* [bug#64446] [PATCH] gnu: Add bliss.
@ 2023-07-03 21:21 David Elsing
2023-07-26 16:10 ` Andreas Enge
2023-07-26 16:22 ` [bug#64446] [PATCH] " Andreas Enge
0 siblings, 2 replies; 6+ messages in thread
From: David Elsing @ 2023-07-03 21:21 UTC (permalink / raw)
To: 64446; +Cc: David Elsing, andreas, efraim, bavier
* gnu/packages/maths.scm (bliss): New variable.
---
The Makefile is rudimentary, so it is easier to call g++ directly.
I did not include GMP, as it is only used to express group sizes exactly.
gnu/packages/maths.scm | 87 ++++++++++++++++++++++++++++++++++++++++++
1 file changed, 87 insertions(+)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 653e76027a..ff0aa6170b 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -8529,3 +8529,90 @@ (define-public scilab
optimization, and modeling, simulation of explicit and implicit dynamical
systems and symbolic manipulations.")
(license license:cecill))) ;CeCILL v2.1
+
+(define-public bliss
+ (package
+ (name "bliss")
+ (version "0.73")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://www.tcs.hut.fi/Software/bliss/bliss-"
+ version ".zip"))
+ (sha256
+ (base32
+ "110ggzyn4fpsq3haisv7pzkgfs5x1m7802r4n5cas30l0hlg6yzm"))))
+ (outputs (list "out" "doc"))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:tests? #f ; No tests
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'fix-string-macro
+ (lambda _
+ (substitute* "bliss.cc"
+ (("\"__DATE__\"") "\" __DATE__ \""))))
+ ;; Move headers under the bliss/ prefix
+ (add-after 'unpack 'move-headers
+ (lambda _
+ (substitute* (find-files "." "\\.(h|hh|cc)$")
+ (("#include \"(.*)\"" all path)
+ (string-append "#include <bliss/" path ">")))
+ (mkdir-p "bliss")
+ (for-each
+ (lambda (file)
+ (rename-file file
+ (string-append "bliss/" (basename file))))
+ (find-files "." "\\.(h|hh)$"))))
+ (add-after 'move-headers 'disable-gmp
+ (lambda _
+ (substitute* "bliss/bignum.hh"
+ (("defined\\(BLISS_USE_GMP\\)") "0"))))
+ (delete 'configure)
+ (replace 'build
+ (lambda _
+ (let ((source-files
+ '("defs" "graph" "partition" "orbit" "uintseqhash" "heap"
+ "timer" "utils")))
+ (for-each
+ (lambda (file)
+ (display (string-append "Compiling " file "\n"))
+ (invoke "g++" "-I." "-fPIC" "-c" "-o"
+ (string-append file ".o")
+ (string-append file ".cc")))
+ source-files)
+ (let ((object-files
+ (map (lambda (file) (string-append file ".o"))
+ source-files)))
+ (display (string-append "Linking shared library\n"))
+ (apply invoke "g++" "-I." "-fPIC" "-shared"
+ "-o" "libbliss.so"
+ "bliss_C.cc"
+ object-files)
+ (display (string-append "Building bliss\n"))
+ (apply invoke "g++" "-I." "-o" "bliss.out" "bliss.cc"
+ "-L." "-lbliss"
+ (string-append "-Wl,-rpath=" #$output:out "/lib")
+ object-files)))))
+ (add-after 'build 'build-doc
+ (lambda _
+ (substitute* "Doxyfile"
+ (("INPUT *=.*") "INPUT = . bliss\n"))
+ (invoke "doxygen")))
+ (replace 'install
+ (lambda _
+ (install-file "libbliss.so" (string-append #$output:out "/lib"))
+ (mkdir-p (string-append #$output:out "/bin/"))
+ (copy-file "bliss.out" (string-append #$output:out "/bin/bliss"))
+ (copy-recursively "bliss"
+ (string-append #$output:out "/include/bliss"))
+ (copy-recursively
+ "html" (string-append #$output:doc "/share/doc/"
+ #$name "-" #$version "/html")))))))
+ (native-inputs (list doxygen unzip))
+ (home-page "http://www.tcs.hut.fi/Software/bliss/index.shtml")
+ (synopsis "Tool for computing automorphism groups and canonical labelings of graphs")
+ (description "@code{bliss} is a library for computing automorphism groups
+and canonical forms of graphs. It has both a command line user interface as
+well as C++ and C programming language APIs.")
