality rather than speed.")
     (license license:bsd-3)))
+
+(define-public yaehmop-tightbind
+  (package
+    (name "yaehmop-tightbind")
+    (version "2022.09.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/greglandrum/yaehmop")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1x0d75m1hgdb411fiv7c5bwq1n4y0swrll0gigh8v5c73kjxrja0"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  (delete-file-recursively "docs")
+                  (delete-file-recursively "examples")
+                  (delete-file-recursively "viewkel")
+                  (delete-file-recursively "tightbind/f2c_files")
+                  (delete-file "tightbind/diag.c")
+                  (delete-file "tightbind/cboris.c")
+                  (delete-file "tightbind/abfns.c")
+                  (delete-file "tightbind/lovlap.c")
+                  #t))))
+    (build-system cmake-build-system)
+    (native-inputs (list gfortran))
+    (inputs (list openblas))
+    (arguments
+     (list
+      #:configure-flags
+      #~(list
+         "-DUSE_BLAS_LAPACK=ON"
+         (string-append "-DPARM_FILE_LOC=" #$output
+                        "/share/" #$name "-" #$version "/eht_parms.dat")
+         "-DBIND_EXE_NAME=yaehmop-bind")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'chdir
+            (lambda _
+              (chdir "tightbind")
+              #t))
+          (add-after 'chdir 'patch-fortran-functions
+            (lambda _
+              (substitute* '("mov.c" "prototypes.h")
+                (("lovlap\\(") "lovlap_(")
+                (("abfns\\(") "abfns_("))
+              #t))
+          (add-after 'chdir 'patch-cmake
+            (lambda _
+              (substitute* "CMakeLists.txt"
+                (("project\\(yaehmop C\\)") "project(yaehmop C Fortran)")
+                (("abfns.c") "fortran77/abfns.f")
+                (("lovlap.c") "fortran77/lovlap.f")
+                (("(set\\(PARM_FILE_LOC.*)\\)" all init)
+                 (string-append init " CACHE STRING \"\")"))
+                (("add_library\\(yaehmop_eht" lib)
+                 (string-append lib " SHARED "))
+                (("target_link_libraries\\(test_eht \\$\\{LAPACK_LIBRARIES\\}.*"
+                  all)
+                 (string-append all "\ntarget_link_libraries(yaehmop_eht "
+                                "${LAPACK_LIBRARIES})\n")))
+              #t))
+          (add-after 'install 'install-eht-parms
+            (lambda _
+              (install-file "../tightbind/eht_parms.dat"
+                            (string-append #$output "/share/"
+                                           #$name "-" #$version))
+              #t))
+          (delete 'check)
+          (add-after 'install-eht-parms 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (invoke "./test_eht"))
+              #t)))))
+    (home-page "https://github.com/greglandrum/yaehmop")
+    (synopsis "Yet Another extended Hueckel Molecular Orbital Package")
+    (description "@code{YAeHMOP} contains a program and library for performing
+extended Hückel calculations.")
+    (license license:bsd-2)))
-- 
2.37.0

[bug#58261] [PATCH 10/11] gnu: Add yaehmop-tightbind.

[Liliana Marie Prikler]

Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
> * gnu/packages/chemistry.scm (yaehmop-tightbind): New variable.
> ---
>  gnu/packages/chemistry.scm | 82
> ++++++++++++++++++++++++++++++++++++++
>  1 file changed, 82 insertions(+)
> 
> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
> index cc26aa329a..a39deff4bf 100644
> --- a/gnu/packages/chemistry.scm
> +++ b/gnu/packages/chemistry.scm
> @@ -42,6 +42,7 @@ (define-module (gnu packages chemistry)
>    #:use-module (gnu packages documentation)
>    #:use-module (gnu packages flex)
>    #:use-module (gnu packages fontutils)
> +  #:use-module (gnu packages gcc)
>    #:use-module (gnu packages gl)
>    #:use-module (gnu packages graphviz)
>    #:use-module (gnu packages gv)
> @@ -817,3 +818,84 @@ (define-public coordgenlibs
>      (description "@code{coordgenlibs} contains algorithms to
> generate 2D
>  coordinates.  It has an emphasis on quality rather than speed.")
>      (license license:bsd-3)))
> +
> +(define-public yaehmop-tightbind
> +  (package
> +    (name "yaehmop-tightbind")
> +    (version "2022.09.1")
> +    (source (origin
> +              (method git-fetch)
> +              (uri (git-reference
> +                    (url "https://github.com/greglandrum/yaehmop")
> +                    (commit (string-append "v" version))))
> +              (file-name (git-file-name name version))
> +              (sha256
> +               (base32
> +               
> "1x0d75m1hgdb411fiv7c5bwq1n4y0swrll0gigh8v5c73kjxrja0"))
> +              (modules '((guix build utils)))
> +              (snippet
> +               '(begin
> +                  (delete-file-recursively "docs")
This one looks suspicious.
> +                  (delete-file-recursively "examples")
As does this.
What gives?
> +                  (delete-file-recursively "viewkel")
> +                  (delete-file-recursively "tightbind/f2c_files")
> +                  (delete-file "tightbind/diag.c")
> +                  (delete-file "tightbind/cboris.c")
> +                  (delete-file "tightbind/abfns.c")
> +                  (delete-file "tightbind/lovlap.c")
> +                  #t))))
> +    (build-system cmake-build-system)
> +    (native-inputs (list gfortran))
> +    (inputs (list openblas))
> +    (arguments
> +     (list
> +      #:configure-flags
> +      #~(list
> +         "-DUSE_BLAS_LAPACK=ON"
> +         (string-append "-DPARM_FILE_LOC=" #$output
> +                        "/share/" #$name "-" #$version
> "/eht_parms.dat")
> +         "-DBIND_EXE_NAME=yaehmop-bind")
> +      #:phases
> +      #~(modify-phases %standard-phases
> +          (add-after 'unpack 'chdir
> +            (lambda _
> +              (chdir "tightbind")
> +              #t))
> +          (add-after 'chdir 'patch-fortran-functions
> +            (lambda _
> +              (substitute* '("mov.c" "prototypes.h")
> +                (("lovlap\\(") "lovlap_(")
> +                (("abfns\\(") "abfns_("))
> +              #t))
> +          (add-after 'chdir 'patch-cmake
> +            (lambda _
> +              (substitute* "CMakeLists.txt"
> +                (("project\\(yaehmop C\\)") "project(yaehmop C
> Fortran)")
> +                (("abfns.c") "fortran77/abfns.f")
> +                (("lovlap.c") "fortran77/lovlap.f")
> +                (("(set\\(PARM_FILE_LOC.*)\\)" all init)
> +                 (string-append init " CACHE STRING \"\")"))
> +                (("add_library\\(yaehmop_eht" lib)
> +                 (string-append lib " SHARED "))
> +                (("target_link_libraries\\(test_eht
> \\$\\{LAPACK_LIBRARIES\\}.*"
> +                  all)
> +                 (string-append all
> "\ntarget_link_libraries(yaehmop_eht "
> +                                "${LAPACK_LIBRARIES})\n")))
> +              #t))
> +          (add-after 'install 'install-eht-parms
> +            (lambda _
> +              (install-file "../tightbind/eht_parms.dat"
> +                            (string-append #$output "/share/"
> +                                           #$name "-" #$version))
> +              #t))
> +          (delete 'check)
> +          (add-after 'install-eht-parms 'check
> +            (lambda* (#:key tests? #:allow-other-keys)
> +              (when tests?
> +                (invoke "./test_eht"))
> +              #t)))))
> +    (home-page "https://github.com/greglandrum/yaehmop")
> +    (synopsis "Yet Another extended Hueckel Molecular Orbital
> Package")
> +    (description "@code{YAeHMOP} contains a program and library for
> performing
> +extended Hückel calculations.")
> +    (license license:bsd-2)))
Looking at this it seems unclear whether you are building yaehmop or
tightbind.  What's going on?

[bug#58261] [PATCH 10/11] gnu: Add yaehmop-tightbind.

[David Elsing]

Liliana Marie Prikler <liliana.prikler@ist.tugraz.at> writes:

> Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
>> * gnu/packages/chemistry.scm (yaehmop-tightbind): New variable.
>> ---
>>  gnu/packages/chemistry.scm | 82
>> ++++++++++++++++++++++++++++++++++++++
>>  1 file changed, 82 insertions(+)
>> 
>> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
>> index cc26aa329a..a39deff4bf 100644
>> --- a/gnu/packages/chemistry.scm
>> +++ b/gnu/packages/chemistry.scm
>> @@ -42,6 +42,7 @@ (define-module (gnu packages chemistry)
>>    #:use-module (gnu packages documentation)
>>    #:use-module (gnu packages flex)
>>    #:use-module (gnu packages fontutils)
>> +  #:use-module (gnu packages gcc)
>>    #:use-module (gnu packages gl)
>>    #:use-module (gnu packages graphviz)
>>    #:use-module (gnu packages gv)
>> @@ -817,3 +818,84 @@ (define-public coordgenlibs
>>      (description "@code{coordgenlibs} contains algorithms to
>> generate 2D
>>  coordinates.  It has an emphasis on quality rather than speed.")
>>      (license license:bsd-3)))
>> +
>> +(define-public yaehmop-tightbind
>> +  (package
>> +    (name "yaehmop-tightbind")
>> +    (version "2022.09.1")
>> +    (source (origin
>> +              (method git-fetch)
>> +              (uri (git-reference
>> +                    (url "https://github.com/greglandrum/yaehmop")
>> +                    (commit (string-append "v" version))))
>> +              (file-name (git-file-name name version))
>> +              (sha256
>> +               (base32
>> +               
>> "1x0d75m1hgdb411fiv7c5bwq1n4y0swrll0gigh8v5c73kjxrja0"))
>> +              (modules '((guix build utils)))
>> +              (snippet
>> +               '(begin
>> +                  (delete-file-recursively "docs")
> This one looks suspicious.
>> +                  (delete-file-recursively "examples")
> As does this.
> What gives?
I did not want to check the documentation in detail and the examples
contain some corrupted "compress" archives of program outputs. :)
But now I build the documentation instead and remove the archives.
There still is one problem: Even though I set FORCE_SOURCE_DATE=1, the
output of pdflatex is still not reproducible. Do you have an idea why
that could be? There are only 3 bytes different in the pdf.
Alternatively, I could just not build the documentation as it is
independent of the build scripts anyway.
>> +                  (delete-file-recursively "viewkel")
>> +                  (delete-file-recursively "tightbind/f2c_files")
>> +                  (delete-file "tightbind/diag.c")
>> +                  (delete-file "tightbind/cboris.c")
>> +                  (delete-file "tightbind/abfns.c")
>> +                  (delete-file "tightbind/lovlap.c")
>> +                  #t))))
>> +    (build-system cmake-build-system)
>> +    (native-inputs (list gfortran))
>> +    (inputs (list openblas))
>> +    (arguments
>> +     (list
>> +      #:configure-flags
>> +      #~(list
>> +         "-DUSE_BLAS_LAPACK=ON"
>> +         (string-append "-DPARM_FILE_LOC=" #$output
>> +                        "/share/" #$name "-" #$version
>> "/eht_parms.dat")
>> +         "-DBIND_EXE_NAME=yaehmop-bind")
>> +      #:phases
>> +      #~(modify-phases %standard-phases
>> +          (add-after 'unpack 'chdir
>> +            (lambda _
>> +              (chdir "tightbind")
>> +              #t))
>> +          (add-after 'chdir 'patch-fortran-functions
>> +            (lambda _
>> +              (substitute* '("mov.c" "prototypes.h")
>> +                (("lovlap\\(") "lovlap_(")
>> +                (("abfns\\(") "abfns_("))
>> +              #t))
>> +          (add-after 'chdir 'patch-cmake
>> +            (lambda _
>> +              (substitute* "CMakeLists.txt"
>> +                (("project\\(yaehmop C\\)") "project(yaehmop C
>> Fortran)")
>> +                (("abfns.c") "fortran77/abfns.f")
>> +                (("lovlap.c") "fortran77/lovlap.f")
>> +                (("(set\\(PARM_FILE_LOC.*)\\)" all init)
>> +                 (string-append init " CACHE STRING \"\")"))
>> +                (("add_library\\(yaehmop_eht" lib)
>> +                 (string-append lib " SHARED "))
>> +                (("target_link_libraries\\(test_eht
>> \\$\\{LAPACK_LIBRARIES\\}.*"
>> +                  all)
>> +                 (string-append all
>> "\ntarget_link_libraries(yaehmop_eht "
>> +                                "${LAPACK_LIBRARIES})\n")))
>> +              #t))
>> +          (add-after 'install 'install-eht-parms
>> +            (lambda _
>> +              (install-file "../tightbind/eht_parms.dat"
>> +                            (string-append #$output "/share/"
>> +                                           #$name "-" #$version))
>> +              #t))
>> +          (delete 'check)
>> +          (add-after 'install-eht-parms 'check
>> +            (lambda* (#:key tests? #:allow-other-keys)
>> +              (when tests?
>> +                (invoke "./test_eht"))
>> +              #t)))))
>> +    (home-page "https://github.com/greglandrum/yaehmop")
>> +    (synopsis "Yet Another extended Hueckel Molecular Orbital
>> Package")
>> +    (description "@code{YAeHMOP} contains a program and library for
>> performing
>> +extended Hückel calculations.")
>> +    (license license:bsd-2)))
> Looking at this it seems unclear whether you are building yaehmop or
> tightbind.  What's going on?
I'm building the yaehmop library (with the source code in tightbind/)
and the "bind" program (which I called yaehmop-bind) that uses the library.
Is it better to just call the package "yaehmop" (which I now did)?
The source also includes a separate visualization program "viewkel",
which does not use the library and would belong in another package in my
opinion.

[bug#58261] [PATCH 10/11] gnu: Add yaehmop-tightbind.

[Liliana Marie Prikler]

Am Freitag, dem 07.10.2022 um 15:12 +0000 schrieb David Elsing:
> Liliana Marie Prikler <liliana.prikler@ist.tugraz.at> writes:
> 
> > Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
> > > * gnu/packages/chemistry.scm (yaehmop-tightbind): New variable.
> > > ---
> > >  gnu/packages/chemistry.scm | 82
> > > ++++++++++++++++++++++++++++++++++++++
> > >  1 file changed, 82 insertions(+)
> > > 
> > > diff --git a/gnu/packages/chemistry.scm
> > > b/gnu/packages/chemistry.scm
> > > index cc26aa329a..a39deff4bf 100644
> > > --- a/gnu/packages/chemistry.scm
> > > +++ b/gnu/packages/chemistry.scm
> > > @@ -42,6 +42,7 @@ (define-module (gnu packages chemistry)
> > >    #:use-module (gnu packages documentation)
> > >    #:use-module (gnu packages flex)
> > >    #:use-module (gnu packages fontutils)
> > > +  #:use-module (gnu packages gcc)
> > >    #:use-module (gnu packages gl)
> > >    #:use-module (gnu packages graphviz)
> > >    #:use-module (gnu packages gv)
> > > @@ -817,3 +818,84 @@ (define-public coordgenlibs
> > >      (description "@code{coordgenlibs} contains algorithms to
> > > generate 2D
> > >  coordinates.  It has an emphasis on quality rather than speed.")
> > >      (license license:bsd-3)))
> > > +
> > > +(define-public yaehmop-tightbind
> > > +  (package
> > > +    (name "yaehmop-tightbind")
> > > +    (version "2022.09.1")
> > > +    (source (origin
> > > +              (method git-fetch)
> > > +              (uri (git-reference
> > > +                    (url
> > > "https://github.com/greglandrum/yaehmop")
> > > +                    (commit (string-append "v" version))))
> > > +              (file-name (git-file-name name version))
> > > +              (sha256
> > > +               (base32
> > > +               
> > > "1x0d75m1hgdb411fiv7c5bwq1n4y0swrll0gigh8v5c73kjxrja0"))
> > > +              (modules '((guix build utils)))
> > > +              (snippet
> > > +               '(begin
> > > +                  (delete-file-recursively "docs")
> > This one looks suspicious.
> > > +                  (delete-file-recursively "examples")
> > As does this.
> > What gives?
> I did not want to check the documentation in detail and the examples
> contain some corrupted "compress" archives of program outputs. :)
> But now I build the documentation instead and remove the archives.
> There still is one problem: Even though I set FORCE_SOURCE_DATE=1,
> the
> output of pdflatex is still not reproducible. Do you have an idea why
> that could be? There are only 3 bytes different in the pdf.
> Alternatively, I could just not build the documentation as it is
> independent of the build scripts anyway.
pdflatex has troubles with reproducible builds, but I can't quite
recall what option makes it not so, but rest assured those are likely 3
very well known bytes.

> > > +                  (delete-file-recursively "viewkel")
> > > +                  (delete-file-recursively
> > > "tightbind/f2c_files")
> > > +                  (delete-file "tightbind/diag.c")
> > > +                  (delete-file "tightbind/cboris.c")
> > > +                  (delete-file "tightbind/abfns.c")
> > > +                  (delete-file "tightbind/lovlap.c")
> > > +                  #t))))
> > > +    (build-system cmake-build-system)
> > > +    (native-inputs (list gfortran))
> > > +    (inputs (list openblas))
> > > +    (arguments
> > > +     (list
> > > +      #:configure-flags
> > > +      #~(list
> > > +         "-DUSE_BLAS_LAPACK=ON"
> > > +         (string-append "-DPARM_FILE_LOC=" #$output
> > > +                        "/share/" #$name "-" #$version
> > > "/eht_parms.dat")
> > > +         "-DBIND_EXE_NAME=yaehmop-bind")
> > > +      #:phases
> > > +      #~(modify-phases %standard-phases
> > > +          (add-after 'unpack 'chdir
> > > +            (lambda _
> > > +              (chdir "tightbind")
> > > +              #t))
> > > +          (add-after 'chdir 'patch-fortran-functions
> > > +            (lambda _
> > > +              (substitute* '("mov.c" "prototypes.h")
> > > +                (("lovlap\\(") "lovlap_(")
> > > +                (("abfns\\(") "abfns_("))
> > > +              #t))
> > > +          (add-after 'chdir 'patch-cmake
> > > +            (lambda _
> > > +              (substitute* "CMakeLists.txt"
> > > +                (("project\\(yaehmop C\\)") "project(yaehmop C
> > > Fortran)")
> > > +                (("abfns.c") "fortran77/abfns.f")
> > > +                (("lovlap.c") "fortran77/lovlap.f")
> > > +                (("(set\\(PARM_FILE_LOC.*)\\)" all init)
> > > +                 (string-append init " CACHE STRING \"\")"))
> > > +                (("add_library\\(yaehmop_eht" lib)
> > > +                 (string-append lib " SHARED "))
> > > +                (("target_link_libraries\\(test_eht
> > > \\$\\{LAPACK_LIBRARIES\\}.*"
> > > +                  all)
> > > +                 (string-append all
> > > "\ntarget_link_libraries(yaehmop_eht "
> > > +                                "${LAPACK_LIBRARIES})\n")))
> > > +              #t))
> > > +          (add-after 'install 'install-eht-parms
> > > +            (lambda _
> > > +              (install-file "../tightbind/eht_parms.dat"
> > > +                            (string-append #$output "/share/"
> > > +                                           #$name "-"
> > > #$version))
> > > +              #t))
> > > +          (delete 'check)
> > > +          (add-after 'install-eht-parms 'check
> > > +            (lambda* (#:key tests? #:allow-other-keys)
> > > +              (when tests?
> > > +                (invoke "./test_eht"))
> > > +              #t)))))
> > > +    (home-page "https://github.com/greglandrum/yaehmop")
> > > +    (synopsis "Yet Another extended Hueckel Molecular Orbital
> > > Package")
> > > +    (description "@code{YAeHMOP} contains a program and library
> > > for
> > > performing
> > > +extended Hückel calculations.")
> > > +    (license license:bsd-2)))
> > Looking at this it seems unclear whether you are building yaehmop
> > or
> > tightbind.  What's going on?
> I'm building the yaehmop library (with the source code in tightbind/)
> and the "bind" program (which I called yaehmop-bind) that uses the
> library.
> Is it better to just call the package "yaehmop" (which I now did)?
> The source also includes a separate visualization program "viewkel",
> which does not use the library and would belong in another package in
> my opinion.
Taking a cursory glance at the CMakeLists, calling it yaehmop is indeed
the correct thing.  I have no idea what viewkel is supposed to do tbh.

[bug#58261] [PATCH 11/11] gnu: Add rdkit.

[David Elsing]

* gnu/packages/chemistry.scm (rdkit): New variable.
---
 gnu/packages/chemistry.scm                    | 198 ++++++++++++++++++
 .../rdkit-cmake-external-dependencies.patch   | 102 +++++++++
 2 files changed, 300 insertions(+)
 create mode 100644 gnu/packages/patches/rdkit-cmake-external-dependencies.patch

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index a39deff4bf..869cf264e3 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -34,6 +34,7 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages backup)
+  #:use-module (gnu packages base)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
@@ -41,10 +42,12 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages cpp)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages flex)
+  #:use-module (gnu packages fonts)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages graphviz)
+  #:use-module (gnu packages gtk)
   #:use-module (gnu packages gv)
   #:use-module (gnu packages image)
   #:use-module (gnu packages maths)
@@ -56,6 +59,7 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages qt)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages sphinx)
+  #:use-module (gnu packages sqlite)
   #:use-module (gnu packages stb)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
@@ -899,3 +903,197 @@ (define-public yaehmop-tightbind
     (description "@code{YAeHMOP} contains a program and library for performing
 extended Hückel calculations.")
     (license license:bsd-2)))
+
+(define-public rdkit
+  (package
+    (name "rdkit")
+    (version "2022.03.5")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/rdkit/rdkit")
+                    (commit
+                     (string-append
+                      "Release_" (string-replace-substring version "." "_")))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9"))
+              (patches
+               (search-patches "rdkit-cmake-external-dependencies.patch"))
+              (modules '((guix build utils)))
+              (snippet
+               #~(begin
+                   ;; Remove pickle files (only used in tests),
+                   ;; as they are compiled programs
+                   (for-each
+                    (lambda (name)
+                      (display (string-append name "\n"))
+                      (delete-file name))
+                    (find-files "." "\\.pkl(\\.gz)?$"))
+                   ;; Remove SQLite data files (can be generated)
+                   (delete-file "Data/RDData.sqlt")
+                   (delete-file "Data/RDTests.sqlt")
+                   #t))))
+    (build-system cmake-build-system)
+    (native-inputs
+     `(("bison" ,bison)
+       ("boost" ,boost)
+       ("catch2" ,catch2)
+       ("eigen" ,eigen)
+       ("flex" ,flex)
+       ("freesasa" ,freesasa)
+       ("pkg-config" ,pkg-config)
+       ("rapidjson" ,rapidjson)
+       ("tar" ,tar)
+       ("avalontoolkit-src"
+        ,(let ((version "1.2.0"))
+           (origin
+             (method url-fetch)
+             (uri (string-append
+                   "http://sourceforge.net/projects/avalontoolkit/files/"
+                   "AvalonToolkit_" (substring version 0 3) "/AvalonToolkit_"
+                   version ".source.tar"))
+             (sha256
+              (base32
+               "0rnnyy6axs2da7aa4q6l30ldavbk49v6l22llj1adn74h1i67bpv"))
+             (modules '((guix build utils) (ice-9 ftw) (srfi srfi-26)))
+             (snippet
+              #~(begin
+                  (chdir "..")
+                  (delete-file-recursively "StandardFiles")
+                  (delete-file-recursively "SourceDistribution/java")
+                  #t)))))
+       ("ringdecomposerlib-src"
+        ,(let ((version "1.1.3"))
+           (origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/rareylab/RingDecomposerLib")
+                   (commit (string-append "v" version "_rdkit"))))
+             (file-name (git-file-name name version))
+             (sha256
+              (base32
+               "1rxzs2wpkkdi40wdzxc4sn0brk7dm7ivgqyfh38gf2f5c7pbg0wi")))))))
+    (inputs
+     (list cairo
+           coordgenlibs
+           font-comic-neue
+           freetype
+           inchi
+           maeparser
+           python
+           sqlite
+           yaehmop-tightbind))
+    (propagated-inputs
+     (list python-numpy python-cairocffi python-pillow))
+    (arguments
+     (list
+      #:imported-modules (append %cmake-build-system-modules
+                                 '((guix build python-build-system)))
+      #:modules '((guix build cmake-build-system)
+                  (guix build utils)
+                  ((guix build python-build-system)
+                   #:select (add-installed-pythonpath)))
+      #:configure-flags
+      #~(list
+         "-DRDK_BUILD_AVALON_SUPPORT=ON"
+         "-DRDK_BUILD_CAIRO_SUPPORT=ON"
+         "-DRDK_BUILD_CPP_TESTS=ON"
+         "-DRDK_BUILD_FREESASA_SUPPORT=ON"
+         "-DRDK_BUILD_INCHI_SUPPORT=ON"
+         "-DRDK_BUILD_YAEHMOP_SUPPORT=ON"
+         (string-append "-DCATCH_DIR="
+                        #$(this-package-native-input "catch2")
+                        "/include/catch2")
+         "-DRDK_INSTALL_DEV_COMPONENT=ON"
+         "-DRDK_INSTALL_INTREE=OFF"
+         "-DRDK_INSTALL_STATIC_LIBS=OFF"
+         (string-append
+          "-DRDK_OPTIMIZE_POPCNT="
+          #$(let ((system (or (%current-target-system)
+                              (%current-system))))
+              (cond
+               ((string-prefix? "x86_64" system) "ON")
+               ((string-prefix? "i686" system) "ON")
+               (else "OFF"))))
+         "-DRDK_USE_BOOST_IOSTREAMS=ON"
+         "-DRDK_USE_FLEXBISON=ON")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'copy-external-dependencies
+            (lambda _
+              (symlink
+               (string-append
+                #$(this-package-input "font-comic-neue")
+                "/share/fonts/truetype/ComicNeue-Regular.ttf")
+               "Data/Fonts/ComicNeue-Regular.ttf")
+              (symlink #$(this-package-native-input "rapidjson")
+                       "External/rapidjson-1.1.0")
+              (invoke "tar" "xvf"
+                      #$(this-package-native-input "avalontoolkit-src")
+                      "-C" "External/AvalonTools")
+              (symlink #$(this-package-native-input "ringdecomposerlib-src")
+                       "External/RingFamilies/RingDecomposerLib")
+              #t))
+          (add-after 'copy-external-dependencies 'patch-source
+            (lambda _
+              (with-directory-excursion "External/AvalonTools"
+                (invoke "patch" "-p0" "-i"
+                        "AvalonToolkit_1.2_patch.txt"))
+              (substitute* "External/YAeHMOP/EHTTools.cpp"
+                (("<yaehmop/tightbind/bind.h>") "<yaehmop/bind.h>"))
+              #t))
+          (add-after 'unpack 'create-sqlite-data-files
+            (lambda _
+              (invoke "sqlite3" "Data/RDData.sqlt"
+                      ".read rdkit/Dbase/test_data/RDData.sqlite")
+              (invoke "sqlite3" "Data/RDTests.sqlt"
+                      ".read rdkit/Dbase/test_data/RDTests.sqlite")
+              #t))
+          (add-after 'unpack 'fix-inchi-include
+            (lambda _
+              (substitute* "Code/cmake/Modules/FindInchi.cmake"
+                (("inchi_api.h.*\\)") "inchi/inchi_api.h)")
+                (("INCHI_LIBRARY NAMES.*\\)")
+                 "INCHI_LIBRARY NAMES inchi PATH_SUFFIXES inchi)")
+                (("find_library" prev)
+                 (string-append
+                  "list(APPEND CMAKE_FIND_LIBRARY_SUFFIXES .so.1)\n"
+                  prev)))
+              (substitute* "External/INCHI-API/inchi.cpp"
+                (("<inchi_api.h>") "<inchi/inchi_api.h>"))
+              #t))
+          (add-before 'build 'enable-bytecode-determinism
+              (lambda _
+                (setenv "PYTHONHASHSEED" "0")
+                (setenv "PYTHONDONTWRITEBYTECODE" "1")
+                #t))
+          (delete 'check)
+          (add-after 'install 'check
+            (lambda* (#:key inputs outputs tests? parallel-tests?
+                      #:allow-other-keys)
+              (when tests?
+                (let
+                    ((job-count (number->string
+                                 (or (and parallel-tests?
+                                          (parallel-job-count))
+                                     1))))
+                  (setenv "RDBASE" (canonicalize-path "../source"))
+                  (add-installed-pythonpath inputs outputs)
+                  (invoke "ctest"
+                          "-j" job-count
+                          "-E" (string-append
+                                ;; need pickled data
+                                "(pyDiscreteValueVect" "|pySparseIntVect"
+                                "|graphmoltestPickler" "|pyPartialCharges"
+                                "|substructLibraryTest" "|pyFeatures"
+                                "|pythonTestDirML" "|pythonTestDirChem"
+                                ;; Catching Python exception fails
+                                "|pyRanker)"))))
+              #t)))))
+    (home-page "https://rdkit.org/")
+    (synopsis "Open-Source Cheminformatics Software")
+    (description "RDKit is a collection of cheminformatics and
+machine-learning software written in C++ and Python.")
+    (license license:bsd-3)))
diff --git a/gnu/packages/patches/rdkit-cmake-external-dependencies.patch b/gnu/packages/patches/rdkit-cmake-external-dependencies.patch
new file mode 100644
index 0000000000..5b73864f51
--- /dev/null
+++ b/gnu/packages/patches/rdkit-cmake-external-dependencies.patch
@@ -0,0 +1,102 @@
+diff -ur a/External/FreeSASA/CMakeLists.txt b/External/FreeSASA/CMakeLists.txt
+--- a/External/FreeSASA/CMakeLists.txt
++++ b/External/FreeSASA/CMakeLists.txt
+@@ -10,7 +10,7 @@
+   endif()
+ endif()
+ 
+-if(needDownload)
++if(FALSE)
+   # don't actually use the md5 here
+   set(FREESASA_VERSION "2.0.3")
+   set(FREESASA_SRC_DIR "${CMAKE_CURRENT_SOURCE_DIR}/freesasa-${FREESASA_VERSION}")
+@@ -66,24 +66,24 @@
+ endif()
+ 
+ set (freesasa_h ${FREESASA_SRC_DIR}/src/freesasa.h)
+-file(READ ${freesasa_h} freesasa_h_data)
++#file(READ ${freesasa_h} freesasa_h_data)
+ string(REGEX REPLACE "(#include <stdio.h>)" "\\1\n#include <RDGeneral/export.h>" freesasa_h_data "${freesasa_h_data}")
+ string(REGEX REPLACE "([^R][^D][^K][^I][^T][^_][^F][^R][^E][^E][^S][^A][^S][^A][^_][^C][^L][^I][^B][^_][^E][^X][^P][^O][^R][^T][^ ])(extern const)" "\\1RDKIT_FREESASA_CLIB_EXPORT \\2" freesasa_h_data "${freesasa_h_data}")
+-file(WRITE ${freesasa_h} "${freesasa_h_data}")
++#file(WRITE ${freesasa_h} "${freesasa_h_data}")
+ 
+ add_definitions(-DUSE_THREADS=0)
+ add_definitions(-DUSE_JSON=0)
+ add_definitions(-DUSE_XML=0)
+-rdkit_library(freesasa_clib ${freesasa_clib_srcs})
+-target_compile_definitions(freesasa_clib PRIVATE RDKIT_FREESASALIB_BUILD)
++#rdkit_library(freesasa_clib ${freesasa_clib_srcs})
++#target_compile_definitions(freesasa_clib PRIVATE RDKIT_FREESASALIB_BUILD)
+ 
+ if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32))
+   set_target_properties(freesasa_clib PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
+ endif()
+-include_directories("${FREESASA_SRC_DIR}/src")
++#include_directories("${FREESASA_SRC_DIR}/src")
+ 
+ rdkit_library(FreeSASALib RDFreeSASA.cpp SHARED 
+-    LINK_LIBRARIES freesasa_clib GraphMol )
++    LINK_LIBRARIES -lfreesasa GraphMol )
+ target_compile_definitions(FreeSASALib PRIVATE RDKIT_FREESASALIB_BUILD)
+ 
+ rdkit_headers(RDFreeSASA.h DEST GraphMol)
+diff -ur a/External/YAeHMOP/CMakeLists.txt b/External/YAeHMOP/CMakeLists.txt
+--- a/External/YAeHMOP/CMakeLists.txt
++++ b/External/YAeHMOP/CMakeLists.txt
+@@ -18,32 +18,32 @@
+ 
+ include_directories( ${RDKit_ExternalDir}/YAeHMOP )
+ 
+-ExternalProject_Add(yaehmop_project
+-  GIT_REPOSITORY https://github.com/greglandrum/yaehmop.git
+-  GIT_TAG master
+-  UPDATE_COMMAND ""
+-  PATCH_COMMAND ""
+-  PREFIX ${CMAKE_CURRENT_SOURCE_DIR}
+-  SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop"
+-  SOURCE_SUBDIR "tightbind"
+-  CMAKE_ARGS -DUSE_BLAS_LAPACK=OFF -DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR} -DCMAKE_C_FLAGS=${CMAKE_C_FLAGS} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+-  TEST_COMMAND "")
+-
+-include_directories(${PROJECT_BINARY_DIR}/include)
+-link_directories(${PROJECT_BINARY_DIR}/lib)
+-link_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build)
+-
+-set(EHT_PARAM_FILE ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat )
+-install(FILES ${EHT_PARAM_FILE}
+-        DESTINATION ${RDKit_ShareDir}/Data
+-        COMPONENT data)
++#ExternalProject_Add(yaehmop_project
++#  GIT_REPOSITORY https://github.com/greglandrum/yaehmop.git
++#  GIT_TAG master
++#  UPDATE_COMMAND ""
++#  PATCH_COMMAND ""
++#  PREFIX ${CMAKE_CURRENT_SOURCE_DIR}
++#  SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop"
++#  SOURCE_SUBDIR "tightbind"
++#  CMAKE_ARGS -DUSE_BLAS_LAPACK=OFF -DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR} -DCMAKE_C_FLAGS=${CMAKE_C_FLAGS} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
++#  TEST_COMMAND "")
++
++#include_directories(${PROJECT_BINARY_DIR}/include)
++#link_directories(${PROJECT_BINARY_DIR}/lib)
++#link_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build)
++
++#set(EHT_PARAM_FILE ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat )
++#install(FILES ${EHT_PARAM_FILE}
++#        DESTINATION ${RDKit_ShareDir}/Data
++#        COMPONENT data)
+ 
+-message("YAeHMOP include_dirs: ${PROJECT_BINARY_DIR}/include")
+-message("YAeHMOP link_dirs: ${PROJECT_BINARY_DIR}/lib ${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build")
++#message("YAeHMOP include_dirs: ${PROJECT_BINARY_DIR}/include")
++#message("YAeHMOP link_dirs: ${PROJECT_BINARY_DIR}/lib ${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build")
+ 
+-rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES yaehmop_eht GraphMol )
++rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES -lyaehmop_eht GraphMol )
+ target_compile_definitions(EHTLib PRIVATE RDKIT_EHTLIB_BUILD)
+-add_dependencies(EHTLib yaehmop_project)
++#add_dependencies(EHTLib yaehmop_project)
+ rdkit_headers(EHTTools.h DEST GraphMol)
+ rdkit_catch_test(testEHTLib1 test1.cpp
+            LINK_LIBRARIES EHTLib FileParsers SmilesParse )
-- 
2.37.0

[bug#58261] [PATCH 11/11] gnu: Add rdkit.

[Liliana Marie Prikler]

Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
> * gnu/packages/chemistry.scm (rdkit): New variable.
> ---
>  gnu/packages/chemistry.scm                    | 198
> ++++++++++++++++++
>  .../rdkit-cmake-external-dependencies.patch   | 102 +++++++++
>  2 files changed, 300 insertions(+)
>  create mode 100644 gnu/packages/patches/rdkit-cmake-external-
> dependencies.patch
> 
> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
> index a39deff4bf..869cf264e3 100644
> --- a/gnu/packages/chemistry.scm
> +++ b/gnu/packages/chemistry.scm
> @@ -34,6 +34,7 @@ (define-module (gnu packages chemistry)
>    #:use-module (gnu packages algebra)
>    #:use-module (gnu packages autotools)
>    #:use-module (gnu packages backup)
> +  #:use-module (gnu packages base)
>    #:use-module (gnu packages bison)
>    #:use-module (gnu packages boost)
>    #:use-module (gnu packages check)
> @@ -41,10 +42,12 @@ (define-module (gnu packages chemistry)
>    #:use-module (gnu packages cpp)
>    #:use-module (gnu packages documentation)
>    #:use-module (gnu packages flex)
> +  #:use-module (gnu packages fonts)
>    #:use-module (gnu packages fontutils)
>    #:use-module (gnu packages gcc)
>    #:use-module (gnu packages gl)
>    #:use-module (gnu packages graphviz)
> +  #:use-module (gnu packages gtk)
>    #:use-module (gnu packages gv)
>    #:use-module (gnu packages image)
>    #:use-module (gnu packages maths)
> @@ -56,6 +59,7 @@ (define-module (gnu packages chemistry)
>    #:use-module (gnu packages qt)
>    #:use-module (gnu packages serialization)
>    #:use-module (gnu packages sphinx)
> +  #:use-module (gnu packages sqlite)
>    #:use-module (gnu packages stb)
>    #:use-module (gnu packages web)
>    #:use-module (gnu packages xml)
> @@ -899,3 +903,197 @@ (define-public yaehmop-tightbind
>      (description "@code{YAeHMOP} contains a program and library for
> performing
>  extended Hückel calculations.")
>      (license license:bsd-2)))
> +
> +(define-public rdkit
> +  (package
> +    (name "rdkit")
> +    (version "2022.03.5")
> +    (source (origin
> +              (method git-fetch)
> +              (uri (git-reference
> +                    (url "https://github.com/rdkit/rdkit")
> +                    (commit
> +                     (string-append
> +                      "Release_" (string-replace-substring version
> "." "_")))))
> +              (file-name (git-file-name name version))
> +              (sha256
> +               (base32
> +               
> "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9"))
> +              (patches
> +               (search-patches "rdkit-cmake-external-
> dependencies.patch"))
> +              (modules '((guix build utils)))
> +              (snippet
> +               #~(begin
> +                   ;; Remove pickle files (only used in tests),
> +                   ;; as they are compiled programs
> +                   (for-each
> +                    (lambda (name)
> +                      (display (string-append name "\n"))
> +                      (delete-file name))
> +                    (find-files "." "\\.pkl(\\.gz)?$"))
> +                   ;; Remove SQLite data files (can be generated)
> +                   (delete-file "Data/RDData.sqlt")
> +                   (delete-file "Data/RDTests.sqlt")
> +                   #t))))
> +    (build-system cmake-build-system)
> +    (native-inputs
> +     `(("bison" ,bison)
> +       ("boost" ,boost)
> +       ("catch2" ,catch2)
> +       ("eigen" ,eigen)
> +       ("flex" ,flex)
> +       ("freesasa" ,freesasa)
> +       ("pkg-config" ,pkg-config)
> +       ("rapidjson" ,rapidjson)
> +       ("tar" ,tar)
> +       ("avalontoolkit-src"
> +        ,(let ((version "1.2.0"))
> +           (origin
> +             (method url-fetch)
> +             (uri (string-append
> +                  
> "http://sourceforge.net/projects/avalontoolkit/files/"
> +                   "AvalonToolkit_" (substring version 0 3)
> "/AvalonToolkit_"
> +                   version ".source.tar"))
> +             (sha256
> +              (base32
> +              
> "0rnnyy6axs2da7aa4q6l30ldavbk49v6l22llj1adn74h1i67bpv"))
> +             (modules '((guix build utils) (ice-9 ftw) (srfi srfi-
> 26)))
> +             (snippet
> +              #~(begin
> +                  (chdir "..")
> +                  (delete-file-recursively "StandardFiles")
> +                  (delete-file-recursively
> "SourceDistribution/java")
> +                  #t)))))
> +       ("ringdecomposerlib-src"
> +        ,(let ((version "1.1.3"))
> +           (origin
> +             (method git-fetch)
> +             (uri (git-reference
> +                   (url
> "https://github.com/rareylab/RingDecomposerLib")
> +                   (commit (string-append "v" version "_rdkit"))))
> +             (file-name (git-file-name name version))
> +             (sha256
> +              (base32
> +              
> "1rxzs2wpkkdi40wdzxc4sn0brk7dm7ivgqyfh38gf2f5c7pbg0wi")))))))
> +    (inputs
> +     (list cairo
> +           coordgenlibs
> +           font-comic-neue
> +           freetype
> +           inchi
> +           maeparser
> +           python
> +           sqlite
> +           yaehmop-tightbind))
> +    (propagated-inputs
> +     (list python-numpy python-cairocffi python-pillow))
> +    (arguments
> +     (list
> +      #:imported-modules (append %cmake-build-system-modules
> +                                 '((guix build python-build-
> system)))
> +      #:modules '((guix build cmake-build-system)
> +                  (guix build utils)
> +                  ((guix build python-build-system)
> +                   #:select (add-installed-pythonpath)))
> +      #:configure-flags
> +      #~(list
> +         "-DRDK_BUILD_AVALON_SUPPORT=ON"
> +         "-DRDK_BUILD_CAIRO_SUPPORT=ON"
> +         "-DRDK_BUILD_CPP_TESTS=ON"
> +         "-DRDK_BUILD_FREESASA_SUPPORT=ON"
> +         "-DRDK_BUILD_INCHI_SUPPORT=ON"
> +         "-DRDK_BUILD_YAEHMOP_SUPPORT=ON"
> +         (string-append "-DCATCH_DIR="
> +                        #$(this-package-native-input "catch2")
> +                        "/include/catch2")
> +         "-DRDK_INSTALL_DEV_COMPONENT=ON"
> +         "-DRDK_INSTALL_INTREE=OFF"
> +         "-DRDK_INSTALL_STATIC_LIBS=OFF"
> +         (string-append
> +          "-DRDK_OPTIMIZE_POPCNT="
> +          #$(let ((system (or (%current-target-system)
> +                              (%current-system))))
> +              (cond
> +               ((string-prefix? "x86_64" system) "ON")
> +               ((string-prefix? "i686" system) "ON")
> +               (else "OFF"))))
> +         "-DRDK_USE_BOOST_IOSTREAMS=ON"
> +         "-DRDK_USE_FLEXBISON=ON")
> +      #:phases
> +      #~(modify-phases %standard-phases
> +          (add-after 'unpack 'copy-external-dependencies
> +            (lambda _
> +              (symlink
> +               (string-append
> +                #$(this-package-input "font-comic-neue")
> +                "/share/fonts/truetype/ComicNeue-Regular.ttf")
> +               "Data/Fonts/ComicNeue-Regular.ttf")
> +              (symlink #$(this-package-native-input "rapidjson")
> +                       "External/rapidjson-1.1.0")
> +              (invoke "tar" "xvf"
> +                      #$(this-package-native-input "avalontoolkit-
> src")
> +                      "-C" "External/AvalonTools")
> +              (symlink #$(this-package-native-input
> "ringdecomposerlib-src")
> +                       "External/RingFamilies/RingDecomposerLib")
> +              #t))
You might want to try unbundling those.  Either way, you should find a
solution that doesn't depend on native-input labels.
> +          (add-after 'copy-external-dependencies 'patch-source
> +            (lambda _
> +              (with-directory-excursion "External/AvalonTools"
> +                (invoke "patch" "-p0" "-i"
> +                        "AvalonToolkit_1.2_patch.txt"))
> +              (substitute* "External/YAeHMOP/EHTTools.cpp"
> +                (("<yaehmop/tightbind/bind.h>") "<yaehmop/bind.h>"))
> +              #t))
See my comment on yaehmop.
> +          (add-after 'unpack 'create-sqlite-data-files
> +            (lambda _
> +              (invoke "sqlite3" "Data/RDData.sqlt"
> +                      ".read rdkit/Dbase/test_data/RDData.sqlite")
> +              (invoke "sqlite3" "Data/RDTests.sqlt"
> +                      ".read rdkit/Dbase/test_data/RDTests.sqlite")
> +              #t))
Do you only need this for tests?  If so, do this in a pre-check phase.
> +          (add-after 'unpack 'fix-inchi-include
> +            (lambda _
> +              (substitute* "Code/cmake/Modules/FindInchi.cmake"
> +                (("inchi_api.h.*\\)") "inchi/inchi_api.h)")
> +                (("INCHI_LIBRARY NAMES.*\\)")
> +                 "INCHI_LIBRARY NAMES inchi PATH_SUFFIXES inchi)")
> +                (("find_library" prev)
> +                 (string-append
> +                  "list(APPEND CMAKE_FIND_LIBRARY_SUFFIXES .so.1)\n"
> +                  prev)))
> +              (substitute* "External/INCHI-API/inchi.cpp"
> +                (("<inchi_api.h>") "<inchi/inchi_api.h>"))
> +              #t))
> +          (add-before 'build 'enable-bytecode-determinism
> +              (lambda _
> +                (setenv "PYTHONHASHSEED" "0")
> +                (setenv "PYTHONDONTWRITEBYTECODE" "1")
> +                #t))
> +          (delete 'check)
> +          (add-after 'install 'check
> +            (lambda* (#:key inputs outputs tests? parallel-tests?
> +                      #:allow-other-keys)
> +              (when tests?
> +                (let
> +                    ((job-count (number->string
> +                                 (or (and parallel-tests?
> +                                          (parallel-job-count))
> +                                     1))))
> +                  (setenv "RDBASE" (canonicalize-path "../source"))
> +                  (add-installed-pythonpath inputs outputs)
This line should also be pre-check, maybe even these two lines.
> +                  (invoke "ctest"
> +                          "-j" job-count
> +                          "-E" (string-append
> +                                ;; need pickled data
> +                                "(pyDiscreteValueVect"
> "|pySparseIntVect"
> +                                "|graphmoltestPickler"
> "|pyPartialCharges"
> +                                "|substructLibraryTest"
> "|pyFeatures"
> +                                "|pythonTestDirML"
> "|pythonTestDirChem"
> +                                ;; Catching Python exception fails
> +                                "|pyRanker)"))))
Use string-join instead.
> +              #t)))))
> +    (home-page "https://rdkit.org/")
> +    (synopsis "Open-Source Cheminformatics Software")
"Open-Source" is meaningless in Guix.
> +    (description "RDKit is a collection of cheminformatics and
> +machine-learning software written in C++ and Python.")
Not particularly descriptive, but then again, neither is rdkit itself.

Cheers

[bug#58261] [PATCH 11/11] gnu: Add rdkit.

