[PATCH] gnu: Add coda.

[PATCH] gnu: Add coda.

[Thomas Danckaert]

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This is a C library wich also presents a python interface.  It can be 
used just as well without python, so I've made python only a native 
input, not a regular input.  There's currently a non-determinism 
issue for the python interface, related to 
https://debbugs.gnu.org/cgi/bugreport.cgi?bug=22533

I also tried to automatically generate the string 
“lib/python3.4/site-packages”, so it's updated automatically when the 
python version changes, but didn't manage to do that (for example I 
tried

   (version-major+minor (package-version python))

but the package variable “python” is not available when the build 
expression is turned into a derivation, as far as I understand it?). 
Advice welcome.

Thomas

[-- Attachment #2: 0001-gnu-Add-coda.patch --]
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From edb38dfcc09afdef4279728c84d10688b9d0fc71 Mon Sep 17 00:00:00 2001
From: Thomas Danckaert <thomas.danckaert@gmail.com>
Date: Wed, 19 Oct 2016 11:44:33 +0200
Subject: [PATCH] gnu: Add coda.

* gnu/packages/maths.scm (coda): New variable.
---
 gnu/packages/maths.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 07934e3..f28d8b4 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -113,6 +113,42 @@ interactive dialogs to guide them.")
    (license license:gpl3+)
    (home-page "http://www.gnu.org/software/c-graph/")))
 
+(define-public coda
+  (package
+    (name "coda")
+    (version "2.17.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/stcorp/coda/releases/download/"
+                           version "/coda-" version ".tar.gz"))
+       (sha256
+        (base32 "04b9l3wzcix0mnfq77mwnil6cbr8h2mki8myvy0lzn236qcwaq1h"))))
+    (native-inputs
+     `(("fortran" ,gfortran)
+       ("python" ,python)
+       ("python-numpy" ,python-numpy)))
+    (inputs
+     `(("zlib" ,zlib)
+       ("hdf4" ,hdf4-alt)
+       ("hdf5" ,hdf5)))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python")))
+    (native-search-paths
+     (list (search-path-specification
+            (variable "PYTHONPATH")
+            (files '("lib/python3.4/site-packages")))))
+    (synopsis "Common interface to various earth observation data formats")
+    (description
+     "The Common Data Access toolbox (CODA) provides a set of interfaces for
+reading remote sensing data from earth observation data files.  These
+interfaces consist of command line applications, libraries, interfaces to
+scientific applications (such as IDL and MATLAB), and interfaces to
+programming languages (such as C, Fortran, Python, and Java).")
+    (home-page "https://stcorp.nl/coda")
+    (license license:gpl2)))
+
 (define-public units
   (package
    (name "units")
-- 
2.7.4

Re: [PATCH] gnu: Add coda.

[Ludovic Courtès]

Thomas Danckaert <post@thomasdanckaert.be> skribis:

> This is a C library wich also presents a python interface.  It can be
> used just as well without python, so I've made python only a native
> input, not a regular input.  There's currently a non-determinism issue
> for the python interface, related to
> https://debbugs.gnu.org/cgi/bugreport.cgi?bug=22533
>
> I also tried to automatically generate the string
> “lib/python3.4/site-packages”, so it's updated automatically when the
> python version changes, but didn't manage to do that (for example I
> tried
>
>   (version-major+minor (package-version python))
>
> but the package variable “python” is not available when the build
> expression is turned into a derivation, as far as I understand
> it?). Advice welcome.

I think this is not needed; see below.

> From edb38dfcc09afdef4279728c84d10688b9d0fc71 Mon Sep 17 00:00:00 2001
> From: Thomas Danckaert <thomas.danckaert@gmail.com>
> Date: Wed, 19 Oct 2016 11:44:33 +0200
> Subject: [PATCH] gnu: Add coda.
>
> * gnu/packages/maths.scm (coda): New variable.

[...]

