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