diff mbox series

[bug#60039] Update GDAL and NetCDF and include lz4 and openjpeg support

Message ID 86v8m5nava.fsf@burningswell.com
State New
Headers show
Series [bug#60039] Update GDAL and NetCDF and include lz4 and openjpeg support | expand

Commit Message

Roman Scherer Dec. 20, 2022, 7:10 p.m. UTC 
Hi Guillaume,

here's the updated patch for Netcdf. I checked the tests again, I
believe I left some of them off by accident after trying a couple of
things. So, I enabled some of them again. They pass. However, I left the
remote and large file tests still turned off.

I believe the remote tests we do not want anyway on Guix CICD
system. Is that correct? And the large file tests seem to take ages. Can
we ignore them, because they are super annoying?

Thanks for the review.

Wdyt?

Roman.
Guillaume Le Vaillant <glv@posteo.net> writes:

> [[PGP Signed Part:Undecided]]
> Roman Scherer <roman.scherer@burningswell.com> skribis:
>
>> Hello Guix,
>>
>> this patch series updates the GDAL, Netcdf and libtiff packages. It also
>> adds support for lz4 and openjpeg to GDAL.
>>
>> Could you please review it?
>>
>> Thanks, Roman.
>>
>> [2. text/x-diff; 0001-gnu-gdal-Update-to-3.6.0.patch]...
>
> Hi,
>
> Instead of this patch 1, I pushed the patch from issue 60159 that updates
> gdal to 3.6.1.
>
>
>> [3. text/x-diff; 0002-gnu-gdal-Add-support-for-lz4-and-openjpeg.patch]...
>
> Patch 2 pushed as 3c6f7b53cea7ea5dc8176fec02271bc3770d7fc1.
>
>
>> [4. text/x-diff; 0003-gnu-libtiff-Update-to-4.4.0.patch]...
>
> As libtiff as over 9000 dependents, it has to be updated on the
> core-updates branch instead of master (see [1]). However, libtiff is
> already at version 4.4.0 on core-updates, so patch 3 is not necessary
> and libtiff 4.4.0 will end up in master when core-updates gets merged.
>
> [1] https://guix.gnu.org/manual/devel/en/guix.html#Submitting-Patches
>
>
>> [5. text/x-diff; 0004-gnu-netcdf-Update-to-4.9.0.patch]...
>
> When adding or removing a patch file to "gnu/packages/patches/...", the
> 'dist_patch_DATA' variable in "gnu/packages/local.mk" has to be updated
> to track the necessary patch files.
> Moreover, as this patch fixes only one line, it is also possible to add
> a custom phase with a '(substitute* ...)' form in the 'arguments' field
> instead of adding a patch file.
> Could you send an updated patch 4?
> Thanks.
>
> Also, many tests are disabled in 'configure-flags'. Are they not working
> at all?
>
> [[End of PGP Signed Part]]

Comments

Guillaume Le Vaillant Dec. 22, 2022, 10:41 a.m. UTC | #1 
Roman Scherer <roman.scherer@burningswell.com> skribis:

> Hi Guillaume,
>
> here's the updated patch for Netcdf. I checked the tests again, I
> believe I left some of them off by accident after trying a couple of
> things. So, I enabled some of them again. They pass. However, I left the
> remote and large file tests still turned off.
>
> I believe the remote tests we do not want anyway on Guix CICD
> system. Is that correct? And the large file tests seem to take ages. Can
> we ignore them, because they are super annoying?
>
> Thanks for the review.
>
> Wdyt?
>
> Roman.
>
> [2. text/x-diff; 0005-gnu-netcdf-Update-to-4.9.0.patch]...

Hi,

The build environment doesn't have network access, so indeed remote
tests have to be disabled.

The netcdf-parallel-openmpi package fails to build with the updated
netcdf. I think it's because the package definition for
netcdf-parallel-openmpi inherits from the package definition for netcdf,
so it has to be updated to take into consideration the build-system
change of netcdf.

There are also some dependents that fail to build (cdo, python-h5netcdf,
python-meshio, qgis). I saw some error messages about conflicting
versions of hdf5, probably because in your patch netcdf uses hdf5-1.12
and the dependents also have hdf5 (v1.10) in their dependency graph in
some way. Maybe this could be fixed by using hdf5 instead of hdf5-1.12
for netcdf...