[David Elsing]

Liliana Marie Prikler <liliana.prikler@ist.tugraz.at> writes:

> Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
>> * gnu/packages/chemistry.scm (rdkit): New variable.
>> ---
>>  gnu/packages/chemistry.scm                    | 198
>> ++++++++++++++++++
>>  .../rdkit-cmake-external-dependencies.patch   | 102 +++++++++
>>  2 files changed, 300 insertions(+)
>>  create mode 100644 gnu/packages/patches/rdkit-cmake-external-
>> dependencies.patch
>> 
>> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
>> index a39deff4bf..869cf264e3 100644
>> --- a/gnu/packages/chemistry.scm
>> +++ b/gnu/packages/chemistry.scm
>> @@ -34,6 +34,7 @@ (define-module (gnu packages chemistry)
>>    #:use-module (gnu packages algebra)
>>    #:use-module (gnu packages autotools)
>>    #:use-module (gnu packages backup)
>> +  #:use-module (gnu packages base)
>>    #:use-module (gnu packages bison)
>>    #:use-module (gnu packages boost)
>>    #:use-module (gnu packages check)
>> @@ -41,10 +42,12 @@ (define-module (gnu packages chemistry)
>>    #:use-module (gnu packages cpp)
>>    #:use-module (gnu packages documentation)
>>    #:use-module (gnu packages flex)
>> +  #:use-module (gnu packages fonts)
>>    #:use-module (gnu packages fontutils)
>>    #:use-module (gnu packages gcc)
>>    #:use-module (gnu packages gl)
>>    #:use-module (gnu packages graphviz)
>> +  #:use-module (gnu packages gtk)
>>    #:use-module (gnu packages gv)
>>    #:use-module (gnu packages image)
>>    #:use-module (gnu packages maths)
>> @@ -56,6 +59,7 @@ (define-module (gnu packages chemistry)
>>    #:use-module (gnu packages qt)
>>    #:use-module (gnu packages serialization)
>>    #:use-module (gnu packages sphinx)
>> +  #:use-module (gnu packages sqlite)
>>    #:use-module (gnu packages stb)
>>    #:use-module (gnu packages web)
>>    #:use-module (gnu packages xml)
>> @@ -899,3 +903,197 @@ (define-public yaehmop-tightbind
>>      (description "@code{YAeHMOP} contains a program and library for
>> performing
>>  extended Hückel calculations.")
>>      (license license:bsd-2)))
>> +
>> +(define-public rdkit
>> +  (package
>> +    (name "rdkit")
>> +    (version "2022.03.5")
>> +    (source (origin
>> +              (method git-fetch)
>> +              (uri (git-reference
>> +                    (url "https://github.com/rdkit/rdkit")
>> +                    (commit
>> +                     (string-append
>> +                      "Release_" (string-replace-substring version
>> "." "_")))))
>> +              (file-name (git-file-name name version))
>> +              (sha256
>> +               (base32
>> +               
>> "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9"))
>> +              (patches
>> +               (search-patches "rdkit-cmake-external-
>> dependencies.patch"))
>> +              (modules '((guix build utils)))
>> +              (snippet
>> +               #~(begin
>> +                   ;; Remove pickle files (only used in tests),
>> +                   ;; as they are compiled programs
>> +                   (for-each
>> +                    (lambda (name)
>> +                      (display (string-append name "\n"))
>> +                      (delete-file name))
>> +                    (find-files "." "\\.pkl(\\.gz)?$"))
>> +                   ;; Remove SQLite data files (can be generated)
>> +                   (delete-file "Data/RDData.sqlt")
>> +                   (delete-file "Data/RDTests.sqlt")
>> +                   #t))))
>> +    (build-system cmake-build-system)
>> +    (native-inputs
>> +     `(("bison" ,bison)
>> +       ("boost" ,boost)
>> +       ("catch2" ,catch2)
>> +       ("eigen" ,eigen)
>> +       ("flex" ,flex)
>> +       ("freesasa" ,freesasa)
>> +       ("pkg-config" ,pkg-config)
>> +       ("rapidjson" ,rapidjson)
>> +       ("tar" ,tar)
>> +       ("avalontoolkit-src"
>> +        ,(let ((version "1.2.0"))
>> +           (origin
>> +             (method url-fetch)
>> +             (uri (string-append
>> +                  
>> "http://sourceforge.net/projects/avalontoolkit/files/"
>> +                   "AvalonToolkit_" (substring version 0 3)
>> "/AvalonToolkit_"
>> +                   version ".source.tar"))
>> +             (sha256
>> +              (base32
>> +              
>> "0rnnyy6axs2da7aa4q6l30ldavbk49v6l22llj1adn74h1i67bpv"))
>> +             (modules '((guix build utils) (ice-9 ftw) (srfi srfi-
>> 26)))
>> +             (snippet
>> +              #~(begin
>> +                  (chdir "..")
>> +                  (delete-file-recursively "StandardFiles")
>> +                  (delete-file-recursively
>> "SourceDistribution/java")
>> +                  #t)))))
>> +       ("ringdecomposerlib-src"
>> +        ,(let ((version "1.1.3"))
>> +           (origin
>> +             (method git-fetch)
>> +             (uri (git-reference
>> +                   (url
>> "https://github.com/rareylab/RingDecomposerLib")
>> +                   (commit (string-append "v" version "_rdkit"))))
>> +             (file-name (git-file-name name version))
>> +             (sha256
>> +              (base32
>> +              
>> "1rxzs2wpkkdi40wdzxc4sn0brk7dm7ivgqyfh38gf2f5c7pbg0wi")))))))
>> +    (inputs
>> +     (list cairo
>> +           coordgenlibs
>> +           font-comic-neue
>> +           freetype
>> +           inchi
>> +           maeparser
>> +           python
>> +           sqlite
>> +           yaehmop-tightbind))
>> +    (propagated-inputs
>> +     (list python-numpy python-cairocffi python-pillow))
>> +    (arguments
>> +     (list
>> +      #:imported-modules (append %cmake-build-system-modules
>> +                                 '((guix build python-build-
>> system)))
>> +      #:modules '((guix build cmake-build-system)
>> +                  (guix build utils)
>> +                  ((guix build python-build-system)
>> +                   #:select (add-installed-pythonpath)))
>> +      #:configure-flags
>> +      #~(list
>> +         "-DRDK_BUILD_AVALON_SUPPORT=ON"
>> +         "-DRDK_BUILD_CAIRO_SUPPORT=ON"
>> +         "-DRDK_BUILD_CPP_TESTS=ON"
>> +         "-DRDK_BUILD_FREESASA_SUPPORT=ON"
>> +         "-DRDK_BUILD_INCHI_SUPPORT=ON"
>> +         "-DRDK_BUILD_YAEHMOP_SUPPORT=ON"
>> +         (string-append "-DCATCH_DIR="
>> +                        #$(this-package-native-input "catch2")
>> +                        "/include/catch2")
>> +         "-DRDK_INSTALL_DEV_COMPONENT=ON"
>> +         "-DRDK_INSTALL_INTREE=OFF"
>> +         "-DRDK_INSTALL_STATIC_LIBS=OFF"
>> +         (string-append
>> +          "-DRDK_OPTIMIZE_POPCNT="
>> +          #$(let ((system (or (%current-target-system)
>> +                              (%current-system))))
>> +              (cond
>> +               ((string-prefix? "x86_64" system) "ON")
>> +               ((string-prefix? "i686" system) "ON")
>> +               (else "OFF"))))
>> +         "-DRDK_USE_BOOST_IOSTREAMS=ON"
>> +         "-DRDK_USE_FLEXBISON=ON")
>> +      #:phases
>> +      #~(modify-phases %standard-phases
>> +          (add-after 'unpack 'copy-external-dependencies
>> +            (lambda _
>> +              (symlink
>> +               (string-append
>> +                #$(this-package-input "font-comic-neue")
>> +                "/share/fonts/truetype/ComicNeue-Regular.ttf")
>> +               "Data/Fonts/ComicNeue-Regular.ttf")
>> +              (symlink #$(this-package-native-input "rapidjson")
>> +                       "External/rapidjson-1.1.0")
>> +              (invoke "tar" "xvf"
>> +                      #$(this-package-native-input "avalontoolkit-
>> src")
>> +                      "-C" "External/AvalonTools")
>> +              (symlink #$(this-package-native-input
>> "ringdecomposerlib-src")
>> +                       "External/RingFamilies/RingDecomposerLib")
>> +              #t))
> You might want to try unbundling those.  Either way, you should find a
> solution that doesn't depend on native-input labels.
Ok, I unbundled them, but the package definitions became a bit long. :)
Do you think it is ok like that?
>> +          (add-after 'copy-external-dependencies 'patch-source
>> +            (lambda _
>> +              (with-directory-excursion "External/AvalonTools"
>> +                (invoke "patch" "-p0" "-i"
>> +                        "AvalonToolkit_1.2_patch.txt"))
>> +              (substitute* "External/YAeHMOP/EHTTools.cpp"
>> +                (("<yaehmop/tightbind/bind.h>") "<yaehmop/bind.h>"))
>> +              #t))
> See my comment on yaehmop.
>> +          (add-after 'unpack 'create-sqlite-data-files
>> +            (lambda _
>> +              (invoke "sqlite3" "Data/RDData.sqlt"
>> +                      ".read rdkit/Dbase/test_data/RDData.sqlite")
>> +              (invoke "sqlite3" "Data/RDTests.sqlt"
>> +                      ".read rdkit/Dbase/test_data/RDTests.sqlite")
>> +              #t))
> Do you only need this for tests?  If so, do this in a pre-check phase.
Ok.
>> +          (add-after 'unpack 'fix-inchi-include
>> +            (lambda _
>> +              (substitute* "Code/cmake/Modules/FindInchi.cmake"
>> +                (("inchi_api.h.*\\)") "inchi/inchi_api.h)")
>> +                (("INCHI_LIBRARY NAMES.*\\)")
>> +                 "INCHI_LIBRARY NAMES inchi PATH_SUFFIXES inchi)")
>> +                (("find_library" prev)
>> +                 (string-append
>> +                  "list(APPEND CMAKE_FIND_LIBRARY_SUFFIXES .so.1)\n"
>> +                  prev)))
>> +              (substitute* "External/INCHI-API/inchi.cpp"
>> +                (("<inchi_api.h>") "<inchi/inchi_api.h>"))
>> +              #t))
>> +          (add-before 'build 'enable-bytecode-determinism
>> +              (lambda _
>> +                (setenv "PYTHONHASHSEED" "0")
>> +                (setenv "PYTHONDONTWRITEBYTECODE" "1")
>> +                #t))
>> +          (delete 'check)
>> +          (add-after 'install 'check
>> +            (lambda* (#:key inputs outputs tests? parallel-tests?
>> +                      #:allow-other-keys)
>> +              (when tests?
>> +                (let
>> +                    ((job-count (number->string
>> +                                 (or (and parallel-tests?
>> +                                          (parallel-job-count))
>> +                                     1))))
>> +                  (setenv "RDBASE" (canonicalize-path "../source"))
>> +                  (add-installed-pythonpath inputs outputs)
> This line should also be pre-check, maybe even these two lines.
>> +                  (invoke "ctest"
>> +                          "-j" job-count
>> +                          "-E" (string-append
>> +                                ;; need pickled data
>> +                                "(pyDiscreteValueVect"
>> "|pySparseIntVect"
>> +                                "|graphmoltestPickler"
>> "|pyPartialCharges"
>> +                                "|substructLibraryTest"
>> "|pyFeatures"
>> +                                "|pythonTestDirML"
>> "|pythonTestDirChem"
>> +                                ;; Catching Python exception fails
>> +                                "|pyRanker)"))))
> Use string-join instead.
Thanks!
>> +              #t)))))
>> +    (home-page "https://rdkit.org/")
>> +    (synopsis "Open-Source Cheminformatics Software")
> "Open-Source" is meaningless in Guix.
>> +    (description "RDKit is a collection of cheminformatics and
>> +machine-learning software written in C++ and Python.")
> Not particularly descriptive, but then again, neither is rdkit itself.
>
> Cheers

[bug#58261] [PATCH 11/11] gnu: Add rdkit.

[Liliana Marie Prikler]

Am Freitag, dem 07.10.2022 um 15:12 +0000 schrieb David Elsing:
> Liliana Marie Prikler <liliana.prikler@ist.tugraz.at> writes:
> 
> > Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
> > > * gnu/packages/chemistry.scm (rdkit): New variable.
> > > ---
> > >  gnu/packages/chemistry.scm                    | 198
> > > ++++++++++++++++++
> > >  .../rdkit-cmake-external-dependencies.patch   | 102 +++++++++
> > >  2 files changed, 300 insertions(+)
> > >  create mode 100644 gnu/packages/patches/rdkit-cmake-external-
> > > dependencies.patch
> > > 
> > > diff --git a/gnu/packages/chemistry.scm
> > > b/gnu/packages/chemistry.scm
> > > index a39deff4bf..869cf264e3 100644
> > > --- a/gnu/packages/chemistry.scm
> > > +++ b/gnu/packages/chemistry.scm
> > > @@ -34,6 +34,7 @@ (define-module (gnu packages chemistry)
> > >    #:use-module (gnu packages algebra)
> > >    #:use-module (gnu packages autotools)
> > >    #:use-module (gnu packages backup)
> > > +  #:use-module (gnu packages base)
> > >    #:use-module (gnu packages bison)
> > >    #:use-module (gnu packages boost)
> > >    #:use-module (gnu packages check)
> > > @@ -41,10 +42,12 @@ (define-module (gnu packages chemistry)
> > >    #:use-module (gnu packages cpp)
> > >    #:use-module (gnu packages documentation)
> > >    #:use-module (gnu packages flex)
> > > +  #:use-module (gnu packages fonts)
> > >    #:use-module (gnu packages fontutils)
> > >    #:use-module (gnu packages gcc)
> > >    #:use-module (gnu packages gl)
> > >    #:use-module (gnu packages graphviz)
> > > +  #:use-module (gnu packages gtk)
> > >    #:use-module (gnu packages gv)
> > >    #:use-module (gnu packages image)
> > >    #:use-module (gnu packages maths)
> > > @@ -56,6 +59,7 @@ (define-module (gnu packages chemistry)
> > >    #:use-module (gnu packages qt)
> > >    #:use-module (gnu packages serialization)
> > >    #:use-module (gnu packages sphinx)
> > > +  #:use-module (gnu packages sqlite)
> > >    #:use-module (gnu packages stb)
> > >    #:use-module (gnu packages web)
> > >    #:use-module (gnu packages xml)
> > > @@ -899,3 +903,197 @@ (define-public yaehmop-tightbind
> > >      (description "@code{YAeHMOP} contains a program and library
> > > for
> > > performing
> > >  extended Hückel calculations.")
> > >      (license license:bsd-2)))
> > > +
> > > +(define-public rdkit
> > > +  (package
> > > +    (name "rdkit")
> > > +    (version "2022.03.5")
> > > +    (source (origin
> > > +              (method git-fetch)
> > > +              (uri (git-reference
> > > +                    (url "https://github.com/rdkit/rdkit")
> > > +                    (commit
> > > +                     (string-append
> > > +                      "Release_" (string-replace-substring
> > > version
> > > "." "_")))))
> > > +              (file-name (git-file-name name version))
> > > +              (sha256
> > > +               (base32
> > > +               
> > > "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9"))
> > > +              (patches
> > > +               (search-patches "rdkit-cmake-external-
> > > dependencies.patch"))
> > > +              (modules '((guix build utils)))
> > > +              (snippet
> > > +               #~(begin
> > > +                   ;; Remove pickle files (only used in tests),
> > > +                   ;; as they are compiled programs
> > > +                   (for-each
> > > +                    (lambda (name)
> > > +                      (display (string-append name "\n"))
> > > +                      (delete-file name))
> > > +                    (find-files "." "\\.pkl(\\.gz)?$"))
> > > +                   ;; Remove SQLite data files (can be
> > > generated)
> > > +                   (delete-file "Data/RDData.sqlt")
> > > +                   (delete-file "Data/RDTests.sqlt")
> > > +                   #t))))
> > > +    (build-system cmake-build-system)
> > > +    (native-inputs
> > > +     `(("bison" ,bison)
> > > +       ("boost" ,boost)
> > > +       ("catch2" ,catch2)
> > > +       ("eigen" ,eigen)
> > > +       ("flex" ,flex)
> > > +       ("freesasa" ,freesasa)
> > > +       ("pkg-config" ,pkg-config)
> > > +       ("rapidjson" ,rapidjson)
> > > +       ("tar" ,tar)
> > > +       ("avalontoolkit-src"
> > > +        ,(let ((version "1.2.0"))
> > > +           (origin
> > > +             (method url-fetch)
> > > +             (uri (string-append
> > > +                  
> > > "http://sourceforge.net/projects/avalontoolkit/files/"
> > > +                   "AvalonToolkit_" (substring version 0 3)
> > > "/AvalonToolkit_"
> > > +                   version ".source.tar"))
> > > +             (sha256
> > > +              (base32
> > > +              
> > > "0rnnyy6axs2da7aa4q6l30ldavbk49v6l22llj1adn74h1i67bpv"))
> > > +             (modules '((guix build utils) (ice-9 ftw) (srfi
> > > srfi-
> > > 26)))
> > > +             (snippet
> > > +              #~(begin
> > > +                  (chdir "..")
> > > +                  (delete-file-recursively "StandardFiles")
> > > +                  (delete-file-recursively
> > > "SourceDistribution/java")
> > > +                  #t)))))
> > > +       ("ringdecomposerlib-src"
> > > +        ,(let ((version "1.1.3"))
> > > +           (origin
> > > +             (method git-fetch)
> > > +             (uri (git-reference
> > > +                   (url
> > > "https://github.com/rareylab/RingDecomposerLib")
> > > +                   (commit (string-append "v" version
> > > "_rdkit"))))
> > > +             (file-name (git-file-name name version))
> > > +             (sha256
> > > +              (base32
> > > +              
> > > "1rxzs2wpkkdi40wdzxc4sn0brk7dm7ivgqyfh38gf2f5c7pbg0wi")))))))
> > > +    (inputs
> > > +     (list cairo
> > > +           coordgenlibs
> > > +           font-comic-neue
> > > +           freetype
> > > +           inchi
> > > +           maeparser
> > > +           python
> > > +           sqlite
> > > +           yaehmop-tightbind))
> > > +    (propagated-inputs
> > > +     (list python-numpy python-cairocffi python-pillow))
> > > +    (arguments
> > > +     (list
> > > +      #:imported-modules (append %cmake-build-system-modules
> > > +                                 '((guix build python-build-
> > > system)))
> > > +      #:modules '((guix build cmake-build-system)
> > > +                  (guix build utils)
> > > +                  ((guix build python-build-system)
> > > +                   #:select (add-installed-pythonpath)))
> > > +      #:configure-flags
> > > +      #~(list
> > > +         "-DRDK_BUILD_AVALON_SUPPORT=ON"
> > > +         "-DRDK_BUILD_CAIRO_SUPPORT=ON"
> > > +         "-DRDK_BUILD_CPP_TESTS=ON"
> > > +         "-DRDK_BUILD_FREESASA_SUPPORT=ON"
> > > +         "-DRDK_BUILD_INCHI_SUPPORT=ON"
> > > +         "-DRDK_BUILD_YAEHMOP_SUPPORT=ON"
> > > +         (string-append "-DCATCH_DIR="
> > > +                        #$(this-package-native-input "catch2")
> > > +                        "/include/catch2")
> > > +         "-DRDK_INSTALL_DEV_COMPONENT=ON"
> > > +         "-DRDK_INSTALL_INTREE=OFF"
> > > +         "-DRDK_INSTALL_STATIC_LIBS=OFF"
> > > +         (string-append
> > > +          "-DRDK_OPTIMIZE_POPCNT="
> > > +          #$(let ((system (or (%current-target-system)
> > > +                              (%current-system))))
> > > +              (cond
> > > +               ((string-prefix? "x86_64" system) "ON")
> > > +               ((string-prefix? "i686" system) "ON")
> > > +               (else "OFF"))))
> > > +         "-DRDK_USE_BOOST_IOSTREAMS=ON"
> > > +         "-DRDK_USE_FLEXBISON=ON")
> > > +      #:phases
> > > +      #~(modify-phases %standard-phases
> > > +          (add-after 'unpack 'copy-external-dependencies
> > > +            (lambda _
> > > +              (symlink
> > > +               (string-append
> > > +                #$(this-package-input "font-comic-neue")
> > > +                "/share/fonts/truetype/ComicNeue-Regular.ttf")
> > > +               "Data/Fonts/ComicNeue-Regular.ttf")
> > > +              (symlink #$(this-package-native-input "rapidjson")
> > > +                       "External/rapidjson-1.1.0")
> > > +              (invoke "tar" "xvf"
> > > +                      #$(this-package-native-input
> > > "avalontoolkit-
> > > src")
> > > +                      "-C" "External/AvalonTools")
> > > +              (symlink #$(this-package-native-input
> > > "ringdecomposerlib-src")
> > > +                      
> > > "External/RingFamilies/RingDecomposerLib")
> > > +              #t))
> > You might want to try unbundling those.  Either way, you should
> > find a
> > solution that doesn't depend on native-input labels.
> Ok, I unbundled them, but the package definitions became a bit long.
> :)  Do you think it is ok like that?
> > 
Long package definitions are not inherently bad (unless of course there
is an obviously less verbose way of writing them).  I'll take a look at
your v2 at a later time.

Cheers

[bug#58261] [PATCH v2 00/13] Add rdkit v2.

[David Elsing]

Thanks a lot for your comments, they are very helpful!
Sorry about the descriptions, I took them mostly from upstream. :)
Are they still too short?

I still have the following problems:
* The tests of tinydir contain a bundled fork of cbehave which uses a
  (bundled) copy of rlutil, so I left them disabled for now.
* Building the documentation of yaehmop with pdflatex is not reproducible even
  though I set FORCE_SOURCE_DATE=1. Is it even necessary to build the
  documentation?
* Using @abbr in the description does not work (I also did not find it in any
  other package).

Greetings,
David

David Elsing (13):
  gnu: Add fast-float.
  gnu: Add pocketfft.
  gnu: Add sajson.
  gnu: Add tinydir.
  gnu: Add optionparser.
  gnu: Add gemmi.
  gnu: Add freesasa.
  gnu: Add maeparser.
  gnu: Add coordgenlibs.
  gnu: Add yaehmop-tightbind.
  gnu: Add avalontoolkit.
  gnu: Add ringdecomposerlib.
  gnu: Add rdkit.

 gnu/packages/chemistry.scm                    | 713 ++++++++++++++++++
 gnu/packages/cpp.scm                          | 232 ++++++
 .../patches/gemmi-fix-sajson-types.patch      |  11 +
 .../rdkit-cmake-external-dependencies.patch   | 102 +++
 .../patches/sajson-build-with-gcc10.patch     |  45 ++
 .../sajson-for-gemmi-build-with-gcc10.patch   |  45 ++
 .../sajson-for-gemmi-numbers-as-strings.patch | 195 +++++
 7 files changed, 1343 insertions(+)
 create mode 100644 gnu/packages/patches/gemmi-fix-sajson-types.patch
 create mode 100644 gnu/packages/patches/rdkit-cmake-external-dependencies.patch
 create mode 100644 gnu/packages/patches/sajson-build-with-gcc10.patch
 create mode 100644 gnu/packages/patches/sajson-for-gemmi-build-with-gcc10.patch
 create mode 100644 gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch

-- 
2.37.0

[bug#58261] [PATCH v2 00/13] Add rdkit v2.

[Liliana Marie Prikler]

Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
> Thanks a lot for your comments, they are very helpful!
> Sorry about the descriptions, I took them mostly from upstream. :)
> Are they still too short?
I don't think we can magically poof good descriptions into existence
when upstreams don't provide them.  That being said, it's best to clean
up whatever's there.  Changing descriptions is a lowball issue, though,
I (or another committer) can do so as we're upstreaming it.

> I still have the following problems:
> * The tests of tinydir contain a bundled fork of cbehave which uses a
>   (bundled) copy of rlutil, so I left them disabled for now.
I mentioned this in a reply to another message already, but the idea
would be to 1. try to use upstream versions or 2. try to package the
bundles. 

> * Building the documentation of yaehmop with pdflatex is not
> reproducible even
>   though I set FORCE_SOURCE_DATE=1. Is it even necessary to build the
>   documentation?
Maybe pdftrailerid can help you?  You could also try to convert the
documentation into a reproducible format -- e.g. using pandoc.

> * Using @abbr in the description does not work (I also did not find
> it in any
>   other package).
My bad, that should be @acronym.

Cheers

[bug#58261] [PATCH v2 00/13] Add rdkit v2.

[David Elsing]

Liliana Marie Prikler <liliana.prikler@gmail.com> writes:

> Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
>> Thanks a lot for your comments, they are very helpful!
>> Sorry about the descriptions, I took them mostly from upstream. :)
>> Are they still too short?
> I don't think we can magically poof good descriptions into existence
> when upstreams don't provide them.  That being said, it's best to clean
> up whatever's there.  Changing descriptions is a lowball issue, though,
> I (or another committer) can do so as we're upstreaming it.
>
>> I still have the following problems:
>> * The tests of tinydir contain a bundled fork of cbehave which uses a
>>   (bundled) copy of rlutil, so I left them disabled for now.
> I mentioned this in a reply to another message already, but the idea
> would be to 1. try to use upstream versions or 2. try to package the
> bundles. 
I noticed that there was only one test anyway, so I just made a patch to
run it with the upstream version (which was last updated in 2013).
>
>> * Building the documentation of yaehmop with pdflatex is not
>> reproducible even
>>   though I set FORCE_SOURCE_DATE=1. Is it even necessary to build the
>>   documentation?
> Maybe pdftrailerid can help you?  You could also try to convert the
> documentation into a reproducible format -- e.g. using pandoc.
It worked with \pdfsuppressptexinfo=-1. :)
>
>> * Using @abbr in the description does not work (I also did not find
>> it in any
>>   other package).
> My bad, that should be @acronym.
Ok thanks!
>
> Cheers

[bug#58261] [PATCH v3 00/15] Add rdkit v3.

[David Elsing]

Thanks again for your comments! Here is the next version. :)
Now all packages were reproducible again after two rounds.

David Elsing (15):
  gnu: Add fast-float.
  gnu: Add pocketfft-cpp.
  gnu: Add sajson.
  gnu: Add cbehave.
  gnu: Add tinydir.
  gnu: Add optionparser.
  gnu: Add sajson-for-gemmi.
  gnu: Add gemmi.
  gnu: Add freesasa.
  gnu: Add maeparser.
  gnu: Add coordgenlibs.
  gnu: Add yaehmop.
  gnu: Add avalon-toolkit.
  gnu: Add ringdecomposerlib.
  gnu: Add rdkit.

 gnu/packages/check.scm                        |  56 ++
 gnu/packages/chemistry.scm                    | 686 ++++++++++++++++++
 gnu/packages/cpp.scm                          | 228 ++++++
 .../patches/gemmi-fix-pegtl-usage.patch       |  31 +
 .../patches/gemmi-fix-sajson-types.patch      |  11 +
 .../pocketfft-cpp-default-disable-simd.patch  | 108 +++
 ...rdkit-unbundle-external-dependencies.patch | 384 ++++++++++
 .../patches/sajson-build-with-gcc10.patch     |  45 ++
 .../sajson-for-gemmi-numbers-as-strings.patch | 195 +++++
 .../patches/tinydir-fix-cbehave-test.patch    |  16 +
 10 files changed, 1760 insertions(+)
 create mode 100644 gnu/packages/patches/gemmi-fix-pegtl-usage.patch
 create mode 100644 gnu/packages/patches/gemmi-fix-sajson-types.patch
 create mode 100644 gnu/packages/patches/pocketfft-cpp-default-disable-simd.patch
 create mode 100644 gnu/packages/patches/rdkit-unbundle-external-dependencies.patch
 create mode 100644 gnu/packages/patches/sajson-build-with-gcc10.patch
 create mode 100644 gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch
 create mode 100644 gnu/packages/patches/tinydir-fix-cbehave-test.patch

-- 
2.37.0

bug#58261: [PATCH v3 00/15] Add rdkit v3.

[Liliana Marie Prikler]

Am Donnerstag, dem 13.10.2022 um 21:04 +0000 schrieb David Elsing:
> Thanks again for your comments! Here is the next version. :)
> Now all packages were reproducible again after two rounds.
I've made some adjustments – some cosmetic, some otherwise – and pushed
this series.

Cheers

[bug#58261] [PATCH v3 00/15] Add rdkit v3.

[David Elsing]

Liliana Marie Prikler <liliana.prikler@gmail.com> writes:

> Am Donnerstag, dem 13.10.2022 um 21:04 +0000 schrieb David Elsing:
>> Thanks again for your comments! Here is the next version. :)
>> Now all packages were reproducible again after two rounds.
> I've made some adjustments – some cosmetic, some otherwise – and pushed
> this series.
>
> Cheers
Thank you!
I'll see whether I can find the reason some tests in freesasa fail on
i686, but it was possible to reproduce them at least.

[bug#58261] [PATCH v3 01/15] gnu: Add fast-float.

[David Elsing]

* gnu/packages/cpp.scm (fast-float): New variable.
---
 gnu/packages/cpp.scm | 50 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)

diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index 805413cc61..eba39ed660 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -29,6 +29,7 @@
 ;;; Copyright © 2022 muradm <mail@muradm.net>
 ;;; Copyright © 2022 Attila Lendvai <attila@lendvai.name>
 ;;; Copyright © 2022 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2022 David Elsing <david.elsing@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1954,3 +1955,52 @@ (define-public crc32c
      "This package provides architecture-specific implementations of the
 CRC32C algorithm, which is specified in RFC 3720, section 12.1.")
     (license license:bsd-3)))
+
+(define-public fast-float
+  (package
+    (name "fast-float")
+    (version "3.5.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/fastfloat/fast_float")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0z3rxxd0pwvw70dbnv63rm67biw829vdqf50y16isxm6g3sbrz8g"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      #~(list
+         "-DFASTFLOAT_TEST=ON"
+         "-DSYSTEM_DOCTEST=ON")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-cmake-tests
+            (lambda _
+              (substitute* "tests/CMakeLists.txt"
+                (("FetchContent_GetProperties\\(supplemental_test_files.*")
+                 "")
+                (("if\\(NOT supplemental_test_files_POPULATED.*")
+                 (string-append
+                  "set(supplemental_test_files_BINARY_DIR "
+                  #$(origin
+                      (method git-fetch)
+                      (uri (git-reference
+                            (url (string-append "https://github.com/fastfloat"
+                                                "/supplemental_test_files.git"))
+                            (commit "97a0b2e638feb479387554cf253e346500541e7e")))
+                      (file-name (git-file-name "fast_float_test-data" version))
+                      (sha256
+                       (base32
+                        "0dxbiyzyh7i847i89ablfzypfc3ckhm7f74w98jsh73v1mppmxlf")))
+                  "/data)\nif(0)\n"))))))))
+    (native-inputs (list doctest))
+    (home-page "https://github.com/fastfloat/fast_float")
+    (synopsis "Floating point number parser for C++")
+    (description "@code{fast_float} is a header-only C++ library for parsing
+floating point numbers from strings.  It implements the C++ from_chars
+functions for the float and double types.")
+    (license (list license:asl2.0 license:expat)))) ; dual licensed
-- 
2.37.0

[bug#58261] [PATCH v3 02/15] gnu: Add pocketfft-cpp.

[David Elsing]

* gnu/packages/cpp.scm (pocketfft-cpp): New variable.
---
 gnu/packages/cpp.scm                          |  29 +++++
 .../pocketfft-cpp-default-disable-simd.patch  | 108 ++++++++++++++++++
 2 files changed, 137 insertions(+)
 create mode 100644 gnu/packages/patches/pocketfft-cpp-default-disable-simd.patch

diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index eba39ed660..2b5841e777 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -2004,3 +2004,32 @@ (define-public fast-float
 floating point numbers from strings.  It implements the C++ from_chars
 functions for the float and double types.")
     (license (list license:asl2.0 license:expat)))) ; dual licensed
+
+(define-public pocketfft-cpp
+  (let ((commit "daa8bb18327bc5c7d22c69428c25cf5dc64167d3")
+        (revision "0"))
+    (package
+      (name "pocketfft-cpp")
+      (version (git-version "0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/mreineck/pocketfft")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1dbkkqkmkxgmz1qjpsqzic5ig3qw1pqndbb3dvjc7xq5f2rdzyq1"))
+                (patches (search-patches
+                          "pocketfft-cpp-default-disable-simd.patch"))))
+      (build-system copy-build-system)
+      (arguments
+       (list
+        #:install-plan
+        #~'(("pocketfft_hdronly.h" "include/"))))
+      (home-page "https://github.com/mreineck/pocketfft")
+      (synopsis "C++11 header-only Fast Fourier Transform library")
+      (description "This package provides a single-header C++11 library for
+computing Fast Fourier transformations.  It supports multidimensional arrays,
+different floating point sizes and complex transformations.")
+      (license license:bsd-3))))
diff --git a/gnu/packages/patches/pocketfft-cpp-default-disable-simd.patch b/gnu/packages/patches/pocketfft-cpp-default-disable-simd.patch
new file mode 100644
index 0000000000..4d2ddae4b5
--- /dev/null
+++ b/gnu/packages/patches/pocketfft-cpp-default-disable-simd.patch
@@ -0,0 +1,108 @@
+Disable SIMD instructions by default.
+They can be enabled by setting -DPOCKETFFT_NO_VECTORS=0.
+
+diff --git a/pocketfft_hdronly.h b/pocketfft_hdronly.h
+index d75ada6..b2d0a23 100644
+--- a/pocketfft_hdronly.h
++++ b/pocketfft_hdronly.h
+@@ -39,6 +39,10 @@ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ #ifndef POCKETFFT_HDRONLY_H
+ #define POCKETFFT_HDRONLY_H
+ 
++#ifndef POCKETFFT_NO_VECTORS
++#define POCKETFFT_NO_VECTORS 1
++#endif
++
+ #ifndef __cplusplus
+ #error This file is C++ and requires a C++ compiler.
+ #endif
+@@ -106,29 +110,29 @@ constexpr bool FORWARD  = true,
+                BACKWARD = false;
+ 
+ // only enable vector support for gcc>=5.0 and clang>=5.0
+-#ifndef POCKETFFT_NO_VECTORS
+-#define POCKETFFT_NO_VECTORS
++#if !(POCKETFFT_NO_VECTORS)
++#define POCKETFFT_NO_VECTORS 1
+ #if defined(__INTEL_COMPILER)
+ // do nothing. This is necessary because this compiler also sets __GNUC__.
+ #elif defined(__clang__)
+ // AppleClang has their own version numbering
+ #ifdef __apple_build_version__
+ #  if (__clang_major__ > 9) || (__clang_major__ == 9 && __clang_minor__ >= 1)
+-#     undef POCKETFFT_NO_VECTORS
++#define POCKETFFT_NO_VECTORS 0
+ #  endif
+ #elif __clang_major__ >= 5
+-#  undef POCKETFFT_NO_VECTORS
++#define POCKETFFT_NO_VECTORS 0
+ #endif
+ #elif defined(__GNUC__)
+ #if __GNUC__>=5
+-#undef POCKETFFT_NO_VECTORS
++#define POCKETFFT_NO_VECTORS 0
+ #endif
+ #endif
+ #endif
+ 
+ template<typename T> struct VLEN { static constexpr size_t val=1; };
+ 
+-#ifndef POCKETFFT_NO_VECTORS
++#if !(POCKETFFT_NO_VECTORS)
+ #if (defined(__AVX512F__))
+ template<> struct VLEN<float> { static constexpr size_t val=16; };
+ template<> struct VLEN<double> { static constexpr size_t val=8; };
+@@ -145,7 +149,7 @@ template<> struct VLEN<double> { static constexpr size_t val=2; };
+ template<> struct VLEN<float> { static constexpr size_t val=4; };
+ template<> struct VLEN<double> { static constexpr size_t val=2; };
+ #else
+-#define POCKETFFT_NO_VECTORS
++#define POCKETFFT_NO_VECTORS 1
+ #endif
+ #endif
+ 
+@@ -180,7 +184,7 @@ template<typename T> class arr
+     T *p;
+     size_t sz;
+ 
+-#if defined(POCKETFFT_NO_VECTORS)
++#if POCKETFFT_NO_VECTORS
+     static T *ralloc(size_t num)
+       {
+       if (num==0) return nullptr;
+@@ -3026,7 +3030,7 @@ class rev_iter
+ template<typename T> struct VTYPE {};
+ template <typename T> using vtype_t = typename VTYPE<T>::type;
+ 
+-#ifndef POCKETFFT_NO_VECTORS
++#if !(POCKETFFT_NO_VECTORS)
+ template<> struct VTYPE<float>
+   {
+   using type = float __attribute__ ((vector_size (VLEN<float>::val*sizeof(float))));
+@@ -3139,7 +3143,7 @@ POCKETFFT_NOINLINE void general_nd(const cndarr<T> &in, ndarr<T> &out,
+         auto storage = alloc_tmp<T0>(in.shape(), len, sizeof(T));
+         const auto &tin(iax==0? in : out);
+         multi_iter<vlen> it(tin, out, axes[iax]);
+-#ifndef POCKETFFT_NO_VECTORS
++#if !(POCKETFFT_NO_VECTORS)
+         if (vlen>1)
+           while (it.remaining()>=vlen)
+             {
+@@ -3245,7 +3249,7 @@ template<typename T> POCKETFFT_NOINLINE void general_r2c(
+     constexpr auto vlen = VLEN<T>::val;
+     auto storage = alloc_tmp<T>(in.shape(), len, sizeof(T));
+     multi_iter<vlen> it(in, out, axis);
+-#ifndef POCKETFFT_NO_VECTORS
++#if !(POCKETFFT_NO_VECTORS)
+     if (vlen>1)
+       while (it.remaining()>=vlen)
+         {
+@@ -3300,7 +3304,7 @@ template<typename T> POCKETFFT_NOINLINE void general_c2r(
+       constexpr auto vlen = VLEN<T>::val;
+       auto storage = alloc_tmp<T>(out.shape(), len, sizeof(T));
+       multi_iter<vlen> it(in, out, axis);
+-#ifndef POCKETFFT_NO_VECTORS
++#if !(POCKETFFT_NO_VECTORS)
+       if (vlen>1)
+         while (it.remaining()>=vlen)
+           {
-- 
2.37.0

[bug#58261] [PATCH v3 03/15] gnu: Add sajson.

[David Elsing]

* gnu/packages/cpp.scm (sajson): New variable.
---
 gnu/packages/cpp.scm                          | 60 +++++++++++++++++++
 .../patches/sajson-build-with-gcc10.patch     | 45 ++++++++++++++
 2 files changed, 105 insertions(+)
 create mode 100644 gnu/packages/patches/sajson-build-with-gcc10.patch

diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index 2b5841e777..b6a0a70ed7 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -57,6 +57,7 @@ (define-module (gnu packages cpp)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system python)
+  #:use-module (guix build-system scons)
   #:use-module (guix modules)
   #:use-module (guix gexp)
   #:use-module (gnu packages)
@@ -2033,3 +2034,62 @@ (define-public pocketfft-cpp
 computing Fast Fourier transformations.  It supports multidimensional arrays,
 different floating point sizes and complex transformations.")
       (license license:bsd-3))))
+
+(define-public sajson
+  (let ((commit "ec644013e34f9984a3cc9ba568cab97a391db9cd")
+        (revision "0"))
+    (package
+      (name "sajson")
+      (version (git-version "1.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/chadaustin/sajson")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (patches
+                 (search-patches "sajson-build-with-gcc10.patch"))
+                (sha256
+                 (base32
+                  "0fjag27w7gvkc5pdhq3ad7yc09rabpzahndw1sgsg04ipznidmmq"))
+                (modules '((guix build utils)))
+                (snippet '(delete-file-recursively "third-party"))))
+      (build-system scons-build-system)
+      (arguments
+       (list
+        #:phases
+        #~(modify-phases %standard-phases
+            (add-after 'unpack 'disable-other-builds
+              (lambda _
+                (substitute* "SConstruct"
+                  (("for name, tools in builds:")
+                   "for name, tools in [('opt', [gcc, opt])]:"))))
+            (add-after 'unpack 'use-external-unittest-cpp
+              (lambda _
+                (substitute* "SConscript"
+                  (("unittestpp_env\\.Library") "_dummy = ")
+                  (("test_env = env.Clone\\(tools=\\[unittestpp, sajson\\]\\)")
+                   (string-append
+                    "test_env = env.Clone(tools=[sajson])\n"
+                    "test_env.Append(CPPPATH='"
+                    (search-input-directory %build-inputs "/include/UnitTest++")
+                    "', LIBPATH='"
+                    (string-append #$(this-package-native-input "unittest-cpp")
+                                   "/lib")
+                    "', LIBS=['UnitTest++'])")))))
+            (replace 'check
+              (lambda* (#:key tests? #:allow-other-keys)
+                (when tests?
+                  (invoke "build/opt/test")
+                  (invoke "build/opt/test_unsorted"))))
+            (replace 'install
+              (lambda _
+                (let ((out (string-append #$output "/include")))
+                  (install-file "include/sajson.h" out)
+                  (install-file "include/sajson_ostream.h" out)))))))
+      (native-inputs (list unittest-cpp))
+      (home-page "https://github.com/chadaustin/sajson")
+      (synopsis "C++11 header-only, in-place JSON parser")
+      (description "@code{sajson} is an in-place JSON parser with support for
+parsing with only a single memory allocation.")
+      (license license:expat))))
diff --git a/gnu/packages/patches/sajson-build-with-gcc10.patch b/gnu/packages/patches/sajson-build-with-gcc10.patch
new file mode 100644
index 0000000000..878706dc79
--- /dev/null
+++ b/gnu/packages/patches/sajson-build-with-gcc10.patch
@@ -0,0 +1,45 @@
+This patch is from the upstream pull request
+https://github.com/chadaustin/sajson/pull/54.
+It fixes linking with GCC.
+
+diff --git a/include/sajson.h b/include/sajson.h
+index 8b4e05a..1bd045b 100644
+--- a/include/sajson.h
++++ b/include/sajson.h
+@@ -138,12 +138,17 @@ constexpr inline size_t make_element(tag t, size_t value) {
+ // header. This trick courtesy of Rich Geldreich's Purple JSON parser.
+ template <typename unused = void>
+ struct globals_struct {
++    static const unsigned char parse_flags[256];
++};
++typedef globals_struct<> globals;
++
+ // clang-format off
+ 
+     // bit 0 (1) - set if: plain ASCII string character
+     // bit 1 (2) - set if: whitespace
+     // bit 4 (0x10) - set if: 0-9 e E .
+-    constexpr static const uint8_t parse_flags[256] = {
++    template <typename unused>
++    const unsigned char globals_struct<unused>::parse_flags[256] = {
+      // 0    1    2    3    4    5    6    7      8    9    A    B    C    D    E    F
+         0,   0,   0,   0,   0,   0,   0,   0,     0,   2,   2,   0,   0,   2,   0,   0, // 0
+         0,   0,   0,   0,   0,   0,   0,   0,     0,   0,   0,   0,   0,   0,   0,   0, // 1
+@@ -162,15 +167,13 @@ struct globals_struct {
+     };
+ 
+ // clang-format on
+-};
+-typedef globals_struct<> globals;
+ 
+-constexpr inline bool is_plain_string_character(char c) {
++inline bool is_plain_string_character(char c) {
+     // return c >= 0x20 && c <= 0x7f && c != 0x22 && c != 0x5c;
+     return (globals::parse_flags[static_cast<unsigned char>(c)] & 1) != 0;
+ }
+ 
+-constexpr inline bool is_whitespace(char c) {
++inline bool is_whitespace(char c) {
+     // return c == '\r' || c == '\n' || c == '\t' || c == ' ';
+     return (globals::parse_flags[static_cast<unsigned char>(c)] & 2) != 0;
+ }
-- 
2.37.0

[bug#58261] [PATCH v3 04/15] gnu: Add cbehave.

[David Elsing]

* gnu/packages/check.scm (cbehave): New variable.
---
 gnu/packages/check.scm | 56 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 797fe71277..70dfbbac27 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -38,6 +38,7 @@
 ;;; Copyright © 2020, 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2021 Hugo Lecomte <hugo.lecomte@inria.fr>
 ;;; Copyright © 2022 Maxime Devos <maximedevos@telenet.be>
+;;; Copyright © 2022 David Elsing <david.elsing@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -3190,3 +3191,58 @@ (define-public python-pytest-regressions
 tables by saving expected data in a data directory (courtesy of pytest-datadir)
 that can be used to verify that future runs produce the same data.")
     (license license:expat)))
+
+(define-public cbehave
+  (let ((commit "5deaea0eaaf52f1c5ccdac0c68c003988f348fb4")
+        (revision "1"))
+    (package
+      (name "cbehave")
+      (version (git-version "0.2.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/bigwhite/cbehave")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0kicawxmxn059n3rmfc7r2q5wfjrqbr6lm8dmsi86ba76ak0f9gi"))
+                (snippet
+                 #~(begin
+                     (for-each
+                      (lambda (file)
+                        (delete-file file))
+                      '("Makefile.in" "aclocal.m4" "config.guess" "config.sub"
+                        "configure" "depcomp" "install-sh" "libtool"
+                        "ltmain.sh" "missing" "src/Makefile.in"
+                        "src/example/Makefile.in"))))))
+      (build-system gnu-build-system)
+      (arguments
+       (list
+        #:configure-flags #~(list "--enable-shared" "--disable-static")
+        #:phases
+        #~(modify-phases %standard-phases
+            (add-before 'bootstrap 'rename-configure.in
+              (lambda _
+                (rename-file "configure.in" "configure.ac")))
+            (add-after 'rename-configure.in 'set-AM_PROG_AR
+              (lambda _
+                (substitute* "configure.ac"
+                  (("^AC_PROG_LIBTOOL.*" orig)
+                   (string-append "AM_PROG_AR\n" orig)))))
+            (add-after 'set-AM_PROG_AR 'enable-tests
+              (lambda _
+                (let ((port (open-file "src/example/Makefile.am" "a")))
+                  (display (string-append "\nTESTS = calculator_test"
+                                          " text_editor_test string_test"
+                                          " product_database_test mock_test\n")
+                           port)
+                  (close-port port))))
+            (add-before 'check 'create-dummy-file
+              (lambda _
+                (invoke "touch" "src/example/foo.txt"))))))
+      (native-inputs (list autoconf automake libtool))
+      (home-page "https://github.com/bigwhite/cbehave")
+      (synopsis "Behavior-driven development framework for C")
+      (description "CBehave is a C framework for behavior-driven development.")
+      (license license:apsl2))))
-- 
2.37.0

[bug#58261] [PATCH v3 05/15] gnu: Add tinydir.

