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2025-04-30gnu: hdf5: Update to 1.14.6.David Elsing
* 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>
2025-04-30gnu: hdf5-blosc: Update to 1.0.1.Andreas Enge
* gnu/packages/maths.scm (hdf5-blosc): Update to 1.0.1. Change-Id: Ie782107c205e8d569a5d6e6ca80dc9f944786542
2025-04-30gnu: hdf5-blosc: Update input.Andreas Enge
* gnu/packages/maths.scm (hdf5-blosc)[inputs]: Remove hdf5-1.10; add hdf5. Change-Id: Ib9356732ffacac001997ac3343b0d57bda14366d
2025-04-30gnu: highs: Cosmetic changes.Andreas Enge
This adds small changes that were forgotten in the previous commit. * gnu/packages/maths.scm (highs): Do not use a git revision since this is a regular release. Change-Id: I56c6401f8569cc3268892dabfe38ac4658ad8953
2025-04-30gnu: Add highs.Wiktor Żelazny
* gnu/packages/maths.scm (highs): New variable. Change-Id: Ie842704d4d9c8a4b531ee45aab34a99e59e4b3c4 Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-04-29gnu: scotch: Update to 7.0.7.Ludovic Courtès
* gnu/packages/maths.scm (scotch): Update to 7.0.7. Change-Id: Idef8e0956d9da1aef13fb423c53db60b6a61b04b Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-04-29gnu: scotch, scotch32, pt-scotch, pt-scotch32: Use gexps.Ludovic Courtès
* gnu/packages/maths.scm (scotch, scotch32) (pt-scotch, pt-scotch32): Use gexps. Change-Id: I93febc994c5345e133eddbd016b1974d08df5bdf Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-04-29gnu: scotch: Remove CMake machinery for the Metis compatibility layer.Ludovic Courtès
This fixes a bug whereby ‘SCOTCHConfig.cmake’ would fail to find ‘scotchmetisTargets.cmake’ because it expects it to be in the same directory as itself, ${CMAKE_CURRENT_LIST_DIR}. * gnu/packages/patches/scotch-cmake-remove-metis.patch: New file. * gnu/packages/maths.scm (scotch)[source]: Use it. * gnu/local.mk (dist_patch_DATA): Add it. Change-Id: If8d8f890852c35cede6e81c33d18b9101988a635 Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-04-29gnu: scotch: Remove “-shared” deprecated aliases.Ludovic Courtès
These aliases were added in commit d4709d78c3b460d7be02f15f6cc6c85f398b1a46, Feb. 2022. * gnu/packages/maths.scm (scotch-shared, pt-scotch-shared): Remove. Change-Id: I971bbf999a9fce5dae05c865316defe55eaeb212 Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-04-29gnu: Remove atlas.Andreas Enge
* gnu/packages/maths.scm (atlas): Delete variable. The package does not build anymore. Its last release dates from 2016. After the removal of shogun there are no other dependent packages. Change-Id: Ibe988d33451b63ef7680b6c0a19cff6430a42a68
2025-04-29gnu: Remove h5check.Andreas Enge
The package has no dependents and appears to be unmaintained. The source code has vanished under the given URL. According to https://issues.guix.gnu.org/64448 it does not compile any more with current versions of hdf5. * gnu/packages/maths.scm (h5check): Delete variable. Change-Id: Ia7ced02059734cf8a5a2db39bbe0f1b38f67df12
2025-04-23gnu: itpp: Add LAPACK support and use gexps.Maxim Cournoyer
This is needed to run some functions needed by the test suite of mia, for example. * gnu/packages/maths.scm (itpp) [arguments]: Use gexps. [inputs]: Add lapack. [native-inputs]: Remove labels. Change-Id: I58b31272ceaf5bdfbbcc0f769ab2418c4b7613d3
2025-04-16gnu: Remove python-networkx-next.Sharlatan Hellseher
It's the same version variant as python-networkx. * gnu/packages/python-xyz.scm (python-networkx-next): Delete variable. * gnu/packages/maths.scm (python-mathics-django) [propagated-inputs]: Remove python-networkx-next; add python-networkx. Change-Id: Iedc48767af728ff258cc7b2d453f979eb1cc70e4
2025-04-16gnu: python-pyglm: Move to maths.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-pyglm): Move from here ... * gnu/packages/maths.scm: ... to here. * gnu/packages/gnome-xyz.scm: Add (gnu packages maths); remove (gnu packages python-science). Change-Id: I49ab732c1070210d005f8753c1e894c9abc3ee8b
