diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 193 |
1 files changed, 139 insertions, 54 deletions
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.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 |