andreas pushed a commit to branch master
in repository guix.
commit 8eeb04e205ac22fdb2eaca1017f46a8adb4210c5
Author: David Elsing <david.els...@posteo.net>
AuthorDate: Wed Apr 30 16:27:03 2025 +0000
gnu: hdf5: Update to 1.14.6.
* 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.
(hdf5-parallel-openmpi)[inputs]: Use modify-inputs and drop labels.
[arguments]<#:configure-flags> Use flags for CMake.
<#:phases>: Delete 'patch-tests phase.
* gnu/packages/patches/hdf5-config-dependencies.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
Change-Id: If3a97fe7e252cc48a050ac396a68a87a02600916
Signed-off-by: Andreas Enge <andr...@enge.fr>
---
gnu/local.mk | 1 +
gnu/packages/maths.scm | 193 +++++++++++++++------
.../patches/hdf5-config-dependencies.patch | 31 ++++
3 files changed, 171 insertions(+), 54 deletions(-)
diff --git a/gnu/local.mk b/gnu/local.mk
index 3efe47fe17..f6f95bbf10 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1575,6 +1575,7 @@ 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 ca24446aa8..0759c82ab6 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -62,7 +62,7 @@
;;; Copyright © 2022 Roman Scherer <roman.sche...@burningswell.com>
;;; Copyright © 2023 Jake Leporte <jakelepo...@outlook.com>
;;; Copyright © 2023 Camilo Q.S. (Distopico) <distop...@riseup.net>
-;;; Copyright © 2023 David Elsing <david.els...@posteo.net>
+;;; Copyright © 2023, 2025 David Elsing <david.els...@posteo.net>
;;; Copyright © 2024 Herman Rimm <her...@rimm.ee>
;;; Copyright © 2024 Foundation Devices, Inc. <he...@foundation.xyz>
;;; Copyright © 2024, 2025 Artyom V. Poptsov <poptsov.art...@gmail.com>
@@ -139,6 +139,7 @@
#: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)
@@ -1836,44 +1837,141 @@ extremely large and complex data collections.")
(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
@@ -2077,32 +2175,19 @@ Swath).")
(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
${HDF5_PACKAGE_NAME}_PACKAGE_EXTLIBS)
+ include
(@PACKAGE_SHARE_INSTALL_DIR@/@ZLIB_PACKAGE_NAME@@HDF_PACKAGE_EXT@-targets.cmake)
++ elseif (${HDF5_PACKAGE_NAME}_ENABLE_Z_LIB_SUPPORT)
++ find_dependency(ZLIB)
+ endif ()
+ if (${HDF5_PACKAGE_NAME}_ENABLE_SZIP_SUPPORT AND
${HDF5_PACKAGE_NAME}_PACKAGE_EXTLIBS)
+ include
(@PACKAGE_SHARE_INSTALL_DIR@/@LIBAEC_PACKAGE_NAME@@HDF_PACKAGE_EXT@-targets.cmake)
++ elseif (${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@@HDF_PACKAGE_EXT@-targets.cmake)
+ endif ()