[David Elsing]

* gnu/packages/cpp.scm (tinydir): New variable.
---
 gnu/packages/cpp.scm                          | 41 +++++++++++++++++++
 .../patches/tinydir-fix-cbehave-test.patch    | 16 ++++++++
 2 files changed, 57 insertions(+)
 create mode 100644 gnu/packages/patches/tinydir-fix-cbehave-test.patch

diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index b6a0a70ed7..7871660611 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -2093,3 +2093,44 @@ (define-public sajson
       (description "@code{sajson} is an in-place JSON parser with support for
 parsing with only a single memory allocation.")
       (license license:expat))))
+
+(define-public tinydir
+  (package
+    (name "tinydir")
+    (version "1.2.5")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/cxong/tinydir")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1nprgdfx4i8wzc1idw6chan4fjfa75b5ll8kghdc0q2278pny259"))
+              (patches (search-patches "tinydir-fix-cbehave-test.patch"))
+              (modules '((guix build utils)))
+              (snippet '(delete-file-recursively "tests/cbehave"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'path-cmake
+            (lambda _
+              (substitute* "tests/CMakeLists.txt"
+                (("^include_dir.*cbehave.*")
+                 (string-append "include_directories("#$cbehave "/include)"))
+                (("^add_subdir.*cbeha.*") ""))))
+          (add-before 'configure 'chdir
+            (lambda _
+              (chdir "tests")))
+          (replace 'install
+            (lambda _
+              (install-file "../tinydir.h"
+                            (string-append #$output "/include")))))))
+    (native-inputs (list cbehave))
+    (home-page "https://github.com/cxong/tinydir")
+    (synopsis "Directory listing wrapper")
+    (description "@code{tinydir} is a header-only C wrapper for listing
+directory contents.")
+    (license license:bsd-2)))
diff --git a/gnu/packages/patches/tinydir-fix-cbehave-test.patch b/gnu/packages/patches/tinydir-fix-cbehave-test.patch
new file mode 100644
index 0000000000..84ecee12c2
--- /dev/null
+++ b/gnu/packages/patches/tinydir-fix-cbehave-test.patch
@@ -0,0 +1,16 @@
+Make test work with upstream cbehave
+(tinydir bundles a modified version)
+
+diff --git a/tests/file_open_test.c b/tests/file_open_test.c
+index 3e659bc..9f6f88d 100644
+--- a/tests/file_open_test.c
++++ b/tests/file_open_test.c
+@@ -19,4 +19,7 @@ FEATURE(file_open, "File open")
+ 	SCENARIO_END
+ FEATURE_END
+ 
+-CBEHAVE_RUN("File open:", TEST_FEATURE(file_open))
++int main(void) {
++	cbehave_feature _cfeatures[] = {{feature_idx(file_open)}};
++	return cbehave_runner("File open:", _cfeatures);
++}
-- 
2.37.0

[bug#58261] [PATCH v3 06/15] gnu: Add optionparser.

[David Elsing]

* gnu/packages/cpp.scm (optionparser): New variable.
---
 gnu/packages/cpp.scm | 48 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index 7871660611..51d146476f 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -2134,3 +2134,51 @@ (define-public tinydir
     (description "@code{tinydir} is a header-only C wrapper for listing
 directory contents.")
     (license license:bsd-2)))
+
+(define-public optionparser
+  (package
+    (name "optionparser")
+    (version "1.7")
+    (source (origin
+              (method url-fetch)
+              (uri
+               (string-append "mirror://sourceforge/optionparser/"
+                              "optionparser-" version ".tar.gz"))
+              (sha256
+               (base32
+                "04gfxrdzwacaynb8scsz6rr7nh64n6yk6w9dh2qdhrxw4caqr0dk"))))
+    (outputs '("out" "doc"))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (delete 'configure)
+          (add-before 'build 'chdir
+            (lambda _ (chdir "src")))
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (begin
+                  (invoke "./example_arg")
+                  (invoke "./testparse")
+                  (invoke "./testprintusage")
+                  (invoke "./testodr")
+                  (invoke "./example")))))
+          (replace 'install
+            (lambda _
+              (install-file "optionparser.h"
+                            (string-append #$output "/include"))))
+          (add-after 'install 'install-doc
+            (lambda _
+              (copy-recursively
+               "../html"
+               (string-append #$output:doc "/share/doc/optionparser/html")))))))
+    (native-inputs (list doxygen))
+    (home-page "https://optionparser.sourceforge.net/")
+    (synopsis "Header-only C++ library to parse command line options")
+    (description "This library can be used to handle the command line
+arguments of a C++ program.  It supports the short and long option formats of
+getopt(), getopt_long() and getopt_long_only(), but has a more convenient
+interface.")
+    (license license:expat)))
-- 
2.37.0

[bug#58261] [PATCH v3 07/15] gnu: Add sajson-for-gemmi.

[David Elsing]

* gnu/packages/chemistry.scm (sajson-for-gemmi): New variable.
---
 gnu/packages/chemistry.scm                    |  23 +++
 .../sajson-for-gemmi-numbers-as-strings.patch | 195 ++++++++++++++++++
 2 files changed, 218 insertions(+)
 create mode 100644 gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index c517610fe8..723b7ee8db 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -6,6 +6,7 @@
 ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
 ;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2022 David Elsing <david.elsing@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -27,6 +28,7 @@ (define-module (gnu packages chemistry)
   #:use-module (guix utils)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix download)
+  #:use-module (guix gexp)
   #:use-module (guix git-download)
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)
@@ -35,6 +37,7 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages cpp)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gl)
@@ -50,8 +53,10 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages qt)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages sphinx)
+  #:use-module (gnu packages stb)
   #:use-module (gnu packages xml)
   #:use-module (guix build-system cmake)
+  #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system python))
 
@@ -566,3 +571,21 @@ (define-public python-pymol
 used to prepare publication-quality figures, to share interactive results with
 your colleagues, or to generate pre-rendered animations.")
     (license license:bsd-3)))
+
+(define-public sajson-for-gemmi
+  (package/inherit sajson
+    (name "sajson-for-gemmi")
+    (source (origin
+              (inherit (package-source sajson))
+              (patches (cons
+                        (search-patch
+                         "sajson-for-gemmi-numbers-as-strings.patch")
+                        (origin-patches (package-source sajson))))))
+    (arguments
+     (substitute-keyword-arguments (package-arguments sajson)
+       ;; This is a modified version used in gemmi, in which numbers are kept
+       ;; as strings. Building the tests fails with the modification.
+       ((#:tests? _ #f) #f)
+       ((#:phases phases)
+        #~(modify-phases #$phases
+            (delete 'build)))))))
diff --git a/gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch b/gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch
new file mode 100644
index 0000000000..6f476b8583
--- /dev/null
+++ b/gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch
@@ -0,0 +1,195 @@
+Patch for gemmi: Keep numbers in JSON file as strings.
+
+Adapted from this commit of the bundled fork of sajson in gemmi:
+https://github.com/project-gemmi/gemmi/commit/fccbca4f6040364ba708613e1429c2251872240d
+
+diff -ur a/include/sajson.h b/include/sajson.h
+--- a/include/sajson.h
++++ b/include/sajson.h
+@@ -411,43 +411,6 @@
+ };
+ } // namespace internal
+ 
+-namespace integer_storage {
+-enum { word_length = 1 };
+-
+-inline int load(const size_t* location) {
+-    int value;
+-    memcpy(&value, location, sizeof(value));
+-    return value;
+-}
+-
+-inline void store(size_t* location, int value) {
+-    // NOTE: Most modern compilers optimize away this constant-size
+-    // memcpy into a single instruction. If any don't, and treat
+-    // punning through a union as legal, they can be special-cased.
+-    static_assert(
+-        sizeof(value) <= sizeof(*location),
+-        "size_t must not be smaller than int");
+-    memcpy(location, &value, sizeof(value));
+-}
+-} // namespace integer_storage
+-
+-namespace double_storage {
+-enum { word_length = sizeof(double) / sizeof(size_t) };
+-
+-inline double load(const size_t* location) {
+-    double value;
+-    memcpy(&value, location, sizeof(double));
+-    return value;
+-}
+-
+-inline void store(size_t* location, double value) {
+-    // NOTE: Most modern compilers optimize away this constant-size
+-    // memcpy into a single instruction. If any don't, and treat
+-    // punning through a union as legal, they can be special-cased.
+-    memcpy(location, &value, sizeof(double));
+-}
+-} // namespace double_storage
+-
+ /// Represents a JSON value.  First, call get_type() to check its type,
+ /// which determines which methods are available.
+ ///
+@@ -585,70 +548,10 @@
+         return length;
+     }
+ 
+-    /// If a numeric value was parsed as a 32-bit integer, returns it.
+-    /// Only legal if get_type() is TYPE_INTEGER.
+-    int get_integer_value() const {
+-        assert_tag(tag::integer);
+-        return integer_storage::load(payload);
+-    }
+-
+-    /// If a numeric value was parsed as a double, returns it.
+-    /// Only legal if get_type() is TYPE_DOUBLE.
+-    double get_double_value() const {
+-        assert_tag(tag::double_);
+-        return double_storage::load(payload);
+-    }
+-
+-    /// Returns a numeric value as a double-precision float.
+-    /// Only legal if get_type() is TYPE_INTEGER or TYPE_DOUBLE.
+-    double get_number_value() const {
+-        assert_tag_2(tag::integer, tag::double_);
+-        if (value_tag == tag::integer) {
+-            return get_integer_value();
+-        } else {
+-            return get_double_value();
+-        }
+-    }
+-
+-    /// Returns true and writes to the output argument if the numeric value
+-    /// fits in a 53-bit integer.  This is useful for timestamps and other
+-    /// situations where integral values with greater than 32-bit precision
+-    /// are used, as 64-bit values are not understood by all JSON
+-    /// implementations or languages.
+-    /// Returns false if the value is not an integer or not in range.
+-    /// Only legal if get_type() is TYPE_INTEGER or TYPE_DOUBLE.
+-    bool get_int53_value(int64_t* out) const {
+-        // Make sure the output variable is always defined to avoid any
+-        // possible situation like
+-        // https://gist.github.com/chadaustin/2c249cb850619ddec05b23ca42cf7a18
+-        *out = 0;
+-
+-        assert_tag_2(tag::integer, tag::double_);
+-        switch (value_tag) {
+-        case tag::integer:
+-            *out = get_integer_value();
+-            return true;
+-        case tag::double_: {
+-            double v = get_double_value();
+-            if (v < -(1LL << 53) || v > (1LL << 53)) {
+-                return false;
+-            }
+-            int64_t as_int = static_cast<int64_t>(v);
+-            if (as_int != v) {
+-                return false;
+-            }
+-            *out = as_int;
+-            return true;
+-        }
+-        default:
+-            return false;
+-        }
+-    }
+-
+     /// Returns the length of the string.
+     /// Only legal if get_type() is TYPE_STRING.
+     size_t get_string_length() const {
+-        assert_tag(tag::string);
++        assert_tag_3(tag::string, tag::integer, tag::double_);
+         return payload[1] - payload[0];
+     }
+ 
+@@ -659,7 +562,7 @@
+     /// embedded NULs.
+     /// Only legal if get_type() is TYPE_STRING.
+     const char* as_cstring() const {
+-        assert_tag(tag::string);
++        assert_tag_3(tag::string, tag::integer, tag::double_);
+         return text + payload[0];
+     }
+ 
+@@ -667,7 +570,7 @@
+     /// Returns a string's value as a std::string.
+     /// Only legal if get_type() is TYPE_STRING.
+     std::string as_string() const {
+-        assert_tag(tag::string);
++        assert_tag_3(tag::string, tag::integer, tag::double_);
+         return std::string(text + payload[0], text + payload[1]);
+     }
+ #endif
+@@ -690,6 +593,10 @@
+         assert(e1 == value_tag || e2 == value_tag);
+     }
+ 
++    void assert_tag_3(tag e1, tag e2, tag e3) const {
++        assert(e1 == value_tag || e2 == value_tag || e3 == value_tag);
++    }
++
+     void assert_in_bounds(size_t i) const { assert(i < get_length()); }
+ 
+     const tag value_tag;
+@@ -2059,6 +1966,8 @@
+     std::pair<char*, internal::tag> parse_number(char* p) {
+         using internal::tag;
+ 
++	size_t start = p - input.get_data();
++
+         // Assume 32-bit, two's complement integers.
+         static constexpr unsigned RISKY = INT_MAX / 10u;
+         unsigned max_digit_after_risky = INT_MAX % 10u;
+@@ -2235,23 +2144,18 @@
+                 u = 0u - u;
+             }
+         }
++
++        bool success;
++        size_t* out = allocator.reserve(2, &success);
++        if (SAJSON_UNLIKELY(!success)) {
++            return std::make_pair(oom(p, "number"), tag::null);
++        }
++        out[0] = start;
++        out[1] = p - input.get_data();
++
+         if (try_double) {
+-            bool success;
+-            size_t* out
+-                = allocator.reserve(double_storage::word_length, &success);
+-            if (SAJSON_UNLIKELY(!success)) {
+-                return std::make_pair(oom(p, "double"), tag::null);
+-            }
+-            double_storage::store(out, d);
+             return std::make_pair(p, tag::double_);
+         } else {
+-            bool success;
+-            size_t* out
+-                = allocator.reserve(integer_storage::word_length, &success);
+-            if (SAJSON_UNLIKELY(!success)) {
+-                return std::make_pair(oom(p, "integer"), tag::null);
+-            }
+-            integer_storage::store(out, static_cast<int>(u));
+             return std::make_pair(p, tag::integer);
+         }
+     }
-- 
2.37.0

[bug#58261] [PATCH v3 08/15] gnu: Add gemmi.

[David Elsing]

* gnu/packages/chemistry.scm (gemmi): New variable.
---
 gnu/packages/chemistry.scm                    | 96 +++++++++++++++++++
 .../patches/gemmi-fix-pegtl-usage.patch       | 31 ++++++
 .../patches/gemmi-fix-sajson-types.patch      | 11 +++
 3 files changed, 138 insertions(+)
 create mode 100644 gnu/packages/patches/gemmi-fix-pegtl-usage.patch
 create mode 100644 gnu/packages/patches/gemmi-fix-sajson-types.patch

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 723b7ee8db..c6b8376248 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -589,3 +589,99 @@ (define-public sajson-for-gemmi
        ((#:phases phases)
         #~(modify-phases #$phases
             (delete 'build)))))))
+
+(define-public gemmi
+  (package
+    (name "gemmi")
+    (version "0.5.7")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/project-gemmi/gemmi")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "00km5q726bslrw7xbfwb3f3mrsk19qbimfnl3hvr4wi1y3z8i18a"))
+              (patches
+               (search-patches "gemmi-fix-sajson-types.patch"
+                               "gemmi-fix-pegtl-usage.patch"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  (delete-file-recursively "include/gemmi/third_party")
+                  (delete-file-recursively "third_party")))))
+    (outputs '("out" "bin" "python"))
+    (build-system cmake-build-system)
+    (native-inputs
+     (list fast-float
+           optionparser
+           pegtl
+           pocketfft-cpp
+           pybind11
+           sajson-for-gemmi
+           stb-sprintf
+           tinydir))
+    (inputs (list python zlib))
+    (arguments
+     (list
+      #:modules '((guix build cmake-build-system)
+                  (guix build utils)
+                  ((guix build python-build-system)
+                   #:select (site-packages)))
+      #:imported-modules (append %cmake-build-system-modules
+                                 '((guix build python-build-system)))
+      #:configure-flags
+      #~(list "-DUSE_PYTHON=ON"
+              (string-append "-DPYTHON_INSTALL_DIR="
+                             (site-packages %build-inputs %outputs)))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-includes
+            (lambda _
+              (substitute*
+                  (list
+                   "include/gemmi/sprintf.hpp"
+                   "include/gemmi/dirwalk.hpp"
+                   "include/gemmi/cif.hpp"
+                   "include/gemmi/json.hpp"
+                   "python/gemmi.cpp"
+                   "include/gemmi/atof.hpp"
+                   "include/gemmi/numb.hpp"
+                   "include/gemmi/fourier.hpp")
+                (("<stb/stb_sprintf.h>") "<stb_sprintf.h>")
+                (("\"third_party/tinydir.h\"") "<tinydir.h>")
+                (("\"third_party/tao/pegtl.hpp\"") "<tao/pegtl.hpp>")
+                (("\"third_party/sajson.h\"") "<sajson.h>")
+                (("\"gemmi/third_party/tao/pegtl/parse_error.hpp\"")
+                 "<tao/pegtl/parse_error.hpp>")
+                (("\"third_party/fast_float.h\"")
+                 "<fast_float/fast_float.h>")
+                (("\"third_party/pocketfft_hdronly.h\"")
+                 "<pocketfft_hdronly.h>"))))
+          (add-after 'unpack 'change-bin-prefix
+            (lambda _
+              (substitute* "CMakeLists.txt"
+                (("install\\(TARGETS program DESTINATION bin\\)")
+                 (string-append
+                  "install(TARGETS program DESTINATION "
+                  #$output:bin "/bin)")))))
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (with-directory-excursion "../source"
+                  (setenv "PYTHONPATH" "../build")
+                  (invoke "python3" "-m" "unittest" "discover" "-v"
+                          "-s" "tests"))))))))
+    (home-page "https://gemmi.readthedocs.io/en/latest/")
+    (synopsis "Macromolecular crystallography library and utilities")
+    (description "GEMMI is a C++ library for macromolecular crystallography.
+It can be used for working with
+@enumerate
+@item macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files),
+@item refinement restraints (CIF files),
+@item reflection data (MTZ and mmCIF formats),
+@item data on a 3D grid (electron density maps, masks, MRC/CCP4 format)
+@item crystallographic symmetry.
+@end enumerate")
+    (license license:mpl2.0)))
diff --git a/gnu/packages/patches/gemmi-fix-pegtl-usage.patch b/gnu/packages/patches/gemmi-fix-pegtl-usage.patch
new file mode 100644
index 0000000000..3667474847
--- /dev/null
+++ b/gnu/packages/patches/gemmi-fix-pegtl-usage.patch
@@ -0,0 +1,31 @@
+Use the definitions from (newer) upstream PEGTL.
+
+diff --git a/include/gemmi/cif.hpp b/include/gemmi/cif.hpp
+index c7ffdb44..35d24210 100644
+--- a/include/gemmi/cif.hpp
++++ b/include/gemmi/cif.hpp
+@@ -37,7 +37,6 @@ namespace pegtl = tao::pegtl;
+ namespace rules {
+ 
+   template<int TableVal> struct lookup_char {
+-    using analyze_t = pegtl::analysis::generic<pegtl::analysis::rule_type::ANY>;
+     template<typename Input> static bool match(Input& in) {
+       if (!in.empty() && cif::char_table(in.peek_char()) == TableVal) {
+         if (TableVal == 2)  // this set includes new-line
+@@ -71,11 +70,11 @@ namespace rules {
+   struct ws_or_eof : pegtl::sor<whitespace, pegtl::eof> {};
+ 
+   // (b) Reserved words.
+-  struct str_data : TAOCPP_PEGTL_ISTRING("data_") {};
+-  struct str_loop : TAOCPP_PEGTL_ISTRING("loop_") {};
+-  struct str_global : TAOCPP_PEGTL_ISTRING("global_") {};
+-  struct str_save : TAOCPP_PEGTL_ISTRING("save_") {};
+-  struct str_stop : TAOCPP_PEGTL_ISTRING("stop_") {};
++  struct str_data : TAO_PEGTL_ISTRING("data_") {};
++  struct str_loop : TAO_PEGTL_ISTRING("loop_") {};
++  struct str_global : TAO_PEGTL_ISTRING("global_") {};
++  struct str_save : TAO_PEGTL_ISTRING("save_") {};
++  struct str_stop : TAO_PEGTL_ISTRING("stop_") {};
+   struct keyword : pegtl::sor<str_data, str_loop, str_global,
+                               str_save, str_stop> {};
+ 
diff --git a/gnu/packages/patches/gemmi-fix-sajson-types.patch b/gnu/packages/patches/gemmi-fix-sajson-types.patch
new file mode 100644
index 0000000000..9633ddac8b
--- /dev/null
+++ b/gnu/packages/patches/gemmi-fix-sajson-types.patch
@@ -0,0 +1,11 @@
+diff -ur a/include/gemmi/json.hpp b/include/gemmi/json.hpp
+--- a/include/gemmi/json.hpp
++++ b/include/gemmi/json.hpp
+@@ -38,6 +38,7 @@
+ 
+ inline std::string as_cif_value(const sajson::value& val) {
+   switch (val.get_type()) {
++    case sajson::TYPE_INTEGER:
+     case sajson::TYPE_DOUBLE:
+       return val.as_string();
+     case sajson::TYPE_NULL:
-- 
2.37.0

[bug#58261] [PATCH v3 09/15] gnu: Add freesasa.

[David Elsing]

* gnu/packages/chemistry.scm (freesasa): New variable.
---
 gnu/packages/chemistry.scm | 86 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 86 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index c6b8376248..a9868ed64d 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -34,11 +34,13 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages backup)
+  #:use-module (gnu packages bison)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cpp)
   #:use-module (gnu packages documentation)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages graphviz)
@@ -54,6 +56,7 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages sphinx)
   #:use-module (gnu packages stb)
+  #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system copy)
@@ -685,3 +688,86 @@ (define-public gemmi
 @item crystallographic symmetry.
 @end enumerate")
     (license license:mpl2.0)))
+
+(define-public freesasa
+  (package
+    (name "freesasa")
+    (version "2.1.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/mittinatten/freesasa")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "07wdnahf3g355ryaiqvfxd5f4rl54wv8jwxcbn0nia89fqysbv0f"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Remove C files generated by Flex and Bison
+                  (for-each delete-file
+                            '("src/parser.c" "src/parser.h"
+                              "src/lexer.c" "src/lexer.h"))))))
+    (outputs '("out" "doc"))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      #~(list "--enable-check"
+              "--enable-parser-generator"
+              "CXXFLAGS=-std=c++17"
+              "--enable-doxygen")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'remove-libc++-linking
+            (lambda _
+              (substitute* "src/Makefile.am"
+                (("-lc\\+\\+") ""))))
+          (add-after 'unpack 'build-shared-library
+            (lambda _
+              (substitute* "src/Makefile.am"
+                (("lib_LIBRARIES") "lib_LTLIBRARIES")
+                (("libfreesasa\\.a") "libfreesasa.la")
+                (("freesasa_LDADD \\+= libfreesasa\\.la" prev)
+                 (string-append prev "\nlibfreesasa_la_LIBADD"
+                                " = -ljson-c ${libxml2_LIBS}\n"))
+                (("_a_SOURCES") "_la_SOURCES"))
+              (substitute* "configure.ac"
+                (("AC_PROG_INSTALL" inst)
+                 (string-append "AM_PROG_LIBTOOL\n" inst)))
+              (substitute* "tests/Makefile.am"
+                (("libfreesasa\\.a") "libfreesasa.la"))))
+          (add-before 'build 'build-lexer-and-parser
+            (lambda _
+              (with-directory-excursion "src"
+                (invoke "make" "lexer.h" "parser.h"))))
+          (add-after 'install 'install-doc
+            (lambda _
+              (copy-recursively
+               "doc/html"
+               (string-append #$output:doc "/share/doc/"
+                              #$name "-" #$version)))))))
+    (native-inputs
+     (list autoconf
+           automake
+           bison
+           check
+           doxygen
+           fast-float
+           flex
+           libtool
+           pegtl
+           perl
+           pkg-config))
+    (inputs
+     (list gemmi json-c libxml2))
+    (home-page "https://freesasa.github.io/")
+    (synopsis "Calculate the solvent accessible surface area (SASA) of
+molecules")
+    (description "FreeSASA is a command line tool and C-library for
+calculating @acronym{SASAs, solvent accessible surface areas}.  By default Lee
+& Richards'algorithm is used, but Shrake & Rupley's is also available.  Both
+can be parameterized to arbitrary precision, and for high resolution versions
+of the algorithms, the calculations give identical results.")
+    (license license:expat)))
-- 
2.37.0

[bug#58261] [PATCH v3 10/15] gnu: Add maeparser.

[David Elsing]

* gnu/packages/chemistry.scm (maeparser): New variable.
---
 gnu/packages/chemistry.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index a9868ed64d..0712c44ad9 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -771,3 +771,24 @@ (define-public freesasa
 can be parameterized to arbitrary precision, and for high resolution versions
 of the algorithms, the calculations give identical results.")
     (license license:expat)))
+
+(define-public maeparser
+  (package
+    (name "maeparser")
+    (version "1.3.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/schrodinger/maeparser")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1yv4y5hn49fhylziigsg922bb244lb57p69r7vg9q899zd3l5b7l"))))
+    (build-system cmake-build-system)
+    (native-inputs (list boost))
+    (inputs (list zlib))
+    (home-page "https://github.com/schrodinger/maeparser")
+    (synopsis "Maestro file parser")
+    (description "maeparser is a parser for Schrodinger Maestro files.")
+    (license license:expat)))
-- 
2.37.0

[bug#58261] [PATCH v3 11/15] gnu: Add coordgenlibs.

[David Elsing]

* gnu/packages/chemistry.scm (coordgenlibs): New variable.
---
 gnu/packages/chemistry.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 0712c44ad9..4da1bc10f1 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -792,3 +792,31 @@ (define-public maeparser
     (synopsis "Maestro file parser")
     (description "maeparser is a parser for Schrodinger Maestro files.")
     (license license:expat)))
+
+(define-public coordgenlibs
+  (package
+    (name "coordgenlibs")
+    (version "3.0.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/schrodinger/coordgenlibs/")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0d09x3v38i9y184bml020bq7xizdrdwng38qmdxlplzfhqkjdidv"))))
+    (build-system cmake-build-system)
+    (native-inputs (list boost))
+    (inputs (list maeparser))
+    (arguments
+     (list
+      #:configure-flags
+      #~(list "-DCOORDGEN_RIGOROUS_BUILD=OFF"
+              "-DCOORDGEN_USE_MAEPARSER=ON")))
+    (home-page "https://github.com/schrodinger/coordgenlibs/")
+    (synopsis "2D molecule coordinate generation")
+    (description "@code{coordgenlibs} contains algorithms to generate 2D
+coordinates of molecules including macrocycles and metal complexes.  It has an
+emphasis on quality rather than speed.")
+    (license license:bsd-3)))
-- 
2.37.0

[bug#58261] [PATCH v3 12/15] gnu: Add yaehmop.

[David Elsing]

* gnu/packages/chemistry.scm (yaehmop): New variable.
---
 gnu/packages/chemistry.scm | 106 +++++++++++++++++++++++++++++++++++++
 1 file changed, 106 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 4da1bc10f1..a1c1dbfa1b 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -42,6 +42,7 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
+  #:use-module (gnu packages gcc)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages gv)
@@ -56,6 +57,7 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages sphinx)
   #:use-module (gnu packages stb)
+  #:use-module (gnu packages tex)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
   #:use-module (guix build-system cmake)
@@ -820,3 +822,107 @@ (define-public coordgenlibs
 coordinates of molecules including macrocycles and metal complexes.  It has an
 emphasis on quality rather than speed.")
     (license license:bsd-3)))
+
+(define-public yaehmop
+  (package
+    (name "yaehmop")
+    (version "2022.09.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/greglandrum/yaehmop")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1x0d75m1hgdb411fiv7c5bwq1n4y0swrll0gigh8v5c73kjxrja0"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Separate program
+                  (delete-file-recursively "viewkel")
+                  ;; Remove example output (some are corrupted)
+                  (for-each delete-file (find-files "examples" "\\.Z$"))
+                  ;; Documentation outputs
+                  (for-each delete-file (find-files "docs" "\\.(ps|pdf)$"))
+                  ;; These are transpiled from Fortran to C, but we build the
+                  ;; Fortran code instead
+                  (delete-file-recursively "tightbind/f2c_files")
+                  (delete-file "tightbind/diag.c")
+                  (delete-file "tightbind/cboris.c")
+                  (delete-file "tightbind/abfns.c")
+                  (delete-file "tightbind/lovlap.c")))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      #~(list
+         "-DUSE_BLAS_LAPACK=ON"
+         (string-append "-DPARM_FILE_LOC=" #$output
+                        "/share/" #$name "-" #$version "/eht_parms.dat")
+         "-DBIND_EXE_NAME=yaehmop-bind")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'chdir
+            (lambda _
+              (chdir "tightbind")))
+          (add-after 'chdir 'patch-fortran-functions
+            (lambda _
+              (substitute* '("mov.c" "prototypes.h")
+                (("lovlap\\(") "lovlap_(")
+                (("abfns\\(") "abfns_("))))
+          (add-after 'chdir 'patch-cmake
+            (lambda _
+              (substitute* "CMakeLists.txt"
+                (("project\\(yaehmop C\\)") "project(yaehmop C Fortran)")
+                (("abfns.c") "fortran77/abfns.f")
+                (("lovlap.c") "fortran77/lovlap.f")
+                (("(set\\(PARM_FILE_LOC.*)\\)" all init)
+                 (string-append init " CACHE STRING \"\")"))
+                (("add_library\\(yaehmop_eht" lib)
+                 (string-append lib " SHARED "))
+                (("target_link_libraries\\(test_eht \\$\\{LAPACK_LIBRARIES\\}.*"
+                  all)
+                 (string-append all "\ntarget_link_libraries(yaehmop_eht "
+                                "${LAPACK_LIBRARIES})\n")))))
+          (add-after 'build 'build-doc
+            (lambda _
+              (with-directory-excursion "../docs"
+                (substitute* "bind_manual.tex"
+                  (("\\\\usepackage\\{bindpage\\}")
+                   (string-append
+                    "\\usepackage[left=2cm,right=2cm,top=4cm,bottom=2cm]"
+                    "{geometry}\n"
+                    "\\pdfsuppressptexinfo=-1\n")))
+                (substitute* "Zmat_appendix.tex"
+                  (("file=dihedral\\.eps")
+                   "file=figs/dihedral.eps"))
+                (setenv "FORCE_SOURCE_DATE" "1")
+                (invoke "latexmk" "-pdf" "bind_manual.tex"))))
+          (add-after 'install 'install-eht-parms
+            (lambda _
+              (install-file "../tightbind/eht_parms.dat"
+                            (string-append #$output "/share/"
+                                           #$name "-" #$version))))
+          (add-after 'install-eht-parms 'install-doc
+            (lambda _
+              (install-file "../docs/bind_manual.pdf"
+                            (string-append #$output "/share/doc/"
+                                           #$name "-" #$version))))
+          (delete 'check)
+          (add-after 'install-doc 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (invoke "./test_eht")))))))
+    (native-inputs
+     (list gfortran
+           (texlive-updmap.cfg (list texlive-fonts-ec
+                                     texlive-latex-graphics
+                                     texlive-latex-geometry))))
+    (inputs (list openblas))
+    (home-page "https://github.com/greglandrum/yaehmop")
+    (synopsis "Perform extended Hückel calculations")
+    (description "@acronym{YAeHMOP, Yet Another extended Hueckel Molecular
+Orbital Package} contains a program and library for performing extended Hückel
+calculations and analyzing the results.")
+    (license license:bsd-2)))
-- 
2.37.0

[bug#58261] [PATCH v3 13/15] gnu: Add avalon-toolkit.

[David Elsing]

* gnu/packages/chemistry.scm (avalon-toolkit): New variable.
---
 gnu/packages/chemistry.scm | 96 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 96 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index a1c1dbfa1b..82bc3ae29e 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -926,3 +926,99 @@ (define-public yaehmop
 Orbital Package} contains a program and library for performing extended Hückel
 calculations and analyzing the results.")
     (license license:bsd-2)))
+
+(define-public avalon-toolkit
+  (package
+    (name "avalon-toolkit")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "mirror://sourceforge/avalontoolkit/"
+             "AvalonToolkit_" (substring version 0 3) "/AvalonToolkit_"
+             version ".source.tar"))
+       (sha256
+        (base32
+         "0rnnyy6axs2da7aa4q6l30ldavbk49v6l22llj1adn74h1i67bpv"))
+       (modules '((guix build utils) (ice-9 ftw)))
+       (snippet
+        #~(begin
+            (delete-file-recursively "../SourceDistribution/java")))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      ;; There are no intended tests
+      #:tests? #f
+      #:phases
+      #~(let ((programs '("canonizer" "matchtest" "sketch" "smi2mol" "struchk")))
+          (modify-phases %standard-phases
+            (delete 'configure)
+            (add-before 'build 'remove-free
+              (lambda _
+                ;; Remove incorrect free of getenv result (patch also in rdkit)
+                (substitute* "common/reaccsio.c"
+                  (("MyFree.*tempdir.*") ""))))
+            ;; The makefile has incorrect compiler flags and is missing some
+            ;; object files, so we build it ourselves.
+            (replace 'build
+              (lambda _
+                (chdir "common")
+                (let* ((parts
+                        (list
+                         "aacheck" "casutils" "denormal" "depictutil" "didepict"
+                         "fixcharges" "forio" "geometry" "graph" "hashcode"
+                         "layout" "local" "pattern" "perceive" "reaccsio"
+                         "rtutils" "set" "shortcut" "sketch" "ssmatch" "stereo"
+                         "symbol_lists" "symboltable" "utilities"))
+                       (objects (map (lambda (name) (string-append name ".o"))
+                                     parts)))
+                  (for-each
+                   (lambda (name)
+                     (display (string-append "Compiling " name ".c\n"))
+                     (invoke "gcc" "-c" "-fPIC" "-O2"
+                             (string-append name ".c")
+                             "-o" (string-append name ".o")))
+                   parts)
+                  (display "Building shared library\n")
+                  (apply invoke "gcc" "-fPIC" "-shared" "-lm"
+                         "-o" "libavalontoolkit.so" "canonizer.c" "smi2mol.c"
+                         "struchk.c" "patclean.c" objects)
+                  ;; patclean is not built here as there is an undeclared
+                  ;; variable in main().
+                  (for-each
+                   (lambda (program)
+                     (display (string-append "Building " program "\n"))
+                     (invoke "gcc" "-L." "-lavalontoolkit" "-lm" "-O2"
+                             (string-append "-Wl,-rpath=" #$output "/lib")
+                             "-DMAIN" (string-append program ".c") "-o" program))
+                   programs))))
+            (replace 'install
+              (lambda _
+                ;; Executables
+                (for-each
+                 (lambda (program)
+                   (install-file program (string-append #$output "/bin")))
+                 programs)
+                (for-each
+                 (lambda (name)
+                   (symlink (string-append #$output "/bin/smi2mol")
+                            (string-append #$output "/bin/" name)))
+                 '("mol2smi" "rdf2smi" "mol2tbl" "mol2sma" "smi2rdf"))
+                ;; Library
+                (install-file "libavalontoolkit.so"
+                              (string-append #$output "/lib"))
+                (for-each
+                 (lambda (file)
+                   (install-file file (string-append #$output
+                                                    "/include/avalontoolkit")))
+                 (find-files "." "\\.h$"))
+                (install-file "../license.txt"
+                              (string-append #$output "/share/doc/"
+                                             #$name "-" #$version "/"))))))))
+    (home-page "https://sourceforge.net/projects/avalontoolkit/")
+    (synopsis "Tools for SMILES and MOL files and for structure fingerprinting")
+    (description "This package contains a library and programs for
+canonicalization of SMILES and MOL files, molecular structure fingerprinting
+and rendering molecules.")
+    (license license:bsd-3)))
-- 
2.37.0

[bug#58261] [PATCH v3 14/15] gnu: Add ringdecomposerlib.

[David Elsing]

* gnu/packages/chemistry.scm (ringdecomposerlib): New variable.
---
 gnu/packages/chemistry.scm | 81 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 81 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 82bc3ae29e..1a80bd1ad5 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -1022,3 +1022,84 @@ (define-public avalon-toolkit
 canonicalization of SMILES and MOL files, molecular structure fingerprinting
 and rendering molecules.")
     (license license:bsd-3)))
+
+(define-public ringdecomposerlib
+  (package
+    (name "ringdecomposerlib")
+    (version "1.1.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/rareylab/RingDecomposerLib")
+                    (commit (string-append "v" version "_rdkit"))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1rxzs2wpkkdi40wdzxc4sn0brk7dm7ivgqyfh38gf2f5c7pbg0wi"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      #~(list "-DBUILD_PYTHON_WRAPPER=ON"
+              "-DPYTHON_EXECUTABLE=python3"
+              (string-append "-DPYTHON_FLAGS=;--prefix=" #$output ";--root=/"))
+      #:imported-modules (append %cmake-build-system-modules
+                                 '((guix build python-build-system)))
+      #:modules '((guix build cmake-build-system)
+                  (guix build utils)
+                  ((guix build python-build-system)
+                   #:select (add-installed-pythonpath)))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'configure 'patch-cmake
+            (lambda _
+              (substitute* (list "src/Test/CMakeLists.txt"
+                                 "src/RingDecomposerLib/CMakeLists.txt")
+                (("build_.*STATIC") "#"))
+              (substitute* "test/CMakeLists.txt"
+                (("STATIC_TEST") "SHARED_TEST"))
+              ;; Link Python library against shared library
+              (substitute* "src/python/CMakeLists.txt"
+                (("RingDecomposerLibStatic") "RingDecomposerLib"))
+              (substitute* "src/python/setup.py.in"
+                (("static_libs =.*") "static_libs = []\n")
+                (("shared_libs\\s*=.*")
+                 (string-append
+                  "shared_libs = ['RingDecomposerLib']"))
+                (("library_dirs\\s*=\\s*\\[\\]")
+                 "library_dirs = ['${CMAKE_BINARY_DIR}/src/RingDecomposerLib']")
+                (("extra_objects=.*")
+                 (string-append
+                  "extra_link_args=['-Wl,-rpath=" #$output "/lib'],\n")))))
+          (add-after 'build 'build-doc
+            (lambda _
+              ;; Disable redundant LaTeX documentation
+              (substitute* "../source/documentation/sphinx/conf.py"
+                (("^(subprocess.*latex|shutil).*") ""))
+              (substitute* "../source/documentation/doxygen.cfg"
+                (("GENERATE_LATEX.*YES") "GENERATE_LATEX = NO"))
+              ;; Build HTML documentation
+              (invoke "sphinx-build" "-b" "html"
+                      "../source/documentation/sphinx" "html")))
+          (add-after 'install 'install-doc
+            (lambda _
+              ;; Not reproducible
+              (delete-file-recursively "html/.doctrees")
+              (copy-recursively "html"
+                                (string-append #$output "/share/doc/"
+                                               #$name "-" #$version "/html"))))
+          (delete 'check)
+          (add-after 'install 'check
+            (assoc-ref %standard-phases 'check))
+          (add-before 'check 'set-pythonpath
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (add-installed-pythonpath inputs outputs))))))
+    (inputs (list python))
+    (native-inputs (list doxygen python python-cython python-sphinx))
+    (home-page "https://github.com/rareylab/RingDecomposerLib")
+    (synopsis "Library for calculating ring topology descriptions such as
+unique ring families")
+    (description "ringdecomposerlib is a library for the calculation of
+unique ring families, relevant cycles, the smallest set of smallest rings and
+other ring topology descriptions.")
+    (license license:bsd-3)))
-- 
2.37.0

[bug#58261] [PATCH v3 15/15] gnu: Add rdkit.

[David Elsing]

* gnu/packages/chemistry.scm (rdkit): New variable.
---
 gnu/packages/chemistry.scm                    | 149 +++++++
 ...rdkit-unbundle-external-dependencies.patch | 384 ++++++++++++++++++
 2 files changed, 533 insertions(+)
 create mode 100644 gnu/packages/patches/rdkit-unbundle-external-dependencies.patch