2025-04-16gnu: glm: Update to 1.0.1.Sharlatan Hellseher
* gnu/packages/maths.scm (glm): Update to 1.0.1. Apply a list style. [source]: Switch to git-fetch. [arguments] <phases>: Remove 'set-environment as <https://github.com/g-truc/glm/pull/1087> is resolved. Use default 'install as <https://github.com/g-truc/glm/pull/968> is resolved. Add 'post-install. Change-Id: Ibda3768102ac94f6ef69057bfccd8716f7f91d0e
2025-04-16gnu: veusz: Update to 3.6.2.Nicolas Graves
* gnu/packages/maths.scm (veusz): Update to 3.6.2. [build-system]: Switch to pyproject-build-system. [arguments]: Improve style, use gexps. {phases}: Remove phase 'fix-sip-dir. Add phase 'fix-pyqt5-include-dir. Refresh phase 'wrap-executable. [native-inputs]: Add python-astropy, python-setuptools, python-wheel. Remove python-sip-4. [inputs]: Add qtwayland-5. Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-04-16gnu: python-quadpy: Deselect one failing test.Sharlatan Hellseher
* gnu/packages/maths.scm (python-quadpy) [arguments] <test-flags>: Deselect one failing test. Change-Id: I29ab3db45afb70928125773644b8704f9b731ada
2025-04-16gnu: python-orthopy: Skip some tests, fix build.Sharlatan Hellseher
* gnu/packages/maths.scm (python-orthopy) [arguments] <test-flags>: Skip 5 failing tests. Change-Id: Ic5e55d9a8a054eaba9f685e134a366dbfaa9bd8d
2025-04-16gnu: openblas: Add debug output.Artyom Bologov
* gnu/packages/maths.scm (openblas): Add "debug" output [outputs]: Add argument, add "debug" output [arguments]<#:make-flags>: Add DEBUG=1 flag
2025-04-16gnu: openblas: Update to 0.3.29.Ricardo Wurmus
* gnu/packages/maths.scm (openblas): Update to 0.3.29. (openblas-0.3.29): Define as alias. Change-Id: I9a17f2efb2af026a2d19cd000f2b9c284cf94197
2025-04-15gnu: opencascade-occt: Move doxygen to native-inputs.nomike
* gnu/packages/maths.scm (opencascade-occt)[inputs]: Move doxygen from here... [native-inputs]: ...to here. Change-Id: I5382f1a1552afebb286d01ffc292dc8cbfbb75af Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-04-15gnu: opencascade-occt: Fix new version detectionnomike
Previously an upgrade from 7.6.2 to the older 2017.73 would be suggested. * gnu/packages/maths.scm (opencascade-occt)[properties]: Add release-tag-prefix and release-tag-version-delimiter. Change-Id: I079accd7da6d5e1ae7438bb0fd8428e9d8733b16 Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-04-07gnu: netcdf-cxx4, netcdf-cxx4-parallel-openmpi: Propagate netcdf.Luca Cirrottola
* gnu/packages/maths.scm (netcdf-cxx4)[inputs]: Move netcdf from here... [propagated-inputs]: ...to here. (netcdf-cxx4-parallel-openmpi)[propagated-inputs]: New field. Change-Id: I6d92e89f75e4e5cbf8d46be6b1ca331999606673 Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-03-31gnu: python-ducc0: Update to 0.37.1.Sharlatan Hellseher
* gnu/packages/maths.scm (python-ducc0): Update to 0.37.1. [arguments] <test-flags>: Run tests in parallel, supported by upstream. [native-inputs]: Remove python-wheel; add cmake-minimal, python-nanobind, python-pytest-xdist, and python-scikit-build-core. Change-Id: Iedc5f5ce49c50f8b72a120f592982baad06be89f
2025-03-31gnu: petsc: Activate higher compiler optimization.Luca Cirrottola
* gnu/packages/maths.scm (petsc)[arguments]<#:configure-flags>: Add compiler optimization flags. Change-Id: Iaadb462e002615448014db44248b0c116b246150 Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-03-31gnu: hdf-java: Update to 1.14.3.David Elsing
* gnu/packages/maths.scm (hdf-java): Update to 1.14.3. [arguments]: Adjust dependency versions in 'unbundle phase. [home-page]: Update. [license]: Update URL. Change-Id: I43db316c3a83f5ddac14b0c670430811dcac6bdc Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-03-31gnu: hdf5: Make hdf5@1.14 the default version.Andreas Enge