> +    (native-search-paths
> +     (list (search-path-specification
> +            (variable "PYTHONPATH")
> +            (files '("lib/python3.4/site-packages")))))

Unless I’m mistaken this is not needed: this ‘native-search-paths’ entry
belongs in Python itself, not in users of Python.

> +    (synopsis "Common interface to various earth observation data formats")
> +    (description
> +     "The Common Data Access toolbox (CODA) provides a set of interfaces for
> +reading remote sensing data from earth observation data files.  These
> +interfaces consist of command line applications, libraries, interfaces to
> +scientific applications (such as IDL and MATLAB), and interfaces to

Let’s remove MATLAB; we can replace it with Octave if it’s valid.

> +    (license license:gpl2)))

Version 2 only?  That is, is the “or any later version” wording missing
from license headers?

Otherwise LGTM.

Could you send an updated patch?

Thank you!

Ludo’.

Re: [PATCH] gnu: Add coda.

[Thomas Danckaert]

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From: ludo@gnu.org (Ludovic Courtès)
Subject: Re: [PATCH] gnu: Add coda.
Date: Wed, 19 Oct 2016 22:13:42 +0200

>> +    (native-search-paths
>> +     (list (search-path-specification
>> +            (variable "PYTHONPATH")
>> +            (files '("lib/python3.4/site-packages")))))
>
> Unless I’m mistaken this is not needed: this ‘native-search-paths’ 
> entry
> belongs in Python itself, not in users of Python.

I used ipython to test the interface, and noticed the PYTHONPATH 
setting was missing.  That's why I added it here.  So probably this 
native-search-paths entry could/should be added to the ipython 
package?

>> +    (synopsis "Common interface to various earth observation data 
>> formats")
>> +    (description
>> +     "The Common Data Access toolbox (CODA) provides a set of 
>> interfaces for
>> +reading remote sensing data from earth observation data files.  
>> These
>> +interfaces consist of command line applications, libraries, 
>> interfaces to
>> +scientific applications (such as IDL and MATLAB), and interfaces 
>> to
>
> Let’s remove MATLAB; we can replace it with Octave if it’s valid.

I removed IDL as well, because it's the same story as Matlab 
(proprietary scripting language for scientific applications).  I 
don't think there's an Octave interface, unless Octave can 
automatically use interfaces written for Matlab (unlikely? I have no 
experience with either).

>> +    (license license:gpl2)))
>
> Version 2 only?  That is, is the “or any later version” wording 
> missing
> from license headers?

gpl2+, indeed.

I've attached an updated patch.

cheers,

Thomas

[-- Attachment #2: 0001-gnu-Add-coda.patch --]
[-- Type: Text/X-Patch, Size: 1836 bytes --]

From f521132ac56e3ad6f7e6169fa1a0fcd56beb77f6 Mon Sep 17 00:00:00 2001
From: Thomas Danckaert <thomas.danckaert@gmail.com>
Date: Wed, 19 Oct 2016 11:44:33 +0200
Subject: [PATCH] gnu: Add coda.

* gnu/packages/maths.scm (coda): New variable.
---
 gnu/packages/maths.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 07934e3..c3c5b68 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -113,6 +113,37 @@ interactive dialogs to guide them.")
    (license license:gpl3+)
    (home-page "http://www.gnu.org/software/c-graph/")))
 
+(define-public coda
+  (package
+    (name "coda")
+    (version "2.17.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/stcorp/coda/releases/download/"
+                           version "/coda-" version ".tar.gz"))
+       (sha256
+        (base32 "04b9l3wzcix0mnfq77mwnil6cbr8h2mki8myvy0lzn236qcwaq1h"))))
+    (native-inputs
+     `(("fortran" ,gfortran)
+       ("python" ,python)
+       ("python-numpy" ,python-numpy)))
+    (inputs
+     `(("zlib" ,zlib)
+       ("hdf4" ,hdf4-alt)
+       ("hdf5" ,hdf5)))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python")))
+    (synopsis "A common interface to various earth observation data formats")
+    (description
+     "The Common Data Access toolbox (CODA) provides a set of interfaces for
+reading remote sensing data from earth observation data files.  It consists of
+command line applications and interfaces to the C, Fortran, Python, and Java
+programming languages.")
+    (home-page "https://stcorp.nl/coda")
+    (license license:gpl2+)))
+
 (define-public units
   (package
    (name "units")
-- 
2.7.4

Re: [PATCH] gnu: Add coda.