Could take a look?
diff mbox series

Patch

From eb2a03112532f6c1482ebaf1634cf3ac67303507 Mon Sep 17 00:00:00 2001
From: r0man <roman@burningswell.com>
Date: Tue, 20 Dec 2022 20:06:57 +0100
Subject: [PATCH] gnu: netcdf: Update to 4.9.0.

* gnu/packages/maths.scm (netcdf): Update to 4.9.0.
---
 gnu/packages/maths.scm | 50 +++++++++++++++++++++++++++++++-----------
 1 file changed, 37 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 050450e12c..a5de0f4016 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1852,16 +1852,16 @@  (define-public itpp
 (define-public netcdf
   (package
     (name "netcdf")
-    (version "4.7.4")
+    (version "4.9.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append
-             "https://www.unidata.ucar.edu/downloads/netcdf/ftp/"
-             "netcdf-c-" version ".tar.gz"))
+             "https://downloads.unidata.ucar.edu/netcdf-c/" version
+             "/netcdf-c-" version ".tar.gz"))
        (sha256
         (base32
-         "1a2fpp15a2rl1m50gcvvzd9y6bavl6vjf9zzf63sz5gdmq06yiqf"))
+         "0j8b814mjdqvqanzmrxpq8hn33n22cdzb3gf9vhya24wnwi615ac"))
        (modules '((guix build utils)))
        (snippet
         ;; Make sure this variable is defined only once.  Failing to do so
@@ -1870,19 +1870,40 @@  (define-public netcdf
         '(substitute* "ncdump/ocprint.c"
            (("^int ocdebug") "static int ocdebug")))
        (patches (search-patches "netcdf-date-time.patch"))))
-    (build-system gnu-build-system)
+    (build-system cmake-build-system)
     (native-inputs
-     (list m4 doxygen graphviz))
+     (list m4 doxygen graphviz unzip))
     (inputs
      `(("hdf4" ,hdf4-alt)
-       ("hdf5" ,hdf5)
+       ("hdf5" ,hdf5-1.12)
        ("curl" ,curl)
        ("zlib" ,zlib)
-       ("libjpeg" ,libjpeg-turbo)))
+       ("libjpeg" ,libjpeg-turbo)
+       ("libxml2" ,libxml2)))
     (arguments
-     `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
-
-       #:phases (modify-phases %standard-phases
+     `(#:configure-flags
+       '("-DENABLE_BYTERANGE=ON"
+         "-DENABLE_CDF5=ON"
+         "-DENABLE_DAP_LONG_TESTS=ON"
+         "-DENABLE_DAP_REMOTE_TESTS=OFF"
+         "-DENABLE_EXAMPLE_TESTS=ON"
+         "-DENABLE_EXTRA_TESTS=ON"
+         "-DENABLE_FILTER_TESTING=ON"
+         "-DENABLE_LARGE_FILE_TESTS=OFF"
+         "-DENABLE_UNIT_TESTS=ON"
+         "-DSOURCE_DATE_EPOCH=0")
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'fix-cmake-typo
+           (lambda _
+             ;; Fix a typo in CMakeLists.txt
+             (substitute* "CMakeLists.txt"
+               (("SET\\(netCDF_LIB_VERSION 19\\}\\)")
+                "SET(netCDF_LIB_VERSION 19)"))
+             #t))
+         (add-before 'configure 'disable-nc-byterange-test
+           (lambda _
+             (invoke "sed" "-i" "/test_byterange/d" "nc_test/CMakeLists.txt")))
          (add-before 'configure 'fix-source-date
            (lambda _
              ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
@@ -1902,8 +1923,11 @@  (define-public netcdf
              (substitute* "libnetcdf.settings"
                (("(/gnu/store/)([0-9A-Za-z]*)" all prefix hash)
                 (string-append prefix (string-take hash 10) "...")))
-             #t)))
-
+             #t))
+         (add-before 'check 'fix-test-rcmerge
+           (lambda _
+             ;; Set HOME, to fix the test-rcmerge.
+             (setenv "HOME" "/tmp"))))
        #:parallel-tests? #f))           ;various race conditions
     (home-page "https://www.unidata.ucar.edu/software/netcdf/")
     (synopsis "Library for scientific data")
-- 
2.38.1