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

[Roman Scherer <roman.scherer@burningswell.com>]

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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.


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From 0fcc8aa4999271d0f50aac8bed9a9c826c88a392 Mon Sep 17 00:00:00 2001
From: r0man <roman@burningswell.com>
Date: Sat, 3 Dec 2022 18:15:04 +0100
Subject: [PATCH 1/4] gnu: gdal: Update to 3.6.0.

* gnu/packages/geo.scm (gdal): Update to 3.6.0.
---
 gnu/packages/geo.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index abfa5963b9..bfce9399c3 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -1043,7 +1043,7 @@ (define-public spatialite-gui
 (define-public gdal
   (package
     (name "gdal")
-    (version "3.5.1")
+    (version "3.6.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1051,7 +1051,7 @@ (define-public gdal
                      version ".tar.gz"))
               (sha256
                (base32
-                "1l93q7xf6qx9ck5axfkf3ygmvclxkvrjd8x00ckn7j0d0750ci3w"))
+                "1nri6p495chlm63dcylq2wwmvlf90pn2kr3jf5ybkby6q3p7jshd"))
               (modules '((guix build utils)))
               (snippet
                 `(begin
-- 
2.38.1


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From d740188e07a5368fd0e01a8aa24a6e515ecebc9e Mon Sep 17 00:00:00 2001
From: r0man <roman@burningswell.com>
Date: Sat, 3 Dec 2022 18:59:02 +0100
Subject: [PATCH 2/4] gnu: gdal: Add support for lz4 and openjpeg.

* gnu/packages/geo.scm (gdal): Add support for lz4 and openjpeg.
---
 gnu/packages/geo.scm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index bfce9399c3..ba348dbb7d 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -1084,8 +1084,10 @@ (define-public gdal
            libpng
            libtiff
            libwebp
+           lz4
            netcdf
            openssl
+           openjpeg
            pcre2
            postgresql ; libpq
            proj
-- 
2.38.1


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From a6deb05aabbbea9b0e0ccb79887e524ddd99e589 Mon Sep 17 00:00:00 2001
From: r0man <roman@burningswell.com>
Date: Sat, 10 Dec 2022 12:16:21 +0100
Subject: [PATCH 3/4] gnu: libtiff: Update to 4.4.0.

* gnu/packages/image.scm (libtiff): Update to 4.4.0.
---
 gnu/packages/image.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index bc1f25627b..9427d022d9 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -569,7 +569,7 @@ (define-public libicns
 (define-public libtiff
   (package
    (name "libtiff")
-   (version "4.3.0")
+   (version "4.4.0")
    (source
      (origin
        (method url-fetch)
@@ -577,7 +577,7 @@ (define-public libtiff
                            version ".tar.gz"))
        (sha256
         (base32
-         "1j3snghqjbhwmnm5vz3dr1zm68dj15mgbx1wqld7vkl7n2nfaihf"))))
+         "1vdbk3sc497c58kxmp02irl6nqkfm9rjs3br7g59m59qfnrj6wli"))))
    (build-system gnu-build-system)
    (outputs '("out"
               "doc"))                           ;1.8 MiB of HTML documentation
-- 
2.38.1


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From 4ab999dfcab8b999d6256e328667a07aa7cb5e76 Mon Sep 17 00:00:00 2001
From: r0man <roman@burningswell.com>
Date: Sat, 10 Dec 2022 12:18:20 +0100
Subject: [PATCH 4/4] gnu: netcdf: Update to 4.9.0.

* gnu/packages/maths.scm (netcdf): Update to 4.9.0.
* gnu/packages/patches/netcdf-4.9.0-fix-cmake-typo.patch
---
 gnu/packages/maths.scm                        | 46 +++++++++++++------
 .../patches/netcdf-4.9.0-fix-cmake-typo.patch | 23 ++++++++++
 2 files changed, 55 insertions(+), 14 deletions(-)
 create mode 100644 gnu/packages/patches/netcdf-4.9.0-fix-cmake-typo.patch

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index aee050735e..057e9651c2 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1850,16 +1850,16 @@ (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
@@ -1867,20 +1867,35 @@ (define-public netcdf
         ;; multiple-definition link error with GCC 10.
         '(substitute* "ncdump/ocprint.c"
            (("^int ocdebug") "static int ocdebug")))
-       (patches (search-patches "netcdf-date-time.patch"))))
-    (build-system gnu-build-system)
+       (patches (search-patches "netcdf-date-time.patch"
+                                "netcdf-4.9.0-fix-cmake-typo.patch"))))
+    (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=OFF"
+         "-DENABLE_DAP_REMOTE_TESTS=OFF"
+         "-DENABLE_EXAMPLE_TESTS=OFF"
+         "-DENABLE_EXTRA_TESTS=OFF"
+         "-DENABLE_FILTER_TESTING=OFF"
+         "-DENABLE_LARGE_FILE_TESTS=OFF"
+         "-DENABLE_UNIT_TESTS=OFF"
+         "-DSOURCE_DATE_EPOCH=0")
+       #:phases
+       (modify-phases %standard-phases
+         (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
@@ -1900,8 +1915,11 @@ (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")
diff --git a/gnu/packages/patches/netcdf-4.9.0-fix-cmake-typo.patch b/gnu/packages/patches/netcdf-4.9.0-fix-cmake-typo.patch
new file mode 100644
index 0000000000..b9c0ed5c10
--- /dev/null
+++ b/gnu/packages/patches/netcdf-4.9.0-fix-cmake-typo.patch
@@ -0,0 +1,23 @@
+From 80a6611cfca98a5979c5ac69cba56a49af8c1e48 Mon Sep 17 00:00:00 2001
+From: Yuriy Chernyshov <thegeorg@yandex-team.com>
+Date: Sun, 19 Jun 2022 19:29:20 +0300
+Subject: [PATCH] Fix typo in CMakeLists.txt
+
+At the time generated dynamic library is named `libnetcdf.so.19}` which looks like a typo.
+---
+ CMakeLists.txt | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 7bf8641bec..18366d24ad 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -39,5 +39,5 @@ SET(NC_VERSION ${netCDF_VERSION})
+ SET(PACKAGE_VERSION ${VERSION})
+
+ # These values should match those in configure.ac
+-SET(netCDF_LIB_VERSION 19})
++SET(netCDF_LIB_VERSION 19)
+ SET(netCDF_SO_VERSION 19)
+
+ # Version of the dispatch table. This must match the value in
-- 
2.38.1


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