[Ludovic Courtès]

Thomas Danckaert <post@thomasdanckaert.be> skribis:

> From: ludo@gnu.org (Ludovic Courtès)
> Subject: Re: [PATCH] gnu: Add coda.
> Date: Wed, 19 Oct 2016 22:13:42 +0200
>
>>> +    (native-search-paths
>>> +     (list (search-path-specification
>>> +            (variable "PYTHONPATH")
>>> +            (files '("lib/python3.4/site-packages")))))
>>
>> Unless I’m mistaken this is not needed: this ‘native-search-paths’
>> entry
>> belongs in Python itself, not in users of Python.
>
> I used ipython to test the interface, and noticed the PYTHONPATH
> setting was missing.  That's why I added it here.  So probably this
> native-search-paths entry could/should be added to the ipython
> package?

Probably not.  I think the problem is as described in
<http://bugs.gnu.org/22138>.

>>> +    (synopsis "Common interface to various earth observation data
>>> formats")
>>> +    (description
>>> +     "The Common Data Access toolbox (CODA) provides a set of
>>> interfaces for
>>> +reading remote sensing data from earth observation data files.
>>> These
>>> +interfaces consist of command line applications, libraries,
>>> interfaces to
>>> +scientific applications (such as IDL and MATLAB), and interfaces
>>> to
>>
>> Let’s remove MATLAB; we can replace it with Octave if it’s valid.
>
> I removed IDL as well, because it's the same story as Matlab
> (proprietary scripting language for scientific applications).  I don't
> think there's an Octave interface, unless Octave can automatically use
> interfaces written for Matlab (unlikely? I have no experience with
> either).

OK.  ISTR Octave can work with “MEX files”, but I’m no expert.

> From f521132ac56e3ad6f7e6169fa1a0fcd56beb77f6 Mon Sep 17 00:00:00 2001
> From: Thomas Danckaert <thomas.danckaert@gmail.com>
> Date: Wed, 19 Oct 2016 11:44:33 +0200
> Subject: [PATCH] gnu: Add coda.
>
> * gnu/packages/maths.scm (coda): New variable.

Applied, thanks!

However I noticed that Coda bundles copies of zlib, pcre, and expat.

Could you send a patch that (1) adds those as inputs and makes sure the
bundled copies are not used (using ‘guix gc --references’ on the
result), and (2) removes the corresponding directories from the source
tree in a ‘snippet’, if possible?

Ludo’.

Re: [PATCH] gnu: Add coda.

[Thomas Danckaert]

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Thanks for applying!

From: ludo@gnu.org (Ludovic Courtès)
Subject: Re: [PATCH] gnu: Add coda.
Date: Mon, 24 Oct 2016 23:24:17 +0200

> However I noticed that Coda bundles copies of zlib, pcre, and expat.

I hadn't noticed that. I've attached a patch.

cheers,

Thomas

[-- Attachment #2: 0001-gnu-coda-Remove-bundled-libraries.patch --]
[-- Type: Text/X-Patch, Size: 5719 bytes --]

From 56ba046e6c176e8f1109bb28ab75a586daa287db Mon Sep 17 00:00:00 2001
From: Thomas Danckaert <thomas.danckaert@gmail.com>
Date: Tue, 25 Oct 2016 10:56:46 +0200
Subject: [PATCH] gnu: coda: Remove bundled libraries.