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 1a80bd1ad5..e72ecd6206 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -34,6 +34,7 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages backup)
+  #:use-module (gnu packages base)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
@@ -41,10 +42,12 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages cpp)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages flex)
+  #:use-module (gnu packages fonts)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages graphviz)
+  #:use-module (gnu packages gtk)
   #:use-module (gnu packages gv)
   #:use-module (gnu packages image)
   #:use-module (gnu packages maths)
@@ -56,6 +59,7 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages qt)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages sphinx)
+  #:use-module (gnu packages sqlite)
   #:use-module (gnu packages stb)
   #:use-module (gnu packages tex)
   #:use-module (gnu packages web)
@@ -1103,3 +1107,148 @@ (define-public ringdecomposerlib
 unique ring families, relevant cycles, the smallest set of smallest rings and
 other ring topology descriptions.")
     (license license:bsd-3)))
+
+(define-public rdkit
+  (package
+    (name "rdkit")
+    (version "2022.03.5")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/rdkit/rdkit")
+                    (commit
+                     (string-append
+                      "Release_" (string-replace-substring version "." "_")))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9"))
+              (patches
+               (search-patches "rdkit-unbundle-external-dependencies.patch"))
+              (modules '((guix build utils)))
+              (snippet
+               #~(begin
+                   ;; Remove pickle files (only used in tests),
+                   ;; as they are compiled programs
+                   (for-each
+                    (lambda (name)
+                      (display (string-append name "\n"))
+                      (delete-file name))
+                    (find-files "." "\\.pkl(\\.gz)?$"))
+                   ;; Remove SQLite data files (can be generated)
+                   (delete-file "Data/RDData.sqlt")
+                   (delete-file "Data/RDTests.sqlt")))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:imported-modules (append %cmake-build-system-modules
+                                 '((guix build python-build-system)))
+      #:modules '((guix build cmake-build-system)
+                  (guix build utils)
+                  ((guix build python-build-system)
+                   #:select (add-installed-pythonpath)))
+      #:configure-flags
+      #~(list
+         "-DRDK_BUILD_AVALON_SUPPORT=ON"
+         "-DRDK_BUILD_CAIRO_SUPPORT=ON"
+         "-DRDK_BUILD_FREESASA_SUPPORT=ON"
+         "-DRDK_BUILD_INCHI_SUPPORT=ON"
+         "-DRDK_BUILD_YAEHMOP_SUPPORT=ON"
+         (string-append "-DCATCH_DIR="
+                        #$(this-package-native-input "catch2")
+                        "/include/catch2")
+         "-DRDK_INSTALL_INTREE=OFF"
+         "-DRDK_INSTALL_STATIC_LIBS=OFF"
+         (string-append
+          "-DRDK_OPTIMIZE_POPCNT="
+          #$(let ((system (or (%current-target-system)
+                              (%current-system))))
+              (cond
+               ((string-prefix? "x86_64" system) "ON")
+               ((string-prefix? "i686" system) "ON")
+               (else "OFF"))))
+         "-DRDK_USE_FLEXBISON=ON"
+         (string-append
+          "-DCMAKE_INCLUDE_PATH="
+          #$(this-package-input "avalon-toolkit") "/include/avalontoolkit"))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'copy-external-dependencies
+            (lambda _
+              (symlink
+               (string-append
+                (search-input-file
+                 %build-inputs "/share/fonts/truetype/ComicNeue-Regular.ttf"))
+               "Data/Fonts/ComicNeue-Regular.ttf")))
+          (add-after 'unpack 'fix-inchi-include
+            (lambda _
+              (substitute* "Code/cmake/Modules/FindInchi.cmake"
+                (("inchi_api.h.*\\)") "inchi/inchi_api.h)")
+                (("INCHI_LIBRARY NAMES.*\\)")
+                 "INCHI_LIBRARY NAMES inchi PATH_SUFFIXES inchi)")
+                (("find_library" prev)
+                 (string-append
+                  "list(APPEND CMAKE_FIND_LIBRARY_SUFFIXES .so.1)\n"
+                  prev)))
+              (substitute* "External/INCHI-API/inchi.cpp"
+                (("<inchi_api.h>") "<inchi/inchi_api.h>"))))
+          (add-before 'build 'enable-bytecode-determinism
+              (lambda _
+                (setenv "PYTHONHASHSEED" "0")
+                (setenv "PYTHONDONTWRITEBYTECODE" "1")))
+          (add-after 'install 'pre-check
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (with-directory-excursion "../source"
+                (invoke "sqlite3" "Data/RDData.sqlt"
+                        ".read rdkit/Dbase/test_data/RDData.sqlite")
+                (invoke "sqlite3" "Data/RDTests.sqlt"
+                        ".read rdkit/Dbase/test_data/RDTests.sqlite")
+                (setenv "RDBASE" (canonicalize-path ".")))
+              (add-installed-pythonpath inputs outputs)))
+          (delete 'check)
+          (add-after 'pre-check 'check
+            (lambda* (#:key tests? parallel-tests? #:allow-other-keys)
+              (when tests?
+                (let ((job-count (number->string
+                                  (if parallel-tests? (parallel-job-count) 1))))
+                  (invoke
+                   "ctest" "-j" job-count
+                   "-E" (string-append
+                         (string-join
+                          '(;; need pickled data
+                            "(pyDiscreteValueVect" "pySparseIntVect"
+                            "graphmoltestPickler" "pyPartialCharges"
+                            "substructLibraryTest" "pyFeatures"
+                            "pythonTestDirML" "pythonTestDirChem"
+                            ;; Catching Python exception fails
+                            "pyRanker)") "|"))))))))))
+    (native-inputs
+     (list bison
+           boost
+           catch2
+           eigen
+           flex
+           freesasa
+           pkg-config
+           rapidjson
+           tar))
+    (inputs
+     (list avalon-toolkit
+           cairo
+           coordgenlibs
+           font-comic-neue
+           freetype
+           inchi
+           maeparser
+           python
+           ringdecomposerlib
+           sqlite
+           yaehmop))
+    (propagated-inputs
+     (list python-numpy python-cairocffi python-pillow))
+    (home-page "https://rdkit.org/")
+    (synopsis "Collection of cheminformatics software")
+    (description "RDKit is a C++ and Python library for cheminformatics, which
+includes (among other things) the analysis and modification of molecules in 2D
+and 3D and descriptor generation for machine learning.")
+    (license license:bsd-3)))
diff --git a/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch b/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch
new file mode 100644
index 0000000000..8ee0611d3b
--- /dev/null
+++ b/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch
@@ -0,0 +1,384 @@
+Remove CMake code for downloading and builing bundled dependencies:
+They are packaged separately as rapidjson, avalon-toolkit, freesasa,
+ringdecomposerlib and yaehmop.
+
+diff --git a/Code/GraphMol/MolInterchange/CMakeLists.txt b/Code/GraphMol/MolInterchange/CMakeLists.txt
+index 1673386a4..c3504e6f1 100644
+--- a/Code/GraphMol/MolInterchange/CMakeLists.txt
++++ b/Code/GraphMol/MolInterchange/CMakeLists.txt
+@@ -1,18 +1,3 @@
+-
+-if(NOT EXISTS "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0")
+-    downloadAndCheckMD5("https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz"
+-          "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz"
+-          "badd12c511e081fec6c89c43a7027bce")
+-    execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
+-      ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz
+-      WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/External)
+-else()
+-  message("-- Found RapidJSON source in ${CMAKE_SOURCE_DIR}/External")
+-endif()
+-
+-include_directories(${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include)
+-
+-
+ rdkit_library(MolInterchange
+               Parser.cpp Writer.cpp
+               LINK_LIBRARIES GraphMol)
+diff --git a/External/AvalonTools/AvalonTools.cpp b/External/AvalonTools/AvalonTools.cpp
+index e6c382123..d83d80668 100644
+--- a/External/AvalonTools/AvalonTools.cpp
++++ b/External/AvalonTools/AvalonTools.cpp
+@@ -24,15 +24,15 @@
+ #include "AvalonTools.h"
+ 
+ extern "C" {
+-#include "local.h"
+-#include "reaccs.h"
+-#include "reaccsio.h"
+-#include "utilities.h"
+-#include "ssmatch.h"
+-#include "smi2mol.h"
+-#include "canonizer.h"
+-#include "layout.h"
+-#include "struchk.h"
++#include <avalontoolkit/local.h>
++#include <avalontoolkit/reaccs.h>
++#include <avalontoolkit/reaccsio.h>
++#include <avalontoolkit/utilities.h>
++#include <avalontoolkit/ssmatch.h>
++#include <avalontoolkit/smi2mol.h>
++#include <avalontoolkit/canonizer.h>
++#include <avalontoolkit/layout.h>
++#include <avalontoolkit/struchk.h>
+ 
+ extern int RunStruchk(struct reaccs_molecule_t **mpp,
+                       struct data_line_t *data_list);
+diff --git a/External/AvalonTools/CMakeLists.txt b/External/AvalonTools/CMakeLists.txt
+index 3e31195fc..314ba35b5 100644
+--- a/External/AvalonTools/CMakeLists.txt
++++ b/External/AvalonTools/CMakeLists.txt
+@@ -2,107 +2,14 @@ if(NOT RDK_BUILD_AVALON_SUPPORT)
+   return()
+ endif(NOT RDK_BUILD_AVALON_SUPPORT)
+ 
+-if(NOT DEFINED AVALONTOOLS_DIR)
+-  set(AVALONTOOLS_DIR "${CMAKE_CURRENT_SOURCE_DIR}/SourceDistribution")
+-  set(fileToPatch "${CMAKE_CURRENT_SOURCE_DIR}/SourceDistribution/common/reaccsio.c")
+-  set(needDownload "TRUE")
+-  if(EXISTS "${fileToPatch}")
+-    file(READ "${fileToPatch}" buffer)
+-    if("${buffer}" MATCHES "//MyFree\\(\\(char \\*\\)tempdir\\);")
+-      set(needDownload "FALSE")
+-    endif()
+-  endif()
+-else()
+-  string(REGEX REPLACE "\\\\" "/" AVALONTOOLS_DIR ${AVALONTOOLS_DIR})
+-  set(needDownload "FALSE")
+-endif()
+-
+-set(AVALON_SRC_PATH ${AVALONTOOLS_DIR}/common)
+-
+-if(needDownload)
+-  if(NOT DEFINED AVALONTOOLS_URL)
+-    set(AVALONTOOLS_URL "https://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.2/AvalonToolkit_1.2.0.source.tar")
+-  endif()
+-  if(NOT DEFINED AVALONTOOLS_MD5SUM)
+-    set(AVALONTOOLS_MD5SUM "092a94f421873f038aa67d4a6cc8cb54")
+-  endif()
+-  if(NOT DEFINED AVALONTOOLS_BASE)
+-    string(REGEX REPLACE "^.*/" "" AVALONTOOLS_BASE "${AVALONTOOLS_URL}")
+-  endif()
+-  downloadAndCheckMD5(${AVALONTOOLS_URL} "${CMAKE_CURRENT_SOURCE_DIR}/${AVALONTOOLS_BASE}" ${AVALONTOOLS_MD5SUM})
+-  execute_process(COMMAND ${CMAKE_COMMAND} -E tar xf
+-    ${CMAKE_CURRENT_SOURCE_DIR}/AvalonToolkit_1.2.0.source.tar
+-    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+-  # apply patch to AvalonTools
+-  configure_file("${fileToPatch}" "${fileToPatch}.orig" COPYONLY)
+-  file(READ "${fileToPatch}" buffer)
+-  string(REGEX REPLACE "MyFree\\(\\(char \\*\\)tempdir\\);"
+-    "//MyFree((char *)tempdir);" buffer "${buffer}")
+-  file(WRITE "${fileToPatch}" "${buffer}")
+-endif()
+ 
+ if (MSVC)
+   add_definitions("/D_CRT_SECURE_NO_WARNINGS")
+   add_compile_options(/wd4224 /wd4101 /wd4018 /wd4996 /wd4244 /wd4305 /wd4013 /wd4146 /wd4334 /wd4715 /wd4715 /nologo)
+ endif(MSVC)
+ 
+-set(avalon_clib_srcs ${AVALON_SRC_PATH}/layout.c
+-	${AVALON_SRC_PATH}/symboltable.c
+-	${AVALON_SRC_PATH}/patclean.c
+-	${AVALON_SRC_PATH}/utilities.c
+-	${AVALON_SRC_PATH}/symbol_lists.c
+-	${AVALON_SRC_PATH}/stereo.c
+-	${AVALON_SRC_PATH}/set.c
+-	${AVALON_SRC_PATH}/perceive.c
+-	${AVALON_SRC_PATH}/local.c
+-	${AVALON_SRC_PATH}/graph.c
+-	${AVALON_SRC_PATH}/geometry.c
+-	${AVALON_SRC_PATH}/forio.c
+-	${AVALON_SRC_PATH}/depictutil.c
+-	${AVALON_SRC_PATH}/denormal.c
+-	${AVALON_SRC_PATH}/casutils.c
+-	${AVALON_SRC_PATH}/ssmatch.c
+-	${AVALON_SRC_PATH}/rtutils.c
+-	${AVALON_SRC_PATH}/smi2mol.c
+-	${AVALON_SRC_PATH}/didepict.c
+-	${AVALON_SRC_PATH}/pattern.c
+-	${AVALON_SRC_PATH}/canonizer.c
+-	${AVALON_SRC_PATH}/aacheck.c
+-	${AVALON_SRC_PATH}/fixcharges.c
+-	${AVALON_SRC_PATH}/struchk.c
+-	${AVALON_SRC_PATH}/reaccsio.c
+-	${AVALON_SRC_PATH}/hashcode.c
+-  )
+-
+-# we need this to ensure that builds continue
+-# to work on linux systems with older versions
+-# of glibc when we're building with gcc-4.1.
+-# Without this flag, we'll endup requiring
+-# glibc 2.7.
+-if(CMAKE_SYSTEM_NAME STREQUAL "Linux")
+-    add_definitions(-D_GNU_SOURCE=1)
+-endif()
+-
+-if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
+-  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-return-type -Wno-implicit-function-declaration -Wno-absolute-value -Wno-parentheses -Wno-logical-op-parentheses -Wno-dangling-else -Wno-format")
+-endif()
+-if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+-  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-unused-result -Wformat-overflow=0 -Wformat=0 -Wno-format-security -Wno-implicit-function-declaration")
+-endif()
+-
+-
+-
+-rdkit_library(avalon_clib ${avalon_clib_srcs})
+-target_compile_definitions(avalon_clib PRIVATE RDKIT_AVALONLIB_BUILD)
+-if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32))
+-  set_target_properties(avalon_clib PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
+-endif()
+-
+-include_directories(${CMAKE_CURRENT_SOURCE_DIR})
+-include_directories(${AVALON_SRC_PATH})
+-
+ rdkit_library(AvalonLib AvalonTools.cpp SHARED 
+-     LINK_LIBRARIES avalon_clib SubstructMatch FileParsers SmilesParse GraphMol DataStructs  )
++     LINK_LIBRARIES -lavalontoolkit SubstructMatch FileParsers SmilesParse GraphMol DataStructs  )
+ target_compile_definitions(AvalonLib PRIVATE RDKIT_AVALONLIB_BUILD)
+ rdkit_headers(AvalonTools.h DEST GraphMol)
+ rdkit_test(testAvalonLib1 test1.cpp
+diff --git a/External/AvalonTools/Wrap/pyAvalonTools.cpp b/External/AvalonTools/Wrap/pyAvalonTools.cpp
+index fb24c497e..31997bc0a 100644
+--- a/External/AvalonTools/Wrap/pyAvalonTools.cpp
++++ b/External/AvalonTools/Wrap/pyAvalonTools.cpp
+@@ -12,7 +12,7 @@
+ #include <boost/cstdint.hpp>
+ 
+ extern "C" {
+-#include "struchk.h"
++#include <avalontoolkit/struchk.h>
+ }
+ 
+ namespace python = boost::python;
+diff --git a/External/FreeSASA/CMakeLists.txt b/External/FreeSASA/CMakeLists.txt
+index 43dfbdc40..81165a143 100644
+--- a/External/FreeSASA/CMakeLists.txt
++++ b/External/FreeSASA/CMakeLists.txt
+@@ -2,88 +2,8 @@ if(NOT RDK_BUILD_FREESASA_SUPPORT)
+   return()
+ endif(NOT RDK_BUILD_FREESASA_SUPPORT)
+ 
+-if(NOT DEFINED FREESASA_DIR)
+-  set(FREESASA_DIR "${CMAKE_CURRENT_SOURCE_DIR}/freesasa")
+-  set(needDownload "TRUE")
+-  if(EXISTS "${FREESASA_DIR}/src/freesasa.h")
+-    set(needDownload "FALSE")
+-  endif()
+-endif()
+-
+-if(needDownload)
+-  # don't actually use the md5 here
+-  set(FREESASA_VERSION "2.0.3")
+-  set(FREESASA_SRC_DIR "${CMAKE_CURRENT_SOURCE_DIR}/freesasa-${FREESASA_VERSION}")
+-  if(NOT EXISTS "${FREESASA_SRC_DIR}/src")
+-    downloadAndCheckMD5("https://github.com/mittinatten/freesasa/releases/download/${FREESASA_VERSION}/freesasa-${FREESASA_VERSION}.tar.gz"
+-          "${CMAKE_CURRENT_SOURCE_DIR}/master.tar.gz"
+-          "")
+-    execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
+-      ${CMAKE_CURRENT_SOURCE_DIR}/master.tar.gz
+-      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+-    message("Copying freesasa2.c to ${FREESASA_SRC_DIR}/src/freesasa2.c")
+-    file(COPY freesasa2.c DESTINATION ${FREESASA_SRC_DIR}/src/)
+-  else()
+-    message("FreeSASA found in ${FREESASA_SRC_DIR}, no download required")
+-  endif()
+-endif()
+-
+-set(CMAKE_C_STANDARD 99)
+-
+-set (freesasa_clib_srcs
+-    ${FREESASA_SRC_DIR}/src/classifier.c
+-    ${FREESASA_SRC_DIR}/src/classifier_naccess.c
+-    ${FREESASA_SRC_DIR}/src/classifier_oons.c
+-    ${FREESASA_SRC_DIR}/src/classifier_protor.c
+-    ${FREESASA_SRC_DIR}/src/coord.c
+-    ${FREESASA_SRC_DIR}/src/freesasa2.c
+-    ${FREESASA_SRC_DIR}/src/lexer.c
+-    ${FREESASA_SRC_DIR}/src/log.c
+-    ${FREESASA_SRC_DIR}/src/nb.c
+-    ${FREESASA_SRC_DIR}/src/node.c
+-    ${FREESASA_SRC_DIR}/src/parser.c
+-    ${FREESASA_SRC_DIR}/src/pdb.c
+-    ${FREESASA_SRC_DIR}/src/rsa.c
+-    ${FREESASA_SRC_DIR}/src/sasa_lr.c
+-    ${FREESASA_SRC_DIR}/src/sasa_sr.c
+-    ${FREESASA_SRC_DIR}/src/selection.c
+-    ${FREESASA_SRC_DIR}/src/structure.c
+-    ${FREESASA_SRC_DIR}/src/util.c
+-    )
+-if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32))
+-  set(freesasa_additional_exports ${CMAKE_CURRENT_SOURCE_DIR}/additional_exports.def)
+-  file(WRITE ${freesasa_additional_exports}
+-    "EXPORTS\n"
+-    "freesasa_default_parameters DATA\n"
+-    "freesasa_protor_classifier DATA\n"
+-    "freesasa_naccess_classifier DATA\n"
+-    "freesasa_oons_classifier DATA\n"
+-  )
+-  set (freesasa_clib_srcs
+-    ${freesasa_clib_srcs}
+-    ${freesasa_additional_exports}
+-  )
+-endif()
+-
+-set (freesasa_h ${FREESASA_SRC_DIR}/src/freesasa.h)
+-file(READ ${freesasa_h} freesasa_h_data)
+-string(REGEX REPLACE "(#include <stdio.h>)" "\\1\n#include <RDGeneral/export.h>" freesasa_h_data "${freesasa_h_data}")
+-string(REGEX REPLACE "([^R][^D][^K][^I][^T][^_][^F][^R][^E][^E][^S][^A][^S][^A][^_][^C][^L][^I][^B][^_][^E][^X][^P][^O][^R][^T][^ ])(extern const)" "\\1RDKIT_FREESASA_CLIB_EXPORT \\2" freesasa_h_data "${freesasa_h_data}")
+-file(WRITE ${freesasa_h} "${freesasa_h_data}")
+-
+-add_definitions(-DUSE_THREADS=0)
+-add_definitions(-DUSE_JSON=0)
+-add_definitions(-DUSE_XML=0)
+-rdkit_library(freesasa_clib ${freesasa_clib_srcs})
+-target_compile_definitions(freesasa_clib PRIVATE RDKIT_FREESASALIB_BUILD)
+-
+-if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32))
+-  set_target_properties(freesasa_clib PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
+-endif()
+-include_directories("${FREESASA_SRC_DIR}/src")
+-
+ rdkit_library(FreeSASALib RDFreeSASA.cpp SHARED 
+-    LINK_LIBRARIES freesasa_clib GraphMol )
++    LINK_LIBRARIES -lfreesasa GraphMol )
+ target_compile_definitions(FreeSASALib PRIVATE RDKIT_FREESASALIB_BUILD)
+ 
+ rdkit_headers(RDFreeSASA.h DEST GraphMol)
+diff --git a/External/RingFamilies/CMakeLists.txt b/External/RingFamilies/CMakeLists.txt
+index 08dd1fe04..66ecd5834 100644
+--- a/External/RingFamilies/CMakeLists.txt
++++ b/External/RingFamilies/CMakeLists.txt
+@@ -1,47 +1,6 @@
+-add_custom_target(ringdecomposerlib_support ALL)
+-
+ if(NOT RDK_USE_URF)
+   return()
+ endif(NOT RDK_USE_URF)
+ 
+-if(NOT DEFINED URFLIB_DIR)
+-    set(URFLIB_DIR "${CMAKE_CURRENT_SOURCE_DIR}/RingDecomposerLib/src/RingDecomposerLib")
+-endif()
+-
+-if(NOT EXISTS "${URFLIB_DIR}/RingDecomposerLib.h")
+-    set(RELEASE_NO "1.1.3_rdkit")
+-    set(MD5 "e9a0bcdda8b921a35e812b9888a9a874")
+-    downloadAndCheckMD5("https://github.com/rareylab/RingDecomposerLib/archive/v${RELEASE_NO}.tar.gz"
+-            "${CMAKE_CURRENT_SOURCE_DIR}/RingDecomposerLib-v${RELEASE_NO}.tar.gz" ${MD5})
+-    execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
+-        ${CMAKE_CURRENT_SOURCE_DIR}/RingDecomposerLib-v${RELEASE_NO}.tar.gz
+-        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+-    file(RENAME "RingDecomposerLib-${RELEASE_NO}" "RingDecomposerLib")
+-else()
+-    message("-- Found RingDecomposerLib source in ${URFLIB_DIR}")
+-endif()
+-
+-set(urflib_INCLUDE_DIRS ${URFLIB_DIR}
+-    CACHE STRING "RingDecomposerLib Include Dir" FORCE)
+-file(GLOB URFSOURCES "${URFLIB_DIR}/*.c")
+-
+-#if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32 AND (NOT RDK_INSTALL_STATIC_LIBS)))
+-if(WIN32)
+-    set (ringdecomposerlib_h ${URFLIB_DIR}/RingDecomposerLib.h)
+-    file(READ ${ringdecomposerlib_h} ringdecomposerlib_h_data)
+-    if (NOT "${ringdecomposerlib_h_data}" MATCHES "RDKIT_URFLIB_BUILD")
+-        string(REGEX REPLACE "(#if[ ]+\\([ ]*defined[ ]*\\([ ]*_WIN32[ ]*\\)[ ]*&&[ ]*)(defined\\([ ]*_MSC_VER[ ]*\\))" "\\1!defined( RDL_WIN_STATIC )" ringdecomposerlib_h_data "${ringdecomposerlib_h_data}")
+-        string(REGEX REPLACE "([ ]*)(#define[ ]+RDL_API[ ]+__declspec)(\\([ ]*dllexport[ ]*\\))" "\\1#ifdef RDKIT_URFLIB_BUILD\n\\1\\1\\2\\3\n\\1#else\n\\1\\1\\2(dllimport)\n\\1#endif" ringdecomposerlib_h_data "${ringdecomposerlib_h_data}")
+-        file(WRITE ${ringdecomposerlib_h} "${ringdecomposerlib_h_data}")
+-    endif()
+-endif()
+-rdkit_library(RingDecomposerLib ${URFSOURCES} SHARED)
+-if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32 AND (NOT RDK_INSTALL_STATIC_LIBS)))
+-    target_compile_definitions(RingDecomposerLib PRIVATE RDKIT_URFLIB_BUILD)
+-endif()
+-install(TARGETS RingDecomposerLib DESTINATION ${RDKit_LibDir})
+-rdkit_headers(${URFLIB_DIR}/RingDecomposerLib.h DEST "")
+-
+-
+-set(RDK_URF_LIBS RingDecomposerLib
+-    CACHE STRING "the libraries for the URF calculation" FORCE)
++rdkit_library(RingDecomposerLib dummy.cpp SHARED LINK_LIBRARIES -lRingDecomposerLib)
++set(RDK_URF_LIBS RingDecomposerLib CACHE STRING "" FORCE)
+diff --git a/External/RingFamilies/dummy.cpp b/External/RingFamilies/dummy.cpp
+new file mode 100644
+index 000000000..e69de29bb
+diff --git a/External/YAeHMOP/CMakeLists.txt b/External/YAeHMOP/CMakeLists.txt
+index f1027b3bd..8bee2f910 100644
+--- a/External/YAeHMOP/CMakeLists.txt
++++ b/External/YAeHMOP/CMakeLists.txt
+@@ -18,32 +18,8 @@ endif()
+ 
+ include_directories( ${RDKit_ExternalDir}/YAeHMOP )
+ 
+-ExternalProject_Add(yaehmop_project
+-  GIT_REPOSITORY https://github.com/greglandrum/yaehmop.git
+-  GIT_TAG master
+-  UPDATE_COMMAND ""
+-  PATCH_COMMAND ""
+-  PREFIX ${CMAKE_CURRENT_SOURCE_DIR}
+-  SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop"
+-  SOURCE_SUBDIR "tightbind"
+-  CMAKE_ARGS -DUSE_BLAS_LAPACK=OFF -DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR} -DCMAKE_C_FLAGS=${CMAKE_C_FLAGS} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+-  TEST_COMMAND "")
+-
+-include_directories(${PROJECT_BINARY_DIR}/include)
+-link_directories(${PROJECT_BINARY_DIR}/lib)
+-link_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build)
+-
+-set(EHT_PARAM_FILE ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat )
+-install(FILES ${EHT_PARAM_FILE}
+-        DESTINATION ${RDKit_ShareDir}/Data
+-        COMPONENT data)
+-
+-message("YAeHMOP include_dirs: ${PROJECT_BINARY_DIR}/include")
+-message("YAeHMOP link_dirs: ${PROJECT_BINARY_DIR}/lib ${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build")
+-
+-rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES yaehmop_eht GraphMol )
++rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES -lyaehmop_eht GraphMol )
+ target_compile_definitions(EHTLib PRIVATE RDKIT_EHTLIB_BUILD)
+-add_dependencies(EHTLib yaehmop_project)
+ rdkit_headers(EHTTools.h DEST GraphMol)
+ rdkit_catch_test(testEHTLib1 test1.cpp
+            LINK_LIBRARIES EHTLib FileParsers SmilesParse )
+diff --git a/External/YAeHMOP/EHTTools.cpp b/External/YAeHMOP/EHTTools.cpp
+index 7a229f51f..71033dc5c 100644
+--- a/External/YAeHMOP/EHTTools.cpp
++++ b/External/YAeHMOP/EHTTools.cpp
+@@ -10,7 +10,7 @@
+ #include <fstream>
+ 
+ extern "C" {
+-#include <yaehmop/tightbind/bind.h>
++#include <yaehmop/bind.h>
+ }
+ 
+ namespace RDKit {
-- 
2.37.0

[bug#58261] [PATCH v2 01/13] gnu: Add fast-float.

[David Elsing]

* gnu/packages/cpp.scm (fast-float): New variable.
---
 gnu/packages/cpp.scm | 54 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)

diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index d03e0bc7e1..a7404df563 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -29,6 +29,7 @@
 ;;; Copyright © 2022 muradm <mail@muradm.net>
 ;;; Copyright © 2022 Attila Lendvai <attila@lendvai.name>
 ;;; Copyright © 2022 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2022 David Elsing <david.elsing@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1907,3 +1908,56 @@ (define-public cpp-mustache
 templated string type for compatibility with any STL-like string (std::string,
 std::wstring, etc).")
     (license license:boost1.0)))
+
+(define-public fast-float
+  (package
+    (name "fast-float")
+    (version "3.5.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/fastfloat/fast_float")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0z3rxxd0pwvw70dbnv63rm67biw829vdqf50y16isxm6g3sbrz8g"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      #~(list
+         "-DFASTFLOAT_TEST=ON"
+         "-DSYSTEM_DOCTEST=ON")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-cmake-tests
+            (lambda _
+              (substitute* "tests/CMakeLists.txt"
+                (("FetchContent_GetProperties\\(supplemental_test_files.*")
+                 "")
+                (("if\\(NOT supplemental_test_files_POPULATED.*")
+                 (string-append
+                  "set(supplemental_test_files_BINARY_DIR "
+                  #$(this-package-native-input "test-data") "/data"
+                  ")\nif(0)\n"))))))))
+    (native-inputs
+     `(("test-data"
+        ,(let ((commit "97a0b2e638feb479387554cf253e346500541e7e"))
+           (origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url
+                    "https://github.com/fastfloat/supplemental_test_files.git")
+                   (commit commit)))
+             (file-name (git-file-name "fast_float_test-data" commit))
+             (sha256
+              (base32
+               "0dxbiyzyh7i847i89ablfzypfc3ckhm7f74w98jsh73v1mppmxlf")))))
+       ("doctest" ,doctest)))
+    (home-page "https://github.com/fastfloat/fast_float")
+    (synopsis "Floating point number parser for C++")
+    (description "@code{fast_float} is a header-only C++ library for parsing
+floating point numbers from strings.  It implements the C++ from_chars
+functions for the float and double types.")
+    (license (list license:asl2.0 license:expat)))) ; dual licensed
-- 
2.37.0

[bug#58261] [PATCH v2 01/13] gnu: Add fast-float.

[Liliana Marie Prikler]

Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
> * gnu/packages/cpp.scm (fast-float): New variable.
> ---
>  gnu/packages/cpp.scm | 54
> ++++++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 54 insertions(+)
> 
> diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
> index d03e0bc7e1..a7404df563 100644
> --- a/gnu/packages/cpp.scm
> +++ b/gnu/packages/cpp.scm
> @@ -29,6 +29,7 @@
>  ;;; Copyright © 2022 muradm <mail@muradm.net>
>  ;;; Copyright © 2022 Attila Lendvai <attila@lendvai.name>
>  ;;; Copyright © 2022 Arun Isaac <arunisaac@systemreboot.net>
> +;;; Copyright © 2022 David Elsing <david.elsing@posteo.net>
>  ;;;
>  ;;; This file is part of GNU Guix.
>  ;;;
> @@ -1907,3 +1908,56 @@ (define-public cpp-mustache
>  templated string type for compatibility with any STL-like string
> (std::string,
>  std::wstring, etc).")
>      (license license:boost1.0)))
> +
> +(define-public fast-float
> +  (package
> +    (name "fast-float")
> +    (version "3.5.1")
> +    (source (origin
> +              (method git-fetch)
> +              (uri (git-reference
> +                    (url "https://github.com/fastfloat/fast_float")
> +                    (commit (string-append "v" version))))
> +              (file-name (git-file-name name version))
> +              (sha256
> +               (base32
> +               
> "0z3rxxd0pwvw70dbnv63rm67biw829vdqf50y16isxm6g3sbrz8g"))))
> +    (build-system cmake-build-system)
> +    (arguments
> +     (list
> +      #:configure-flags
> +      #~(list
> +         "-DFASTFLOAT_TEST=ON"
> +         "-DSYSTEM_DOCTEST=ON")
> +      #:phases
> +      #~(modify-phases %standard-phases
> +          (add-after 'unpack 'patch-cmake-tests
> +            (lambda _
> +              (substitute* "tests/CMakeLists.txt"
> +               
> (("FetchContent_GetProperties\\(supplemental_test_files.*")
> +                 "")
> +                (("if\\(NOT supplemental_test_files_POPULATED.*")
> +                 (string-append
> +                  "set(supplemental_test_files_BINARY_DIR "
> +                  #$(this-package-native-input "test-data") "/data"
> +                  ")\nif(0)\n"))))))))
> +    (native-inputs
> +     `(("test-data"
> +        ,(let ((commit "97a0b2e638feb479387554cf253e346500541e7e"))
> +           (origin
> +             (method git-fetch)
> +             (uri (git-reference
> +                   (url
> +                   
> "https://github.com/fastfloat/supplemental_test_files.git")
> +                   (commit commit)))
> +             (file-name (git-file-name "fast_float_test-data"
> commit))
> +             (sha256
> +              (base32
> +              
> "0dxbiyzyh7i847i89ablfzypfc3ckhm7f74w98jsh73v1mppmxlf")))))
You can use the origin directly in the recipe via #$.  Alternatively,
search-input-directory "data" would probably also work.
> +       ("doctest" ,doctest)))
> +    (home-page "https://github.com/fastfloat/fast_float")
> +    (synopsis "Floating point number parser for C++")
> +    (description "@code{fast_float} is a header-only C++ library for
> parsing
> +floating point numbers from strings.  It implements the C++
> from_chars
> +functions for the float and double types.")
> +    (license (list license:asl2.0 license:expat)))) ; dual licensed
Cheers

[bug#58261] [PATCH v2 02/13] gnu: Add pocketfft.

[David Elsing]

* gnu/packages/cpp.scm (pocketfft): New variable.
---
 gnu/packages/cpp.scm | 44 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index a7404df563..38a2a9e829 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -1961,3 +1961,47 @@ (define-public fast-float
 floating point numbers from strings.  It implements the C++ from_chars
 functions for the float and double types.")
     (license (list license:asl2.0 license:expat)))) ; dual licensed
+
+(define-public pocketfft-cpp
+  (let ((commit "daa8bb18327bc5c7d22c69428c25cf5dc64167d3")
+        (revision "0"))
+    (package
+      (name "pocketfft-cpp")
+      (version (git-version "0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/mreineck/pocketfft")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1dbkkqkmkxgmz1qjpsqzic5ig3qw1pqndbb3dvjc7xq5f2rdzyq1"))))
+      (build-system copy-build-system)
+      (arguments
+       (list
+        #:install-plan
+        #~'(("pocketfft_hdronly.h" "include/"))
+        #:phases
+        #~(modify-phases %standard-phases
+            (add-before 'install 'patch-novectors
+              (lambda _
+                (substitute* "pocketfft_hdronly.h"
+                  (("#ifndef POCKETFFT_NO_VECTORS")
+                   "#if !(POCKETFFT_NO_VECTORS)")
+                  (("#if defined\\(POCKETFFT_NO_VECTORS\\)")
+                   "#if POCKETFFT_NO_VECTORS")
+                  (("#define POCKETFFT_NO_VECTORS")
+                   "#define POCKETFFT_NO_VECTORS 1")
+                  (("#\\s*undef POCKETFFT_NO_VECTORS")
+                   "#define POCKETFFT_NO_VECTORS 0")
+                  (("#define POCKETFFT_HDRONLY_H.*" orig)
+                   (string-append
+                    orig "\n#ifndef POCKETFFT_NO_VECTORS\n"
+                    "#define POCKETFFT_NO_VECTORS 1\n" "#endif\n"))))))))
+      (home-page "https://github.com/mreineck/pocketfft")
+      (synopsis "C++11 header-only Fast Fourier Transform library")
+      (description "This package provides a single-header C++11 library for
+computing Fast Fourier transformations.  It supports multidimensional arrays,
+different floating point sizes and complex transformations.")
+      (license license:bsd-3))))
-- 
2.37.0

[bug#58261] [PATCH v2 02/13] gnu: Add pocketfft.

[Liliana Marie Prikler]

Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
> * gnu/packages/cpp.scm (pocketfft): New variable.
> ---
>  gnu/packages/cpp.scm | 44
> ++++++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 44 insertions(+)
> 
> diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
> index a7404df563..38a2a9e829 100644
> --- a/gnu/packages/cpp.scm
> +++ b/gnu/packages/cpp.scm
> @@ -1961,3 +1961,47 @@ (define-public fast-float
>  floating point numbers from strings.  It implements the C++
> from_chars
>  functions for the float and double types.")
>      (license (list license:asl2.0 license:expat)))) ; dual licensed
> +
> +(define-public pocketfft-cpp
> +  (let ((commit "daa8bb18327bc5c7d22c69428c25cf5dc64167d3")
> +        (revision "0"))
> +    (package
> +      (name "pocketfft-cpp")
> +      (version (git-version "0" revision commit))
> +      (source (origin
> +                (method git-fetch)
> +                (uri (git-reference
> +                      (url "https://github.com/mreineck/pocketfft")
> +                      (commit commit)))
> +                (file-name (git-file-name name version))
> +                (sha256
> +                 (base32
> +                 
> "1dbkkqkmkxgmz1qjpsqzic5ig3qw1pqndbb3dvjc7xq5f2rdzyq1"))))
> +      (build-system copy-build-system)
> +      (arguments
> +       (list
> +        #:install-plan
> +        #~'(("pocketfft_hdronly.h" "include/"))
> +        #:phases
> +        #~(modify-phases %standard-phases
> +            (add-before 'install 'patch-novectors
> +              (lambda _
> +                (substitute* "pocketfft_hdronly.h"
> +                  (("#ifndef POCKETFFT_NO_VECTORS")
> +                   "#if !(POCKETFFT_NO_VECTORS)")
> +                  (("#if defined\\(POCKETFFT_NO_VECTORS\\)")
> +                   "#if POCKETFFT_NO_VECTORS")
> +                  (("#define POCKETFFT_NO_VECTORS")
> +                   "#define POCKETFFT_NO_VECTORS 1")
This one I don't think changes anything.
> +                  (("#\\s*undef POCKETFFT_NO_VECTORS")
> +                   "#define POCKETFFT_NO_VECTORS 0")
Here too, I think you can ignore that.
> +                  (("#define POCKETFFT_HDRONLY_H.*" orig)
> +                   (string-append
> +                    orig "\n#ifndef POCKETFFT_NO_VECTORS\n"
> +                    "#define POCKETFFT_NO_VECTORS 1\n"
> "#endif\n"))))))))
More importantly, I think this should be done with a snippet or even
better a patch – I'd recommend the latter because I think it'd be
easier to reason about.
> +      (home-page "https://github.com/mreineck/pocketfft")
> +      (synopsis "C++11 header-only Fast Fourier Transform library")
> +      (description "This package provides a single-header C++11
> library for
> +computing Fast Fourier transformations.  It supports
> multidimensional arrays,
> +different floating point sizes and complex transformations.")
> +      (license license:bsd-3))))

[bug#58261] [PATCH v2 03/13] gnu: Add sajson.

[David Elsing]

* gnu/packages/cpp.scm (sajson): New variable.
---
 gnu/packages/cpp.scm                          | 60 +++++++++++++++++++
 .../patches/sajson-build-with-gcc10.patch     | 45 ++++++++++++++
 2 files changed, 105 insertions(+)
 create mode 100644 gnu/packages/patches/sajson-build-with-gcc10.patch

diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index 38a2a9e829..dca0245df5 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -57,6 +57,7 @@ (define-module (gnu packages cpp)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system python)
+  #:use-module (guix build-system scons)
   #:use-module (guix modules)
   #:use-module (guix gexp)
   #:use-module (gnu packages)
@@ -2005,3 +2006,62 @@ (define-public pocketfft-cpp
 computing Fast Fourier transformations.  It supports multidimensional arrays,
 different floating point sizes and complex transformations.")
       (license license:bsd-3))))
+
+(define-public sajson
+  (let ((commit "ec644013e34f9984a3cc9ba568cab97a391db9cd")
+        (revision "0"))
+    (package
+      (name "sajson")
+      (version (git-version "1.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/chadaustin/sajson")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (patches
+                 (search-patches "sajson-build-with-gcc10.patch"))
+                (sha256
+                 (base32
+                  "0fjag27w7gvkc5pdhq3ad7yc09rabpzahndw1sgsg04ipznidmmq"))
+                (modules '((guix build utils)))
+                (snippet '(delete-file-recursively "third-party"))))
+      (build-system scons-build-system)
+      (arguments
+       (list
+        #:phases
+        #~(modify-phases %standard-phases
+            (add-after 'unpack 'disable-other-builds
+              (lambda _
+                (substitute* "SConstruct"
+                  (("for name, tools in builds:")
+                   "for name, tools in [('opt', [gcc, opt])]:"))))
+            (add-after 'unpack 'use-external-unittest-cpp
+              (lambda* (#:key inputs #:allow-other-keys)
+                (substitute* "SConscript"
+                  (("unittestpp_env\\.Library") "_dummy = ")
+                  (("test_env = env.Clone\\(tools=\\[unittestpp, sajson\\]\\)")
+                   (string-append
+                    "test_env = env.Clone(tools=[sajson])\n"
+                    "test_env.Append(CPPPATH='"
+                    (search-input-directory inputs "/include/UnitTest++")
+                    "', LIBPATH='"
+                    (string-append #$(this-package-native-input "unittest-cpp")
+                                   "/lib")
+                    "', LIBS=['UnitTest++'])")))))
+            (replace 'check
+              (lambda* (#:key tests? #:allow-other-keys)
+                (when tests?
+                  (invoke "build/opt/test")
+                  (invoke "build/opt/test_unsorted"))))
+            (replace 'install
+              (lambda _
+                (let ((out (string-append #$output "/include")))
+                  (install-file "include/sajson.h" out)
+                  (install-file "include/sajson_ostream.h" out)))))))
+      (native-inputs (list unittest-cpp))
+      (home-page "https://github.com/chadaustin/sajson")
+      (synopsis "C++11 header-only, in-place JSON parser")
+      (description "@code{sajson} is an in-place JSON parser with support for
+parsing with only a single memory allocation.")
+      (license license:expat))))
diff --git a/gnu/packages/patches/sajson-build-with-gcc10.patch b/gnu/packages/patches/sajson-build-with-gcc10.patch
new file mode 100644
index 0000000000..878706dc79
--- /dev/null
+++ b/gnu/packages/patches/sajson-build-with-gcc10.patch
@@ -0,0 +1,45 @@
+This patch is from the upstream pull request
+https://github.com/chadaustin/sajson/pull/54.
+It fixes linking with GCC.
+
+diff --git a/include/sajson.h b/include/sajson.h
+index 8b4e05a..1bd045b 100644
+--- a/include/sajson.h
++++ b/include/sajson.h
+@@ -138,12 +138,17 @@ constexpr inline size_t make_element(tag t, size_t value) {
+ // header. This trick courtesy of Rich Geldreich's Purple JSON parser.
+ template <typename unused = void>
+ struct globals_struct {
++    static const unsigned char parse_flags[256];
++};
++typedef globals_struct<> globals;
++
+ // clang-format off
+ 
+     // bit 0 (1) - set if: plain ASCII string character
+     // bit 1 (2) - set if: whitespace
+     // bit 4 (0x10) - set if: 0-9 e E .
+-    constexpr static const uint8_t parse_flags[256] = {
++    template <typename unused>
++    const unsigned char globals_struct<unused>::parse_flags[256] = {
+      // 0    1    2    3    4    5    6    7      8    9    A    B    C    D    E    F
+         0,   0,   0,   0,   0,   0,   0,   0,     0,   2,   2,   0,   0,   2,   0,   0, // 0
+         0,   0,   0,   0,   0,   0,   0,   0,     0,   0,   0,   0,   0,   0,   0,   0, // 1
+@@ -162,15 +167,13 @@ struct globals_struct {
+     };
+ 
+ // clang-format on
+-};
+-typedef globals_struct<> globals;
+ 
+-constexpr inline bool is_plain_string_character(char c) {
++inline bool is_plain_string_character(char c) {
+     // return c >= 0x20 && c <= 0x7f && c != 0x22 && c != 0x5c;
+     return (globals::parse_flags[static_cast<unsigned char>(c)] & 1) != 0;
+ }
+ 
+-constexpr inline bool is_whitespace(char c) {
++inline bool is_whitespace(char c) {
+     // return c == '\r' || c == '\n' || c == '\t' || c == ' ';
+     return (globals::parse_flags[static_cast<unsigned char>(c)] & 2) != 0;
+ }
-- 
2.37.0

[bug#58261] [PATCH v2 03/13] gnu: Add sajson.

[Liliana Marie Prikler]

Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
> * gnu/packages/cpp.scm (sajson): New variable.
> ---
>  gnu/packages/cpp.scm                          | 60
> +++++++++++++++++++
>  .../patches/sajson-build-with-gcc10.patch     | 45 ++++++++++++++
>  2 files changed, 105 insertions(+)
>  create mode 100644 gnu/packages/patches/sajson-build-with-
> gcc10.patch
> 
> diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
> index 38a2a9e829..dca0245df5 100644
> --- a/gnu/packages/cpp.scm
> +++ b/gnu/packages/cpp.scm
> @@ -57,6 +57,7 @@ (define-module (gnu packages cpp)
>    #:use-module (guix build-system gnu)
>    #:use-module (guix build-system meson)
>    #:use-module (guix build-system python)
> +  #:use-module (guix build-system scons)
>    #:use-module (guix modules)
>    #:use-module (guix gexp)
>    #:use-module (gnu packages)
> @@ -2005,3 +2006,62 @@ (define-public pocketfft-cpp
>  computing Fast Fourier transformations.  It supports
> multidimensional arrays,
>  different floating point sizes and complex transformations.")
>        (license license:bsd-3))))
> +
> +(define-public sajson
> +  (let ((commit "ec644013e34f9984a3cc9ba568cab97a391db9cd")
> +        (revision "0"))
> +    (package
> +      (name "sajson")
> +      (version (git-version "1.0" revision commit))
> +      (source (origin
> +                (method git-fetch)
> +                (uri (git-reference
> +                      (url "https://github.com/chadaustin/sajson")
> +                      (commit commit)))
> +                (file-name (git-file-name name version))
> +                (patches
> +                 (search-patches "sajson-build-with-gcc10.patch"))
> +                (sha256
> +                 (base32
> +                 
> "0fjag27w7gvkc5pdhq3ad7yc09rabpzahndw1sgsg04ipznidmmq"))
> +                (modules '((guix build utils)))
> +                (snippet '(delete-file-recursively "third-party"))))
> +      (build-system scons-build-system)
> +      (arguments
> +       (list
> +        #:phases
> +        #~(modify-phases %standard-phases
> +            (add-after 'unpack 'disable-other-builds
> +              (lambda _
> +                (substitute* "SConstruct"
> +                  (("for name, tools in builds:")
> +                   "for name, tools in [('opt', [gcc, opt])]:"))))
> +            (add-after 'unpack 'use-external-unittest-cpp
> +              (lambda* (#:key inputs #:allow-other-keys)
> +                (substitute* "SConscript"
> +                  (("unittestpp_env\\.Library") "_dummy = ")
> +                  (("test_env = env.Clone\\(tools=\\[unittestpp,
> sajson\\]\\)")
> +                   (string-append
> +                    "test_env = env.Clone(tools=[sajson])\n"
> +                    "test_env.Append(CPPPATH='"
> +                    (search-input-directory inputs
> "/include/UnitTest++")
Note that you need (or native-inputs inputs) wherever you wrote inputs.
> +                    "', LIBPATH='"
> +                    (string-append #$(this-package-native-input
> "unittest-cpp")
> +                                   "/lib")
> +                    "', LIBS=['UnitTest++'])")))))
> +            (replace 'check
> +              (lambda* (#:key tests? #:allow-other-keys)
> +                (when tests?
> +                  (invoke "build/opt/test")
> +                  (invoke "build/opt/test_unsorted"))))
> +            (replace 'install
> +              (lambda _
> +                (let ((out (string-append #$output "/include")))
> +                  (install-file "include/sajson.h" out)
> +                  (install-file "include/sajson_ostream.h"
> out)))))))
For the record, what would a regular install do?
> +      (native-inputs (list unittest-cpp))
> +      (home-page "https://github.com/chadaustin/sajson")
> +      (synopsis "C++11 header-only, in-place JSON parser")
> +      (description "@code{sajson} is an in-place JSON parser with
> support for
> +parsing with only a single memory allocation.")
> +      (license license:expat))))
> diff --git a/gnu/packages/patches/sajson-build-with-gcc10.patch
> b/gnu/packages/patches/sajson-build-with-gcc10.patch
> new file mode 100644
> index 0000000000..878706dc79
> --- /dev/null
> +++ b/gnu/packages/patches/sajson-build-with-gcc10.patch
> @@ -0,0 +1,45 @@
> +This patch is from the upstream pull request
> +https://github.com/chadaustin/sajson/pull/54.
> +It fixes linking with GCC.
> +
> +diff --git a/include/sajson.h b/include/sajson.h
> +index 8b4e05a..1bd045b 100644
> +--- a/include/sajson.h
> ++++ b/include/sajson.h
> +@@ -138,12 +138,17 @@ constexpr inline size_t make_element(tag t,
> size_t value) {
> + // header. This trick courtesy of Rich Geldreich's Purple JSON
> parser.
> + template <typename unused = void>
> + struct globals_struct {
> ++    static const unsigned char parse_flags[256];
> ++};
> ++typedef globals_struct<> globals;
> ++
> + // clang-format off
> + 
> +     // bit 0 (1) - set if: plain ASCII string character
> +     // bit 1 (2) - set if: whitespace
> +     // bit 4 (0x10) - set if: 0-9 e E .
> +-    constexpr static const uint8_t parse_flags[256] = {
> ++    template <typename unused>
> ++    const unsigned char globals_struct<unused>::parse_flags[256] =
> {
> +      // 0    1    2    3    4    5    6    7      8    9    A   
> B    C    D    E    F
> +         0,   0,   0,   0,   0,   0,   0,   0,     0,   2,   2,  
> 0,   0,   2,   0,   0, // 0
> +         0,   0,   0,   0,   0,   0,   0,   0,     0,   0,   0,  
> 0,   0,   0,   0,   0, // 1
> +@@ -162,15 +167,13 @@ struct globals_struct {
> +     };
> + 
> + // clang-format on
> +-};
> +-typedef globals_struct<> globals;
> + 
> +-constexpr inline bool is_plain_string_character(char c) {
> ++inline bool is_plain_string_character(char c) {
> +     // return c >= 0x20 && c <= 0x7f && c != 0x22 && c != 0x5c;
> +     return (globals::parse_flags[static_cast<unsigned char>(c)] &
> 1) != 0;
> + }
> + 
> +-constexpr inline bool is_whitespace(char c) {
> ++inline bool is_whitespace(char c) {
> +     // return c == '\r' || c == '\n' || c == '\t' || c == ' ';
> +     return (globals::parse_flags[static_cast<unsigned char>(c)] &
> 2) != 0;
> + }

[bug#58261] [PATCH v2 03/13] gnu: Add sajson.

