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gnu: hdf5: Update to 1.14.6.

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* 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 <andreas@enge.fr>
This commit is contained in:
David Elsing 2025-04-30 16:27:03 +00:00 • committed by Andreas Enge
parent 9d7da25ab2
commit 8eeb04e205
No known key found for this signature in database
GPG key ID: F7D5C9BF765C61E3
3 changed files with 171 additions and 54 deletions
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193
gnu/packages/maths.scm
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@ -62,7 +62,7 @@
;;; Copyright © 2022 Roman Scherer <roman.scherer@burningswell.com>
;;; Copyright © 2023 Jake Leporte <jakeleporte@outlook.com>
;;; Copyright © 2023 Camilo Q.S. (Distopico) <distopico@riseup.net>
;;; Copyright © 2023 David Elsing <david.elsing@posteo.net>
;;; Copyright © 2023, 2025 David Elsing <david.elsing@posteo.net>
;;; Copyright © 2024 Herman Rimm <herman@rimm.ee>
;;; Copyright © 2024 Foundation Devices, Inc. <hello@foundation.xyz>
;;; Copyright © 2024, 2025 Artyom V. Poptsov <poptsov.artyom@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