+ (license license:lgpl3)))
--
2.40.1
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [bug#64446] [PATCH] gnu: Add bliss.
2023-07-03 21:21 [bug#64446] [PATCH] gnu: Add bliss David Elsing
@ 2023-07-26 16:10 ` Andreas Enge
2023-09-20 22:14 ` David Elsing
2023-07-26 16:22 ` [bug#64446] [PATCH] " Andreas Enge
1 sibling, 1 reply; 6+ messages in thread
From: Andreas Enge @ 2023-07-26 16:10 UTC (permalink / raw)
To: David Elsing; +Cc: 64446, efraim, bavier
Hello,
I have spent quite a long time on this package, trying to simplify your
recipe.
Am Mon, Jul 03, 2023 at 09:21:32PM +0000 schrieb David Elsing:
> + (add-after 'unpack 'fix-string-macro
> + (lambda _
> + (substitute* "bliss.cc"
> + (("\"__DATE__\"") "\" __DATE__ \""))))
This so far is only a warning with newer gcc versions, so we do not really
need it.
> + ;; Move headers under the bliss/ prefix
> + (add-after 'unpack 'move-headers
> + (lambda _
> + (substitute* (find-files "." "\\.(h|hh|cc)$")
> + (("#include \"(.*)\"" all path)
> + (string-append "#include <bliss/" path ">")))
> + (mkdir-p "bliss")
> + (for-each
> + (lambda (file)
> + (rename-file file
> + (string-append "bliss/" (basename file))))
> + (find-files "." "\\.(h|hh)$"))))
All surprising phases need more comments for their rationale.
I added this:
;; Move headers under the bliss/ prefix. This is a Guix choice,
;; since the header names are sufficiently generic to cause
;; confusions with other packages ("heap.hh").
> + (add-after 'move-headers 'disable-gmp
> + (lambda _
> + (substitute* "bliss/bignum.hh"
> + (("defined\\(BLISS_USE_GMP\\)") "0"))))
This looks like it is not needed if using the Makefile.
> + (replace 'build
Here I am not convinced. You end up rewriting the Makefile in Guile.
The Makefile works, but it tries to create a binary "bliss", which
collides with the new file for the headers. This could be solved by
moving the content of the 'move-headers phase between the installation
of the bliss binary (after which it can be deleted) and the installation
of the headers.
Moreover, the Makefile does not create a dynamic, but only a static
library, and your build phase adds a dynamic library. Is this our role
as packagers?
According to the time stamps of the files inside the .zip, the software
dates from 2015 and is apparently unmaintained (otherwise I would have
suggested to get in touch with the developers to improve the Makefile).
So I wonder whether this software meets the quality standards for inclusion
into Guix.
Hm, I just found a new version here:
https://users.aalto.fi/~tjunttil/bliss/index.html :
"Compiling
In Linux and macOS, one can use GNU Make to compile the bliss executable, as well as the static and shared libraries, with (...)"!
And the author is here:
https://users.aalto.fi/~tjunttil/
Would you like to give it another try, David? And maybe discuss with the
author whether they would be willing to implement the bliss/ subdirectory
for the headers? (Given that there are now separate src/ and build/
subdirectories that would be quite easy.) And add an "install" target?
Andreas
^ permalink raw reply [flat|nested] 6+ messages in thread
* [bug#64446] [PATCH] gnu: Add bliss.