[David Elsing]

Liliana Marie Prikler <liliana.prikler@gmail.com> writes:

> Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
>> * gnu/packages/cpp.scm (sajson): New variable.
>> ---
>>  gnu/packages/cpp.scm                          | 60
>> +++++++++++++++++++
>>  .../patches/sajson-build-with-gcc10.patch     | 45 ++++++++++++++
>>  2 files changed, 105 insertions(+)
>>  create mode 100644 gnu/packages/patches/sajson-build-with-
>> gcc10.patch
>> 
>> diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
>> index 38a2a9e829..dca0245df5 100644
>> --- a/gnu/packages/cpp.scm
>> +++ b/gnu/packages/cpp.scm
>> @@ -57,6 +57,7 @@ (define-module (gnu packages cpp)
>>    #:use-module (guix build-system gnu)
>>    #:use-module (guix build-system meson)
>>    #:use-module (guix build-system python)
>> +  #:use-module (guix build-system scons)
>>    #:use-module (guix modules)
>>    #:use-module (guix gexp)
>>    #:use-module (gnu packages)
>> @@ -2005,3 +2006,62 @@ (define-public pocketfft-cpp
>>  computing Fast Fourier transformations.  It supports
>> multidimensional arrays,
>>  different floating point sizes and complex transformations.")
>>        (license license:bsd-3))))
>> +
>> +(define-public sajson
>> +  (let ((commit "ec644013e34f9984a3cc9ba568cab97a391db9cd")
>> +        (revision "0"))
>> +    (package
>> +      (name "sajson")
>> +      (version (git-version "1.0" revision commit))
>> +      (source (origin
>> +                (method git-fetch)
>> +                (uri (git-reference
>> +                      (url "https://github.com/chadaustin/sajson")
>> +                      (commit commit)))
>> +                (file-name (git-file-name name version))
>> +                (patches
>> +                 (search-patches "sajson-build-with-gcc10.patch"))
>> +                (sha256
>> +                 (base32
>> +                 
>> "0fjag27w7gvkc5pdhq3ad7yc09rabpzahndw1sgsg04ipznidmmq"))
>> +                (modules '((guix build utils)))
>> +                (snippet '(delete-file-recursively "third-party"))))
>> +      (build-system scons-build-system)
>> +      (arguments
>> +       (list
>> +        #:phases
>> +        #~(modify-phases %standard-phases
>> +            (add-after 'unpack 'disable-other-builds
>> +              (lambda _
>> +                (substitute* "SConstruct"
>> +                  (("for name, tools in builds:")
>> +                   "for name, tools in [('opt', [gcc, opt])]:"))))
>> +            (add-after 'unpack 'use-external-unittest-cpp
>> +              (lambda* (#:key inputs #:allow-other-keys)
>> +                (substitute* "SConscript"
>> +                  (("unittestpp_env\\.Library") "_dummy = ")
>> +                  (("test_env = env.Clone\\(tools=\\[unittestpp,
>> sajson\\]\\)")
>> +                   (string-append
>> +                    "test_env = env.Clone(tools=[sajson])\n"
>> +                    "test_env.Append(CPPPATH='"
>> +                    (search-input-directory inputs
>> "/include/UnitTest++")
> Note that you need (or native-inputs inputs) wherever you wrote inputs.
Is %build-inputs ok?
>> +                    "', LIBPATH='"
>> +                    (string-append #$(this-package-native-input
>> "unittest-cpp")
>> +                                   "/lib")
>> +                    "', LIBS=['UnitTest++'])")))))
>> +            (replace 'check
>> +              (lambda* (#:key tests? #:allow-other-keys)
>> +                (when tests?
>> +                  (invoke "build/opt/test")
>> +                  (invoke "build/opt/test_unsorted"))))
>> +            (replace 'install
>> +              (lambda _
>> +                (let ((out (string-append #$output "/include")))
>> +                  (install-file "include/sajson.h" out)
>> +                  (install-file "include/sajson_ostream.h"
>> out)))))))
> For the record, what would a regular install do?
Just nothing.
>> +      (native-inputs (list unittest-cpp))
>> +      (home-page "https://github.com/chadaustin/sajson")
>> +      (synopsis "C++11 header-only, in-place JSON parser")
>> +      (description "@code{sajson} is an in-place JSON parser with
>> support for
>> +parsing with only a single memory allocation.")
>> +      (license license:expat))))
>> diff --git a/gnu/packages/patches/sajson-build-with-gcc10.patch
>> b/gnu/packages/patches/sajson-build-with-gcc10.patch
>> new file mode 100644
>> index 0000000000..878706dc79
>> --- /dev/null
>> +++ b/gnu/packages/patches/sajson-build-with-gcc10.patch
>> @@ -0,0 +1,45 @@
>> +This patch is from the upstream pull request
>> +https://github.com/chadaustin/sajson/pull/54.
>> +It fixes linking with GCC.
>> +
>> +diff --git a/include/sajson.h b/include/sajson.h
>> +index 8b4e05a..1bd045b 100644
>> +--- a/include/sajson.h
>> ++++ b/include/sajson.h
>> +@@ -138,12 +138,17 @@ constexpr inline size_t make_element(tag t,
>> size_t value) {
>> + // header. This trick courtesy of Rich Geldreich's Purple JSON
>> parser.
>> + template <typename unused = void>
>> + struct globals_struct {
>> ++    static const unsigned char parse_flags[256];
>> ++};
>> ++typedef globals_struct<> globals;
>> ++
>> + // clang-format off
>> + 
>> +     // bit 0 (1) - set if: plain ASCII string character
>> +     // bit 1 (2) - set if: whitespace
>> +     // bit 4 (0x10) - set if: 0-9 e E .
>> +-    constexpr static const uint8_t parse_flags[256] = {
>> ++    template <typename unused>
>> ++    const unsigned char globals_struct<unused>::parse_flags[256] =
>> {
>> +      // 0    1    2    3    4    5    6    7      8    9    A   
>> B    C    D    E    F
>> +         0,   0,   0,   0,   0,   0,   0,   0,     0,   2,   2,  
>> 0,   0,   2,   0,   0, // 0
>> +         0,   0,   0,   0,   0,   0,   0,   0,     0,   0,   0,  
>> 0,   0,   0,   0,   0, // 1
>> +@@ -162,15 +167,13 @@ struct globals_struct {
>> +     };
>> + 
>> + // clang-format on
>> +-};
>> +-typedef globals_struct<> globals;
>> + 
>> +-constexpr inline bool is_plain_string_character(char c) {
>> ++inline bool is_plain_string_character(char c) {
>> +     // return c >= 0x20 && c <= 0x7f && c != 0x22 && c != 0x5c;
>> +     return (globals::parse_flags[static_cast<unsigned char>(c)] &
>> 1) != 0;
>> + }
>> + 
>> +-constexpr inline bool is_whitespace(char c) {
>> ++inline bool is_whitespace(char c) {
>> +     // return c == '\r' || c == '\n' || c == '\t' || c == ' ';
>> +     return (globals::parse_flags[static_cast<unsigned char>(c)] &
>> 2) != 0;
>> + }

[bug#58261] [PATCH v2 03/13] gnu: Add sajson.

[Liliana Marie Prikler]

Am Donnerstag, dem 13.10.2022 um 20:59 +0000 schrieb David Elsing:
> Liliana Marie Prikler <liliana.prikler@gmail.com> writes:
> 
> > Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
> > > * gnu/packages/cpp.scm (sajson): New variable.
> > > ---
> > >  gnu/packages/cpp.scm                          | 60
> > > +++++++++++++++++++
> > >  .../patches/sajson-build-with-gcc10.patch     | 45
> > > ++++++++++++++
> > >  2 files changed, 105 insertions(+)
> > >  create mode 100644 gnu/packages/patches/sajson-build-with-
> > > gcc10.patch
> > > 
> > > diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
> > > index 38a2a9e829..dca0245df5 100644
> > > --- a/gnu/packages/cpp.scm
> > > +++ b/gnu/packages/cpp.scm
> > > @@ -57,6 +57,7 @@ (define-module (gnu packages cpp)
> > >    #:use-module (guix build-system gnu)
> > >    #:use-module (guix build-system meson)
> > >    #:use-module (guix build-system python)
> > > +  #:use-module (guix build-system scons)
> > >    #:use-module (guix modules)
> > >    #:use-module (guix gexp)
> > >    #:use-module (gnu packages)
> > > @@ -2005,3 +2006,62 @@ (define-public pocketfft-cpp
> > >  computing Fast Fourier transformations.  It supports
> > > multidimensional arrays,
> > >  different floating point sizes and complex transformations.")
> > >        (license license:bsd-3))))
> > > +
> > > +(define-public sajson
> > > +  (let ((commit "ec644013e34f9984a3cc9ba568cab97a391db9cd")
> > > +        (revision "0"))
> > > +    (package
> > > +      (name "sajson")
> > > +      (version (git-version "1.0" revision commit))
> > > +      (source (origin
> > > +                (method git-fetch)
> > > +                (uri (git-reference
> > > +                      (url
> > > "https://github.com/chadaustin/sajson")
> > > +                      (commit commit)))
> > > +                (file-name (git-file-name name version))
> > > +                (patches
> > > +                 (search-patches "sajson-build-with-
> > > gcc10.patch"))
> > > +                (sha256
> > > +                 (base32
> > > +                 
> > > "0fjag27w7gvkc5pdhq3ad7yc09rabpzahndw1sgsg04ipznidmmq"))
> > > +                (modules '((guix build utils)))
> > > +                (snippet '(delete-file-recursively "third-
> > > party"))))
> > > +      (build-system scons-build-system)
> > > +      (arguments
> > > +       (list
> > > +        #:phases
> > > +        #~(modify-phases %standard-phases
> > > +            (add-after 'unpack 'disable-other-builds
> > > +              (lambda _
> > > +                (substitute* "SConstruct"
> > > +                  (("for name, tools in builds:")
> > > +                   "for name, tools in [('opt', [gcc,
> > > opt])]:"))))
> > > +            (add-after 'unpack 'use-external-unittest-cpp
> > > +              (lambda* (#:key inputs #:allow-other-keys)
> > > +                (substitute* "SConscript"
> > > +                  (("unittestpp_env\\.Library") "_dummy = ")
> > > +                  (("test_env = env.Clone\\(tools=\\[unittestpp,
> > > sajson\\]\\)")
> > > +                   (string-append
> > > +                    "test_env = env.Clone(tools=[sajson])\n"
> > > +                    "test_env.Append(CPPPATH='"
> > > +                    (search-input-directory inputs
> > > "/include/UnitTest++")
> > Note that you need (or native-inputs inputs) wherever you wrote
> > inputs.
> Is %build-inputs ok?
No, we only use this in trivial-build-system and other places where we
don't have the split.
> > > +                    "', LIBPATH='"
> > > +                    (string-append #$(this-package-native-input
> > > "unittest-cpp")
> > > +                                   "/lib")
> > > +                    "', LIBS=['UnitTest++'])")))))
> > > +            (replace 'check
> > > +              (lambda* (#:key tests? #:allow-other-keys)
> > > +                (when tests?
> > > +                  (invoke "build/opt/test")
> > > +                  (invoke "build/opt/test_unsorted"))))
> > > +            (replace 'install
> > > +              (lambda _
> > > +                (let ((out (string-append #$output "/include")))
> > > +                  (install-file "include/sajson.h" out)
> > > +                  (install-file "include/sajson_ostream.h"
> > > out)))))))
> > For the record, what would a regular install do?
> Just nothing.
Fair enough.
> > > +      (native-inputs (list unittest-cpp))
> > > +      (home-page "https://github.com/chadaustin/sajson")
> > > +      (synopsis "C++11 header-only, in-place JSON parser")
> > > +      (description "@code{sajson} is an in-place JSON parser
> > > with
> > > support for
> > > +parsing with only a single memory allocation.")
> > > +      (license license:expat))))
> > > diff --git a/gnu/packages/patches/sajson-build-with-gcc10.patch
> > > b/gnu/packages/patches/sajson-build-with-gcc10.patch
> > > new file mode 100644
> > > index 0000000000..878706dc79
> > > --- /dev/null
> > > +++ b/gnu/packages/patches/sajson-build-with-gcc10.patch
> > > @@ -0,0 +1,45 @@
> > > +This patch is from the upstream pull request
> > > +https://github.com/chadaustin/sajson/pull/54.
> > > +It fixes linking with GCC.
> > > +
> > > +diff --git a/include/sajson.h b/include/sajson.h
> > > +index 8b4e05a..1bd045b 100644
> > > +--- a/include/sajson.h
> > > ++++ b/include/sajson.h
> > > +@@ -138,12 +138,17 @@ constexpr inline size_t make_element(tag
> > > t,
> > > size_t value) {
> > > + // header. This trick courtesy of Rich Geldreich's Purple JSON
> > > parser.
> > > + template <typename unused = void>
> > > + struct globals_struct {
> > > ++    static const unsigned char parse_flags[256];
> > > ++};
> > > ++typedef globals_struct<> globals;
> > > ++
> > > + // clang-format off
> > > + 
> > > +     // bit 0 (1) - set if: plain ASCII string character
> > > +     // bit 1 (2) - set if: whitespace
> > > +     // bit 4 (0x10) - set if: 0-9 e E .
> > > +-    constexpr static const uint8_t parse_flags[256] = {
> > > ++    template <typename unused>
> > > ++    const unsigned char
> > > globals_struct<unused>::parse_flags[256] =
> > > {
> > > +      // 0    1    2    3    4    5    6    7      8    9   
> > > A   
> > > B    C    D    E    F
> > > +         0,   0,   0,   0,   0,   0,   0,   0,     0,   2,  
> > > 2,  
> > > 0,   0,   2,   0,   0, // 0
> > > +         0,   0,   0,   0,   0,   0,   0,   0,     0,   0,  
> > > 0,  
> > > 0,   0,   0,   0,   0, // 1
> > > +@@ -162,15 +167,13 @@ struct globals_struct {
> > > +     };
> > > + 
> > > + // clang-format on
> > > +-};
> > > +-typedef globals_struct<> globals;
> > > + 
> > > +-constexpr inline bool is_plain_string_character(char c) {
> > > ++inline bool is_plain_string_character(char c) {
> > > +     // return c >= 0x20 && c <= 0x7f && c != 0x22 && c != 0x5c;
> > > +     return (globals::parse_flags[static_cast<unsigned char>(c)]
> > > &
> > > 1) != 0;
> > > + }
> > > + 
> > > +-constexpr inline bool is_whitespace(char c) {
> > > ++inline bool is_whitespace(char c) {
> > > +     // return c == '\r' || c == '\n' || c == '\t' || c == ' ';
> > > +     return (globals::parse_flags[static_cast<unsigned char>(c)]
> > > &
> > > 2) != 0;
> > > + }

[bug#58261] [PATCH v2 04/13] gnu: Add tinydir.

[David Elsing]

* gnu/packages/cpp.scm (tinydir): New variable.
---
 gnu/packages/cpp.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index dca0245df5..e99fdcecd8 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -2065,3 +2065,30 @@ (define-public sajson
       (description "@code{sajson} is an in-place JSON parser with support for
 parsing with only a single memory allocation.")
       (license license:expat))))
+
+(define-public tinydir
+  (package
+    (name "tinydir")
+    (version "1.2.5")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/cxong/tinydir")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1nprgdfx4i8wzc1idw6chan4fjfa75b5ll8kghdc0q2278pny259"))
+              (modules '((guix build utils)))
+              (snippet '(delete-file-recursively "tests/cbehave"))))
+    (build-system copy-build-system)
+    (arguments
+     (list
+      ;; TODO: Tests contain a private fork of cbehave and a bundled copy of rlutil
+      #:install-plan
+      #~'(("tinydir.h" "include/"))))
+    (home-page "https://github.com/cxong/tinydir")
+    (synopsis "C header-only directory and file reader")
+    (description "@code{tinydir} is a header-only C library to portably read
+files and directories.")
+    (license license:bsd-2)))
-- 
2.37.0

[bug#58261] [PATCH v2 04/13] gnu: Add tinydir.

[Liliana Marie Prikler]

Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
> * gnu/packages/cpp.scm (tinydir): New variable.
> ---
>  gnu/packages/cpp.scm | 27 +++++++++++++++++++++++++++
>  1 file changed, 27 insertions(+)
> 
> diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
> index dca0245df5..e99fdcecd8 100644
> --- a/gnu/packages/cpp.scm
> +++ b/gnu/packages/cpp.scm
> @@ -2065,3 +2065,30 @@ (define-public sajson
>        (description "@code{sajson} is an in-place JSON parser with
> support for
>  parsing with only a single memory allocation.")
>        (license license:expat))))
> +
> +(define-public tinydir
> +  (package
> +    (name "tinydir")
> +    (version "1.2.5")
> +    (source (origin
> +              (method git-fetch)
> +              (uri (git-reference
> +                    (url "https://github.com/cxong/tinydir")
> +                    (commit version)))
> +              (file-name (git-file-name name version))
> +              (sha256
> +               (base32
> +               
> "1nprgdfx4i8wzc1idw6chan4fjfa75b5ll8kghdc0q2278pny259"))
> +              (modules '((guix build utils)))
> +              (snippet '(delete-file-recursively "tests/cbehave"))))
> +    (build-system copy-build-system)
> +    (arguments
> +     (list
> +      ;; TODO: Tests contain a private fork of cbehave and a bundled
> copy of rlutil
> +      #:install-plan
> +      #~'(("tinydir.h" "include/"))))
> +    (home-page "https://github.com/cxong/tinydir")
> +    (synopsis "C header-only directory and file reader")
Just "Directory and file reader", though I'm not too sure whether it
actually reads files.
> +    (description "@code{tinydir} is a header-only C library to
> portably read
> +files and directories.")
Since in this case "portable" means "works on the Microsoft OS and
Unix", I'm pretty sure it's but a buzzword.
> +    (license license:bsd-2)))

[bug#58261] [PATCH v2 05/13] gnu: Add optionparser.

[David Elsing]

* gnu/packages/cpp.scm (optionparser): New variable.
---
 gnu/packages/cpp.scm | 47 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)

diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index e99fdcecd8..d1c580a1fc 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -2092,3 +2092,50 @@ (define-public tinydir
     (description "@code{tinydir} is a header-only C library to portably read
 files and directories.")
     (license license:bsd-2)))
+
+(define-public optionparser
+  (package
+    (name "optionparser")
+    (version "1.7")
+    (source (origin
+              (method url-fetch)
+              (uri
+               (string-append "mirror://sourceforge/optionparser/"
+                              "optionparser-" version ".tar.gz"))
+              (sha256
+               (base32
+                "04gfxrdzwacaynb8scsz6rr7nh64n6yk6w9dh2qdhrxw4caqr0dk"))))
+    (outputs '("out" "doc"))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (delete 'configure)
+          (add-before 'build 'chdir
+            (lambda _ (chdir "src")))
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                  (begin
+                    (invoke "./example_arg")
+                    (invoke "./testparse")
+                    (invoke "./testprintusage")
+                    (invoke "./testodr")
+                    (invoke "./example")))))
+          (replace 'install
+            (lambda _
+              (install-file "optionparser.h" (string-append #$output "/include"))))
+          (add-after 'install 'install-doc
+            (lambda _
+              (copy-recursively
+               "../html"
+               (string-append #$output:doc "/share/doc/optionparser/html")))))))
+    (native-inputs (list doxygen))
+    (home-page "https://optionparser.sourceforge.net/")
+    (synopsis "Header-only C++ library to parse command line options")
+    (description "This library can be used to handle the command line
+arguments of a C++ program.  It supports the short and long option formats of
+getopt(), getopt_long() and getopt_long_only(), but has a more convenient
+interface.")
+    (license license:expat)))
-- 
2.37.0

[bug#58261] [PATCH v2 06/13] gnu: Add gemmi.

[David Elsing]

* gnu/packages/chemistry.scm (gemmi): New variable.
---
 gnu/packages/chemistry.scm                    | 118 +++++++++++
 .../patches/gemmi-fix-sajson-types.patch      |  11 +
 .../sajson-for-gemmi-build-with-gcc10.patch   |  45 ++++
 .../sajson-for-gemmi-numbers-as-strings.patch | 195 ++++++++++++++++++
 4 files changed, 369 insertions(+)
 create mode 100644 gnu/packages/patches/gemmi-fix-sajson-types.patch
 create mode 100644 gnu/packages/patches/sajson-for-gemmi-build-with-gcc10.patch
 create mode 100644 gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index c517610fe8..d8f1608a3a 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -6,6 +6,7 @@
 ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
 ;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2022 David Elsing <david.elsing@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -23,6 +24,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages chemistry)
+  #:use-module (guix gexp)
   #:use-module (guix packages)
   #:use-module (guix utils)
   #:use-module ((guix licenses) #:prefix license:)
@@ -35,6 +37,7 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages cpp)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gl)
@@ -50,8 +53,10 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages qt)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages sphinx)
+  #:use-module (gnu packages stb)
   #:use-module (gnu packages xml)
   #:use-module (guix build-system cmake)
+  #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system python))
 
@@ -566,3 +571,116 @@ (define-public python-pymol
 used to prepare publication-quality figures, to share interactive results with
 your colleagues, or to generate pre-rendered animations.")
     (license license:bsd-3)))
+
+(define-public sajson-for-gemmi
+  (package/inherit sajson
+    (name "sajson-for-gemmi")
+    (source (origin
+              (inherit (package-source sajson))
+              (patches (search-patches
+                        "sajson-for-gemmi-numbers-as-strings.patch"
+                        "sajson-for-gemmi-build-with-gcc10.patch"))))
+    (arguments
+     (substitute-keyword-arguments (package-arguments sajson)
+       ((#:tests? _ #f) #f)
+       ((#:phases phases)
+        #~(modify-phases #$phases
+            (delete 'build)))))))
+
+(define-public gemmi
+  (package
+    (name "gemmi")
+    (version "0.5.7")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/project-gemmi/gemmi")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "00km5q726bslrw7xbfwb3f3mrsk19qbimfnl3hvr4wi1y3z8i18a"))
+              (patches
+               (search-patches "gemmi-fix-sajson-types.patch"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  (delete-file-recursively "include/gemmi/third_party")
+                  (delete-file-recursively "third_party")))))
+    (outputs '("out" "bin" "python"))
+    (build-system cmake-build-system)
+    (native-inputs
+     (list fast-float
+           optionparser
+           pegtl
+           pocketfft-cpp
+           pybind11
+           sajson-for-gemmi
+           stb-sprintf
+           tinydir))
+    (inputs (list python zlib))
+    (arguments
+     (list
+      #:configure-flags
+      #~(let* ((python-lib
+                (string-append
+                 #$output:python "/lib/python"
+                 #$(version-major+minor (package-version python))
+                 "/site-packages")))
+          (list "-DUSE_PYTHON=ON"
+                (string-append "-DPYTHON_INSTALL_DIR=" python-lib)))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-includes
+            (lambda _
+              (substitute* "include/gemmi/sprintf.hpp"
+                (("<stb/stb_sprintf.h>") "<stb_sprintf.h>"))
+              (substitute* "include/gemmi/dirwalk.hpp"
+                (("\"third_party/tinydir.h\"") "<tinydir.h>"))
+              (substitute* "include/gemmi/cif.hpp"
+                (("\"third_party/tao/pegtl.hpp\"") "<tao/pegtl.hpp>"))
+              (substitute* "include/gemmi/json.hpp"
+                (("\"third_party/sajson.h\"") "<sajson.h>"))
+              (substitute* "python/gemmi.cpp"
+                (("\"gemmi/third_party/tao/pegtl/parse_error.hpp\"")
+                 "<tao/pegtl/parse_error.hpp>"))
+              (substitute* '("include/gemmi/atof.hpp"
+                             "include/gemmi/numb.hpp")
+                (("\"third_party/fast_float.h\"")
+                 "<fast_float/fast_float.h>"))
+              (substitute* "include/gemmi/fourier.hpp"
+                (("\"third_party/pocketfft_hdronly.h\"")
+                 "<pocketfft_hdronly.h>"))))
+          (add-after 'patch-includes 'patch-cif
+            (lambda _
+              (substitute* "include/gemmi/cif.hpp"
+                (((string-append
+                   "^.*using analyze_t = pegtl::analysis::generic"
+                   "<pegtl::analysis::rule_type::ANY>;.*$")) "")
+                (("TAOCPP_PEGTL_") "TAO_PEGTL_"))))
+          (add-after 'unpack 'change-bin-prefix
+            (lambda _
+              (substitute* "CMakeLists.txt"
+                (("install\\(TARGETS program DESTINATION bin\\)")
+                 (string-append
+                  "install(TARGETS program DESTINATION "
+                  #$output:bin "/bin)")))))
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (with-directory-excursion "../source"
+                  (setenv "PYTHONPATH" "../build")
+                  (invoke "python3" "-m" "unittest" "discover" "-v"
+                          "-s" "tests"))))))))
+    (home-page "https://gemmi.readthedocs.io/en/latest/")
+    (synopsis "Macromolecular crystallography library and utilities")
+    (description "GEMMI is a C++ library for macromolecular crystallography.
+It can be used for working with
+@enumerate
+@item macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files),
+@item refinement restraints (CIF files),
+@item reflection data (MTZ and mmCIF formats),
+@item data on a 3D grid (electron density maps, masks, MRC/CCP4 format)
+@item crystallographic symmetry.
+@end enumerate")
+    (license license:mpl2.0)))
diff --git a/gnu/packages/patches/gemmi-fix-sajson-types.patch b/gnu/packages/patches/gemmi-fix-sajson-types.patch
new file mode 100644
index 0000000000..9633ddac8b
--- /dev/null
+++ b/gnu/packages/patches/gemmi-fix-sajson-types.patch
@@ -0,0 +1,11 @@
+diff -ur a/include/gemmi/json.hpp b/include/gemmi/json.hpp
+--- a/include/gemmi/json.hpp
++++ b/include/gemmi/json.hpp
+@@ -38,6 +38,7 @@
+ 
+ inline std::string as_cif_value(const sajson::value& val) {
+   switch (val.get_type()) {
++    case sajson::TYPE_INTEGER:
+     case sajson::TYPE_DOUBLE:
+       return val.as_string();
+     case sajson::TYPE_NULL:
diff --git a/gnu/packages/patches/sajson-for-gemmi-build-with-gcc10.patch b/gnu/packages/patches/sajson-for-gemmi-build-with-gcc10.patch
new file mode 100644
index 0000000000..878706dc79
--- /dev/null
+++ b/gnu/packages/patches/sajson-for-gemmi-build-with-gcc10.patch
@@ -0,0 +1,45 @@
+This patch is from the upstream pull request
+https://github.com/chadaustin/sajson/pull/54.
+It fixes linking with GCC.
+
+diff --git a/include/sajson.h b/include/sajson.h
+index 8b4e05a..1bd045b 100644
+--- a/include/sajson.h
++++ b/include/sajson.h
+@@ -138,12 +138,17 @@ constexpr inline size_t make_element(tag t, size_t value) {
+ // header. This trick courtesy of Rich Geldreich's Purple JSON parser.
+ template <typename unused = void>
+ struct globals_struct {
++    static const unsigned char parse_flags[256];
++};
++typedef globals_struct<> globals;
++
+ // clang-format off
+ 
+     // bit 0 (1) - set if: plain ASCII string character
+     // bit 1 (2) - set if: whitespace
+     // bit 4 (0x10) - set if: 0-9 e E .
+-    constexpr static const uint8_t parse_flags[256] = {
++    template <typename unused>
++    const unsigned char globals_struct<unused>::parse_flags[256] = {
+      // 0    1    2    3    4    5    6    7      8    9    A    B    C    D    E    F
+         0,   0,   0,   0,   0,   0,   0,   0,     0,   2,   2,   0,   0,   2,   0,   0, // 0
+         0,   0,   0,   0,   0,   0,   0,   0,     0,   0,   0,   0,   0,   0,   0,   0, // 1
+@@ -162,15 +167,13 @@ struct globals_struct {
+     };
+ 
+ // clang-format on
+-};
+-typedef globals_struct<> globals;
+ 
+-constexpr inline bool is_plain_string_character(char c) {
++inline bool is_plain_string_character(char c) {
+     // return c >= 0x20 && c <= 0x7f && c != 0x22 && c != 0x5c;
+     return (globals::parse_flags[static_cast<unsigned char>(c)] & 1) != 0;
+ }
+ 
+-constexpr inline bool is_whitespace(char c) {
++inline bool is_whitespace(char c) {
+     // return c == '\r' || c == '\n' || c == '\t' || c == ' ';
+     return (globals::parse_flags[static_cast<unsigned char>(c)] & 2) != 0;
+ }
diff --git a/gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch b/gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch
new file mode 100644
index 0000000000..6f476b8583
--- /dev/null
+++ b/gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch
@@ -0,0 +1,195 @@
+Patch for gemmi: Keep numbers in JSON file as strings.
+
+Adapted from this commit of the bundled fork of sajson in gemmi:
+https://github.com/project-gemmi/gemmi/commit/fccbca4f6040364ba708613e1429c2251872240d
+
+diff -ur a/include/sajson.h b/include/sajson.h
+--- a/include/sajson.h
++++ b/include/sajson.h
+@@ -411,43 +411,6 @@
+ };
+ } // namespace internal
+ 
+-namespace integer_storage {
+-enum { word_length = 1 };
+-
+-inline int load(const size_t* location) {
+-    int value;
+-    memcpy(&value, location, sizeof(value));
+-    return value;
+-}
+-
+-inline void store(size_t* location, int value) {
+-    // NOTE: Most modern compilers optimize away this constant-size
+-    // memcpy into a single instruction. If any don't, and treat
+-    // punning through a union as legal, they can be special-cased.
+-    static_assert(
+-        sizeof(value) <= sizeof(*location),
+-        "size_t must not be smaller than int");
+-    memcpy(location, &value, sizeof(value));
+-}
+-} // namespace integer_storage
+-
+-namespace double_storage {
+-enum { word_length = sizeof(double) / sizeof(size_t) };
+-
+-inline double load(const size_t* location) {
+-    double value;
+-    memcpy(&value, location, sizeof(double));
+-    return value;
+-}
+-
+-inline void store(size_t* location, double value) {
+-    // NOTE: Most modern compilers optimize away this constant-size
+-    // memcpy into a single instruction. If any don't, and treat
+-    // punning through a union as legal, they can be special-cased.
+-    memcpy(location, &value, sizeof(double));
+-}
+-} // namespace double_storage
+-
+ /// Represents a JSON value.  First, call get_type() to check its type,
+ /// which determines which methods are available.
+ ///
+@@ -585,70 +548,10 @@
+         return length;
+     }
+ 
+-    /// If a numeric value was parsed as a 32-bit integer, returns it.
+-    /// Only legal if get_type() is TYPE_INTEGER.
+-    int get_integer_value() const {
+-        assert_tag(tag::integer);
+-        return integer_storage::load(payload);
+-    }
+-
+-    /// If a numeric value was parsed as a double, returns it.
+-    /// Only legal if get_type() is TYPE_DOUBLE.
+-    double get_double_value() const {
+-        assert_tag(tag::double_);
+-        return double_storage::load(payload);
+-    }
+-
+-    /// Returns a numeric value as a double-precision float.
+-    /// Only legal if get_type() is TYPE_INTEGER or TYPE_DOUBLE.
+-    double get_number_value() const {
+-        assert_tag_2(tag::integer, tag::double_);
+-        if (value_tag == tag::integer) {
+-            return get_integer_value();
+-        } else {
+-            return get_double_value();
+-        }
+-    }
+-
+-    /// Returns true and writes to the output argument if the numeric value
+-    /// fits in a 53-bit integer.  This is useful for timestamps and other
+-    /// situations where integral values with greater than 32-bit precision
+-    /// are used, as 64-bit values are not understood by all JSON
+-    /// implementations or languages.
+-    /// Returns false if the value is not an integer or not in range.
+-    /// Only legal if get_type() is TYPE_INTEGER or TYPE_DOUBLE.
+-    bool get_int53_value(int64_t* out) const {
+-        // Make sure the output variable is always defined to avoid any
+-        // possible situation like
+-        // https://gist.github.com/chadaustin/2c249cb850619ddec05b23ca42cf7a18
+-        *out = 0;
+-
+-        assert_tag_2(tag::integer, tag::double_);
+-        switch (value_tag) {
+-        case tag::integer:
+-            *out = get_integer_value();
+-            return true;
+-        case tag::double_: {
+-            double v = get_double_value();
+-            if (v < -(1LL << 53) || v > (1LL << 53)) {
+-                return false;
+-            }
+-            int64_t as_int = static_cast<int64_t>(v);
+-            if (as_int != v) {
+-                return false;
+-            }
+-            *out = as_int;
+-            return true;
+-        }
+-        default:
+-            return false;
+-        }
+-    }
+-
+     /// Returns the length of the string.
+     /// Only legal if get_type() is TYPE_STRING.
+     size_t get_string_length() const {
+-        assert_tag(tag::string);
++        assert_tag_3(tag::string, tag::integer, tag::double_);
+         return payload[1] - payload[0];
+     }
+ 
+@@ -659,7 +562,7 @@
+     /// embedded NULs.
+     /// Only legal if get_type() is TYPE_STRING.
+     const char* as_cstring() const {
+-        assert_tag(tag::string);
++        assert_tag_3(tag::string, tag::integer, tag::double_);
+         return text + payload[0];
+     }
+ 
+@@ -667,7 +570,7 @@
+     /// Returns a string's value as a std::string.
+     /// Only legal if get_type() is TYPE_STRING.
+     std::string as_string() const {
+-        assert_tag(tag::string);
++        assert_tag_3(tag::string, tag::integer, tag::double_);
+         return std::string(text + payload[0], text + payload[1]);
+     }
+ #endif
+@@ -690,6 +593,10 @@
+         assert(e1 == value_tag || e2 == value_tag);
+     }
+ 
++    void assert_tag_3(tag e1, tag e2, tag e3) const {
++        assert(e1 == value_tag || e2 == value_tag || e3 == value_tag);
++    }
++
+     void assert_in_bounds(size_t i) const { assert(i < get_length()); }
+ 
+     const tag value_tag;
+@@ -2059,6 +1966,8 @@
+     std::pair<char*, internal::tag> parse_number(char* p) {
+         using internal::tag;
+ 
++	size_t start = p - input.get_data();
++
+         // Assume 32-bit, two's complement integers.
+         static constexpr unsigned RISKY = INT_MAX / 10u;
+         unsigned max_digit_after_risky = INT_MAX % 10u;
+@@ -2235,23 +2144,18 @@
+                 u = 0u - u;
+             }
+         }
++
++        bool success;
++        size_t* out = allocator.reserve(2, &success);
++        if (SAJSON_UNLIKELY(!success)) {
++            return std::make_pair(oom(p, "number"), tag::null);
++        }
++        out[0] = start;
++        out[1] = p - input.get_data();
++
+         if (try_double) {
+-            bool success;
+-            size_t* out
+-                = allocator.reserve(double_storage::word_length, &success);
+-            if (SAJSON_UNLIKELY(!success)) {
+-                return std::make_pair(oom(p, "double"), tag::null);
+-            }
+-            double_storage::store(out, d);
+             return std::make_pair(p, tag::double_);
+         } else {
+-            bool success;
+-            size_t* out
+-                = allocator.reserve(integer_storage::word_length, &success);
+-            if (SAJSON_UNLIKELY(!success)) {
+-                return std::make_pair(oom(p, "integer"), tag::null);
+-            }
+-            integer_storage::store(out, static_cast<int>(u));
+             return std::make_pair(p, tag::integer);
+         }
+     }
-- 
2.37.0

[bug#58261] [PATCH v2 06/13] gnu: Add gemmi.

[Liliana Marie Prikler]

Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
> * gnu/packages/chemistry.scm (gemmi): New variable.
> ---
>  gnu/packages/chemistry.scm                    | 118 +++++++++++
>  .../patches/gemmi-fix-sajson-types.patch      |  11 +
>  .../sajson-for-gemmi-build-with-gcc10.patch   |  45 ++++
>  .../sajson-for-gemmi-numbers-as-strings.patch | 195
> ++++++++++++++++++
>  4 files changed, 369 insertions(+)
>  create mode 100644 gnu/packages/patches/gemmi-fix-sajson-types.patch
>  create mode 100644 gnu/packages/patches/sajson-for-gemmi-build-with-
> gcc10.patch
>  create mode 100644 gnu/packages/patches/sajson-for-gemmi-numbers-as-
> strings.patch
> 
> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
> index c517610fe8..d8f1608a3a 100644
> --- a/gnu/packages/chemistry.scm
> +++ b/gnu/packages/chemistry.scm
> @@ -6,6 +6,7 @@
>  ;;; Copyright © 2020 Björn Höfling
> <bjoern.hoefling@bjoernhoefling.de>
>  ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
>  ;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
> +;;; Copyright © 2022 David Elsing <david.elsing@posteo.net>
>  ;;;
>  ;;; This file is part of GNU Guix.
>  ;;;
> @@ -23,6 +24,7 @@
>  ;;; along with GNU Guix.  If not, see
> <http://www.gnu.org/licenses/>.
>  
>  (define-module (gnu packages chemistry)
> +  #:use-module (guix gexp)
>    #:use-module (guix packages)
>    #:use-module (guix utils)
>    #:use-module ((guix licenses) #:prefix license:)
> @@ -35,6 +37,7 @@ (define-module (gnu packages chemistry)
>    #:use-module (gnu packages boost)
>    #:use-module (gnu packages check)
>    #:use-module (gnu packages compression)
> +  #:use-module (gnu packages cpp)
>    #:use-module (gnu packages documentation)
>    #:use-module (gnu packages fontutils)
>    #:use-module (gnu packages gl)
> @@ -50,8 +53,10 @@ (define-module (gnu packages chemistry)
>    #:use-module (gnu packages qt)
>    #:use-module (gnu packages serialization)
>    #:use-module (gnu packages sphinx)
> +  #:use-module (gnu packages stb)
>    #:use-module (gnu packages xml)
>    #:use-module (guix build-system cmake)
> +  #:use-module (guix build-system copy)
>    #:use-module (guix build-system gnu)
>    #:use-module (guix build-system python))
>  
> @@ -566,3 +571,116 @@ (define-public python-pymol
>  used to prepare publication-quality figures, to share interactive
> results with
>  your colleagues, or to generate pre-rendered animations.")
>      (license license:bsd-3)))
> +
> +(define-public sajson-for-gemmi
> +  (package/inherit sajson
> +    (name "sajson-for-gemmi")
> +    (source (origin
> +              (inherit (package-source sajson))
> +              (patches (search-patches
> +                        "sajson-for-gemmi-numbers-as-strings.patch"
> +                        "sajson-for-gemmi-build-with-
> gcc10.patch"))))
> +    (arguments
> +     (substitute-keyword-arguments (package-arguments sajson)
> +       ((#:tests? _ #f) #f)
Don't forget the comment as to why they're disabled.
> +       ((#:phases phases)
> +        #~(modify-phases #$phases
> +            (delete 'build)))))))
Why is the build deleted?

Split here.
> +(define-public gemmi
> +  (package
> +    (name "gemmi")
> +    (version "0.5.7")
> +    (source (origin
> +              (method git-fetch)
> +              (uri (git-reference
> +                    (url "https://github.com/project-gemmi/gemmi")
> +                    (commit (string-append "v" version))))
> +              (file-name (git-file-name name version))
> +              (sha256
> +               (base32
> +               
> "00km5q726bslrw7xbfwb3f3mrsk19qbimfnl3hvr4wi1y3z8i18a"))
> +              (patches
> +               (search-patches "gemmi-fix-sajson-types.patch"))
> +              (modules '((guix build utils)))
> +              (snippet
> +               '(begin
> +                  (delete-file-recursively
> "include/gemmi/third_party")
> +                  (delete-file-recursively "third_party")))))
> +    (outputs '("out" "bin" "python"))
> +    (build-system cmake-build-system)
> +    (native-inputs
> +     (list fast-float
> +           optionparser
> +           pegtl
> +           pocketfft-cpp
> +           pybind11
> +           sajson-for-gemmi
> +           stb-sprintf
> +           tinydir))
> +    (inputs (list python zlib))
> +    (arguments
> +     (list
> +      #:configure-flags
> +      #~(let* ((python-lib
> +                (string-append
> +                 #$output:python "/lib/python"
> +                 #$(version-major+minor (package-version python))
> +                 "/site-packages")))
Note that python-build-system has a (site-packages) procedure.  Writing
the boilerplate to include it in the build shouldn't be much worse in
terms of lines than what you're doing here.
> +          (list "-DUSE_PYTHON=ON"
> +                (string-append "-DPYTHON_INSTALL_DIR=" python-lib)))
> +      #:phases
> +      #~(modify-phases %standard-phases
> +          (add-after 'unpack 'patch-includes
> +            (lambda _
> +              (substitute* "include/gemmi/sprintf.hpp"
> +                (("<stb/stb_sprintf.h>") "<stb_sprintf.h>"))
> +              (substitute* "include/gemmi/dirwalk.hpp"
> +                (("\"third_party/tinydir.h\"") "<tinydir.h>"))
> +              (substitute* "include/gemmi/cif.hpp"
> +                (("\"third_party/tao/pegtl.hpp\"")
> "<tao/pegtl.hpp>"))
> +              (substitute* "include/gemmi/json.hpp"
> +                (("\"third_party/sajson.h\"") "<sajson.h>"))
> +              (substitute* "python/gemmi.cpp"
> +                (("\"gemmi/third_party/tao/pegtl/parse_error.hpp\"")
> +                 "<tao/pegtl/parse_error.hpp>"))
> +              (substitute* '("include/gemmi/atof.hpp"
> +                             "include/gemmi/numb.hpp")
> +                (("\"third_party/fast_float.h\"")
> +                 "<fast_float/fast_float.h>"))
> +              (substitute* "include/gemmi/fourier.hpp"
> +                (("\"third_party/pocketfft_hdronly.h\"")
> +                 "<pocketfft_hdronly.h>"))))
I'd collect all the files into a (list ...) and then write out the
substitutes.

> +          (add-after 'patch-includes 'patch-cif
> +            (lambda _
> +              (substitute* "include/gemmi/cif.hpp"
> +                (((string-append
> +                   "^.*using analyze_t = pegtl::analysis::generic"
> +                   "<pegtl::analysis::rule_type::ANY>;.*$")) "")
> +                (("TAOCPP_PEGTL_") "TAO_PEGTL_"))))
Uhm... I think I'd prefer a patch for this one.
> +          (add-after 'unpack 'change-bin-prefix
> +            (lambda _
> +              (substitute* "CMakeLists.txt"
> +                (("install\\(TARGETS program DESTINATION bin\\)")
> +                 (string-append
> +                  "install(TARGETS program DESTINATION "
> +                  #$output:bin "/bin)")))))
> +          (replace 'check
> +            (lambda* (#:key tests? #:allow-other-keys)
> +              (when tests?
> +                (with-directory-excursion "../source"
> +                  (setenv "PYTHONPATH" "../build")
> +                  (invoke "python3" "-m" "unittest" "discover" "-v"
> +                          "-s" "tests"))))))))
> +    (home-page "https://gemmi.readthedocs.io/en/latest/")
> +    (synopsis "Macromolecular crystallography library and
> utilities")
> +    (description "GEMMI is a C++ library for macromolecular
> crystallography.
> +It can be used for working with
> +@enumerate
> +@item macromolecular models (content of PDB, PDBx/mmCIF and mmJSON
> files),
> +@item refinement restraints (CIF files),
> +@item reflection data (MTZ and mmCIF formats),
> +@item data on a 3D grid (electron density maps, masks, MRC/CCP4
> format)
> +@item crystallographic symmetry.
> +@end enumerate")
> +    (license license:mpl2.0)))
> diff --git a/gnu/packages/patches/gemmi-fix-sajson-types.patch
> b/gnu/packages/patches/gemmi-fix-sajson-types.patch
> new file mode 100644
> index 0000000000..9633ddac8b
> --- /dev/null
> +++ b/gnu/packages/patches/gemmi-fix-sajson-types.patch
> @@ -0,0 +1,11 @@
> +diff -ur a/include/gemmi/json.hpp b/include/gemmi/json.hpp
> +--- a/include/gemmi/json.hpp
> ++++ b/include/gemmi/json.hpp
> +@@ -38,6 +38,7 @@
> + 
> + inline std::string as_cif_value(const sajson::value& val) {
> +   switch (val.get_type()) {
> ++    case sajson::TYPE_INTEGER:
> +     case sajson::TYPE_DOUBLE:
> +       return val.as_string();
> +     case sajson::TYPE_NULL:
> diff --git a/gnu/packages/patches/sajson-for-gemmi-build-with-
> gcc10.patch b/gnu/packages/patches/sajson-for-gemmi-build-with-
> gcc10.patch
> new file mode 100644
> index 0000000000..878706dc79
> --- /dev/null
> +++ b/gnu/packages/patches/sajson-for-gemmi-build-with-gcc10.patch
> @@ -0,0 +1,45 @@
> +This patch is from the upstream pull request
> +https://github.com/chadaustin/sajson/pull/54.
> +It fixes linking with GCC.
> +
> +diff --git a/include/sajson.h b/include/sajson.h
> +index 8b4e05a..1bd045b 100644
> +--- a/include/sajson.h
> ++++ b/include/sajson.h
> +@@ -138,12 +138,17 @@ constexpr inline size_t make_element(tag t,
> size_t value) {
> + // header. This trick courtesy of Rich Geldreich's Purple JSON
> parser.
> + template <typename unused = void>
> + struct globals_struct {
> ++    static const unsigned char parse_flags[256];
> ++};
> ++typedef globals_struct<> globals;
> ++
> + // clang-format off
> + 
> +     // bit 0 (1) - set if: plain ASCII string character
> +     // bit 1 (2) - set if: whitespace
> +     // bit 4 (0x10) - set if: 0-9 e E .
> +-    constexpr static const uint8_t parse_flags[256] = {
> ++    template <typename unused>
> ++    const unsigned char globals_struct<unused>::parse_flags[256] =
> {
> +      // 0    1    2    3    4    5    6    7      8    9    A   
> B    C    D    E    F
> +         0,   0,   0,   0,   0,   0,   0,   0,     0,   2,   2,  
> 0,   0,   2,   0,   0, // 0
> +         0,   0,   0,   0,   0,   0,   0,   0,     0,   0,   0,  
> 0,   0,   0,   0,   0, // 1
> +@@ -162,15 +167,13 @@ struct globals_struct {
> +     };
> + 
> + // clang-format on
> +-};
> +-typedef globals_struct<> globals;
> + 
> +-constexpr inline bool is_plain_string_character(char c) {
> ++inline bool is_plain_string_character(char c) {
> +     // return c >= 0x20 && c <= 0x7f && c != 0x22 && c != 0x5c;
> +     return (globals::parse_flags[static_cast<unsigned char>(c)] &
> 1) != 0;
> + }
> + 
> +-constexpr inline bool is_whitespace(char c) {
> ++inline bool is_whitespace(char c) {
> +     // return c == '\r' || c == '\n' || c == '\t' || c == ' ';
> +     return (globals::parse_flags[static_cast<unsigned char>(c)] &
> 2) != 0;
> + }
> diff --git a/gnu/packages/patches/sajson-for-gemmi-numbers-as-
> strings.patch b/gnu/packages/patches/sajson-for-gemmi-numbers-as-
> strings.patch
> new file mode 100644
> index 0000000000..6f476b8583
> --- /dev/null
> +++ b/gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch
> @@ -0,0 +1,195 @@
> +Patch for gemmi: Keep numbers in JSON file as strings.
> +
> +Adapted from this commit of the bundled fork of sajson in gemmi:
> +
> https://github.com/project-gemmi/gemmi/commit/fccbca4f6040364ba708613e
> 1429c2251872240d
> +
> +diff -ur a/include/sajson.h b/include/sajson.h
> +--- a/include/sajson.h
> ++++ b/include/sajson.h
> +@@ -411,43 +411,6 @@
> + };
> + } // namespace internal
> + 
> +-namespace integer_storage {
> +-enum { word_length = 1 };
> +-
> +-inline int load(const size_t* location) {
> +-    int value;
> +-    memcpy(&value, location, sizeof(value));
> +-    return value;
> +-}
> +-
> +-inline void store(size_t* location, int value) {
> +-    // NOTE: Most modern compilers optimize away this constant-size
> +-    // memcpy into a single instruction. If any don't, and treat
> +-    // punning through a union as legal, they can be special-cased.
> +-    static_assert(
> +-        sizeof(value) <= sizeof(*location),
> +-        "size_t must not be smaller than int");
> +-    memcpy(location, &value, sizeof(value));
> +-}
> +-} // namespace integer_storage
> +-
> +-namespace double_storage {
> +-enum { word_length = sizeof(double) / sizeof(size_t) };
> +-
> +-inline double load(const size_t* location) {
> +-    double value;
> +-    memcpy(&value, location, sizeof(double));
> +-    return value;
> +-}
> +-
> +-inline void store(size_t* location, double value) {
> +-    // NOTE: Most modern compilers optimize away this constant-size
> +-    // memcpy into a single instruction. If any don't, and treat
> +-    // punning through a union as legal, they can be special-cased.
> +-    memcpy(location, &value, sizeof(double));
> +-}
> +-} // namespace double_storage
> +-
> + /// Represents a JSON value.  First, call get_type() to check its
> type,
> + /// which determines which methods are available.
> + ///
> +@@ -585,70 +548,10 @@
> +         return length;
> +     }
> + 
> +-    /// If a numeric value was parsed as a 32-bit integer, returns
> it.
> +-    /// Only legal if get_type() is TYPE_INTEGER.
> +-    int get_integer_value() const {
> +-        assert_tag(tag::integer);
> +-        return integer_storage::load(payload);
> +-    }
> +-
> +-    /// If a numeric value was parsed as a double, returns it.
> +-    /// Only legal if get_type() is TYPE_DOUBLE.
> +-    double get_double_value() const {
> +-        assert_tag(tag::double_);
> +-        return double_storage::load(payload);
> +-    }
> +-
> +-    /// Returns a numeric value as a double-precision float.
> +-    /// Only legal if get_type() is TYPE_INTEGER or TYPE_DOUBLE.
> +-    double get_number_value() const {
> +-        assert_tag_2(tag::integer, tag::double_);
> +-        if (value_tag == tag::integer) {
> +-            return get_integer_value();
> +-        } else {
> +-            return get_double_value();
> +-        }
> +-    }
> +-
> +-    /// Returns true and writes to the output argument if the
> numeric value
> +-    /// fits in a 53-bit integer.  This is useful for timestamps
> and other
> +-    /// situations where integral values with greater than 32-bit
> precision
> +-    /// are used, as 64-bit values are not understood by all JSON
> +-    /// implementations or languages.
> +-    /// Returns false if the value is not an integer or not in
> range.
> +-    /// Only legal if get_type() is TYPE_INTEGER or TYPE_DOUBLE.
> +-    bool get_int53_value(int64_t* out) const {
> +-        // Make sure the output variable is always defined to avoid
> any
> +-        // possible situation like
> +-        //
> https://gist.github.com/chadaustin/2c249cb850619ddec05b23ca42cf7a18
> +-        *out = 0;
> +-
> +-        assert_tag_2(tag::integer, tag::double_);
> +-        switch (value_tag) {
> +-        case tag::integer:
> +-            *out = get_integer_value();
> +-            return true;
> +-        case tag::double_: {
> +-            double v = get_double_value();
> +-            if (v < -(1LL << 53) || v > (1LL << 53)) {
> +-                return false;
> +-            }
> +-            int64_t as_int = static_cast<int64_t>(v);
> +-            if (as_int != v) {
> +-                return false;
> +-            }
> +-            *out = as_int;
> +-            return true;
> +-        }
> +-        default:
> +-            return false;
> +-        }
> +-    }
> +-
> +     /// Returns the length of the string.
> +     /// Only legal if get_type() is TYPE_STRING.
> +     size_t get_string_length() const {
> +-        assert_tag(tag::string);
> ++        assert_tag_3(tag::string, tag::integer, tag::double_);
> +         return payload[1] - payload[0];
> +     }
> + 
> +@@ -659,7 +562,7 @@
> +     /// embedded NULs.
> +     /// Only legal if get_type() is TYPE_STRING.
> +     const char* as_cstring() const {
> +-        assert_tag(tag::string);
> ++        assert_tag_3(tag::string, tag::integer, tag::double_);
> +         return text + payload[0];
> +     }
> + 
> +@@ -667,7 +570,7 @@
> +     /// Returns a string's value as a std::string.
> +     /// Only legal if get_type() is TYPE_STRING.
> +     std::string as_string() const {
> +-        assert_tag(tag::string);
> ++        assert_tag_3(tag::string, tag::integer, tag::double_);
> +         return std::string(text + payload[0], text + payload[1]);
> +     }
> + #endif
> +@@ -690,6 +593,10 @@
> +         assert(e1 == value_tag || e2 == value_tag);
> +     }
> + 
> ++    void assert_tag_3(tag e1, tag e2, tag e3) const {
> ++        assert(e1 == value_tag || e2 == value_tag || e3 ==
> value_tag);
> ++    }
> ++
> +     void assert_in_bounds(size_t i) const { assert(i <
> get_length()); }
> + 
> +     const tag value_tag;
> +@@ -2059,6 +1966,8 @@
> +     std::pair<char*, internal::tag> parse_number(char* p) {
> +         using internal::tag;
> + 
> ++      size_t start = p - input.get_data();
> ++
> +         // Assume 32-bit, two's complement integers.
> +         static constexpr unsigned RISKY = INT_MAX / 10u;
> +         unsigned max_digit_after_risky = INT_MAX % 10u;
> +@@ -2235,23 +2144,18 @@
> +                 u = 0u - u;
> +             }
> +         }
> ++
> ++        bool success;
> ++        size_t* out = allocator.reserve(2, &success);
> ++        if (SAJSON_UNLIKELY(!success)) {
> ++            return std::make_pair(oom(p, "number"), tag::null);
> ++        }
> ++        out[0] = start;
> ++        out[1] = p - input.get_data();
> ++
> +         if (try_double) {
> +-            bool success;
> +-            size_t* out
> +-                = allocator.reserve(double_storage::word_length,
> &success);
> +-            if (SAJSON_UNLIKELY(!success)) {
> +-                return std::make_pair(oom(p, "double"), tag::null);
> +-            }
> +-            double_storage::store(out, d);
> +             return std::make_pair(p, tag::double_);
> +         } else {
> +-            bool success;
> +-            size_t* out
> +-                = allocator.reserve(integer_storage::word_length,
> &success);
> +-            if (SAJSON_UNLIKELY(!success)) {
> +-                return std::make_pair(oom(p, "integer"),
> tag::null);
> +-            }
> +-            integer_storage::store(out, static_cast<int>(u));
> +             return std::make_pair(p, tag::integer);
> +         }
> +     }

[bug#58261] [PATCH v2 06/13] gnu: Add gemmi.

