Subject: [bug#77590] [PATCH v4 1/5] gnu: hdf5: Update to 1.14.6.

From: David Elsing <[email-masked]>
Date: Mon, 14 Apr 2025 17:09:24 +0000

* gnu/packages/maths.scm (hdf5): Update to 1.14.6. Do not inherit from
hdf5-1.8.
[name, version]: New field.
[source]: Switch to git-fetch. Add modules and snippet fields. Use different
patch file.
[build-system]: New field. Use CMake.
[inputs]: New field.
[native-inputs]: New field. Add bison, flex and which.
[arguments]: Do not inherit from hdf5-1.8.
<#:configure-flags>: New field.
<#:phases>: New field. Use gexps. Remove 'patch-configure, 'patch-settings,
'patch-references, 'split, 'skip-version-test and
'patch-configure-build-settings phases.  Add 'make-gen-deterministic,
'generate-flexbison, 'patch-trace-shebang, 'fix-fortran-i686-test and
'generate-headers phases.
[home-page, synopsis, description]: New fields.
[license]: New field. Adjust URL.
* gnu/packages/patches/hdf5-config-dependencies.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
---
 gnu/local.mk                                  |   1 +
 gnu/packages/maths.scm                        | 193 +++++++++++++-----
 .../patches/hdf5-config-dependencies.patch    |  31 +++
 3 files changed, 171 insertions(+), 54 deletions(-)
 create mode 100644 gnu/packages/patches/hdf5-config-dependencies.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 8ff2af1474..714798768f 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1572,6 +1572,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/hdf4-reproducibility.patch 		\
   %D%/packages/patches/hdf4-shared-fortran.patch 		\
   %D%/packages/patches/hdf5-config-date.patch			\
+  %D%/packages/patches/hdf5-config-dependencies.patch		\
   %D%/packages/patches/hdf-eos2-build-shared.patch 		\
   %D%/packages/patches/hdf-eos2-remove-gctp.patch		\
   %D%/packages/patches/hdf-eos2-fortrantests.patch		\
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 11a86216aa..ddea48a046 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -62,7 +62,7 @@
 ;;; Copyright © 2022 Roman Scherer <[email-masked]>
 ;;; Copyright © 2023 Jake Leporte <[email-masked]>
 ;;; Copyright © 2023 Camilo Q.S. (Distopico) <[email-masked]>
-;;; Copyright © 2023 David Elsing <[email-masked]>
+;;; Copyright © 2023, 2025 David Elsing <[email-masked]>
 ;;; Copyright © 2024 Herman Rimm <[email-masked]>
 ;;; Copyright © 2024 Foundation Devices, Inc. <[email-masked]>
 ;;; Copyright © 2024, 2025 Artyom V. Poptsov <[email-masked]>
@@ -137,6 +137,7 @@ (define-module (gnu packages maths)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gd)
+  #:use-module (gnu packages geo)
   #:use-module (gnu packages ghostscript)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gperf)
@@ -1834,44 +1835,141 @@ (define-public hdf5-1.10
         (base32 "14gih7kmjx4h3lc7pg4fwcl28hf1qqkf2x7rljpxqvzkjrqbxi00"))
        (patches (search-patches "hdf5-config-date.patch"))))))
 