2023-07-03 21:21 [bug#64446] [PATCH] gnu: Add bliss David Elsing
2023-07-26 16:10 ` Andreas Enge
@ 2023-07-26 16:22 ` Andreas Enge
1 sibling, 0 replies; 6+ messages in thread
From: Andreas Enge @ 2023-07-26 16:22 UTC (permalink / raw)
To: David Elsing; +Cc: 64446, efraim, bavier
Am Mon, Jul 03, 2023 at 09:21:32PM +0000 schrieb David Elsing:
> + (outputs (list "out" "doc"))
Oh, and I think the documentation is sufficiently small to be kept in the
same package.
Andreas
^ permalink raw reply [flat|nested] 6+ messages in thread
* [bug#64446] [PATCH] gnu: Add bliss.
2023-07-26 16:10 ` Andreas Enge
@ 2023-09-20 22:14 ` David Elsing
2023-09-20 22:19 ` [bug#64446] [PATCH v2] " David Elsing
0 siblings, 1 reply; 6+ messages in thread
From: David Elsing @ 2023-09-20 22:14 UTC (permalink / raw)
To: Andreas Enge; +Cc: 64446, efraim, bavier
Andreas Enge <andreas@enge.fr> writes:
Hello,
thanks for your comments! I noticed that igraph actually contains a
bundled copy of bliss which uses GMP, so I added it as a dependency
here.
> ;; Move headers under the bliss/ prefix. This is a Guix choice,
> ;; since the header names are sufficiently generic to cause
> ;; confusions with other packages ("heap.hh").
In igraph, the bundled copy also has the files under the bliss/ prefix,
so I think it's good we do the same.
> Would you like to give it another try, David? And maybe discuss with the
> author whether they would be willing to implement the bliss/ subdirectory
> for the headers? (Given that there are now separate src/ and build/
> subdirectories that would be quite easy.) And add an "install" target?
I updated the package using the CMake build files in the new version.
During unbundling bliss from igraph, I saw that it also contains
a copy of CXSparse, which led me to split SuiteSparse into its
subpackages: https://issues.guix.gnu.org/66129.
When updating the igraph package, it would be good to use the
suitesparse-cxsparse package right away, so I did not include it yet.
The build with the bliss package succeeds however.
Cheers,
David
^ permalink raw reply [flat|nested] 6+ messages in thread
* [bug#64446] [PATCH v2] gnu: Add bliss.
2023-09-20 22:14 ` David Elsing
@ 2023-09-20 22:19 ` David Elsing
2023-10-11 17:11 ` bug#64446: " Ludovic Courtès
0 siblings, 1 reply; 6+ messages in thread
From: David Elsing @ 2023-09-20 22:19 UTC (permalink / raw)
To: 64446; +Cc: David Elsing
* gnu/packages/maths.scm (bliss): New variable.
---
gnu/packages/maths.scm | 85 ++++++++++++++++++++++++++++++++++++++++++
1 file changed, 85 insertions(+)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 6141c09886..76ac34a5d9 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -8567,3 +8567,88 @@ (define-public ruy
architecture.")
(license license:asl2.0))))
+(define-public bliss
+ (package
+ (name "bliss")
+ (version "0.77")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://users.aalto.fi/~tjunttil/bliss/downloads/bliss-"
+ version ".zip"))
+ (sha256
+ (base32
+ "193jb63kdwfas2cf61xj3fgkvhb6v2mnbwwpr0jas3zk6j0bkj5c"))))
+ (build-system cmake-build-system)
+ (arguments
+ (list
+ ;; There are no tests
+ #:tests? #f
+ #:configure-flags #~(list "-DUSE_GMP=ON") ; Used by igraph
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; Ensure that GMP is used, otherwise the BigNum type changes.
+ (add-after 'unpack 'define-use-gmp
+ (lambda _
+ (substitute* "src/bignum.hh"
+ (("#pragma once.*" all)
+ (string-append all "#define BLISS_USE_GMP")))))
+ ;; Move headers under the bliss/ prefix. This is a Guix choice,
+ ;; since there are no upstream installation instructions and the
+ ;; header names are sufficiently generic to cause confusions with
+ ;; other packages (e.g. "heap.hh").