[David Elsing]

Liliana Marie Prikler <liliana.prikler@gmail.com> writes:

> Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
>> * gnu/packages/chemistry.scm (gemmi): New variable.
>> ---
>>  gnu/packages/chemistry.scm                    | 118 +++++++++++
>>  .../patches/gemmi-fix-sajson-types.patch      |  11 +
>>  .../sajson-for-gemmi-build-with-gcc10.patch   |  45 ++++
>>  .../sajson-for-gemmi-numbers-as-strings.patch | 195
>> ++++++++++++++++++
>>  4 files changed, 369 insertions(+)
>>  create mode 100644 gnu/packages/patches/gemmi-fix-sajson-types.patch
>>  create mode 100644 gnu/packages/patches/sajson-for-gemmi-build-with-
>> gcc10.patch
>>  create mode 100644 gnu/packages/patches/sajson-for-gemmi-numbers-as-
>> strings.patch
>> 
>> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
>> index c517610fe8..d8f1608a3a 100644
>> --- a/gnu/packages/chemistry.scm
>> +++ b/gnu/packages/chemistry.scm
>> @@ -6,6 +6,7 @@
>>  ;;; Copyright © 2020 Björn Höfling
>> <bjoern.hoefling@bjoernhoefling.de>
>>  ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
>>  ;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
>> +;;; Copyright © 2022 David Elsing <david.elsing@posteo.net>
>>  ;;;
>>  ;;; This file is part of GNU Guix.
>>  ;;;
>> @@ -23,6 +24,7 @@
>>  ;;; along with GNU Guix.  If not, see
>> <http://www.gnu.org/licenses/>.
>>  
>>  (define-module (gnu packages chemistry)
>> +  #:use-module (guix gexp)
>>    #:use-module (guix packages)
>>    #:use-module (guix utils)
>>    #:use-module ((guix licenses) #:prefix license:)
>> @@ -35,6 +37,7 @@ (define-module (gnu packages chemistry)
>>    #:use-module (gnu packages boost)
>>    #:use-module (gnu packages check)
>>    #:use-module (gnu packages compression)
>> +  #:use-module (gnu packages cpp)
>>    #:use-module (gnu packages documentation)
>>    #:use-module (gnu packages fontutils)
>>    #:use-module (gnu packages gl)
>> @@ -50,8 +53,10 @@ (define-module (gnu packages chemistry)
>>    #:use-module (gnu packages qt)
>>    #:use-module (gnu packages serialization)
>>    #:use-module (gnu packages sphinx)
>> +  #:use-module (gnu packages stb)
>>    #:use-module (gnu packages xml)
>>    #:use-module (guix build-system cmake)
>> +  #:use-module (guix build-system copy)
>>    #:use-module (guix build-system gnu)
>>    #:use-module (guix build-system python))
>>  
>> @@ -566,3 +571,116 @@ (define-public python-pymol
>>  used to prepare publication-quality figures, to share interactive
>> results with
>>  your colleagues, or to generate pre-rendered animations.")
>>      (license license:bsd-3)))
>> +
>> +(define-public sajson-for-gemmi
>> +  (package/inherit sajson
>> +    (name "sajson-for-gemmi")
>> +    (source (origin
>> +              (inherit (package-source sajson))
>> +              (patches (search-patches
>> +                        "sajson-for-gemmi-numbers-as-strings.patch"
>> +                        "sajson-for-gemmi-build-with-
>> gcc10.patch"))))
>> +    (arguments
>> +     (substitute-keyword-arguments (package-arguments sajson)
>> +       ((#:tests? _ #f) #f)
> Don't forget the comment as to why they're disabled.
>> +       ((#:phases phases)
>> +        #~(modify-phases #$phases
>> +            (delete 'build)))))))
> Why is the build deleted?
It fails due to the change and only builds the tests anyway.
>
> Split here.
>> +(define-public gemmi
>> +  (package
>> +    (name "gemmi")
>> +    (version "0.5.7")
>> +    (source (origin
>> +              (method git-fetch)
>> +              (uri (git-reference
>> +                    (url "https://github.com/project-gemmi/gemmi")
>> +                    (commit (string-append "v" version))))
>> +              (file-name (git-file-name name version))
>> +              (sha256
>> +               (base32
>> +               
>> "00km5q726bslrw7xbfwb3f3mrsk19qbimfnl3hvr4wi1y3z8i18a"))
>> +              (patches
>> +               (search-patches "gemmi-fix-sajson-types.patch"))
>> +              (modules '((guix build utils)))
>> +              (snippet
>> +               '(begin
>> +                  (delete-file-recursively
>> "include/gemmi/third_party")
>> +                  (delete-file-recursively "third_party")))))
>> +    (outputs '("out" "bin" "python"))
>> +    (build-system cmake-build-system)
>> +    (native-inputs
>> +     (list fast-float
>> +           optionparser
>> +           pegtl
>> +           pocketfft-cpp
>> +           pybind11
>> +           sajson-for-gemmi
>> +           stb-sprintf
>> +           tinydir))
>> +    (inputs (list python zlib))
>> +    (arguments
>> +     (list
>> +      #:configure-flags
>> +      #~(let* ((python-lib
>> +                (string-append
>> +                 #$output:python "/lib/python"
>> +                 #$(version-major+minor (package-version python))
>> +                 "/site-packages")))
> Note that python-build-system has a (site-packages) procedure.  Writing
> the boilerplate to include it in the build shouldn't be much worse in
> terms of lines than what you're doing here.
>> +          (list "-DUSE_PYTHON=ON"
>> +                (string-append "-DPYTHON_INSTALL_DIR=" python-lib)))
>> +      #:phases
>> +      #~(modify-phases %standard-phases
>> +          (add-after 'unpack 'patch-includes
>> +            (lambda _
>> +              (substitute* "include/gemmi/sprintf.hpp"
>> +                (("<stb/stb_sprintf.h>") "<stb_sprintf.h>"))
>> +              (substitute* "include/gemmi/dirwalk.hpp"
>> +                (("\"third_party/tinydir.h\"") "<tinydir.h>"))
>> +              (substitute* "include/gemmi/cif.hpp"
>> +                (("\"third_party/tao/pegtl.hpp\"")
>> "<tao/pegtl.hpp>"))
>> +              (substitute* "include/gemmi/json.hpp"
>> +                (("\"third_party/sajson.h\"") "<sajson.h>"))
>> +              (substitute* "python/gemmi.cpp"
>> +                (("\"gemmi/third_party/tao/pegtl/parse_error.hpp\"")
>> +                 "<tao/pegtl/parse_error.hpp>"))
>> +              (substitute* '("include/gemmi/atof.hpp"
>> +                             "include/gemmi/numb.hpp")
>> +                (("\"third_party/fast_float.h\"")
>> +                 "<fast_float/fast_float.h>"))
>> +              (substitute* "include/gemmi/fourier.hpp"
>> +                (("\"third_party/pocketfft_hdronly.h\"")
>> +                 "<pocketfft_hdronly.h>"))))
> I'd collect all the files into a (list ...) and then write out the
> substitutes.
Is it preferred to put list elements on separate lines (also in inputs)?
>
>> +          (add-after 'patch-includes 'patch-cif
>> +            (lambda _
>> +              (substitute* "include/gemmi/cif.hpp"
>> +                (((string-append
>> +                   "^.*using analyze_t = pegtl::analysis::generic"
>> +                   "<pegtl::analysis::rule_type::ANY>;.*$")) "")
>> +                (("TAOCPP_PEGTL_") "TAO_PEGTL_"))))
> Uhm... I think I'd prefer a patch for this one.
>> +          (add-after 'unpack 'change-bin-prefix
>> +            (lambda _
>> +              (substitute* "CMakeLists.txt"
>> +                (("install\\(TARGETS program DESTINATION bin\\)")
>> +                 (string-append
>> +                  "install(TARGETS program DESTINATION "
>> +                  #$output:bin "/bin)")))))
>> +          (replace 'check
>> +            (lambda* (#:key tests? #:allow-other-keys)
>> +              (when tests?
>> +                (with-directory-excursion "../source"
>> +                  (setenv "PYTHONPATH" "../build")
>> +                  (invoke "python3" "-m" "unittest" "discover" "-v"
>> +                          "-s" "tests"))))))))
>> +    (home-page "https://gemmi.readthedocs.io/en/latest/")
>> +    (synopsis "Macromolecular crystallography library and
>> utilities")
>> +    (description "GEMMI is a C++ library for macromolecular
>> crystallography.
>> +It can be used for working with
>> +@enumerate
>> +@item macromolecular models (content of PDB, PDBx/mmCIF and mmJSON
>> files),
>> +@item refinement restraints (CIF files),
>> +@item reflection data (MTZ and mmCIF formats),
>> +@item data on a 3D grid (electron density maps, masks, MRC/CCP4
>> format)
>> +@item crystallographic symmetry.
>> +@end enumerate")
>> +    (license license:mpl2.0)))
>> diff --git a/gnu/packages/patches/gemmi-fix-sajson-types.patch
>> b/gnu/packages/patches/gemmi-fix-sajson-types.patch
>> new file mode 100644
>> index 0000000000..9633ddac8b
>> --- /dev/null
>> +++ b/gnu/packages/patches/gemmi-fix-sajson-types.patch
>> @@ -0,0 +1,11 @@
>> +diff -ur a/include/gemmi/json.hpp b/include/gemmi/json.hpp
>> +--- a/include/gemmi/json.hpp
>> ++++ b/include/gemmi/json.hpp
>> +@@ -38,6 +38,7 @@
>> + 
>> + inline std::string as_cif_value(const sajson::value& val) {
>> +   switch (val.get_type()) {
>> ++    case sajson::TYPE_INTEGER:
>> +     case sajson::TYPE_DOUBLE:
>> +       return val.as_string();
>> +     case sajson::TYPE_NULL:
>> diff --git a/gnu/packages/patches/sajson-for-gemmi-build-with-
>> gcc10.patch b/gnu/packages/patches/sajson-for-gemmi-build-with-
>> gcc10.patch
>> new file mode 100644
>> index 0000000000..878706dc79
>> --- /dev/null
>> +++ b/gnu/packages/patches/sajson-for-gemmi-build-with-gcc10.patch
>> @@ -0,0 +1,45 @@
>> +This patch is from the upstream pull request
>> +https://github.com/chadaustin/sajson/pull/54.
>> +It fixes linking with GCC.
>> +
>> +diff --git a/include/sajson.h b/include/sajson.h
>> +index 8b4e05a..1bd045b 100644
>> +--- a/include/sajson.h
>> ++++ b/include/sajson.h
>> +@@ -138,12 +138,17 @@ constexpr inline size_t make_element(tag t,
>> size_t value) {
>> + // header. This trick courtesy of Rich Geldreich's Purple JSON
>> parser.
>> + template <typename unused = void>
>> + struct globals_struct {
>> ++    static const unsigned char parse_flags[256];
>> ++};
>> ++typedef globals_struct<> globals;
>> ++
>> + // clang-format off
>> + 
>> +     // bit 0 (1) - set if: plain ASCII string character
>> +     // bit 1 (2) - set if: whitespace
>> +     // bit 4 (0x10) - set if: 0-9 e E .
>> +-    constexpr static const uint8_t parse_flags[256] = {
>> ++    template <typename unused>
>> ++    const unsigned char globals_struct<unused>::parse_flags[256] =
>> {
>> +      // 0    1    2    3    4    5    6    7      8    9    A   
>> B    C    D    E    F
>> +         0,   0,   0,   0,   0,   0,   0,   0,     0,   2,   2,  
>> 0,   0,   2,   0,   0, // 0
>> +         0,   0,   0,   0,   0,   0,   0,   0,     0,   0,   0,  
>> 0,   0,   0,   0,   0, // 1
>> +@@ -162,15 +167,13 @@ struct globals_struct {
>> +     };
>> + 
>> + // clang-format on
>> +-};
>> +-typedef globals_struct<> globals;
>> + 
>> +-constexpr inline bool is_plain_string_character(char c) {
>> ++inline bool is_plain_string_character(char c) {
>> +     // return c >= 0x20 && c <= 0x7f && c != 0x22 && c != 0x5c;
>> +     return (globals::parse_flags[static_cast<unsigned char>(c)] &
>> 1) != 0;
>> + }
>> + 
>> +-constexpr inline bool is_whitespace(char c) {
>> ++inline bool is_whitespace(char c) {
>> +     // return c == '\r' || c == '\n' || c == '\t' || c == ' ';
>> +     return (globals::parse_flags[static_cast<unsigned char>(c)] &
>> 2) != 0;
>> + }
>> diff --git a/gnu/packages/patches/sajson-for-gemmi-numbers-as-
>> strings.patch b/gnu/packages/patches/sajson-for-gemmi-numbers-as-
>> strings.patch
>> new file mode 100644
>> index 0000000000..6f476b8583
>> --- /dev/null
>> +++ b/gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch
>> @@ -0,0 +1,195 @@
>> +Patch for gemmi: Keep numbers in JSON file as strings.
>> +
>> +Adapted from this commit of the bundled fork of sajson in gemmi:
>> +
>> https://github.com/project-gemmi/gemmi/commit/fccbca4f6040364ba708613e
>> 1429c2251872240d
>> +
>> +diff -ur a/include/sajson.h b/include/sajson.h
>> +--- a/include/sajson.h
>> ++++ b/include/sajson.h
>> +@@ -411,43 +411,6 @@
>> + };
>> + } // namespace internal
>> + 
>> +-namespace integer_storage {
>> +-enum { word_length = 1 };
>> +-
>> +-inline int load(const size_t* location) {
>> +-    int value;
>> +-    memcpy(&value, location, sizeof(value));
>> +-    return value;
>> +-}
>> +-
>> +-inline void store(size_t* location, int value) {
>> +-    // NOTE: Most modern compilers optimize away this constant-size
>> +-    // memcpy into a single instruction. If any don't, and treat
>> +-    // punning through a union as legal, they can be special-cased.
>> +-    static_assert(
>> +-        sizeof(value) <= sizeof(*location),
>> +-        "size_t must not be smaller than int");
>> +-    memcpy(location, &value, sizeof(value));
>> +-}
>> +-} // namespace integer_storage
>> +-
>> +-namespace double_storage {
>> +-enum { word_length = sizeof(double) / sizeof(size_t) };
>> +-
>> +-inline double load(const size_t* location) {
>> +-    double value;
>> +-    memcpy(&value, location, sizeof(double));
>> +-    return value;
>> +-}
>> +-
>> +-inline void store(size_t* location, double value) {
>> +-    // NOTE: Most modern compilers optimize away this constant-size
>> +-    // memcpy into a single instruction. If any don't, and treat
>> +-    // punning through a union as legal, they can be special-cased.
>> +-    memcpy(location, &value, sizeof(double));
>> +-}
>> +-} // namespace double_storage
>> +-
>> + /// Represents a JSON value.  First, call get_type() to check its
>> type,
>> + /// which determines which methods are available.
>> + ///
>> +@@ -585,70 +548,10 @@
>> +         return length;
>> +     }
>> + 
>> +-    /// If a numeric value was parsed as a 32-bit integer, returns
>> it.
>> +-    /// Only legal if get_type() is TYPE_INTEGER.
>> +-    int get_integer_value() const {
>> +-        assert_tag(tag::integer);
>> +-        return integer_storage::load(payload);
>> +-    }
>> +-
>> +-    /// If a numeric value was parsed as a double, returns it.
>> +-    /// Only legal if get_type() is TYPE_DOUBLE.
>> +-    double get_double_value() const {
>> +-        assert_tag(tag::double_);
>> +-        return double_storage::load(payload);
>> +-    }
>> +-
>> +-    /// Returns a numeric value as a double-precision float.
>> +-    /// Only legal if get_type() is TYPE_INTEGER or TYPE_DOUBLE.
>> +-    double get_number_value() const {
>> +-        assert_tag_2(tag::integer, tag::double_);
>> +-        if (value_tag == tag::integer) {
>> +-            return get_integer_value();
>> +-        } else {
>> +-            return get_double_value();
>> +-        }
>> +-    }
>> +-
>> +-    /// Returns true and writes to the output argument if the
>> numeric value
>> +-    /// fits in a 53-bit integer.  This is useful for timestamps
>> and other
>> +-    /// situations where integral values with greater than 32-bit
>> precision
>> +-    /// are used, as 64-bit values are not understood by all JSON
>> +-    /// implementations or languages.
>> +-    /// Returns false if the value is not an integer or not in
>> range.
>> +-    /// Only legal if get_type() is TYPE_INTEGER or TYPE_DOUBLE.
>> +-    bool get_int53_value(int64_t* out) const {
>> +-        // Make sure the output variable is always defined to avoid
>> any
>> +-        // possible situation like
>> +-        //
>> https://gist.github.com/chadaustin/2c249cb850619ddec05b23ca42cf7a18
>> +-        *out = 0;
>> +-
>> +-        assert_tag_2(tag::integer, tag::double_);
>> +-        switch (value_tag) {
>> +-        case tag::integer:
>> +-            *out = get_integer_value();
>> +-            return true;
>> +-        case tag::double_: {
>> +-            double v = get_double_value();
>> +-            if (v < -(1LL << 53) || v > (1LL << 53)) {
>> +-                return false;
>> +-            }
>> +-            int64_t as_int = static_cast<int64_t>(v);
>> +-            if (as_int != v) {
>> +-                return false;
>> +-            }
>> +-            *out = as_int;
>> +-            return true;
>> +-        }
>> +-        default:
>> +-            return false;
>> +-        }
>> +-    }
>> +-
>> +     /// Returns the length of the string.
>> +     /// Only legal if get_type() is TYPE_STRING.
>> +     size_t get_string_length() const {
>> +-        assert_tag(tag::string);
>> ++        assert_tag_3(tag::string, tag::integer, tag::double_);
>> +         return payload[1] - payload[0];
>> +     }
>> + 
>> +@@ -659,7 +562,7 @@
>> +     /// embedded NULs.
>> +     /// Only legal if get_type() is TYPE_STRING.
>> +     const char* as_cstring() const {
>> +-        assert_tag(tag::string);
>> ++        assert_tag_3(tag::string, tag::integer, tag::double_);
>> +         return text + payload[0];
>> +     }
>> + 
>> +@@ -667,7 +570,7 @@
>> +     /// Returns a string's value as a std::string.
>> +     /// Only legal if get_type() is TYPE_STRING.
>> +     std::string as_string() const {
>> +-        assert_tag(tag::string);
>> ++        assert_tag_3(tag::string, tag::integer, tag::double_);
>> +         return std::string(text + payload[0], text + payload[1]);
>> +     }
>> + #endif
>> +@@ -690,6 +593,10 @@
>> +         assert(e1 == value_tag || e2 == value_tag);
>> +     }
>> + 
>> ++    void assert_tag_3(tag e1, tag e2, tag e3) const {
>> ++        assert(e1 == value_tag || e2 == value_tag || e3 ==
>> value_tag);
>> ++    }
>> ++
>> +     void assert_in_bounds(size_t i) const { assert(i <
>> get_length()); }
>> + 
>> +     const tag value_tag;
>> +@@ -2059,6 +1966,8 @@
>> +     std::pair<char*, internal::tag> parse_number(char* p) {
>> +         using internal::tag;
>> + 
>> ++      size_t start = p - input.get_data();
>> ++
>> +         // Assume 32-bit, two's complement integers.
>> +         static constexpr unsigned RISKY = INT_MAX / 10u;
>> +         unsigned max_digit_after_risky = INT_MAX % 10u;
>> +@@ -2235,23 +2144,18 @@
>> +                 u = 0u - u;
>> +             }
>> +         }
>> ++
>> ++        bool success;
>> ++        size_t* out = allocator.reserve(2, &success);
>> ++        if (SAJSON_UNLIKELY(!success)) {
>> ++            return std::make_pair(oom(p, "number"), tag::null);
>> ++        }
>> ++        out[0] = start;
>> ++        out[1] = p - input.get_data();
>> ++
>> +         if (try_double) {
>> +-            bool success;
>> +-            size_t* out
>> +-                = allocator.reserve(double_storage::word_length,
>> &success);
>> +-            if (SAJSON_UNLIKELY(!success)) {
>> +-                return std::make_pair(oom(p, "double"), tag::null);
>> +-            }
>> +-            double_storage::store(out, d);
>> +             return std::make_pair(p, tag::double_);
>> +         } else {
>> +-            bool success;
>> +-            size_t* out
>> +-                = allocator.reserve(integer_storage::word_length,
>> &success);
>> +-            if (SAJSON_UNLIKELY(!success)) {
>> +-                return std::make_pair(oom(p, "integer"),
>> tag::null);
>> +-            }
>> +-            integer_storage::store(out, static_cast<int>(u));
>> +             return std::make_pair(p, tag::integer);
>> +         }
>> +     }

[bug#58261] [PATCH v2 06/13] gnu: Add gemmi.

[Liliana Marie Prikler]

Am Donnerstag, dem 13.10.2022 um 21:00 +0000 schrieb David Elsing:
> Liliana Marie Prikler <liliana.prikler@gmail.com> writes:
> 
> > Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
> > > * gnu/packages/chemistry.scm (gemmi): New variable.
> > > ---
> > >  gnu/packages/chemistry.scm                    | 118 +++++++++++
> > >  .../patches/gemmi-fix-sajson-types.patch      |  11 +
> > >  .../sajson-for-gemmi-build-with-gcc10.patch   |  45 ++++
> > >  .../sajson-for-gemmi-numbers-as-strings.patch | 195
> > > ++++++++++++++++++
> > >  4 files changed, 369 insertions(+)
> > >  create mode 100644 gnu/packages/patches/gemmi-fix-sajson-
> > > types.patch
> > >  create mode 100644 gnu/packages/patches/sajson-for-gemmi-build-
> > > with-
> > > gcc10.patch
> > >  create mode 100644 gnu/packages/patches/sajson-for-gemmi-
> > > numbers-as-
> > > strings.patch
> > > 
> > > diff --git a/gnu/packages/chemistry.scm
> > > b/gnu/packages/chemistry.scm
> > > index c517610fe8..d8f1608a3a 100644
> > > --- a/gnu/packages/chemistry.scm
> > > +++ b/gnu/packages/chemistry.scm
> > > @@ -6,6 +6,7 @@
> > >  ;;; Copyright © 2020 Björn Höfling
> > > <bjoern.hoefling@bjoernhoefling.de>
> > >  ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
> > >  ;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
> > > +;;; Copyright © 2022 David Elsing <david.elsing@posteo.net>
> > >  ;;;
> > >  ;;; This file is part of GNU Guix.
> > >  ;;;
> > > @@ -23,6 +24,7 @@
> > >  ;;; along with GNU Guix.  If not, see
> > > <http://www.gnu.org/licenses/>.
> > >  
> > >  (define-module (gnu packages chemistry)
> > > +  #:use-module (guix gexp)
> > >    #:use-module (guix packages)
> > >    #:use-module (guix utils)
> > >    #:use-module ((guix licenses) #:prefix license:)
> > > @@ -35,6 +37,7 @@ (define-module (gnu packages chemistry)
> > >    #:use-module (gnu packages boost)
> > >    #:use-module (gnu packages check)
> > >    #:use-module (gnu packages compression)
> > > +  #:use-module (gnu packages cpp)
> > >    #:use-module (gnu packages documentation)
> > >    #:use-module (gnu packages fontutils)
> > >    #:use-module (gnu packages gl)
> > > @@ -50,8 +53,10 @@ (define-module (gnu packages chemistry)
> > >    #:use-module (gnu packages qt)
> > >    #:use-module (gnu packages serialization)
> > >    #:use-module (gnu packages sphinx)
> > > +  #:use-module (gnu packages stb)
> > >    #:use-module (gnu packages xml)
> > >    #:use-module (guix build-system cmake)
> > > +  #:use-module (guix build-system copy)
> > >    #:use-module (guix build-system gnu)
> > >    #:use-module (guix build-system python))
> > >  
> > > @@ -566,3 +571,116 @@ (define-public python-pymol
> > >  used to prepare publication-quality figures, to share
> > > interactive
> > > results with
> > >  your colleagues, or to generate pre-rendered animations.")
> > >      (license license:bsd-3)))
> > > +
> > > +(define-public sajson-for-gemmi
> > > +  (package/inherit sajson
> > > +    (name "sajson-for-gemmi")
> > > +    (source (origin
> > > +              (inherit (package-source sajson))
> > > +              (patches (search-patches
> > > +                        "sajson-for-gemmi-numbers-as-
> > > strings.patch"
> > > +                        "sajson-for-gemmi-build-with-
> > > gcc10.patch"))))
> > > +    (arguments
> > > +     (substitute-keyword-arguments (package-arguments sajson)
> > > +       ((#:tests? _ #f) #f)
> > Don't forget the comment as to why they're disabled.
> > > +       ((#:phases phases)
> > > +        #~(modify-phases #$phases
> > > +            (delete 'build)))))))
> > Why is the build deleted?
> It fails due to the change and only builds the tests anyway.
> > 
> > Split here.
> > > +(define-public gemmi
> > > +  (package
> > > +    (name "gemmi")
> > > +    (version "0.5.7")
> > > +    (source (origin
> > > +              (method git-fetch)
> > > +              (uri (git-reference
> > > +                    (url
> > > "https://github.com/project-gemmi/gemmi")
> > > +                    (commit (string-append "v" version))))
> > > +              (file-name (git-file-name name version))
> > > +              (sha256
> > > +               (base32
> > > +               
> > > "00km5q726bslrw7xbfwb3f3mrsk19qbimfnl3hvr4wi1y3z8i18a"))
> > > +              (patches
> > > +               (search-patches "gemmi-fix-sajson-types.patch"))
> > > +              (modules '((guix build utils)))
> > > +              (snippet
> > > +               '(begin
> > > +                  (delete-file-recursively
> > > "include/gemmi/third_party")
> > > +                  (delete-file-recursively "third_party")))))
> > > +    (outputs '("out" "bin" "python"))
> > > +    (build-system cmake-build-system)
> > > +    (native-inputs
> > > +     (list fast-float
> > > +           optionparser
> > > +           pegtl
> > > +           pocketfft-cpp
> > > +           pybind11
> > > +           sajson-for-gemmi
> > > +           stb-sprintf
> > > +           tinydir))
> > > +    (inputs (list python zlib))
> > > +    (arguments
> > > +     (list
> > > +      #:configure-flags
> > > +      #~(let* ((python-lib
> > > +                (string-append
> > > +                 #$output:python "/lib/python"
> > > +                 #$(version-major+minor (package-version
> > > python))
> > > +                 "/site-packages")))
> > Note that python-build-system has a (site-packages) procedure. 
> > Writing
> > the boilerplate to include it in the build shouldn't be much worse
> > in
> > terms of lines than what you're doing here.
> > > +          (list "-DUSE_PYTHON=ON"
> > > +                (string-append "-DPYTHON_INSTALL_DIR=" python-
> > > lib)))
> > > +      #:phases
> > > +      #~(modify-phases %standard-phases
> > > +          (add-after 'unpack 'patch-includes
> > > +            (lambda _
> > > +              (substitute* "include/gemmi/sprintf.hpp"
> > > +                (("<stb/stb_sprintf.h>") "<stb_sprintf.h>"))
> > > +              (substitute* "include/gemmi/dirwalk.hpp"
> > > +                (("\"third_party/tinydir.h\"") "<tinydir.h>"))
> > > +              (substitute* "include/gemmi/cif.hpp"
> > > +                (("\"third_party/tao/pegtl.hpp\"")
> > > "<tao/pegtl.hpp>"))
> > > +              (substitute* "include/gemmi/json.hpp"
> > > +                (("\"third_party/sajson.h\"") "<sajson.h>"))
> > > +              (substitute* "python/gemmi.cpp"
> > > +               
> > > (("\"gemmi/third_party/tao/pegtl/parse_error.hpp\"")
> > > +                 "<tao/pegtl/parse_error.hpp>"))
> > > +              (substitute* '("include/gemmi/atof.hpp"
> > > +                             "include/gemmi/numb.hpp")
> > > +                (("\"third_party/fast_float.h\"")
> > > +                 "<fast_float/fast_float.h>"))
> > > +              (substitute* "include/gemmi/fourier.hpp"
> > > +                (("\"third_party/pocketfft_hdronly.h\"")
> > > +                 "<pocketfft_hdronly.h>"))))
> > I'd collect all the files into a (list ...) and then write out the
> > substitutes.
> Is it preferred to put list elements on separate lines (also in
> inputs)?
> 
Depends on the length, but in this case I'd say yes.
However, if things neatly fit into one line, you don't have to add a
new line.

Cheers

[bug#58261] [PATCH v2 07/13] gnu: Add freesasa.

[David Elsing]

* gnu/packages/chemistry.scm (freesasa): New variable.
---
 gnu/packages/chemistry.scm | 86 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 86 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index d8f1608a3a..681e026186 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -34,11 +34,13 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages backup)
+  #:use-module (gnu packages bison)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cpp)
   #:use-module (gnu packages documentation)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages graphviz)
@@ -54,6 +56,7 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages sphinx)
   #:use-module (gnu packages stb)
+  #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system copy)
@@ -684,3 +687,86 @@ (define-public gemmi
 @item crystallographic symmetry.
 @end enumerate")
     (license license:mpl2.0)))
+
+(define-public freesasa
+  (package
+    (name "freesasa")
+    (version "2.1.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/mittinatten/freesasa")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "07wdnahf3g355ryaiqvfxd5f4rl54wv8jwxcbn0nia89fqysbv0f"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Remove C files generated by Flex and Bison
+                  (for-each delete-file
+                            '("src/parser.c" "src/parser.h"
+                              "src/lexer.c" "src/lexer.h"))))))
+    (outputs '("out" "doc"))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      #~(list "--enable-check"
+              "--enable-parser-generator"
+              "CXXFLAGS=-std=c++17"
+              "--enable-doxygen")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'remove-libc++-linking
+            (lambda _
+              (substitute* "src/Makefile.am"
+                (("-lc\\+\\+") ""))))
+          (add-after 'unpack 'build-shared-library
+            (lambda _
+              (substitute* "src/Makefile.am"
+                (("lib_LIBRARIES") "lib_LTLIBRARIES")
+                (("libfreesasa\\.a") "libfreesasa.la")
+                (("freesasa_LDADD \\+= libfreesasa\\.la" prev)
+                 (string-append prev "\nlibfreesasa_la_LIBADD"
+                                " = -ljson-c ${libxml2_LIBS}\n"))
+                (("_a_SOURCES") "_la_SOURCES"))
+              (substitute* "configure.ac"
+                (("AC_PROG_INSTALL" inst)
+                 (string-append "AM_PROG_LIBTOOL\n" inst)))
+              (substitute* "tests/Makefile.am"
+                (("libfreesasa\\.a") "libfreesasa.la"))))
+          (add-before 'build 'build-lexer-and-parser
+            (lambda _
+              (with-directory-excursion "src"
+                (invoke "make" "lexer.h" "parser.h"))))
+          (add-after 'install 'install-doc
+            (lambda _
+              (copy-recursively
+               "doc/html"
+               (string-append #$output:doc "/share/doc/" #$name "-" #$version)))))))
+    (native-inputs
+     (list autoconf
+           automake
+           bison
+           check
+           doxygen
+           fast-float
+           flex
+           libtool
+           pegtl
+           perl
+           pkg-config))
+    (inputs
+     (list gemmi json-c libxml2))
+    (home-page "https://freesasa.github.io/")
+    (synopsis "Calculate the solvent accessible surface area (SASA) of
+molecules")
+    ;; TODO: @abbr
+    (description "FreeSASA is a command line tool and C-library for
+calculating solvent accessible surface areas.  By default Lee & Richards'
+algorithm is used, but Shrake & Rupley's is also available.  Both can be
+parameterized to arbitrary precision, and for high resolution versions of the
+algorithms, the calculations give identical results.")
+    (license license:expat)))
-- 
2.37.0

[bug#58261] [PATCH v2 08/13] gnu: Add maeparser.

[David Elsing]

* gnu/packages/chemistry.scm (maeparser): New variable.
---
 gnu/packages/chemistry.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 681e026186..6eb1e4a694 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -770,3 +770,24 @@ (define-public freesasa
 parameterized to arbitrary precision, and for high resolution versions of the
 algorithms, the calculations give identical results.")
     (license license:expat)))
+
+(define-public maeparser
+  (package
+    (name "maeparser")
+    (version "1.3.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/schrodinger/maeparser")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1yv4y5hn49fhylziigsg922bb244lb57p69r7vg9q899zd3l5b7l"))))
+    (build-system cmake-build-system)
+    (native-inputs (list boost))
+    (inputs (list zlib))
+    (home-page "https://github.com/schrodinger/maeparser")
+    (synopsis "Maestro file parser")
+    (description "maeparser is a parser for Schrodinger Maestro files.")
+    (license license:expat)))
-- 
2.37.0

[bug#58261] [PATCH v2 09/13] gnu: Add coordgenlibs.

[David Elsing]

* gnu/packages/chemistry.scm (coordgenlibs): New variable.
---
 gnu/packages/chemistry.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 6eb1e4a694..1510cbab41 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -791,3 +791,30 @@ (define-public maeparser
     (synopsis "Maestro file parser")
     (description "maeparser is a parser for Schrodinger Maestro files.")
     (license license:expat)))
+
+(define-public coordgenlibs
+  (package
+    (name "coordgenlibs")
+    (version "3.0.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/schrodinger/coordgenlibs/")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0d09x3v38i9y184bml020bq7xizdrdwng38qmdxlplzfhqkjdidv"))))
+    (build-system cmake-build-system)
+    (native-inputs (list boost))
+    (inputs (list maeparser))
+    (arguments
+     (list
+      #:configure-flags
+      #~(list "-DCOORDGEN_RIGOROUS_BUILD=OFF"
+              "-DCOORDGEN_USE_MAEPARSER=ON")))
+    (home-page "https://github.com/schrodinger/coordgenlibs/")
+    (synopsis "2D coordinate generation")
+    (description "@code{coordgenlibs} contains algorithms to generate 2D
+coordinates.  It has an emphasis on quality rather than speed.")
+    (license license:bsd-3)))
-- 
2.37.0

[bug#58261] [PATCH v2 09/13] gnu: Add coordgenlibs.

[Liliana Marie Prikler]

Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
> * gnu/packages/chemistry.scm (coordgenlibs): New variable.
> ---
>  gnu/packages/chemistry.scm | 27 +++++++++++++++++++++++++++
>  1 file changed, 27 insertions(+)
> 
> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
> index 6eb1e4a694..1510cbab41 100644
> --- a/gnu/packages/chemistry.scm
> +++ b/gnu/packages/chemistry.scm
> @@ -791,3 +791,30 @@ (define-public maeparser
>      (synopsis "Maestro file parser")
>      (description "maeparser is a parser for Schrodinger Maestro
> files.")
>      (license license:expat)))
> +
> +(define-public coordgenlibs
> +  (package
> +    (name "coordgenlibs")
> +    (version "3.0.1")
> +    (source (origin
> +              (method git-fetch)
> +              (uri (git-reference
> +                    (url
> "https://github.com/schrodinger/coordgenlibs/")
> +                    (commit (string-append "v" version))))
> +              (file-name (git-file-name name version))
> +              (sha256
> +               (base32
> +               
> "0d09x3v38i9y184bml020bq7xizdrdwng38qmdxlplzfhqkjdidv"))))
> +    (build-system cmake-build-system)
> +    (native-inputs (list boost))
> +    (inputs (list maeparser))
> +    (arguments
> +     (list
> +      #:configure-flags
> +      #~(list "-DCOORDGEN_RIGOROUS_BUILD=OFF"
> +              "-DCOORDGEN_USE_MAEPARSER=ON")))
> +    (home-page "https://github.com/schrodinger/coordgenlibs/")
> +    (synopsis "2D coordinate generation")
> +    (description "@code{coordgenlibs} contains algorithms to
> generate 2D
> +coordinates.  It has an emphasis on quality rather than speed.")
It emphasises quality over speed.  That being said, is it that hard to
generate points?  What's the full context here?
> +    (license license:bsd-3)))

[bug#58261] [PATCH v2 09/13] gnu: Add coordgenlibs.

[David Elsing]

Liliana Marie Prikler <liliana.prikler@gmail.com> writes:

> Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
>> * gnu/packages/chemistry.scm (coordgenlibs): New variable.
>> ---
>>  gnu/packages/chemistry.scm | 27 +++++++++++++++++++++++++++
>>  1 file changed, 27 insertions(+)
>> 
>> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
>> index 6eb1e4a694..1510cbab41 100644
>> --- a/gnu/packages/chemistry.scm
>> +++ b/gnu/packages/chemistry.scm
>> @@ -791,3 +791,30 @@ (define-public maeparser
>>      (synopsis "Maestro file parser")
>>      (description "maeparser is a parser for Schrodinger Maestro
>> files.")
>>      (license license:expat)))
>> +
>> +(define-public coordgenlibs
>> +  (package
>> +    (name "coordgenlibs")
>> +    (version "3.0.1")
>> +    (source (origin
>> +              (method git-fetch)
>> +              (uri (git-reference
>> +                    (url
>> "https://github.com/schrodinger/coordgenlibs/")
>> +                    (commit (string-append "v" version))))
>> +              (file-name (git-file-name name version))
>> +              (sha256
>> +               (base32
>> +               
>> "0d09x3v38i9y184bml020bq7xizdrdwng38qmdxlplzfhqkjdidv"))))
>> +    (build-system cmake-build-system)
>> +    (native-inputs (list boost))
>> +    (inputs (list maeparser))
>> +    (arguments
>> +     (list
>> +      #:configure-flags
>> +      #~(list "-DCOORDGEN_RIGOROUS_BUILD=OFF"
>> +              "-DCOORDGEN_USE_MAEPARSER=ON")))
>> +    (home-page "https://github.com/schrodinger/coordgenlibs/")
>> +    (synopsis "2D coordinate generation")
>> +    (description "@code{coordgenlibs} contains algorithms to
>> generate 2D
>> +coordinates.  It has an emphasis on quality rather than speed.")
> It emphasises quality over speed.  That being said, is it that hard to
> generate points?  What's the full context here?
Ah, it's 2D coordinates for molecules. :)
>> +    (license license:bsd-3)))

[bug#58261] [PATCH v2 10/13] gnu: Add yaehmop-tightbind.

[David Elsing]

* gnu/packages/chemistry.scm (yaehmop-tightbind): New variable.
---
 gnu/packages/chemistry.scm | 110 +++++++++++++++++++++++++++++++++++++
 1 file changed, 110 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 1510cbab41..68d28a52c3 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -42,6 +42,7 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
+  #:use-module (gnu packages gcc)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages gv)
@@ -56,6 +57,7 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages sphinx)
   #:use-module (gnu packages stb)
+  #:use-module (gnu packages tex)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
   #:use-module (guix build-system cmake)
@@ -818,3 +820,111 @@ (define-public coordgenlibs
     (description "@code{coordgenlibs} contains algorithms to generate 2D
 coordinates.  It has an emphasis on quality rather than speed.")
     (license license:bsd-3)))
+
+(define-public yaehmop
+  (package
+    (name "yaehmop")
+    (version "2022.09.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/greglandrum/yaehmop")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1x0d75m1hgdb411fiv7c5bwq1n4y0swrll0gigh8v5c73kjxrja0"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Separate program
+                  (delete-file-recursively "viewkel")
+                  ;; Remove example output (some are corrupted)
+                  (for-each delete-file (find-files "examples" "\\.Z$"))
+                  ;; Documentation outputs
+                  (for-each delete-file (find-files "docs" "\\.(ps|pdf)$"))
+                  ;; These are transpiled from Fortran to C, but we build the
+                  ;; Fortran code instead
+                  (delete-file-recursively "tightbind/f2c_files")
+                  (delete-file "tightbind/diag.c")
+                  (delete-file "tightbind/cboris.c")
+                  (delete-file "tightbind/abfns.c")
+                  (delete-file "tightbind/lovlap.c")))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      #~(list
+         "-DUSE_BLAS_LAPACK=ON"
+         (string-append "-DPARM_FILE_LOC=" #$output
+                        "/share/" #$name "-" #$version "/eht_parms.dat")
+         "-DBIND_EXE_NAME=yaehmop-bind")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'chdir
+            (lambda _
+              (chdir "tightbind")))
+          (add-after 'chdir 'patch-fortran-functions
+            (lambda _
+              (substitute* '("mov.c" "prototypes.h")
+                (("lovlap\\(") "lovlap_(")
+                (("abfns\\(") "abfns_("))))
+          (add-after 'chdir 'patch-cmake
+            (lambda _
+              (substitute* "CMakeLists.txt"
+                (("project\\(yaehmop C\\)") "project(yaehmop C Fortran)")
+                (("abfns.c") "fortran77/abfns.f")
+                (("lovlap.c") "fortran77/lovlap.f")
+                (("(set\\(PARM_FILE_LOC.*)\\)" all init)
+                 (string-append init " CACHE STRING \"\")"))
+                (("add_library\\(yaehmop_eht" lib)
+                 (string-append lib " SHARED "))
+                (("target_link_libraries\\(test_eht \\$\\{LAPACK_LIBRARIES\\}.*"
+                  all)
+                 (string-append all "\ntarget_link_libraries(yaehmop_eht "
+                                "${LAPACK_LIBRARIES})\n")))))
+          (add-after 'build 'fix-latex
+            (lambda _
+              (chdir "../docs")
+              (substitute* "bind_manual.tex"
+                (("\\\\usepackage\\{bindpage\\}")
+                 (string-append
+                  "\\usepackage[left=2cm,right=2cm,top=4cm,bottom=2cm]"
+                  "{geometry}")))
+              (substitute* "Zmat_appendix.tex"
+                (("file=dihedral\\.eps")
+                 "file=figs/dihedral.eps"))))
+          (add-after 'fix-latex 'build-doc
+            (lambda _
+              ;; TODO: not reproducible
+              (setenv "FORCE_SOURCE_DATE" "1")
+              ;; Needs to run twice to compile completely
+              (invoke "pdflatex" "bind_manual.tex")
+              (invoke "pdflatex" "bind_manual.tex")
+              (chdir "../build")))
+          (add-after 'install 'install-eht-parms
+            (lambda _
+              (install-file "../tightbind/eht_parms.dat"
+                            (string-append #$output "/share/"
+                                           #$name "-" #$version))))
+          (add-after 'install-eht-parms 'install-doc
+            (lambda _
+              (install-file "../docs/bind_manual.pdf"
+                            (string-append #$output "/share/doc/"
+                                           #$name "-" #$version))))
+          (delete 'check)
+          (add-after 'install-doc 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (invoke "./test_eht")))))))
+    (native-inputs
+     `(("gfortran" ,gfortran)
+       ("texlive" ,(texlive-updmap.cfg (list texlive-fonts-ec
+                                             texlive-latex-graphics
+                                             texlive-latex-geometry)))))
+    (inputs (list openblas))
+    (home-page "https://github.com/greglandrum/yaehmop")
+    (synopsis "Yet Another extended Hueckel Molecular Orbital Package")
+    (description "@code{YAeHMOP} contains a program and library for performing
+extended Hückel calculations.")
+    (license license:bsd-2)))
-- 
2.37.0

[bug#58261] [PATCH v2 10/13] gnu: Add yaehmop-tightbind.