* gnu/packages/maths.scm (coda): Remove bundled libraries.
[source]: Add patch and snippet to remove bundled zlib, pcre and expat.
[inputs]: Add system zlib, pcre and expat.
* gnu/packages/patches/coda-use-system-libs.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
---
 gnu/local.mk                                    |  1 +
 gnu/packages/maths.scm                          | 13 +++++--
 gnu/packages/patches/coda-use-system-libs.patch | 46 +++++++++++++++++++++++++
 3 files changed, 58 insertions(+), 2 deletions(-)
 create mode 100644 gnu/packages/patches/coda-use-system-libs.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 51849f4..4ffd37a 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -484,6 +484,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/clucene-pkgconfig.patch			\
   %D%/packages/patches/clx-remove-demo.patch			\
   %D%/packages/patches/cmake-fix-tests.patch			\
+  %D%/packages/patches/coda-use-system-libs.patch		\
   %D%/packages/patches/cpio-CVE-2016-2037.patch			\
   %D%/packages/patches/cpufrequtils-fix-aclocal.patch		\
   %D%/packages/patches/cracklib-CVE-2016-6318.patch		\
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 2928cb6..70a6212 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -123,18 +123,27 @@ interactive dialogs to guide them.")
        (uri (string-append "https://github.com/stcorp/coda/releases/download/"
                            version "/coda-" version ".tar.gz"))
        (sha256
-        (base32 "04b9l3wzcix0mnfq77mwnil6cbr8h2mki8myvy0lzn236qcwaq1h"))))
+        (base32 "04b9l3wzcix0mnfq77mwnil6cbr8h2mki8myvy0lzn236qcwaq1h"))
+       (patches (search-patches "coda-use-system-libs.patch"))
+       (modules '((guix build utils)))
+       (snippet ;; Make sure we don't use the bundled software.
+        '(map (lambda (d)
+                (delete-file-recursively (string-append "libcoda/" d) ))
+              '("zlib" "pcre" "expat")))))
     (native-inputs
      `(("fortran" ,gfortran)
        ("python" ,python)
        ("python-numpy" ,python-numpy)))
     (inputs
      `(("zlib" ,zlib)
+       ("pcre" ,pcre)
+       ("expat" ,expat)
        ("hdf4" ,hdf4-alt)
        ("hdf5" ,hdf5)))
     (build-system gnu-build-system)
     (arguments
-     '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python")))
+     '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
+                           "LIBS= -lz -lpcre -lexpat")))
     (synopsis "A common interface to various earth observation data formats")
     (description
      "The Common Data Access toolbox (CODA) provides a set of interfaces for
diff --git a/gnu/packages/patches/coda-use-system-libs.patch b/gnu/packages/patches/coda-use-system-libs.patch
new file mode 100644
index 0000000..fbf8441
--- /dev/null
+++ b/gnu/packages/patches/coda-use-system-libs.patch
@@ -0,0 +1,46 @@
+Remove dependencies on bundled zlib, pcre and expat.
+
+diff --git a/Makefile.in b/Makefile.in
+index 4360a26..80f9f59 100644
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -210,8 +210,7 @@ coda_matlab_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \
+ @BUILD_MATLAB_TRUE@@SUBPACKAGE_MODE_FALSE@	-rpath \
+ @BUILD_MATLAB_TRUE@@SUBPACKAGE_MODE_FALSE@	$(matlabmexexecdir)
+ am__DEPENDENCIES_1 =