+ (add-after 'define-use-gmp 'move-headers
+ (lambda _
+ (substitute* (find-files "src")
+ (("#include \"(.*)\"" _ path)
+ (string-append "#include <bliss/" path ">")))
+ (mkdir-p "include/bliss")
+ (for-each
+ (lambda (file)
+ (rename-file file
+ (string-append "include/bliss/" (basename file))))
+ (find-files "src" "\\.(h|hh)$"))
+ (substitute* "Doxyfile"
+ (("INPUT *=.*") "INPUT = bliss"))))
+ (add-after 'move-headers 'patch-cmake
+ (lambda _
+ (let ((port (open-file "CMakeLists.txt" "a")))
+ (display
+ (apply
+ string-append
+ ;; Install the executable and the shared library.
+ "install(TARGETS bliss)\n"
+ "install(TARGETS bliss-executable)\n"
+ "install(DIRECTORY include/bliss DESTINATION include)\n"
+ "target_link_libraries(bliss PUBLIC ${GMP_LIBRARIES})\n"
+ ;; Missing include directories.
+ (map
+ (lambda (name)
+ (string-append
+ "target_include_directories(" name " PUBLIC\n"
+ "${CMAKE_CURRENT_SOURCE_DIR}/include"
+ " ${GMP_INCLUDE_DIR})\n"))
+ '("bliss" "bliss_static" "bliss-executable")))
+ port)
+ (close-port port))))
+ (add-after 'build 'build-doc
+ (lambda _
+ (mkdir "doc")
+ (with-directory-excursion "doc"
+ (let ((srcdir (string-append "../../bliss-" #$version)))
+ (copy-recursively (string-append srcdir "/include/bliss")
+ "bliss")
+ (invoke "doxygen" (string-append srcdir "/Doxyfile"))))))
+ (add-after 'install 'install-doc
+ (lambda _
+ (copy-recursively
+ "doc/html" (string-append #$output "/share/doc/"
+ #$name "-" #$version "/html")))))))
+ (native-inputs (list doxygen graphviz unzip))
+ (propagated-inputs (list gmp))
+ (home-page "https://users.aalto.fi/~tjunttil/bliss/index.html")
+ (synopsis "Tool for computing automorphism groups and canonical labelings of graphs")
+ (description "@code{bliss} is a library for computing automorphism groups
++and canonical forms of graphs. It has both a command line user interface as
++well as C++ and C programming language APIs.")
+ (license license:lgpl3)))
--
2.41.0
^ permalink raw reply related [flat|nested] 6+ messages in thread
* bug#64446: [PATCH v2] gnu: Add bliss.
2023-09-20 22:19 ` [bug#64446] [PATCH v2] " David Elsing
@ 2023-10-11 17:11 ` Ludovic Courtès
0 siblings, 0 replies; 6+ messages in thread
From: Ludovic Courtès @ 2023-10-11 17:11 UTC (permalink / raw)
To: David Elsing; +Cc: Andreas Enge, 64446-done
Hi,
David Elsing <david.elsing@posteo.net> skribis:
> * gnu/packages/maths.scm (bliss): New variable.
I believe this version addresses the concerns Andreas raised. Applied!
Ludo’.
^ permalink raw reply [flat|nested] 6+ messages in thread
end of thread, other threads:[~2023-10-11 17:12 UTC | newest]
Thread overview: 6+ messages (download: mbox.gz / follow: Atom feed)
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2023-07-03 21:21 [bug#64446] [PATCH] gnu: Add bliss David Elsing
2023-07-26 16:10 ` Andreas Enge
2023-09-20 22:14 ` David Elsing
2023-09-20 22:19 ` [bug#64446] [PATCH v2] " David Elsing
2023-10-11 17:11 ` bug#64446: " Ludovic Courtès
2023-07-26 16:22 ` [bug#64446] [PATCH] " Andreas Enge
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