[Liliana Marie Prikler]

Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
> * gnu/packages/chemistry.scm (yaehmop-tightbind): New variable.
Don't forget to update the ChangeLog.
> ---
>  gnu/packages/chemistry.scm | 110
> +++++++++++++++++++++++++++++++++++++
>  1 file changed, 110 insertions(+)
> 
> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
> index 1510cbab41..68d28a52c3 100644
> --- a/gnu/packages/chemistry.scm
> +++ b/gnu/packages/chemistry.scm
> @@ -42,6 +42,7 @@ (define-module (gnu packages chemistry)
>    #:use-module (gnu packages documentation)
>    #:use-module (gnu packages flex)
>    #:use-module (gnu packages fontutils)
> +  #:use-module (gnu packages gcc)
>    #:use-module (gnu packages gl)
>    #:use-module (gnu packages graphviz)
>    #:use-module (gnu packages gv)
> @@ -56,6 +57,7 @@ (define-module (gnu packages chemistry)
>    #:use-module (gnu packages serialization)
>    #:use-module (gnu packages sphinx)
>    #:use-module (gnu packages stb)
> +  #:use-module (gnu packages tex)
>    #:use-module (gnu packages web)
>    #:use-module (gnu packages xml)
>    #:use-module (guix build-system cmake)
> @@ -818,3 +820,111 @@ (define-public coordgenlibs
>      (description "@code{coordgenlibs} contains algorithms to
> generate 2D
>  coordinates.  It has an emphasis on quality rather than speed.")
>      (license license:bsd-3)))
> +
> +(define-public yaehmop
> +  (package
> +    (name "yaehmop")
> +    (version "2022.09.1")
> +    (source (origin
> +              (method git-fetch)
> +              (uri (git-reference
> +                    (url "https://github.com/greglandrum/yaehmop")
> +                    (commit (string-append "v" version))))
> +              (file-name (git-file-name name version))
> +              (sha256
> +               (base32
> +               
> "1x0d75m1hgdb411fiv7c5bwq1n4y0swrll0gigh8v5c73kjxrja0"))
> +              (modules '((guix build utils)))
> +              (snippet
> +               '(begin
> +                  ;; Separate program
> +                  (delete-file-recursively "viewkel")
> +                  ;; Remove example output (some are corrupted)
> +                  (for-each delete-file (find-files "examples"
> "\\.Z$"))
> +                  ;; Documentation outputs
> +                  (for-each delete-file (find-files "docs"
> "\\.(ps|pdf)$"))
> +                  ;; These are transpiled from Fortran to C, but we
> build the
> +                  ;; Fortran code instead
> +                  (delete-file-recursively "tightbind/f2c_files")
> +                  (delete-file "tightbind/diag.c")
> +                  (delete-file "tightbind/cboris.c")
> +                  (delete-file "tightbind/abfns.c")
> +                  (delete-file "tightbind/lovlap.c")))))
> +    (build-system cmake-build-system)
> +    (arguments
> +     (list
> +      #:configure-flags
> +      #~(list
> +         "-DUSE_BLAS_LAPACK=ON"
> +         (string-append "-DPARM_FILE_LOC=" #$output
> +                        "/share/" #$name "-" #$version
> "/eht_parms.dat")
> +         "-DBIND_EXE_NAME=yaehmop-bind")
> +      #:phases
> +      #~(modify-phases %standard-phases
> +          (add-after 'unpack 'chdir
> +            (lambda _
> +              (chdir "tightbind")))
> +          (add-after 'chdir 'patch-fortran-functions
> +            (lambda _
> +              (substitute* '("mov.c" "prototypes.h")
> +                (("lovlap\\(") "lovlap_(")
> +                (("abfns\\(") "abfns_("))))
> +          (add-after 'chdir 'patch-cmake
> +            (lambda _
> +              (substitute* "CMakeLists.txt"
> +                (("project\\(yaehmop C\\)") "project(yaehmop C
> Fortran)")
> +                (("abfns.c") "fortran77/abfns.f")
> +                (("lovlap.c") "fortran77/lovlap.f")
> +                (("(set\\(PARM_FILE_LOC.*)\\)" all init)
> +                 (string-append init " CACHE STRING \"\")"))
> +                (("add_library\\(yaehmop_eht" lib)
> +                 (string-append lib " SHARED "))
> +                (("target_link_libraries\\(test_eht
> \\$\\{LAPACK_LIBRARIES\\}.*"
> +                  all)
> +                 (string-append all
> "\ntarget_link_libraries(yaehmop_eht "
> +                                "${LAPACK_LIBRARIES})\n")))))
> +          (add-after 'build 'fix-latex
> +            (lambda _
> +              (chdir "../docs")
> +              (substitute* "bind_manual.tex"
> +                (("\\\\usepackage\\{bindpage\\}")
> +                 (string-append
> +                 
> "\\usepackage[left=2cm,right=2cm,top=4cm,bottom=2cm]"
> +                  "{geometry}")))
> +              (substitute* "Zmat_appendix.tex"
> +                (("file=dihedral\\.eps")
> +                 "file=figs/dihedral.eps"))))
> +          (add-after 'fix-latex 'build-doc
> +            (lambda _
> +              ;; TODO: not reproducible
> +              (setenv "FORCE_SOURCE_DATE" "1")
> +              ;; Needs to run twice to compile completely
> +              (invoke "pdflatex" "bind_manual.tex")
> +              (invoke "pdflatex" "bind_manual.tex")
> +              (chdir "../build")))
Note that we have rubber to automate building PDFs.  Also prefer "with-
directory-excursion" over chdir where possible.
> +          (add-after 'install 'install-eht-parms
> +            (lambda _
> +              (install-file "../tightbind/eht_parms.dat"
> +                            (string-append #$output "/share/"
> +                                           #$name "-" #$version))))
> +          (add-after 'install-eht-parms 'install-doc
> +            (lambda _
> +              (install-file "../docs/bind_manual.pdf"
> +                            (string-append #$output "/share/doc/"
> +                                           #$name "-" #$version))))
> +          (delete 'check)
> +          (add-after 'install-doc 'check
> +            (lambda* (#:key tests? #:allow-other-keys)
> +              (when tests?
> +                (invoke "./test_eht")))))))
> +    (native-inputs
> +     `(("gfortran" ,gfortran)
> +       ("texlive" ,(texlive-updmap.cfg (list texlive-fonts-ec
> +                                             texlive-latex-graphics
> +                                             texlive-latex-
> geometry)))))
I think you can do without labels here (see my comment regarding
rubber).
> +    (inputs (list openblas))
> +    (home-page "https://github.com/greglandrum/yaehmop")
> +    (synopsis "Yet Another extended Hueckel Molecular Orbital
> Package")
You can use this as an @acronym in the description.  For the synopsis,
I'd use something else, e.g. "Perform Hückel calculations".
> +    (description "@code{YAeHMOP} contains a program and library for
> performing
> +extended Hückel calculations.")
I recommend adding "and analyzing and visualizing the results." (see
plug_it.tex)
> +    (license license:bsd-2)))

Cheers

[bug#58261] [PATCH v2 10/13] gnu: Add yaehmop-tightbind.

[David Elsing]

Liliana Marie Prikler <liliana.prikler@gmail.com> writes:

> Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
>> * gnu/packages/chemistry.scm (yaehmop-tightbind): New variable.
> Don't forget to update the ChangeLog.
Ah thanks. :)
>> ---
>>  gnu/packages/chemistry.scm | 110
>> +++++++++++++++++++++++++++++++++++++
>>  1 file changed, 110 insertions(+)
>> 
>> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
>> index 1510cbab41..68d28a52c3 100644
>> --- a/gnu/packages/chemistry.scm
>> +++ b/gnu/packages/chemistry.scm
>> @@ -42,6 +42,7 @@ (define-module (gnu packages chemistry)
>>    #:use-module (gnu packages documentation)
>>    #:use-module (gnu packages flex)
>>    #:use-module (gnu packages fontutils)
>> +  #:use-module (gnu packages gcc)
>>    #:use-module (gnu packages gl)
>>    #:use-module (gnu packages graphviz)
>>    #:use-module (gnu packages gv)
>> @@ -56,6 +57,7 @@ (define-module (gnu packages chemistry)
>>    #:use-module (gnu packages serialization)
>>    #:use-module (gnu packages sphinx)
>>    #:use-module (gnu packages stb)
>> +  #:use-module (gnu packages tex)
>>    #:use-module (gnu packages web)
>>    #:use-module (gnu packages xml)
>>    #:use-module (guix build-system cmake)
>> @@ -818,3 +820,111 @@ (define-public coordgenlibs
>>      (description "@code{coordgenlibs} contains algorithms to
>> generate 2D
>>  coordinates.  It has an emphasis on quality rather than speed.")
>>      (license license:bsd-3)))
>> +
>> +(define-public yaehmop
>> +  (package
>> +    (name "yaehmop")
>> +    (version "2022.09.1")
>> +    (source (origin
>> +              (method git-fetch)
>> +              (uri (git-reference
>> +                    (url "https://github.com/greglandrum/yaehmop")
>> +                    (commit (string-append "v" version))))
>> +              (file-name (git-file-name name version))
>> +              (sha256
>> +               (base32
>> +               
>> "1x0d75m1hgdb411fiv7c5bwq1n4y0swrll0gigh8v5c73kjxrja0"))
>> +              (modules '((guix build utils)))
>> +              (snippet
>> +               '(begin
>> +                  ;; Separate program
>> +                  (delete-file-recursively "viewkel")
>> +                  ;; Remove example output (some are corrupted)
>> +                  (for-each delete-file (find-files "examples"
>> "\\.Z$"))
>> +                  ;; Documentation outputs
>> +                  (for-each delete-file (find-files "docs"
>> "\\.(ps|pdf)$"))
>> +                  ;; These are transpiled from Fortran to C, but we
>> build the
>> +                  ;; Fortran code instead
>> +                  (delete-file-recursively "tightbind/f2c_files")
>> +                  (delete-file "tightbind/diag.c")
>> +                  (delete-file "tightbind/cboris.c")
>> +                  (delete-file "tightbind/abfns.c")
>> +                  (delete-file "tightbind/lovlap.c")))))
>> +    (build-system cmake-build-system)
>> +    (arguments
>> +     (list
>> +      #:configure-flags
>> +      #~(list
>> +         "-DUSE_BLAS_LAPACK=ON"
>> +         (string-append "-DPARM_FILE_LOC=" #$output
>> +                        "/share/" #$name "-" #$version
>> "/eht_parms.dat")
>> +         "-DBIND_EXE_NAME=yaehmop-bind")
>> +      #:phases
>> +      #~(modify-phases %standard-phases
>> +          (add-after 'unpack 'chdir
>> +            (lambda _
>> +              (chdir "tightbind")))
>> +          (add-after 'chdir 'patch-fortran-functions
>> +            (lambda _
>> +              (substitute* '("mov.c" "prototypes.h")
>> +                (("lovlap\\(") "lovlap_(")
>> +                (("abfns\\(") "abfns_("))))
>> +          (add-after 'chdir 'patch-cmake
>> +            (lambda _
>> +              (substitute* "CMakeLists.txt"
>> +                (("project\\(yaehmop C\\)") "project(yaehmop C
>> Fortran)")
>> +                (("abfns.c") "fortran77/abfns.f")
>> +                (("lovlap.c") "fortran77/lovlap.f")
>> +                (("(set\\(PARM_FILE_LOC.*)\\)" all init)
>> +                 (string-append init " CACHE STRING \"\")"))
>> +                (("add_library\\(yaehmop_eht" lib)
>> +                 (string-append lib " SHARED "))
>> +                (("target_link_libraries\\(test_eht
>> \\$\\{LAPACK_LIBRARIES\\}.*"
>> +                  all)
>> +                 (string-append all
>> "\ntarget_link_libraries(yaehmop_eht "
>> +                                "${LAPACK_LIBRARIES})\n")))))
>> +          (add-after 'build 'fix-latex
>> +            (lambda _
>> +              (chdir "../docs")
>> +              (substitute* "bind_manual.tex"
>> +                (("\\\\usepackage\\{bindpage\\}")
>> +                 (string-append
>> +                 
>> "\\usepackage[left=2cm,right=2cm,top=4cm,bottom=2cm]"
>> +                  "{geometry}")))
>> +              (substitute* "Zmat_appendix.tex"
>> +                (("file=dihedral\\.eps")
>> +                 "file=figs/dihedral.eps"))))
>> +          (add-after 'fix-latex 'build-doc
>> +            (lambda _
>> +              ;; TODO: not reproducible
>> +              (setenv "FORCE_SOURCE_DATE" "1")
>> +              ;; Needs to run twice to compile completely
>> +              (invoke "pdflatex" "bind_manual.tex")
>> +              (invoke "pdflatex" "bind_manual.tex")
>> +              (chdir "../build")))
> Note that we have rubber to automate building PDFs.  Also prefer "with-
> directory-excursion" over chdir where possible.
I used latexmk as it's already included in texlive-bin
(it is also reproducible with \pdfsuppressptexinfo=-1).
>> +          (add-after 'install 'install-eht-parms
>> +            (lambda _
>> +              (install-file "../tightbind/eht_parms.dat"
>> +                            (string-append #$output "/share/"
>> +                                           #$name "-" #$version))))
>> +          (add-after 'install-eht-parms 'install-doc
>> +            (lambda _
>> +              (install-file "../docs/bind_manual.pdf"
>> +                            (string-append #$output "/share/doc/"
>> +                                           #$name "-" #$version))))
>> +          (delete 'check)
>> +          (add-after 'install-doc 'check
>> +            (lambda* (#:key tests? #:allow-other-keys)
>> +              (when tests?
>> +                (invoke "./test_eht")))))))
>> +    (native-inputs
>> +     `(("gfortran" ,gfortran)
>> +       ("texlive" ,(texlive-updmap.cfg (list texlive-fonts-ec
>> +                                             texlive-latex-graphics
>> +                                             texlive-latex-
>> geometry)))))
> I think you can do without labels here (see my comment regarding
> rubber).
>> +    (inputs (list openblas))
>> +    (home-page "https://github.com/greglandrum/yaehmop")
>> +    (synopsis "Yet Another extended Hueckel Molecular Orbital
>> Package")
> You can use this as an @acronym in the description.  For the synopsis,
> I'd use something else, e.g. "Perform Hückel calculations".
>> +    (description "@code{YAeHMOP} contains a program and library for
>> performing
>> +extended Hückel calculations.")
> I recommend adding "and analyzing and visualizing the results." (see
> plug_it.tex)
The visualization program is not built, so maybe without visualizing?
>> +    (license license:bsd-2)))
>
> Cheers

[bug#58261] [PATCH v2 10/13] gnu: Add yaehmop-tightbind.

[Liliana Marie Prikler]

Am Donnerstag, dem 13.10.2022 um 21:00 +0000 schrieb David Elsing:
> Liliana Marie Prikler <liliana.prikler@gmail.com> writes:
> 
> > Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
> > > * gnu/packages/chemistry.scm (yaehmop-tightbind): New variable.
> > Don't forget to update the ChangeLog.
> Ah thanks. :)
> > > ---
> > >  gnu/packages/chemistry.scm | 110
> > > +++++++++++++++++++++++++++++++++++++
> > >  1 file changed, 110 insertions(+)
> > > 
> > > diff --git a/gnu/packages/chemistry.scm
> > > b/gnu/packages/chemistry.scm
> > > index 1510cbab41..68d28a52c3 100644
> > > --- a/gnu/packages/chemistry.scm
> > > +++ b/gnu/packages/chemistry.scm
> > > @@ -42,6 +42,7 @@ (define-module (gnu packages chemistry)
> > >    #:use-module (gnu packages documentation)
> > >    #:use-module (gnu packages flex)
> > >    #:use-module (gnu packages fontutils)
> > > +  #:use-module (gnu packages gcc)
> > >    #:use-module (gnu packages gl)
> > >    #:use-module (gnu packages graphviz)
> > >    #:use-module (gnu packages gv)
> > > @@ -56,6 +57,7 @@ (define-module (gnu packages chemistry)
> > >    #:use-module (gnu packages serialization)
> > >    #:use-module (gnu packages sphinx)
> > >    #:use-module (gnu packages stb)
> > > +  #:use-module (gnu packages tex)
> > >    #:use-module (gnu packages web)
> > >    #:use-module (gnu packages xml)
> > >    #:use-module (guix build-system cmake)
> > > @@ -818,3 +820,111 @@ (define-public coordgenlibs
> > >      (description "@code{coordgenlibs} contains algorithms to
> > > generate 2D
> > >  coordinates.  It has an emphasis on quality rather than speed.")
> > >      (license license:bsd-3)))
> > > +
> > > +(define-public yaehmop
> > > +  (package
> > > +    (name "yaehmop")
> > > +    (version "2022.09.1")
> > > +    (source (origin
> > > +              (method git-fetch)
> > > +              (uri (git-reference
> > > +                    (url
> > > "https://github.com/greglandrum/yaehmop")
> > > +                    (commit (string-append "v" version))))
> > > +              (file-name (git-file-name name version))
> > > +              (sha256
> > > +               (base32
> > > +               
> > > "1x0d75m1hgdb411fiv7c5bwq1n4y0swrll0gigh8v5c73kjxrja0"))
> > > +              (modules '((guix build utils)))
> > > +              (snippet
> > > +               '(begin
> > > +                  ;; Separate program
> > > +                  (delete-file-recursively "viewkel")
> > > +                  ;; Remove example output (some are corrupted)
> > > +                  (for-each delete-file (find-files "examples"
> > > "\\.Z$"))
> > > +                  ;; Documentation outputs
> > > +                  (for-each delete-file (find-files "docs"
> > > "\\.(ps|pdf)$"))
> > > +                  ;; These are transpiled from Fortran to C, but
> > > we
> > > build the
> > > +                  ;; Fortran code instead
> > > +                  (delete-file-recursively
> > > "tightbind/f2c_files")
> > > +                  (delete-file "tightbind/diag.c")
> > > +                  (delete-file "tightbind/cboris.c")
> > > +                  (delete-file "tightbind/abfns.c")
> > > +                  (delete-file "tightbind/lovlap.c")))))
> > > +    (build-system cmake-build-system)
> > > +    (arguments
> > > +     (list
> > > +      #:configure-flags
> > > +      #~(list
> > > +         "-DUSE_BLAS_LAPACK=ON"
> > > +         (string-append "-DPARM_FILE_LOC=" #$output
> > > +                        "/share/" #$name "-" #$version
> > > "/eht_parms.dat")
> > > +         "-DBIND_EXE_NAME=yaehmop-bind")
> > > +      #:phases
> > > +      #~(modify-phases %standard-phases
> > > +          (add-after 'unpack 'chdir
> > > +            (lambda _
> > > +              (chdir "tightbind")))
> > > +          (add-after 'chdir 'patch-fortran-functions
> > > +            (lambda _
> > > +              (substitute* '("mov.c" "prototypes.h")
> > > +                (("lovlap\\(") "lovlap_(")
> > > +                (("abfns\\(") "abfns_("))))
> > > +          (add-after 'chdir 'patch-cmake
> > > +            (lambda _
> > > +              (substitute* "CMakeLists.txt"
> > > +                (("project\\(yaehmop C\\)") "project(yaehmop C
> > > Fortran)")
> > > +                (("abfns.c") "fortran77/abfns.f")
> > > +                (("lovlap.c") "fortran77/lovlap.f")
> > > +                (("(set\\(PARM_FILE_LOC.*)\\)" all init)
> > > +                 (string-append init " CACHE STRING \"\")"))
> > > +                (("add_library\\(yaehmop_eht" lib)
> > > +                 (string-append lib " SHARED "))
> > > +                (("target_link_libraries\\(test_eht
> > > \\$\\{LAPACK_LIBRARIES\\}.*"
> > > +                  all)
> > > +                 (string-append all
> > > "\ntarget_link_libraries(yaehmop_eht "
> > > +                                "${LAPACK_LIBRARIES})\n")))))
> > > +          (add-after 'build 'fix-latex
> > > +            (lambda _
> > > +              (chdir "../docs")
> > > +              (substitute* "bind_manual.tex"
> > > +                (("\\\\usepackage\\{bindpage\\}")
> > > +                 (string-append
> > > +                 
> > > "\\usepackage[left=2cm,right=2cm,top=4cm,bottom=2cm]"
> > > +                  "{geometry}")))
> > > +              (substitute* "Zmat_appendix.tex"
> > > +                (("file=dihedral\\.eps")
> > > +                 "file=figs/dihedral.eps"))))
> > > +          (add-after 'fix-latex 'build-doc
> > > +            (lambda _
> > > +              ;; TODO: not reproducible
> > > +              (setenv "FORCE_SOURCE_DATE" "1")
> > > +              ;; Needs to run twice to compile completely
> > > +              (invoke "pdflatex" "bind_manual.tex")
> > > +              (invoke "pdflatex" "bind_manual.tex")
> > > +              (chdir "../build")))
> > Note that we have rubber to automate building PDFs.  Also prefer
> > "with-
> > directory-excursion" over chdir where possible.
> I used latexmk as it's already included in texlive-bin
> (it is also reproducible with \pdfsuppressptexinfo=-1).
> > > +          (add-after 'install 'install-eht-parms
> > > +            (lambda _
> > > +              (install-file "../tightbind/eht_parms.dat"
> > > +                            (string-append #$output "/share/"
> > > +                                           #$name "-"
> > > #$version))))
> > > +          (add-after 'install-eht-parms 'install-doc
> > > +            (lambda _
> > > +              (install-file "../docs/bind_manual.pdf"
> > > +                            (string-append #$output
> > > "/share/doc/"
> > > +                                           #$name "-"
> > > #$version))))
> > > +          (delete 'check)
> > > +          (add-after 'install-doc 'check
> > > +            (lambda* (#:key tests? #:allow-other-keys)
> > > +              (when tests?
> > > +                (invoke "./test_eht")))))))
> > > +    (native-inputs
> > > +     `(("gfortran" ,gfortran)
> > > +       ("texlive" ,(texlive-updmap.cfg (list texlive-fonts-ec
> > > +                                             texlive-latex-
> > > graphics
> > > +                                             texlive-latex-
> > > geometry)))))
> > I think you can do without labels here (see my comment regarding
> > rubber).
> > > +    (inputs (list openblas))
> > > +    (home-page "https://github.com/greglandrum/yaehmop")
> > > +    (synopsis "Yet Another extended Hueckel Molecular Orbital
> > > Package")
> > You can use this as an @acronym in the description.  For the
> > synopsis,
> > I'd use something else, e.g. "Perform Hückel calculations".
> > > +    (description "@code{YAeHMOP} contains a program and library
> > > for
> > > performing
> > > +extended Hückel calculations.")
> > I recommend adding "and analyzing and visualizing the results."
> > (see
> > plug_it.tex)
> The visualization program is not built, so maybe without visualizing?
SGTM

[bug#58261] [PATCH v2 11/13] gnu: Add avalontoolkit.

[David Elsing]

* gnu/packages/chemistry.scm (avalontoolkit): New variable.
---
 gnu/packages/chemistry.scm | 93 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 93 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 68d28a52c3..e52dd2f3b6 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -928,3 +928,96 @@ (define-public yaehmop
     (description "@code{YAeHMOP} contains a program and library for performing
 extended Hückel calculations.")
     (license license:bsd-2)))
+
+(define-public avalontoolkit
+  (package
+    (name "avalontoolkit")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "mirror://sourceforge/avalontoolkit/"
+             "AvalonToolkit_" (substring version 0 3) "/AvalonToolkit_"
+             version ".source.tar"))
+       (sha256
+        (base32
+         "0rnnyy6axs2da7aa4q6l30ldavbk49v6l22llj1adn74h1i67bpv"))
+       (modules '((guix build utils) (ice-9 ftw)))
+       (snippet
+        #~(begin
+            (chdir "..")
+            (delete-file-recursively "SourceDistribution/java")))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      ;; There are no tests
+      #:tests? #f
+      #:phases
+      #~(let ((programs '("canonizer" "matchtest" "smi2mol" "struchk")))
+          (modify-phases %standard-phases
+            (delete 'configure)
+            (add-before 'build 'remove-free
+              (lambda _
+                ;; Remove incorrect free of getenv result (patch also in rdkit)
+                (substitute* "common/reaccsio.c"
+                  (("MyFree.*tempdir.*") ""))))
+            (replace 'build
+              (lambda _
+                (chdir "common")
+                (let* ((parts
+                        (list
+                         "aacheck" "casutils" "denormal" "depictutil"
+                         "didepict" "fixcharges" "forio" "geometry" "graph"
+                         "hashcode" "layout" "local" "patclean" "pattern"
+                         "perceive" "reaccsio" "rtutils" "set" "shortcut"
+                         "sketch" "ssmatch" "stereo" "symbol_lists"
+                         "symboltable" "utilities"))
+                       (objects (map (lambda (name) (string-append name ".o"))
+                                     parts)))
+                  (for-each
+                   (lambda (name)
+                     (display (string-append "Compiling " name ".c\n"))
+                     (invoke "gcc" "-c" "-fPIC" "-O2"
+                             (string-append name ".c")
+                             "-o" (string-append name ".o")))
+                   parts)
+                  (display "Building shared library\n")
+                  (apply invoke "gcc" "-fPIC" "-shared" "-lm"
+                         "-o" "libavalontoolkit.so"
+                         "canonizer.c" "smi2mol.c" "struchk.c" objects)
+                  (for-each
+                   (lambda (program)
+                     (display (string-append "Building " program "\n"))
+                     (invoke "gcc" "-L." "-lavalontoolkit" "-lm" "-O2"
+                             (string-append "-Wl,-rpath=" #$output "/lib")
+                             "-DMAIN" (string-append program ".c") "-o" program))
+                   programs))))
+            (replace 'install
+              (lambda _
+                ;; Executables
+                (for-each
+                 (lambda (program)
+                   (install-file program (string-append #$output "/bin")))
+                 programs)
+                (for-each
+                 (lambda (name)
+                   (symlink (string-append #$output "/bin/smi2mol")
+                            (string-append #$output "/bin/" name)))
+                 '("mol2smi" "rdf2smi" "mol2tbl" "mol2sma" "smi2rdf"))
+                ;; Library
+                (install-file "libavalontoolkit.so" (string-append #$output "/lib"))
+                (for-each
+                 (lambda (file)
+                   (install-file file (string-append #$output
+                                                    "/include/avalontoolkit")))
+                 (find-files "." "\\.h$"))
+                (install-file "../license.txt"
+                              (string-append #$output "/share/doc/"
+                                             #$name "-" #$version "/"))))))))
+    (home-page "https://sourceforge.net/projects/avalontoolkit/")
+    (synopsis "Tools for SMILES and MOL files and for structure fingerprinting")
+    (description "This package contains a library and programs for
+canonicalization of SMILES and MOL files, molecular structure fingerprinting
+and rendering molecules.")
+    (license license:bsd-3)))
-- 
2.37.0

[bug#58261] [PATCH v2 11/13] gnu: Add avalontoolkit.

[Liliana Marie Prikler]

Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
> * gnu/packages/chemistry.scm (avalontoolkit): New variable.
> ---
>  gnu/packages/chemistry.scm | 93
> ++++++++++++++++++++++++++++++++++++++
>  1 file changed, 93 insertions(+)
> 
> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
> index 68d28a52c3..e52dd2f3b6 100644
> --- a/gnu/packages/chemistry.scm
> +++ b/gnu/packages/chemistry.scm
> @@ -928,3 +928,96 @@ (define-public yaehmop
>      (description "@code{YAeHMOP} contains a program and library for
> performing
>  extended Hückel calculations.")
>      (license license:bsd-2)))
> +
> +(define-public avalontoolkit
> +  (package
> +    (name "avalontoolkit")
I think we could do a hyphen between avalon and toolkit.
> +    (version "1.2.0")
> +    (source
> +     (origin
> +       (method url-fetch)
> +       (uri (string-append
> +             "mirror://sourceforge/avalontoolkit/"
> +             "AvalonToolkit_" (substring version 0 3)
> "/AvalonToolkit_"
> +             version ".source.tar"))
> +       (sha256
> +        (base32
> +         "0rnnyy6axs2da7aa4q6l30ldavbk49v6l22llj1adn74h1i67bpv"))
> +       (modules '((guix build utils) (ice-9 ftw)))
> +       (snippet
> +        #~(begin
> +            (chdir "..")
> +            (delete-file-recursively "SourceDistribution/java")))))
> +    (build-system gnu-build-system)
> +    (arguments
> +     (list
> +      ;; There are no tests
> +      #:tests? #f
> +      #:phases
> +      #~(let ((programs '("canonizer" "matchtest" "smi2mol"
> "struchk")))
> +          (modify-phases %standard-phases
> +            (delete 'configure)
> +            (add-before 'build 'remove-free
> +              (lambda _
> +                ;; Remove incorrect free of getenv result (patch
> also in rdkit)
> +                (substitute* "common/reaccsio.c"
> +                  (("MyFree.*tempdir.*") ""))))
> +            (replace 'build
> +              (lambda _
> +                (chdir "common")
> +                (let* ((parts
> +                        (list
> +                         "aacheck" "casutils" "denormal"
> "depictutil"
> +                         "didepict" "fixcharges" "forio" "geometry"
> "graph"
> +                         "hashcode" "layout" "local" "patclean"
> "pattern"
> +                         "perceive" "reaccsio" "rtutils" "set"
> "shortcut"
> +                         "sketch" "ssmatch" "stereo" "symbol_lists"
> +                         "symboltable" "utilities"))
> +                       (objects (map (lambda (name) (string-append
> name ".o"))
> +                                     parts)))
> +                  (for-each
> +                   (lambda (name)
> +                     (display (string-append "Compiling " name
> ".c\n"))
> +                     (invoke "gcc" "-c" "-fPIC" "-O2"
> +                             (string-append name ".c")
> +                             "-o" (string-append name ".o")))
> +                   parts)
> +                  (display "Building shared library\n")
> +                  (apply invoke "gcc" "-fPIC" "-shared" "-lm"
> +                         "-o" "libavalontoolkit.so"
> +                         "canonizer.c" "smi2mol.c" "struchk.c"
> objects)
> +                  (for-each
> +                   (lambda (program)
> +                     (display (string-append "Building " program
> "\n"))
> +                     (invoke "gcc" "-L." "-lavalontoolkit" "-lm" "-
> O2"
> +                             (string-append "-Wl,-rpath=" #$output
> "/lib")
> +                             "-DMAIN" (string-append program ".c")
> "-o" program))
> +                   programs))))
Uhm... is the Makefile that unusable?
> +            (replace 'install
> +              (lambda _
> +                ;; Executables
> +                (for-each
> +                 (lambda (program)
> +                   (install-file program (string-append #$output
> "/bin")))
> +                 programs)
> +                (for-each
> +                 (lambda (name)
> +                   (symlink (string-append #$output "/bin/smi2mol")
> +                            (string-append #$output "/bin/" name)))
> +                 '("mol2smi" "rdf2smi" "mol2tbl" "mol2sma"
> "smi2rdf"))
> +                ;; Library
> +                (install-file "libavalontoolkit.so" (string-append
> #$output "/lib"))
> +                (for-each
> +                 (lambda (file)
> +                   (install-file file (string-append #$output
> +                                                   
> "/include/avalontoolkit")))
> +                 (find-files "." "\\.h$"))
> +                (install-file "../license.txt"
> +                              (string-append #$output "/share/doc/"
> +                                             #$name "-" #$version
> "/"))))))))
Same as above.
> +    (home-page "https://sourceforge.net/projects/avalontoolkit/")
> +    (synopsis "Tools for SMILES and MOL files and for structure
> fingerprinting")
> +    (description "This package contains a library and programs for
> +canonicalization of SMILES and MOL files, molecular structure
> fingerprinting
> +and rendering molecules.")
> +    (license license:bsd-3)))

[bug#58261] [PATCH v2 11/13] gnu: Add avalontoolkit.

[David Elsing]

Liliana Marie Prikler <liliana.prikler@gmail.com> writes:

> Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
>> * gnu/packages/chemistry.scm (avalontoolkit): New variable.
>> ---
>>  gnu/packages/chemistry.scm | 93
>> ++++++++++++++++++++++++++++++++++++++
>>  1 file changed, 93 insertions(+)
>> 
>> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
>> index 68d28a52c3..e52dd2f3b6 100644
>> --- a/gnu/packages/chemistry.scm
>> +++ b/gnu/packages/chemistry.scm
>> @@ -928,3 +928,96 @@ (define-public yaehmop
>>      (description "@code{YAeHMOP} contains a program and library for
>> performing
>>  extended Hückel calculations.")
>>      (license license:bsd-2)))
>> +
>> +(define-public avalontoolkit
>> +  (package
>> +    (name "avalontoolkit")
> I think we could do a hyphen between avalon and toolkit.
>> +    (version "1.2.0")
>> +    (source
>> +     (origin
>> +       (method url-fetch)
>> +       (uri (string-append
>> +             "mirror://sourceforge/avalontoolkit/"
>> +             "AvalonToolkit_" (substring version 0 3)
>> "/AvalonToolkit_"
>> +             version ".source.tar"))
>> +       (sha256
>> +        (base32
>> +         "0rnnyy6axs2da7aa4q6l30ldavbk49v6l22llj1adn74h1i67bpv"))
>> +       (modules '((guix build utils) (ice-9 ftw)))
>> +       (snippet
>> +        #~(begin
>> +            (chdir "..")
>> +            (delete-file-recursively "SourceDistribution/java")))))
>> +    (build-system gnu-build-system)
>> +    (arguments
>> +     (list
>> +      ;; There are no tests
>> +      #:tests? #f
>> +      #:phases
>> +      #~(let ((programs '("canonizer" "matchtest" "smi2mol"
>> "struchk")))
>> +          (modify-phases %standard-phases
>> +            (delete 'configure)
>> +            (add-before 'build 'remove-free
>> +              (lambda _
>> +                ;; Remove incorrect free of getenv result (patch
>> also in rdkit)
>> +                (substitute* "common/reaccsio.c"
>> +                  (("MyFree.*tempdir.*") ""))))
>> +            (replace 'build
>> +              (lambda _
>> +                (chdir "common")
>> +                (let* ((parts
>> +                        (list
>> +                         "aacheck" "casutils" "denormal"
>> "depictutil"
>> +                         "didepict" "fixcharges" "forio" "geometry"
>> "graph"
>> +                         "hashcode" "layout" "local" "patclean"
>> "pattern"
>> +                         "perceive" "reaccsio" "rtutils" "set"
>> "shortcut"
>> +                         "sketch" "ssmatch" "stereo" "symbol_lists"
>> +                         "symboltable" "utilities"))
>> +                       (objects (map (lambda (name) (string-append
>> name ".o"))
>> +                                     parts)))
>> +                  (for-each
>> +                   (lambda (name)
>> +                     (display (string-append "Compiling " name
>> ".c\n"))
>> +                     (invoke "gcc" "-c" "-fPIC" "-O2"
>> +                             (string-append name ".c")
>> +                             "-o" (string-append name ".o")))
>> +                   parts)
>> +                  (display "Building shared library\n")
>> +                  (apply invoke "gcc" "-fPIC" "-shared" "-lm"
>> +                         "-o" "libavalontoolkit.so"
>> +                         "canonizer.c" "smi2mol.c" "struchk.c"
>> objects)
>> +                  (for-each
>> +                   (lambda (program)
>> +                     (display (string-append "Building " program
>> "\n"))
>> +                     (invoke "gcc" "-L." "-lavalontoolkit" "-lm" "-
>> O2"
>> +                             (string-append "-Wl,-rpath=" #$output
>> "/lib")
>> +                             "-DMAIN" (string-append program ".c")
>> "-o" program))
>> +                   programs))))
> Uhm... is the Makefile that unusable?
Pretty much: Not all programs are built, the compiler and linker options
need to be adjusted in several places and the shared library is missing
some object files. :)
>> +            (replace 'install
>> +              (lambda _
>> +                ;; Executables
>> +                (for-each
>> +                 (lambda (program)
>> +                   (install-file program (string-append #$output
>> "/bin")))
>> +                 programs)
>> +                (for-each
>> +                 (lambda (name)
>> +                   (symlink (string-append #$output "/bin/smi2mol")
>> +                            (string-append #$output "/bin/" name)))
>> +                 '("mol2smi" "rdf2smi" "mol2tbl" "mol2sma"
>> "smi2rdf"))
>> +                ;; Library
>> +                (install-file "libavalontoolkit.so" (string-append
>> #$output "/lib"))
>> +                (for-each
>> +                 (lambda (file)
>> +                   (install-file file (string-append #$output
>> +                                                   
>> "/include/avalontoolkit")))
>> +                 (find-files "." "\\.h$"))
>> +                (install-file "../license.txt"
>> +                              (string-append #$output "/share/doc/"
>> +                                             #$name "-" #$version
>> "/"))))))))
> Same as above.
There is no install target.
>> +    (home-page "https://sourceforge.net/projects/avalontoolkit/")
>> +    (synopsis "Tools for SMILES and MOL files and for structure
>> fingerprinting")
>> +    (description "This package contains a library and programs for
>> +canonicalization of SMILES and MOL files, molecular structure
>> fingerprinting
>> +and rendering molecules.")
>> +    (license license:bsd-3)))

[bug#58261] [PATCH v2 12/13] gnu: Add ringdecomposerlib.

[David Elsing]

* gnu/packages/chemistry.scm (ringdecomposerlib): New variable.
---
 gnu/packages/chemistry.scm | 80 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 80 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index e52dd2f3b6..43953238cd 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -1021,3 +1021,83 @@ (define-public avalontoolkit
 canonicalization of SMILES and MOL files, molecular structure fingerprinting
 and rendering molecules.")
     (license license:bsd-3)))
+
+(define-public ringdecomposerlib
+  (package
+    (name "ringdecomposerlib")
+    (version "1.1.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/rareylab/RingDecomposerLib")
+                    (commit (string-append "v" version "_rdkit"))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1rxzs2wpkkdi40wdzxc4sn0brk7dm7ivgqyfh38gf2f5c7pbg0wi"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      #~(list "-DBUILD_PYTHON_WRAPPER=ON"
+              "-DPYTHON_EXECUTABLE=python3"
+              (string-append "-DPYTHON_FLAGS=;--prefix=" #$output ";--root=/"))
+      #:imported-modules (append %cmake-build-system-modules
+                                 '((guix build python-build-system)))
+      #:modules '((guix build cmake-build-system)
+                  (guix build utils)
+                  ((guix build python-build-system)
+                   #:select (add-installed-pythonpath)))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'configure 'patch-cmake
+            (lambda _
+              (substitute* (list "src/Test/CMakeLists.txt"
+                                 "src/RingDecomposerLib/CMakeLists.txt")
+                (("build_.*STATIC") "#"))
+              (substitute* "test/CMakeLists.txt"
+                (("STATIC_TEST") "SHARED_TEST"))
+              ;; Link Python library against shared library
+              (substitute* "src/python/CMakeLists.txt"
+                (("RingDecomposerLibStatic") "RingDecomposerLib"))
+              (substitute* "src/python/setup.py.in"
+                (("static_libs =.*") "static_libs = []\n")
+                (("shared_libs\\s*=.*")
+                 (string-append
+                  "shared_libs = ['RingDecomposerLib']"))
+                (("library_dirs\\s*=\\s*\\[\\]")
+                 "library_dirs = ['${CMAKE_BINARY_DIR}/src/RingDecomposerLib']")
+                (("extra_objects=.*")
+                 (string-append "extra_link_args=['-Wl,-rpath=" #$output "/lib'],\n")))))
+          (add-after 'build 'build-doc
+            (lambda _
+              ;; Disable redundant LaTeX documentation
+              (substitute* "../source/documentation/sphinx/conf.py"
+                (("^(subprocess.*latex|shutil).*") ""))
+              (substitute* "../source/documentation/doxygen.cfg"
+                (("GENERATE_LATEX.*YES") "GENERATE_LATEX = NO"))
+              ;; Build HTML documentation
+              (invoke "sphinx-build" "-b" "html"
+                      "../source/documentation/sphinx" "html")))
+          (add-after 'install 'install-doc
+            (lambda _
+              ;; Not reproducible
+              (delete-file-recursively "html/.doctrees")
+              (copy-recursively "html"
+                                (string-append #$output "/share/doc/"
+                                               #$name "-" #$version "/html"))))
+          (delete 'check)
+          (add-after 'install 'check
+            (assoc-ref %standard-phases 'check))
+          (add-before 'check 'set-pythonpath
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (add-installed-pythonpath inputs outputs))))))
+    (inputs (list python))
+    (native-inputs (list doxygen python python-cython python-sphinx))
+    (home-page "https://github.com/rareylab/RingDecomposerLib")
+    (synopsis "Library for calculating ring topology descriptions such as
+unique ring families")
+    (description "ringdecomposerlib is a library for the calculation of
+unique ring families, relevant cycles, the smallest set of smallest rings and
+other ring topology descriptions.")
+    (license license:bsd-3)))
-- 
2.37.0

[bug#58261] [PATCH v2 13/13] gnu: Add rdkit.