-;; When updating this package, please also update hdf-java.
 (define-public hdf5
   (package
-    (inherit hdf5-1.8)
-    (version "1.14.3")
+    (name "hdf5")
+    (version "1.14.6")
     (source
      (origin
-       (method url-fetch)
-       (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
-                                 "hdf5-" (version-major+minor version)
-                                 "/hdf5-" version "/src/hdf5-"
-                                 version ".tar.bz2")
-                  (string-append "https://support.hdfgroup.org/ftp/HDF5/"
-                                 "current"
-                                 (apply string-append
-                                        (take (string-split version #\.) 2))
-                                 "/src/hdf5-" version ".tar.bz2")))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/HDFGroup/hdf5")
+             (commit (string-append "hdf5_" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "05zr11y3bivfwrbvzbky1q2gjf6r7n92cvvdnh5jilbmxljg49cl"))
-       (patches (search-patches "hdf5-config-date.patch"))))
+        (base32
+         "1f7yv0xra465c3qy8c79fzddib653wzj5dsakb0bs02nwp3xm54q"))
+       (modules '((guix build utils)))
+       (snippet
+        '(for-each
+          delete-file
+          (append
+           (find-files "." "Makefile\\.in$")
+           (find-files "java/lib" "\\.jar$")
+           (list "aclocal.m4"
+                 "bin/compile"
+                 "bin/config.guess"
+                 "bin/config.sub"
+                 "bin/depcomp"
+                 "bin/install-sh"
+                 "bin/ltmain.sh"
+                 "bin/missing"
+                 "bin/test-driver"
+                 "configure"
+                 "HDF5Examples/aclocal.m4"
+                 "HDF5Examples/compile"
+                 "HDF5Examples/configure"
+                 "HDF5Examples/depcomp"
+                 "HDF5Examples/missing"
+                 "HDF5Examples/test-driver"
+                 "hl/src/H5LTanalyze.c"
+                 "hl/src/H5LTparse.c"
+                 "hl/src/H5LTparse.h"
+                 "hl/tools/gif2h5/testfiles/ex_image2.h5"
+                 "hl/tools/gif2h5/testfiles/h52giftst.h5"
+                 "m4/ax_prog_doxygen.m4"
+                 "m4/libtool.m4"
+                 "m4/lt~obsolete.m4"
+                 "m4/ltoptions.m4"
+                 "m4/ltsugar.m4"
+                 "m4/ltversion.m4"
+                 "src/H5config.h.in"
+                 "src/H5Edefin.h"
+                 "src/H5Einit.h"
+                 "src/H5Epubgen.h"
+                 "src/H5Eterm.h"
+                 "src/H5overflow.h"
+                 "src/H5version.h"))))
+       (patches (search-patches "hdf5-config-dependencies.patch"))))
+    (build-system cmake-build-system)
     (arguments
-     (substitute-keyword-arguments (package-arguments hdf5-1.8)
-       ((#:phases phases #~%standard-phases)
-        #~(modify-phases #$phases
-            (add-after 'configure 'skip-version-test
-              (lambda _
-                ;; Skip test_check_version since the 'patch-settings' phase
-                ;; modifies the test reference.
-                (substitute* "test/test_check_version.sh.in"
-                  (("TESTING\\(\\).*" all)
-                   (string-append all "\nSKIP; exit 0\n")))))
-            (add-after 'patch-configure 'patch-configure-build-settings
-              (lambda _
-                (substitute* "src/H5build_settings.autotools.c.in"
-                  ;; Don't record the build-time kernel version to make the
-                  ;; library file reproducible.
-                  (("@UNAME_INFO@")
-                   "Linux"))))))))))
+     (list
+      ;; Some of the users, notably Flann, need the C++ interface.
+      #:configure-flags
+      #~(list
+         (string-append "-DHDF5_INSTALL_CMAKE_DIR=" #$output "/lib/cmake")
+         "-DHDF5_BUILD_CPP_LIB=ON"
+         "-DHDF5_BUILD_FORTRAN=ON"
+         ;; Build a thread-safe library.  Unfortunately, CMakeLists.txt
+         ;; invites you to either turn off C++, Fortran, and the high-level
+         ;; interface (HL), or to enable 'ALLOW_UNSUPPORTED'.  Debian
+         ;; packagers chose to pass '--enable-unsupported' to the 'configure'
+         ;; script and we follow their lead here.
+         "-DHDF5_ENABLE_THREADSAFE=ON"
+         "-DALLOW_UNSUPPORTED=ON"
+         "-DHDF5_BUILD_DOC=ON")
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; XXX: src/H5private.h includes <fenv.h> and fails to find the
+          ;; stdlib types when the gfortran header is used.  Remove gfortran
+          ;; from CPLUS_INCLUDE_PATH as a workaround.
+          (add-after 'set-paths 'hide-gfortran
+            (lambda _
+              (let ((gfortran #$(this-package-native-input "gfortran")))
+                (setenv "CPLUS_INCLUDE_PATH"
+                        (string-join
+                         (delete (string-append gfortran "/include/c++")
+                                 (string-split (getenv "CPLUS_INCLUDE_PATH") #\:))
+                         ":")))))
+          (add-after 'unpack 'make-gen-deterministic
+            (lambda _
+              (substitute* "bin/make_err"
+                (("keys %major" all)
+                 (string-append "sort " all))
+                (("while.*each \\(%section\\).*")
+                 (string-append
+                  "foreach $sect_name (sort keys %section) {\n"
+                  "        $sect_desc = $section{$sect_name};\n")))))
+          (add-after 'unpack 'generate-flexbison
+            (lambda _
+              (invoke "bash" "bin/genparser" "hl/src")))
+          (add-after 'unpack 'patch-trace-shebang
+            (lambda _
+              (for-each patch-shebang
+                        (find-files "bin" (lambda (file stat)
+                                            (executable-file? file))))))
+          ;; This is a known issue on i686, see
+          ;; https://github.com/HDFGroup/hdf5/issues/4926
+          (add-after 'unpack 'fix-fortran-i686-test
+            (lambda _
+              (substitute* "fortran/test/tH5R.F90"
+                (((string-append
+                   "CALL h5rget_obj_name_f\\(C_LOC\\(ref_ptr\\(2\\)\\),"
+                   " \"\", error, name_len=buf_size \\)"))
+                 (string-append
+                  "CALL h5rget_obj_name_f(C_LOC(ref_ptr(2)),"
+                  " \"xxxxxxxxxxxxxx\", error, name_len=buf_size)")))))
+          (add-after 'unpack 'generate-headers
+            (lambda _
+              (invoke "perl" "bin/make_err" "src/H5err.txt")
+              (invoke "perl" "bin/make_vers" "src/H5vers.txt")
+              (invoke "perl" "bin/make_overflow" "src/H5overflow.txt"))))))
+    (inputs (list libaec zlib))
+    (native-inputs
+     (list bison
+           doxygen
+           flex
+           gfortran
+           graphviz
+           ;; Needed to generate some headers and for tests
+           perl
+           which))
+    (home-page "https://www.hdfgroup.org")
+    (synopsis "Management suite for extremely large and complex data")
+    (description "HDF5 is a suite that makes possible the management of
+extremely large and complex data collections.")
+    (license (license:x11-style
+              "https://support.hdfgroup.org/ftp/HDF5/releases/COPYING.html"))))
 