+-libcoda_la_DEPENDENCIES = @LTLIBOBJS@ libexpat_internal.la \
+-	libpcre_internal.la libz_internal.la $(am__DEPENDENCIES_1) \
++libcoda_la_DEPENDENCIES = @LTLIBOBJS@ $(am__DEPENDENCIES_1) \
+ 	$(am__DEPENDENCIES_1)
+ am__libcoda_la_SOURCES_DIST = libcoda/coda-ascbin-cursor.c \
+ 	libcoda/coda-ascbin.h libcoda/coda-ascii-cursor.c \
+@@ -306,8 +305,7 @@ libcoda_la_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
+ 	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
+ 	$(libcoda_la_LDFLAGS) $(LDFLAGS) -o $@
+ @SUBPACKAGE_MODE_FALSE@am_libcoda_la_rpath = -rpath $(libdir)
+-am__DEPENDENCIES_2 = @LTLIBOBJS@ libexpat_internal.la \
+-	libpcre_internal.la libz_internal.la $(am__DEPENDENCIES_1) \
++am__DEPENDENCIES_2 = @LTLIBOBJS@ $(am__DEPENDENCIES_1) \
+ 	$(am__DEPENDENCIES_1)
+ libcoda_internal_la_DEPENDENCIES = $(am__DEPENDENCIES_2)
+ am__libcoda_internal_la_SOURCES_DIST = libcoda/coda-ascbin-cursor.c \
+@@ -898,8 +896,8 @@ INSTALL_DATA_HOOK_TARGETS = $(am__append_1)
+ UNINSTALL_HOOK_TARGETS = 
+ CLEAN_LOCAL_TARGETS = $(am__append_11)
+ ALL_LOCAL_TARGETS = 
+-@SUBPACKAGE_MODE_FALSE@noinst_LTLIBRARIES = libcoda_internal.la libexpat_internal.la libpcre_internal.la libz_internal.la
+-@SUBPACKAGE_MODE_TRUE@noinst_LTLIBRARIES = libcoda_internal.la libexpat_internal.la libpcre_internal.la libz_internal.la
++@SUBPACKAGE_MODE_FALSE@noinst_LTLIBRARIES = libcoda_internal.la
++@SUBPACKAGE_MODE_TRUE@noinst_LTLIBRARIES = libcoda_internal.la
+ 
+ # libraries (+ related files)
+ @SUBPACKAGE_MODE_FALSE@lib_LTLIBRARIES = libcoda.la
+@@ -1048,7 +1046,7 @@ libcoda_hdf5_files = \
+ 
+ libcoda_la_CPPFLAGS = -Ilibcoda/expat -I$(srcdir)/libcoda/expat -Ilibcoda/pcre -I$(srcdir)/libcoda/pcre -Ilibcoda/zlib -I$(srcdir)/libcoda/zlib $(AM_CPPFLAGS)
+ libcoda_la_LDFLAGS = -no-undefined -version-info $(LIBCODA_CURRENT):$(LIBCODA_REVISION):$(LIBCODA_AGE)
+-libcoda_la_LIBADD = @LTLIBOBJS@ libexpat_internal.la libpcre_internal.la libz_internal.la $(HDF4LIBS) $(HDF5LIBS)
++libcoda_la_LIBADD = @LTLIBOBJS@ $(HDF4LIBS) $(HDF5LIBS)
+ libcoda_internal_la_SOURCES = libcoda/coda-ascbin-cursor.c \
+ 	libcoda/coda-ascbin.h libcoda/coda-ascii-cursor.c \
+ 	libcoda/coda-ascii-internal.h libcoda/coda-ascii.c \
-- 
2.7.4

Re: [PATCH] gnu: Add coda.

[Ludovic Courtès]

Thomas Danckaert <post@thomasdanckaert.be> skribis:

> From 56ba046e6c176e8f1109bb28ab75a586daa287db Mon Sep 17 00:00:00 2001
> From: Thomas Danckaert <thomas.danckaert@gmail.com>
> Date: Tue, 25 Oct 2016 10:56:46 +0200
> Subject: [PATCH] gnu: coda: Remove bundled libraries.
>
> * gnu/packages/maths.scm (coda): Remove bundled libraries.
> [source]: Add patch and snippet to remove bundled zlib, pcre and expat.
> [inputs]: Add system zlib, pcre and expat.
> * gnu/packages/patches/coda-use-system-libs.patch: New file.
> * gnu/local.mk (dist_patch_DATA): Add it.

Woow, that was fast!

> +       (snippet ;; Make sure we don't use the bundled software.
> +        '(map (lambda (d)
> +                (delete-file-recursively (string-append "libcoda/" d) ))
                                                                        ^
I changed ‘map’ to ‘for-each’, to make it clear that this expression is
used for effects, and removed the extra space above.

Pushed, thanks!

Ludo’.