[David Elsing]

* gnu/packages/chemistry.scm (rdkit): New variable.
---
 gnu/packages/chemistry.scm                    | 178 ++++++++++++++++++
 .../rdkit-cmake-external-dependencies.patch   | 102 ++++++++++
 2 files changed, 280 insertions(+)
 create mode 100644 gnu/packages/patches/rdkit-cmake-external-dependencies.patch

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 43953238cd..4b34a38797 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -34,6 +34,7 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages backup)
+  #:use-module (gnu packages base)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
@@ -41,10 +42,12 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages cpp)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages flex)
+  #:use-module (gnu packages fonts)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages graphviz)
+  #:use-module (gnu packages gtk)
   #:use-module (gnu packages gv)
   #:use-module (gnu packages image)
   #:use-module (gnu packages maths)
@@ -56,6 +59,7 @@ (define-module (gnu packages chemistry)
   #:use-module (gnu packages qt)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages sphinx)
+  #:use-module (gnu packages sqlite)
   #:use-module (gnu packages stb)
   #:use-module (gnu packages tex)
   #:use-module (gnu packages web)
@@ -1101,3 +1105,177 @@ (define-public ringdecomposerlib
 unique ring families, relevant cycles, the smallest set of smallest rings and
 other ring topology descriptions.")
     (license license:bsd-3)))
+
+(define-public rdkit
+  (package
+    (name "rdkit")
+    (version "2022.03.5")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/rdkit/rdkit")
+                    (commit
+                     (string-append
+                      "Release_" (string-replace-substring version "." "_")))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9"))
+              (patches
+               (search-patches "rdkit-cmake-external-dependencies.patch"))
+              (modules '((guix build utils)))
+              (snippet
+               #~(begin
+                   ;; Remove pickle files (only used in tests),
+                   ;; as they are compiled programs
+                   (for-each
+                    (lambda (name)
+                      (display (string-append name "\n"))
+                      (delete-file name))
+                    (find-files "." "\\.pkl(\\.gz)?$"))
+                   ;; Remove SQLite data files (can be generated)
+                   (delete-file "Data/RDData.sqlt")
+                   (delete-file "Data/RDTests.sqlt")))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:imported-modules (append %cmake-build-system-modules
+                                 '((guix build python-build-system)))
+      #:modules '((guix build cmake-build-system)
+                  (guix build utils)
+                  ((guix build python-build-system)
+                   #:select (add-installed-pythonpath)))
+      #:configure-flags
+      #~(list
+         "-DRDK_BUILD_AVALON_SUPPORT=ON"
+         "-DRDK_BUILD_CAIRO_SUPPORT=ON"
+         "-DRDK_BUILD_CPP_TESTS=ON"
+         "-DRDK_BUILD_FREESASA_SUPPORT=ON"
+         "-DRDK_BUILD_INCHI_SUPPORT=ON"
+         "-DRDK_BUILD_YAEHMOP_SUPPORT=ON"
+         (string-append "-DCATCH_DIR="
+                        #$(this-package-native-input "catch2")
+                        "/include/catch2")
+         "-DRDK_INSTALL_DEV_COMPONENT=ON"
+         "-DRDK_INSTALL_INTREE=OFF"
+         "-DRDK_INSTALL_STATIC_LIBS=OFF"
+         (string-append
+          "-DRDK_OPTIMIZE_POPCNT="
+          #$(let ((system (or (%current-target-system)
+                              (%current-system))))
+              (cond
+               ((string-prefix? "x86_64" system) "ON")
+               ((string-prefix? "i686" system) "ON")
+               (else "OFF"))))
+         "-DRDK_USE_BOOST_IOSTREAMS=ON"
+         "-DRDK_USE_FLEXBISON=ON")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'copy-external-dependencies
+            (lambda _
+              (symlink
+               (string-append
+                #$(this-package-input "font-comic-neue")
+                "/share/fonts/truetype/ComicNeue-Regular.ttf")
+               "Data/Fonts/ComicNeue-Regular.ttf")))
+          (add-after 'copy-external-dependencies 'patch-source
+            (lambda _
+              (substitute* "External/AvalonTools/CMakeLists.txt"
+                (("^if\\(NOT RDK_BUILD" orig)
+                 (string-append "if(0)\n" orig))
+                (("include_directories.*AVALON_SRC_PATH.*")
+                 (string-append "endif()\ninclude_directories("
+                                #$avalontoolkit "/include/avalontoolkit)\n"))
+                (("LINK_LIBRARIES avalon_clib")
+                 (string-append
+                  "LINK_LIBRARIES -L" #$avalontoolkit "/lib -lavalontoolkit")))
+              (let ((port
+                     (open-file "External/RingFamilies/dummy.cpp" "w")))
+                (display "" port)
+                (close port))
+              (let ((port
+                     (open-file "External/RingFamilies/CMakeLists.txt" "w")))
+                (display (string-append
+                          "rdkit_library(RingDecomposerLib dummy.cpp SHARED"
+                          " LINK_LIBRARIES -lRingDecomposerLib)\n"
+                          "set(RDK_URF_LIBS RingDecomposerLib CACHE STRING \"\" FORCE)\n")
+                         port)
+                (close port))
+              (substitute* "Code/GraphMol/MolInterchange/CMakeLists.txt"
+                (("if\\(NOT" orig)
+                 (string-append "if(0)\n" orig))
+                (("^include_directories.*") "endif()\n"))
+              (substitute* "External/YAeHMOP/EHTTools.cpp"
+                (("<yaehmop/tightbind/bind.h>") "<yaehmop/bind.h>"))))
+          (add-after 'unpack 'fix-inchi-include
+            (lambda _
+              (substitute* "Code/cmake/Modules/FindInchi.cmake"
+                (("inchi_api.h.*\\)") "inchi/inchi_api.h)")
+                (("INCHI_LIBRARY NAMES.*\\)")
+                 "INCHI_LIBRARY NAMES inchi PATH_SUFFIXES inchi)")
+                (("find_library" prev)
+                 (string-append
+                  "list(APPEND CMAKE_FIND_LIBRARY_SUFFIXES .so.1)\n"
+                  prev)))
+              (substitute* "External/INCHI-API/inchi.cpp"
+                (("<inchi_api.h>") "<inchi/inchi_api.h>"))))
+          (add-before 'build 'enable-bytecode-determinism
+              (lambda _
+                (setenv "PYTHONHASHSEED" "0")
+                (setenv "PYTHONDONTWRITEBYTECODE" "1")))
+          (add-after 'install 'pre-check
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (with-directory-excursion "../source"
+                (invoke "sqlite3" "Data/RDData.sqlt"
+                        ".read rdkit/Dbase/test_data/RDData.sqlite")
+                (invoke "sqlite3" "Data/RDTests.sqlt"
+                        ".read rdkit/Dbase/test_data/RDTests.sqlite")
+                (setenv "RDBASE" (canonicalize-path ".")))
+              (add-installed-pythonpath inputs outputs)))
+          (delete 'check)
+          (add-after 'pre-check 'check
+            (lambda* (#:key tests? parallel-tests? #:allow-other-keys)
+              (when tests?
+                (let ((job-count (number->string
+                                  (if parallel-tests? (parallel-job-count) 1))))
+                  (invoke
+                   "ctest" "-j" job-count
+                   "-E" (string-append
+                         "(" (string-join
+                              '(;; need pickled data
+                                "(pyDiscreteValueVect" "pySparseIntVect"
+                                "graphmoltestPickler" "pyPartialCharges"
+                                "substructLibraryTest" "pyFeatures"
+                                "pythonTestDirML" "pythonTestDirChem"
+                                ;; Catching Python exception fails
+                                "pyRanker)") "|") ")")))))))))
+    (native-inputs
+     (list bison
+           boost
+           catch2
+           eigen
+           flex
+           freesasa
+           pkg-config
+           rapidjson
+           tar))
+    (inputs
+     (list avalontoolkit
+           cairo
+           coordgenlibs
+           font-comic-neue
+           freetype
+           inchi
+           maeparser
+           python
+           ringdecomposerlib
+           sqlite
+           yaehmop))
+    (propagated-inputs
+     (list python-numpy python-cairocffi python-pillow))
+    (home-page "https://rdkit.org/")
+    (synopsis "Collection of cheminformatics software")
+    (description "RDKit is a C++ and Python library for cheminformatics, which
+includes (among other things) the analysis and modification of molecules in 2D
+and 3D and descriptor generation for machine learning.")
+    (license license:bsd-3)))
diff --git a/gnu/packages/patches/rdkit-cmake-external-dependencies.patch b/gnu/packages/patches/rdkit-cmake-external-dependencies.patch
new file mode 100644
index 0000000000..5b73864f51
--- /dev/null
+++ b/gnu/packages/patches/rdkit-cmake-external-dependencies.patch
@@ -0,0 +1,102 @@
+diff -ur a/External/FreeSASA/CMakeLists.txt b/External/FreeSASA/CMakeLists.txt
+--- a/External/FreeSASA/CMakeLists.txt
++++ b/External/FreeSASA/CMakeLists.txt
+@@ -10,7 +10,7 @@
+   endif()
+ endif()
+ 
+-if(needDownload)
++if(FALSE)
+   # don't actually use the md5 here
+   set(FREESASA_VERSION "2.0.3")
+   set(FREESASA_SRC_DIR "${CMAKE_CURRENT_SOURCE_DIR}/freesasa-${FREESASA_VERSION}")
+@@ -66,24 +66,24 @@
+ endif()
+ 
+ set (freesasa_h ${FREESASA_SRC_DIR}/src/freesasa.h)
+-file(READ ${freesasa_h} freesasa_h_data)
++#file(READ ${freesasa_h} freesasa_h_data)
+ string(REGEX REPLACE "(#include <stdio.h>)" "\\1\n#include <RDGeneral/export.h>" freesasa_h_data "${freesasa_h_data}")
+ string(REGEX REPLACE "([^R][^D][^K][^I][^T][^_][^F][^R][^E][^E][^S][^A][^S][^A][^_][^C][^L][^I][^B][^_][^E][^X][^P][^O][^R][^T][^ ])(extern const)" "\\1RDKIT_FREESASA_CLIB_EXPORT \\2" freesasa_h_data "${freesasa_h_data}")
+-file(WRITE ${freesasa_h} "${freesasa_h_data}")
++#file(WRITE ${freesasa_h} "${freesasa_h_data}")
+ 
+ add_definitions(-DUSE_THREADS=0)
+ add_definitions(-DUSE_JSON=0)
+ add_definitions(-DUSE_XML=0)
+-rdkit_library(freesasa_clib ${freesasa_clib_srcs})
+-target_compile_definitions(freesasa_clib PRIVATE RDKIT_FREESASALIB_BUILD)
++#rdkit_library(freesasa_clib ${freesasa_clib_srcs})
++#target_compile_definitions(freesasa_clib PRIVATE RDKIT_FREESASALIB_BUILD)
+ 
+ if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32))
+   set_target_properties(freesasa_clib PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
+ endif()
+-include_directories("${FREESASA_SRC_DIR}/src")
++#include_directories("${FREESASA_SRC_DIR}/src")
+ 
+ rdkit_library(FreeSASALib RDFreeSASA.cpp SHARED 
+-    LINK_LIBRARIES freesasa_clib GraphMol )
++    LINK_LIBRARIES -lfreesasa GraphMol )
+ target_compile_definitions(FreeSASALib PRIVATE RDKIT_FREESASALIB_BUILD)
+ 
+ rdkit_headers(RDFreeSASA.h DEST GraphMol)
+diff -ur a/External/YAeHMOP/CMakeLists.txt b/External/YAeHMOP/CMakeLists.txt
+--- a/External/YAeHMOP/CMakeLists.txt
++++ b/External/YAeHMOP/CMakeLists.txt
+@@ -18,32 +18,32 @@
+ 
+ include_directories( ${RDKit_ExternalDir}/YAeHMOP )
+ 
+-ExternalProject_Add(yaehmop_project
+-  GIT_REPOSITORY https://github.com/greglandrum/yaehmop.git
+-  GIT_TAG master
+-  UPDATE_COMMAND ""
+-  PATCH_COMMAND ""
+-  PREFIX ${CMAKE_CURRENT_SOURCE_DIR}
+-  SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop"
+-  SOURCE_SUBDIR "tightbind"
+-  CMAKE_ARGS -DUSE_BLAS_LAPACK=OFF -DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR} -DCMAKE_C_FLAGS=${CMAKE_C_FLAGS} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+-  TEST_COMMAND "")
+-
+-include_directories(${PROJECT_BINARY_DIR}/include)
+-link_directories(${PROJECT_BINARY_DIR}/lib)
+-link_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build)
+-
+-set(EHT_PARAM_FILE ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat )
+-install(FILES ${EHT_PARAM_FILE}
+-        DESTINATION ${RDKit_ShareDir}/Data
+-        COMPONENT data)
++#ExternalProject_Add(yaehmop_project
++#  GIT_REPOSITORY https://github.com/greglandrum/yaehmop.git
++#  GIT_TAG master
++#  UPDATE_COMMAND ""
++#  PATCH_COMMAND ""
++#  PREFIX ${CMAKE_CURRENT_SOURCE_DIR}
++#  SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop"
++#  SOURCE_SUBDIR "tightbind"
++#  CMAKE_ARGS -DUSE_BLAS_LAPACK=OFF -DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR} -DCMAKE_C_FLAGS=${CMAKE_C_FLAGS} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
++#  TEST_COMMAND "")
++
++#include_directories(${PROJECT_BINARY_DIR}/include)
++#link_directories(${PROJECT_BINARY_DIR}/lib)
++#link_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build)
++
++#set(EHT_PARAM_FILE ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat )
++#install(FILES ${EHT_PARAM_FILE}
++#        DESTINATION ${RDKit_ShareDir}/Data
++#        COMPONENT data)
+ 
+-message("YAeHMOP include_dirs: ${PROJECT_BINARY_DIR}/include")
+-message("YAeHMOP link_dirs: ${PROJECT_BINARY_DIR}/lib ${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build")
++#message("YAeHMOP include_dirs: ${PROJECT_BINARY_DIR}/include")
++#message("YAeHMOP link_dirs: ${PROJECT_BINARY_DIR}/lib ${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build")
+ 
+-rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES yaehmop_eht GraphMol )
++rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES -lyaehmop_eht GraphMol )
+ target_compile_definitions(EHTLib PRIVATE RDKIT_EHTLIB_BUILD)
+-add_dependencies(EHTLib yaehmop_project)
++#add_dependencies(EHTLib yaehmop_project)
+ rdkit_headers(EHTTools.h DEST GraphMol)
+ rdkit_catch_test(testEHTLib1 test1.cpp
+            LINK_LIBRARIES EHTLib FileParsers SmilesParse )
-- 
2.37.0

[bug#58261] [PATCH v2 13/13] gnu: Add rdkit.

[Liliana Marie Prikler]

Am Freitag, dem 07.10.2022 um 15:22 +0000 schrieb David Elsing:
> * gnu/packages/chemistry.scm (rdkit): New variable.
> ---
>  gnu/packages/chemistry.scm                    | 178
> ++++++++++++++++++
>  .../rdkit-cmake-external-dependencies.patch   | 102 ++++++++++
>  2 files changed, 280 insertions(+)
>  create mode 100644 gnu/packages/patches/rdkit-cmake-external-
> dependencies.patch
> 
> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
> index 43953238cd..4b34a38797 100644
> --- a/gnu/packages/chemistry.scm
> +++ b/gnu/packages/chemistry.scm
> @@ -34,6 +34,7 @@ (define-module (gnu packages chemistry)
>    #:use-module (gnu packages algebra)
>    #:use-module (gnu packages autotools)
>    #:use-module (gnu packages backup)
> +  #:use-module (gnu packages base)
>    #:use-module (gnu packages bison)
>    #:use-module (gnu packages boost)
>    #:use-module (gnu packages check)
> @@ -41,10 +42,12 @@ (define-module (gnu packages chemistry)
>    #:use-module (gnu packages cpp)
>    #:use-module (gnu packages documentation)
>    #:use-module (gnu packages flex)
> +  #:use-module (gnu packages fonts)
>    #:use-module (gnu packages fontutils)
>    #:use-module (gnu packages gcc)
>    #:use-module (gnu packages gl)
>    #:use-module (gnu packages graphviz)
> +  #:use-module (gnu packages gtk)
>    #:use-module (gnu packages gv)
>    #:use-module (gnu packages image)
>    #:use-module (gnu packages maths)
> @@ -56,6 +59,7 @@ (define-module (gnu packages chemistry)
>    #:use-module (gnu packages qt)
>    #:use-module (gnu packages serialization)
>    #:use-module (gnu packages sphinx)
> +  #:use-module (gnu packages sqlite)
>    #:use-module (gnu packages stb)
>    #:use-module (gnu packages tex)
>    #:use-module (gnu packages web)
> @@ -1101,3 +1105,177 @@ (define-public ringdecomposerlib
>  unique ring families, relevant cycles, the smallest set of smallest
> rings and
>  other ring topology descriptions.")
>      (license license:bsd-3)))
> +
> +(define-public rdkit
> +  (package
> +    (name "rdkit")
> +    (version "2022.03.5")
> +    (source (origin
> +              (method git-fetch)
> +              (uri (git-reference
> +                    (url "https://github.com/rdkit/rdkit")
> +                    (commit
> +                     (string-append
> +                      "Release_" (string-replace-substring version
> "." "_")))))
> +              (file-name (git-file-name name version))
> +              (sha256
> +               (base32
> +               
> "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9"))
> +              (patches
> +               (search-patches "rdkit-cmake-external-
> dependencies.patch"))
> +              (modules '((guix build utils)))
> +              (snippet
> +               #~(begin
> +                   ;; Remove pickle files (only used in tests),
> +                   ;; as they are compiled programs
> +                   (for-each
> +                    (lambda (name)
> +                      (display (string-append name "\n"))
> +                      (delete-file name))
> +                    (find-files "." "\\.pkl(\\.gz)?$"))
> +                   ;; Remove SQLite data files (can be generated)
> +                   (delete-file "Data/RDData.sqlt")
> +                   (delete-file "Data/RDTests.sqlt")))))
> +    (build-system cmake-build-system)
> +    (arguments
> +     (list
> +      #:imported-modules (append %cmake-build-system-modules
> +                                 '((guix build python-build-
> system)))
> +      #:modules '((guix build cmake-build-system)
> +                  (guix build utils)
> +                  ((guix build python-build-system)
> +                   #:select (add-installed-pythonpath)))
> +      #:configure-flags
> +      #~(list
> +         "-DRDK_BUILD_AVALON_SUPPORT=ON"
> +         "-DRDK_BUILD_CAIRO_SUPPORT=ON"
> +         "-DRDK_BUILD_CPP_TESTS=ON"
> +         "-DRDK_BUILD_FREESASA_SUPPORT=ON"
> +         "-DRDK_BUILD_INCHI_SUPPORT=ON"
> +         "-DRDK_BUILD_YAEHMOP_SUPPORT=ON"
Are any of these implied or do they have to be explicitly enabled?
> +         (string-append "-DCATCH_DIR="
> +                        #$(this-package-native-input "catch2")
> +                        "/include/catch2")
> +         "-DRDK_INSTALL_DEV_COMPONENT=ON"
> +         "-DRDK_INSTALL_INTREE=OFF"
> +         "-DRDK_INSTALL_STATIC_LIBS=OFF"
> +         (string-append
> +          "-DRDK_OPTIMIZE_POPCNT="
> +          #$(let ((system (or (%current-target-system)
> +                              (%current-system))))
> +              (cond
> +               ((string-prefix? "x86_64" system) "ON")
> +               ((string-prefix? "i686" system) "ON")
> +               (else "OFF"))))
> +         "-DRDK_USE_BOOST_IOSTREAMS=ON"
> +         "-DRDK_USE_FLEXBISON=ON")
> +      #:phases
> +      #~(modify-phases %standard-phases
> +          (add-after 'unpack 'copy-external-dependencies
> +            (lambda _
> +              (symlink
> +               (string-append
> +                #$(this-package-input "font-comic-neue")
> +                "/share/fonts/truetype/ComicNeue-Regular.ttf")
> +               "Data/Fonts/ComicNeue-Regular.ttf")))
Try (search-input-file) instead.
> +          (add-after 'copy-external-dependencies 'patch-source
> +            (lambda _
> +              (substitute* "External/AvalonTools/CMakeLists.txt"
> +                (("^if\\(NOT RDK_BUILD" orig)
> +                 (string-append "if(0)\n" orig))
> +                (("include_directories.*AVALON_SRC_PATH.*")
> +                 (string-append "endif()\ninclude_directories("
> +                                #$avalontoolkit
> "/include/avalontoolkit)\n"))
> +                (("LINK_LIBRARIES avalon_clib")
> +                 (string-append
> +                  "LINK_LIBRARIES -L" #$avalontoolkit "/lib -
> lavalontoolkit")))
> +              (let ((port
> +                     (open-file "External/RingFamilies/dummy.cpp"
> "w")))
> +                (display "" port)
> +                (close port))
> +              (let ((port
> +                     (open-file
> "External/RingFamilies/CMakeLists.txt" "w")))
> +                (display (string-append
> +                          "rdkit_library(RingDecomposerLib dummy.cpp
> SHARED"
> +                          " LINK_LIBRARIES -lRingDecomposerLib)\n"
> +                          "set(RDK_URF_LIBS RingDecomposerLib CACHE
> STRING \"\" FORCE)\n")
> +                         port)
> +                (close port))
> +              (substitute*
> "Code/GraphMol/MolInterchange/CMakeLists.txt"
> +                (("if\\(NOT" orig)
> +                 (string-append "if(0)\n" orig))
> +                (("^include_directories.*") "endif()\n"))
> +              (substitute* "External/YAeHMOP/EHTTools.cpp"
> +                (("<yaehmop/tightbind/bind.h>")
> "<yaehmop/bind.h>"))))
I think you might want to unbundle these with a patch.
> +          (add-after 'unpack 'fix-inchi-include
> +            (lambda _
> +              (substitute* "Code/cmake/Modules/FindInchi.cmake"
> +                (("inchi_api.h.*\\)") "inchi/inchi_api.h)")
> +                (("INCHI_LIBRARY NAMES.*\\)")
> +                 "INCHI_LIBRARY NAMES inchi PATH_SUFFIXES inchi)")
> +                (("find_library" prev)
> +                 (string-append
> +                  "list(APPEND CMAKE_FIND_LIBRARY_SUFFIXES .so.1)\n"
> +                  prev)))
> +              (substitute* "External/INCHI-API/inchi.cpp"
> +                (("<inchi_api.h>") "<inchi/inchi_api.h>"))))
> +          (add-before 'build 'enable-bytecode-determinism
> +              (lambda _
> +                (setenv "PYTHONHASHSEED" "0")
> +                (setenv "PYTHONDONTWRITEBYTECODE" "1")))
> +          (add-after 'install 'pre-check
> +            (lambda* (#:key inputs outputs #:allow-other-keys)
> +              (with-directory-excursion "../source"
> +                (invoke "sqlite3" "Data/RDData.sqlt"
> +                        ".read rdkit/Dbase/test_data/RDData.sqlite")
> +                (invoke "sqlite3" "Data/RDTests.sqlt"
> +                        ".read
> rdkit/Dbase/test_data/RDTests.sqlite")
> +                (setenv "RDBASE" (canonicalize-path ".")))
> +              (add-installed-pythonpath inputs outputs)))
> +          (delete 'check)
> +          (add-after 'pre-check 'check
> +            (lambda* (#:key tests? parallel-tests? #:allow-other-
> keys)
> +              (when tests?
> +                (let ((job-count (number->string
> +                                  (if parallel-tests? (parallel-job-
> count) 1))))
> +                  (invoke
> +                   "ctest" "-j" job-count
> +                   "-E" (string-append
> +                         "(" (string-join
> +                              '(;; need pickled data
> +                                "(pyDiscreteValueVect"
> "pySparseIntVect"
> +                                "graphmoltestPickler"
> "pyPartialCharges"
> +                                "substructLibraryTest" "pyFeatures"
> +                                "pythonTestDirML"
> "pythonTestDirChem"
> +                                ;; Catching Python exception fails
> +                                "pyRanker)") "|") ")")))))))))
I think you have two layers of brackets now – delete the inner ones.
> +    (native-inputs
> +     (list bison
> +           boost
> +           catch2
> +           eigen
> +           flex
> +           freesasa
> +           pkg-config
> +           rapidjson
> +           tar))
> +    (inputs
> +     (list avalontoolkit
> +           cairo
> +           coordgenlibs
> +           font-comic-neue
> +           freetype
> +           inchi
> +           maeparser
> +           python
> +           ringdecomposerlib
> +           sqlite
> +           yaehmop))
> +    (propagated-inputs
> +     (list python-numpy python-cairocffi python-pillow))
> +    (home-page "https://rdkit.org/")
> +    (synopsis "Collection of cheminformatics software")
> +    (description "RDKit is a C++ and Python library for
> cheminformatics, which
> +includes (among other things) the analysis and modification of
> molecules in 2D
> +and 3D and descriptor generation for machine learning.")
> +    (license license:bsd-3)))
> diff --git a/gnu/packages/patches/rdkit-cmake-external-
> dependencies.patch b/gnu/packages/patches/rdkit-cmake-external-
> dependencies.patch
> new file mode 100644
> index 0000000000..5b73864f51
> --- /dev/null
> +++ b/gnu/packages/patches/rdkit-cmake-external-dependencies.patch
> @@ -0,0 +1,102 @@
> +diff -ur a/External/FreeSASA/CMakeLists.txt
> b/External/FreeSASA/CMakeLists.txt
> +--- a/External/FreeSASA/CMakeLists.txt
> ++++ b/External/FreeSASA/CMakeLists.txt
> +@@ -10,7 +10,7 @@
> +   endif()
> + endif()
> + 
> +-if(needDownload)
> ++if(FALSE)
> +   # don't actually use the md5 here
> +   set(FREESASA_VERSION "2.0.3")
> +   set(FREESASA_SRC_DIR "${CMAKE_CURRENT_SOURCE_DIR}/freesasa-
> ${FREESASA_VERSION}")
> +@@ -66,24 +66,24 @@
> + endif()
> + 
> + set (freesasa_h ${FREESASA_SRC_DIR}/src/freesasa.h)
> +-file(READ ${freesasa_h} freesasa_h_data)
> ++#file(READ ${freesasa_h} freesasa_h_data)
> + string(REGEX REPLACE "(#include <stdio.h>)" "\\1\n#include
> <RDGeneral/export.h>" freesasa_h_data "${freesasa_h_data}")
> + string(REGEX REPLACE
> "([^R][^D][^K][^I][^T][^_][^F][^R][^E][^E][^S][^A][^S][^A][^_][^C][^L
> ][^I][^B][^_][^E][^X][^P][^O][^R][^T][^ ])(extern const)"
> "\\1RDKIT_FREESASA_CLIB_EXPORT \\2" freesasa_h_data
> "${freesasa_h_data}")
> +-file(WRITE ${freesasa_h} "${freesasa_h_data}")
> ++#file(WRITE ${freesasa_h} "${freesasa_h_data}")
> + 
> + add_definitions(-DUSE_THREADS=0)
> + add_definitions(-DUSE_JSON=0)
> + add_definitions(-DUSE_XML=0)
> +-rdkit_library(freesasa_clib ${freesasa_clib_srcs})
> +-target_compile_definitions(freesasa_clib PRIVATE
> RDKIT_FREESASALIB_BUILD)
> ++#rdkit_library(freesasa_clib ${freesasa_clib_srcs})
> ++#target_compile_definitions(freesasa_clib PRIVATE
> RDKIT_FREESASALIB_BUILD)
> + 
> + if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32))
> +   set_target_properties(freesasa_clib PROPERTIES
> WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
> + endif()
> +-include_directories("${FREESASA_SRC_DIR}/src")
> ++#include_directories("${FREESASA_SRC_DIR}/src")
> + 
> + rdkit_library(FreeSASALib RDFreeSASA.cpp SHARED 
> +-    LINK_LIBRARIES freesasa_clib GraphMol )
> ++    LINK_LIBRARIES -lfreesasa GraphMol )
> + target_compile_definitions(FreeSASALib PRIVATE
> RDKIT_FREESASALIB_BUILD)
> + 
> + rdkit_headers(RDFreeSASA.h DEST GraphMol)
> +diff -ur a/External/YAeHMOP/CMakeLists.txt
> b/External/YAeHMOP/CMakeLists.txt
> +--- a/External/YAeHMOP/CMakeLists.txt
> ++++ b/External/YAeHMOP/CMakeLists.txt
> +@@ -18,32 +18,32 @@
> + 
> + include_directories( ${RDKit_ExternalDir}/YAeHMOP )
> + 
> +-ExternalProject_Add(yaehmop_project
> +-  GIT_REPOSITORY https://github.com/greglandrum/yaehmop.git
> +-  GIT_TAG master
> +-  UPDATE_COMMAND ""
> +-  PATCH_COMMAND ""
> +-  PREFIX ${CMAKE_CURRENT_SOURCE_DIR}
> +-  SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop"
> +-  SOURCE_SUBDIR "tightbind"
> +-  CMAKE_ARGS -DUSE_BLAS_LAPACK=OFF -
> DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR} -
> DCMAKE_C_FLAGS=${CMAKE_C_FLAGS} -
> DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
> +-  TEST_COMMAND "")
> +-
> +-include_directories(${PROJECT_BINARY_DIR}/include)
> +-link_directories(${PROJECT_BINARY_DIR}/lib)
> +-link_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-
> build)
> +-
> +-set(EHT_PARAM_FILE
> ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat )
> +-install(FILES ${EHT_PARAM_FILE}
> +-        DESTINATION ${RDKit_ShareDir}/Data
> +-        COMPONENT data)
> ++#ExternalProject_Add(yaehmop_project
> ++#  GIT_REPOSITORY https://github.com/greglandrum/yaehmop.git
> ++#  GIT_TAG master
> ++#  UPDATE_COMMAND ""
> ++#  PATCH_COMMAND ""
> ++#  PREFIX ${CMAKE_CURRENT_SOURCE_DIR}
> ++#  SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop"
> ++#  SOURCE_SUBDIR "tightbind"
> ++#  CMAKE_ARGS -DUSE_BLAS_LAPACK=OFF -
> DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR} -
> DCMAKE_C_FLAGS=${CMAKE_C_FLAGS} -
> DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
> ++#  TEST_COMMAND "")
> ++
> ++#include_directories(${PROJECT_BINARY_DIR}/include)
> ++#link_directories(${PROJECT_BINARY_DIR}/lib)
> ++#link_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-
> build)
> ++
> ++#set(EHT_PARAM_FILE
> ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat )
> ++#install(FILES ${EHT_PARAM_FILE}
> ++#        DESTINATION ${RDKit_ShareDir}/Data
> ++#        COMPONENT data)
> + 
> +-message("YAeHMOP include_dirs: ${PROJECT_BINARY_DIR}/include")
> +-message("YAeHMOP link_dirs: ${PROJECT_BINARY_DIR}/lib
> ${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build")
> ++#message("YAeHMOP include_dirs: ${PROJECT_BINARY_DIR}/include")
> ++#message("YAeHMOP link_dirs: ${PROJECT_BINARY_DIR}/lib
> ${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build")
> + 
> +-rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES yaehmop_eht
> GraphMol )
> ++rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES -
> lyaehmop_eht GraphMol )
> + target_compile_definitions(EHTLib PRIVATE RDKIT_EHTLIB_BUILD)
> +-add_dependencies(EHTLib yaehmop_project)
> ++#add_dependencies(EHTLib yaehmop_project)
> + rdkit_headers(EHTTools.h DEST GraphMol)
> + rdkit_catch_test(testEHTLib1 test1.cpp
> +            LINK_LIBRARIES EHTLib FileParsers SmilesParse )
Cheers

[bug#58261] [PATCH v2 13/13] gnu: Add rdkit.

[David Elsing]

Liliana Marie Prikler <liliana.prikler@gmail.com> writes:

> Am Freitag, dem 07.10.2022 um 15:22 +0000 schrieb David Elsing:
>> * gnu/packages/chemistry.scm (rdkit): New variable.
>> ---
>>  gnu/packages/chemistry.scm                    | 178
>> ++++++++++++++++++
>>  .../rdkit-cmake-external-dependencies.patch   | 102 ++++++++++
>>  2 files changed, 280 insertions(+)
>>  create mode 100644 gnu/packages/patches/rdkit-cmake-external-
>> dependencies.patch
>> 
>> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
>> index 43953238cd..4b34a38797 100644
>> --- a/gnu/packages/chemistry.scm
>> +++ b/gnu/packages/chemistry.scm
>> @@ -34,6 +34,7 @@ (define-module (gnu packages chemistry)
>>    #:use-module (gnu packages algebra)
>>    #:use-module (gnu packages autotools)
>>    #:use-module (gnu packages backup)
>> +  #:use-module (gnu packages base)
>>    #:use-module (gnu packages bison)
>>    #:use-module (gnu packages boost)
>>    #:use-module (gnu packages check)
>> @@ -41,10 +42,12 @@ (define-module (gnu packages chemistry)
>>    #:use-module (gnu packages cpp)
>>    #:use-module (gnu packages documentation)
>>    #:use-module (gnu packages flex)
>> +  #:use-module (gnu packages fonts)
>>    #:use-module (gnu packages fontutils)
>>    #:use-module (gnu packages gcc)
>>    #:use-module (gnu packages gl)
>>    #:use-module (gnu packages graphviz)
>> +  #:use-module (gnu packages gtk)
>>    #:use-module (gnu packages gv)
>>    #:use-module (gnu packages image)
>>    #:use-module (gnu packages maths)
>> @@ -56,6 +59,7 @@ (define-module (gnu packages chemistry)
>>    #:use-module (gnu packages qt)
>>    #:use-module (gnu packages serialization)
>>    #:use-module (gnu packages sphinx)
>> +  #:use-module (gnu packages sqlite)
>>    #:use-module (gnu packages stb)
>>    #:use-module (gnu packages tex)
>>    #:use-module (gnu packages web)
>> @@ -1101,3 +1105,177 @@ (define-public ringdecomposerlib
>>  unique ring families, relevant cycles, the smallest set of smallest
>> rings and
>>  other ring topology descriptions.")
>>      (license license:bsd-3)))
>> +
>> +(define-public rdkit
>> +  (package
>> +    (name "rdkit")
>> +    (version "2022.03.5")
>> +    (source (origin
>> +              (method git-fetch)
>> +              (uri (git-reference
>> +                    (url "https://github.com/rdkit/rdkit")
>> +                    (commit
>> +                     (string-append
>> +                      "Release_" (string-replace-substring version
>> "." "_")))))
>> +              (file-name (git-file-name name version))
>> +              (sha256
>> +               (base32
>> +               
>> "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9"))
>> +              (patches
>> +               (search-patches "rdkit-cmake-external-
>> dependencies.patch"))
>> +              (modules '((guix build utils)))
>> +              (snippet
>> +               #~(begin
>> +                   ;; Remove pickle files (only used in tests),
>> +                   ;; as they are compiled programs
>> +                   (for-each
>> +                    (lambda (name)
>> +                      (display (string-append name "\n"))
>> +                      (delete-file name))
>> +                    (find-files "." "\\.pkl(\\.gz)?$"))
>> +                   ;; Remove SQLite data files (can be generated)
>> +                   (delete-file "Data/RDData.sqlt")
>> +                   (delete-file "Data/RDTests.sqlt")))))
>> +    (build-system cmake-build-system)
>> +    (arguments
>> +     (list
>> +      #:imported-modules (append %cmake-build-system-modules
>> +                                 '((guix build python-build-
>> system)))
>> +      #:modules '((guix build cmake-build-system)
>> +                  (guix build utils)
>> +                  ((guix build python-build-system)
>> +                   #:select (add-installed-pythonpath)))
>> +      #:configure-flags
>> +      #~(list
>> +         "-DRDK_BUILD_AVALON_SUPPORT=ON"
>> +         "-DRDK_BUILD_CAIRO_SUPPORT=ON"
>> +         "-DRDK_BUILD_CPP_TESTS=ON"
>> +         "-DRDK_BUILD_FREESASA_SUPPORT=ON"
>> +         "-DRDK_BUILD_INCHI_SUPPORT=ON"
>> +         "-DRDK_BUILD_YAEHMOP_SUPPORT=ON"
> Are any of these implied or do they have to be explicitly enabled?
Oops, I overlooked some, now only flags changing the default are specified.
>> +         (string-append "-DCATCH_DIR="
>> +                        #$(this-package-native-input "catch2")
>> +                        "/include/catch2")
>> +         "-DRDK_INSTALL_DEV_COMPONENT=ON"
>> +         "-DRDK_INSTALL_INTREE=OFF"
>> +         "-DRDK_INSTALL_STATIC_LIBS=OFF"
>> +         (string-append
>> +          "-DRDK_OPTIMIZE_POPCNT="
>> +          #$(let ((system (or (%current-target-system)
>> +                              (%current-system))))
>> +              (cond
>> +               ((string-prefix? "x86_64" system) "ON")
>> +               ((string-prefix? "i686" system) "ON")
>> +               (else "OFF"))))
>> +         "-DRDK_USE_BOOST_IOSTREAMS=ON"
>> +         "-DRDK_USE_FLEXBISON=ON")
>> +      #:phases
>> +      #~(modify-phases %standard-phases
>> +          (add-after 'unpack 'copy-external-dependencies
>> +            (lambda _
>> +              (symlink
>> +               (string-append
>> +                #$(this-package-input "font-comic-neue")
>> +                "/share/fonts/truetype/ComicNeue-Regular.ttf")
>> +               "Data/Fonts/ComicNeue-Regular.ttf")))
> Try (search-input-file) instead.
>> +          (add-after 'copy-external-dependencies 'patch-source
>> +            (lambda _
>> +              (substitute* "External/AvalonTools/CMakeLists.txt"
>> +                (("^if\\(NOT RDK_BUILD" orig)
>> +                 (string-append "if(0)\n" orig))
>> +                (("include_directories.*AVALON_SRC_PATH.*")
>> +                 (string-append "endif()\ninclude_directories("
>> +                                #$avalontoolkit
>> "/include/avalontoolkit)\n"))
>> +                (("LINK_LIBRARIES avalon_clib")
>> +                 (string-append
>> +                  "LINK_LIBRARIES -L" #$avalontoolkit "/lib -
>> lavalontoolkit")))
>> +              (let ((port
>> +                     (open-file "External/RingFamilies/dummy.cpp"
>> "w")))
>> +                (display "" port)
>> +                (close port))
>> +              (let ((port
>> +                     (open-file
>> "External/RingFamilies/CMakeLists.txt" "w")))
>> +                (display (string-append
>> +                          "rdkit_library(RingDecomposerLib dummy.cpp
>> SHARED"
>> +                          " LINK_LIBRARIES -lRingDecomposerLib)\n"
>> +                          "set(RDK_URF_LIBS RingDecomposerLib CACHE
>> STRING \"\" FORCE)\n")
>> +                         port)
>> +                (close port))
>> +              (substitute*
>> "Code/GraphMol/MolInterchange/CMakeLists.txt"
>> +                (("if\\(NOT" orig)
>> +                 (string-append "if(0)\n" orig))
>> +                (("^include_directories.*") "endif()\n"))
>> +              (substitute* "External/YAeHMOP/EHTTools.cpp"
>> +                (("<yaehmop/tightbind/bind.h>")
>> "<yaehmop/bind.h>"))))
> I think you might want to unbundle these with a patch.
Is the patch ok?
>> +          (add-after 'unpack 'fix-inchi-include
>> +            (lambda _
>> +              (substitute* "Code/cmake/Modules/FindInchi.cmake"
>> +                (("inchi_api.h.*\\)") "inchi/inchi_api.h)")
>> +                (("INCHI_LIBRARY NAMES.*\\)")
>> +                 "INCHI_LIBRARY NAMES inchi PATH_SUFFIXES inchi)")
>> +                (("find_library" prev)
>> +                 (string-append
>> +                  "list(APPEND CMAKE_FIND_LIBRARY_SUFFIXES .so.1)\n"
>> +                  prev)))
>> +              (substitute* "External/INCHI-API/inchi.cpp"
>> +                (("<inchi_api.h>") "<inchi/inchi_api.h>"))))
>> +          (add-before 'build 'enable-bytecode-determinism
>> +              (lambda _
>> +                (setenv "PYTHONHASHSEED" "0")
>> +                (setenv "PYTHONDONTWRITEBYTECODE" "1")))
>> +          (add-after 'install 'pre-check
>> +            (lambda* (#:key inputs outputs #:allow-other-keys)
>> +              (with-directory-excursion "../source"
>> +                (invoke "sqlite3" "Data/RDData.sqlt"
>> +                        ".read rdkit/Dbase/test_data/RDData.sqlite")
>> +                (invoke "sqlite3" "Data/RDTests.sqlt"
>> +                        ".read
>> rdkit/Dbase/test_data/RDTests.sqlite")
>> +                (setenv "RDBASE" (canonicalize-path ".")))
>> +              (add-installed-pythonpath inputs outputs)))
>> +          (delete 'check)
>> +          (add-after 'pre-check 'check
>> +            (lambda* (#:key tests? parallel-tests? #:allow-other-
>> keys)
>> +              (when tests?
>> +                (let ((job-count (number->string
>> +                                  (if parallel-tests? (parallel-job-
>> count) 1))))
>> +                  (invoke
>> +                   "ctest" "-j" job-count
>> +                   "-E" (string-append
>> +                         "(" (string-join
>> +                              '(;; need pickled data
>> +                                "(pyDiscreteValueVect"
>> "pySparseIntVect"
>> +                                "graphmoltestPickler"
>> "pyPartialCharges"
>> +                                "substructLibraryTest" "pyFeatures"
>> +                                "pythonTestDirML"
>> "pythonTestDirChem"
>> +                                ;; Catching Python exception fails
>> +                                "pyRanker)") "|") ")")))))))))
> I think you have two layers of brackets now – delete the inner ones.
Oh thanks!
>> +    (native-inputs
>> +     (list bison
>> +           boost
>> +           catch2
>> +           eigen
>> +           flex
>> +           freesasa
>> +           pkg-config
>> +           rapidjson
>> +           tar))
>> +    (inputs
>> +     (list avalontoolkit
>> +           cairo
>> +           coordgenlibs
>> +           font-comic-neue
>> +           freetype
>> +           inchi
>> +           maeparser
>> +           python
>> +           ringdecomposerlib
>> +           sqlite
>> +           yaehmop))
>> +    (propagated-inputs
>> +     (list python-numpy python-cairocffi python-pillow))
>> +    (home-page "https://rdkit.org/")
>> +    (synopsis "Collection of cheminformatics software")
>> +    (description "RDKit is a C++ and Python library for
>> cheminformatics, which
>> +includes (among other things) the analysis and modification of
>> molecules in 2D
>> +and 3D and descriptor generation for machine learning.")
>> +    (license license:bsd-3)))
>> diff --git a/gnu/packages/patches/rdkit-cmake-external-
>> dependencies.patch b/gnu/packages/patches/rdkit-cmake-external-
>> dependencies.patch
>> new file mode 100644
>> index 0000000000..5b73864f51
>> --- /dev/null
>> +++ b/gnu/packages/patches/rdkit-cmake-external-dependencies.patch
>> @@ -0,0 +1,102 @@
>> +diff -ur a/External/FreeSASA/CMakeLists.txt
>> b/External/FreeSASA/CMakeLists.txt
>> +--- a/External/FreeSASA/CMakeLists.txt
>> ++++ b/External/FreeSASA/CMakeLists.txt
>> +@@ -10,7 +10,7 @@
>> +   endif()
>> + endif()
>> + 
>> +-if(needDownload)
>> ++if(FALSE)
>> +   # don't actually use the md5 here
>> +   set(FREESASA_VERSION "2.0.3")
>> +   set(FREESASA_SRC_DIR "${CMAKE_CURRENT_SOURCE_DIR}/freesasa-
>> ${FREESASA_VERSION}")
>> +@@ -66,24 +66,24 @@
>> + endif()
>> + 
>> + set (freesasa_h ${FREESASA_SRC_DIR}/src/freesasa.h)
>> +-file(READ ${freesasa_h} freesasa_h_data)
>> ++#file(READ ${freesasa_h} freesasa_h_data)
>> + string(REGEX REPLACE "(#include <stdio.h>)" "\\1\n#include
>> <RDGeneral/export.h>" freesasa_h_data "${freesasa_h_data}")
>> + string(REGEX REPLACE
>> "([^R][^D][^K][^I][^T][^_][^F][^R][^E][^E][^S][^A][^S][^A][^_][^C][^L
>> ][^I][^B][^_][^E][^X][^P][^O][^R][^T][^ ])(extern const)"
>> "\\1RDKIT_FREESASA_CLIB_EXPORT \\2" freesasa_h_data
>> "${freesasa_h_data}")
>> +-file(WRITE ${freesasa_h} "${freesasa_h_data}")
>> ++#file(WRITE ${freesasa_h} "${freesasa_h_data}")
>> + 
>> + add_definitions(-DUSE_THREADS=0)
>> + add_definitions(-DUSE_JSON=0)
>> + add_definitions(-DUSE_XML=0)
>> +-rdkit_library(freesasa_clib ${freesasa_clib_srcs})
>> +-target_compile_definitions(freesasa_clib PRIVATE
>> RDKIT_FREESASALIB_BUILD)
>> ++#rdkit_library(freesasa_clib ${freesasa_clib_srcs})
>> ++#target_compile_definitions(freesasa_clib PRIVATE
>> RDKIT_FREESASALIB_BUILD)
>> + 
>> + if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32))
>> +   set_target_properties(freesasa_clib PROPERTIES
>> WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
>> + endif()
>> +-include_directories("${FREESASA_SRC_DIR}/src")
>> ++#include_directories("${FREESASA_SRC_DIR}/src")
>> + 
>> + rdkit_library(FreeSASALib RDFreeSASA.cpp SHARED 
>> +-    LINK_LIBRARIES freesasa_clib GraphMol )
>> ++    LINK_LIBRARIES -lfreesasa GraphMol )
>> + target_compile_definitions(FreeSASALib PRIVATE
>> RDKIT_FREESASALIB_BUILD)
>> + 
>> + rdkit_headers(RDFreeSASA.h DEST GraphMol)
>> +diff -ur a/External/YAeHMOP/CMakeLists.txt
>> b/External/YAeHMOP/CMakeLists.txt
>> +--- a/External/YAeHMOP/CMakeLists.txt
>> ++++ b/External/YAeHMOP/CMakeLists.txt
>> +@@ -18,32 +18,32 @@
>> + 
>> + include_directories( ${RDKit_ExternalDir}/YAeHMOP )
>> + 
>> +-ExternalProject_Add(yaehmop_project
>> +-  GIT_REPOSITORY https://github.com/greglandrum/yaehmop.git
>> +-  GIT_TAG master
>> +-  UPDATE_COMMAND ""
>> +-  PATCH_COMMAND ""
>> +-  PREFIX ${CMAKE_CURRENT_SOURCE_DIR}
>> +-  SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop"
>> +-  SOURCE_SUBDIR "tightbind"
>> +-  CMAKE_ARGS -DUSE_BLAS_LAPACK=OFF -
>> DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR} -
>> DCMAKE_C_FLAGS=${CMAKE_C_FLAGS} -
>> DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
>> +-  TEST_COMMAND "")
>> +-
>> +-include_directories(${PROJECT_BINARY_DIR}/include)
>> +-link_directories(${PROJECT_BINARY_DIR}/lib)
>> +-link_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-
>> build)
>> +-
>> +-set(EHT_PARAM_FILE
>> ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat )
>> +-install(FILES ${EHT_PARAM_FILE}
>> +-        DESTINATION ${RDKit_ShareDir}/Data
>> +-        COMPONENT data)
>> ++#ExternalProject_Add(yaehmop_project
>> ++#  GIT_REPOSITORY https://github.com/greglandrum/yaehmop.git
>> ++#  GIT_TAG master
>> ++#  UPDATE_COMMAND ""
>> ++#  PATCH_COMMAND ""
>> ++#  PREFIX ${CMAKE_CURRENT_SOURCE_DIR}
>> ++#  SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop"
>> ++#  SOURCE_SUBDIR "tightbind"
>> ++#  CMAKE_ARGS -DUSE_BLAS_LAPACK=OFF -
>> DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR} -
>> DCMAKE_C_FLAGS=${CMAKE_C_FLAGS} -
>> DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
>> ++#  TEST_COMMAND "")
>> ++
>> ++#include_directories(${PROJECT_BINARY_DIR}/include)
>> ++#link_directories(${PROJECT_BINARY_DIR}/lib)
>> ++#link_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-
>> build)
>> ++
>> ++#set(EHT_PARAM_FILE
>> ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat )
>> ++#install(FILES ${EHT_PARAM_FILE}
>> ++#        DESTINATION ${RDKit_ShareDir}/Data
>> ++#        COMPONENT data)
>> + 
>> +-message("YAeHMOP include_dirs: ${PROJECT_BINARY_DIR}/include")
>> +-message("YAeHMOP link_dirs: ${PROJECT_BINARY_DIR}/lib
>> ${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build")
>> ++#message("YAeHMOP include_dirs: ${PROJECT_BINARY_DIR}/include")
>> ++#message("YAeHMOP link_dirs: ${PROJECT_BINARY_DIR}/lib
>> ${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build")
>> + 
>> +-rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES yaehmop_eht
>> GraphMol )
>> ++rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES -
>> lyaehmop_eht GraphMol )
>> + target_compile_definitions(EHTLib PRIVATE RDKIT_EHTLIB_BUILD)
>> +-add_dependencies(EHTLib yaehmop_project)
>> ++#add_dependencies(EHTLib yaehmop_project)
>> + rdkit_headers(EHTTools.h DEST GraphMol)
>> + rdkit_catch_test(testEHTLib1 test1.cpp
>> +            LINK_LIBRARIES EHTLib FileParsers SmilesParse )
> Cheers