 ;; Keep this in sync with the current hdf5 package.
 (define-public hdf-java
@@ -2075,32 +2173,19 @@ (define-public hdf-eos5
 (define-public hdf5-parallel-openmpi
   (package/inherit hdf5
     (name "hdf5-parallel-openmpi")
-    (inputs
-     `(("mpi" ,openmpi)
-       ,@(package-inputs hdf5)))
+    (inputs (modify-inputs (package-inputs hdf5)
+              (prepend openmpi)))
     (arguments
      (substitute-keyword-arguments (package-arguments hdf5)
-       ((#:configure-flags flags)
-        #~(cons "--enable-parallel"
-                (delete "--enable-cxx"
-                        (delete "--enable-threadsafe" #$flags))))
+       ((#:configure-flags _ #f)
+        ''("-DHDF5_ENABLE_THREADSAFE=OFF"
+           "-DHDF5_ENABLE_PARALLEL=ON"
+           "-DHDF5_BUILD_CPP_LIB=OFF"
+           "-DHDF5_BUILD_DOC=ON"))
        ((#:phases phases)
         #~(modify-phases #$phases
             (add-after 'build 'mpi-setup
-              #$%openmpi-setup)
-            (add-before 'check 'patch-tests
-              (lambda _
-                ;; OpenMPI's mpirun will exit with non-zero status if it
-                ;; detects an "abnormal termination", i.e. any process not
-                ;; calling MPI_Finalize().  Since the test is explicitly
-                ;; avoiding MPI_Finalize so as not to have at_exit and thus
-                ;; H5C_flush_cache from being called, mpirun will always
-                ;; complain, so turn this test off.
-                (substitute* "testpar/Makefile"
-                  (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
-                   (string-append front back "\n")))
-                (substitute* "tools/test/h5diff/testph5diff.sh"
-                  (("/bin/sh") (which "sh")))))))))
+              #$%openmpi-setup)))))
     (synopsis "Management suite for data with parallel IO support")))
 
 (define-public hdf5-blosc
diff --git a/gnu/packages/patches/hdf5-config-dependencies.patch b/gnu/packages/patches/hdf5-config-dependencies.patch
new file mode 100644
index 0000000000..cf448dac44
--- /dev/null
+++ b/gnu/packages/patches/hdf5-config-dependencies.patch
@@ -0,0 +1,31 @@
+The installed CMake configuration is missing targets for zlib and
+libaec. Taken from
+https://github.com/microsoft/vcpkg/blob/e36fe7110deac47a3aff8eda3dcc7cfb894a2ebf/ports/hdf5/hdf5_config.patch
+
+diff --git a/config/cmake/hdf5-config.cmake.in b/config/cmake/hdf5-config.cmake.in
+index 1a3fb7bbf2..79081ce040 100644
+--- a/config/cmake/hdf5-config.cmake.in
++++ b/config/cmake/hdf5-config.cmake.in
+@@ -120,12 +114,22 @@ set (${HDF5_PACKAGE_NAME}_VERSION_MINOR  @HDF5_VERSION_MINOR@)
+ # Don't include targets if this file is being picked up by another
+ # project which has already built hdf5 as a subproject
+ #-----------------------------------------------------------------------------
++include(CMakeFindDependencyMacro)
+ if (NOT TARGET "@HDF5_PACKAGE@")
+   if (${HDF5_PACKAGE_NAME}_ENABLE_Z_LIB_SUPPORT AND ${HDF5_PACKAGE_NAME}_PACKAGE_EXTLIBS)
+     include (@PACKAGE_SHARE_INSTALL_DIR@/@ZLIB_PACKAGE_NAME@@[email-masked])
++  elseif (${HDF5_PACKAGE_NAME}_ENABLE_Z_LIB_SUPPORT)
++    find_dependency(ZLIB)
+   endif ()
+   if (${HDF5_PACKAGE_NAME}_ENABLE_SZIP_SUPPORT AND ${HDF5_PACKAGE_NAME}_PACKAGE_EXTLIBS)
+     include (@PACKAGE_SHARE_INSTALL_DIR@/@LIBAEC_PACKAGE_NAME@@[email-masked])
++  elseif (${HDF5_PACKAGE_NAME}_ENABLE_SZIP_SUPPORT)
++    if (${HDF5_PACKAGE_NAME}_BUILD_STATIC_LIBS)
++      set(libaec_USE_STATIC_LIBS ON)
++    else()
++      set(libaec_USE_STATIC_LIBS OFF)
++    endif()
++    find_dependency(libaec)
+   endif ()
+   include (@PACKAGE_SHARE_INSTALL_DIR@/@HDF5_PACKAGE@@[email-masked])
+ endif ()
-- 
2.48.1