This replaces all inputs hdf5@1.10 by hdf5@1.14 unless explicitly specified otherwise. * gnu/packages/maths.scm (hdf5-1.14): Rename to... (hdf5): ...this, which was previously defined as hdf5-1.10. (hdf-eos5, hdf5-parallel-openmpi, scilab): Adapt variable names. * gnu/packages/bioinformatics.scm (fast5, ncbi-vdb), gnu/packages/cran.scm (r-h5), gnu/packages/image.scm (vigra)[inputs]: Keep hdf5-1.10. Change-Id: Ie43a13ecbb4da597ec1d3f7c0428102b45881485
2025-03-28gnu: hypre: Fix documentation.Luca Cirrottola
* gnu/packages/maths.scm (hypre)[native-inputs]: Add ghostscript. [arguments]<phases>{build-docs}: Set $HOME so that fontconfig finds a directory for writing its cache. Change-Id: I46635f262a0d3ecd4114d1d673da635232522915 Co-authored-by: Andreas Enge <andreas@enge.fr> Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-03-28gnu: hypre: Update to 2.32.0.Luca Cirrottola
* gnu/packages/maths.scm (hypre): Update to 2.32.0. [inputs]: Add python-sphinx-rtd-theme. Change-Id: I278cb9ac088cdd40075b2b10d10cef9451cd17cc Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-03-26gnu: Add lis.Liliana Marie Prikler
* gnu/packages/maths.scm (lis): New variable. Change-Id: I68bf93787346815912d02b919cb5c9acf884483e
2025-03-22gnu: yices: Use gexp variables.Maxim Cournoyer
* gnu/packages/maths.scm (yices): [phases] <fix-build-files>: Use gexp variable. Change-Id: If40f787e3c6535edd14aec833de8beff79213d95
2025-03-12gnu: octave: Update to 9.4.0Andy Tai
* gnu/packages/maths.scm (octave-cli): Update to 9.4.0 Change-Id: I9891e6f2a85b5909725f5fa5b45edaaa65594cfa Signed-off-by: Eric Bavier <bavier@posteo.net>
2025-03-10gnu: python-mathics-django: Update to 8.0.1.Danny Milosavljevic
* gnu/packages/maths.scm (python-mathics-django): Update to 8.0.1. Change-Id: I6c00d8e43457c1541b205b052e0219991ce06805
2025-03-10gnu: python-mathics-core: Update to 8.0.1.Danny Milosavljevic
* gnu/packages/maths.scm (python-mathics-core): Update to 8.0.1. Change-Id: I97d568dbabde8d074525bc5e850f247d9e17fcfd
2025-03-03gnu: pnetcdf: Add missing zlib input.Lars Bilke
* gnu/packages/maths.scm (pnetcdf): Add missing zlib input. Change-Id: I8b0c143cce016d6cfb2ffe8923f1380452a7e8ac Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2025-02-19gnu: Fix some misspellings.Efraim Flashner
Change-Id: I316652aff7418af4b8e83bea24638b1513f8aa97
2025-02-17gnu: Fix typos in description and synopsis in various packages.Vagrant Cascadian
* gnu/packages/crates-database.scm (rust-sqlformat-0.2)[description]: Fix spelling of "formatting". * gnu/packages/emacs-xyz.scm (emacs-arei)[synopsis]: Fix spelling of "Asynchronous". (emacs-ob-racket)[description]: Fix spelling of "support". * gnu/packages/firmware.scm (fcode-utils)[description]: Fix spelling of "utilities". (sgabios)[description]: Fix spelling of "capabilities". * gnu/packages/games.scm (qcheckers)[description]: Fix spelling of "formerly". * gnu/packages/geo.scm (python-ogr2osm)[description]: Fix spelling of "PostgreSQL". * gnu/packages/guile-xyz.scm (guile-ares-rs)[synopsis]: Fix spelling of "Asynchronous". (guile-rsv)[description]: Fix spelling of "Separated". * gnu/packages/julia-xyz.scm (julia-multivariatepolynomials)[description]: Fix spelling of "implementing". * gnu/packages/language.scm (mecab)[description]: Fix spelling of "developed". * gnu/packages/lisp-xyz.scm (sbcl-cl-json-pointer)[description]: Fix spelling of "library". * gnu/packages/machine-learning.scm (ideep-pytorch)[synopsis]: Fix spelling of "internal". * gnu/packages/maths.scm (suitesparse-cholmod)[description]: Fix spelling of "routines". * gnu/packages/ocaml.scm (ocamlc-loc)[description]: Fix spelling of "compiler". * gnu/packages/pdf.scm (capypdf)[description]: Fix spelling of "library". * gnu/packages/ruby.scm ruby-silent-stream)[description]: Fix spelling of "Extensions". (ruby-fileutils)[synopsis]: Fix spelling of "library". * gnu/packages/rust-apps.scm (kibi)[description]: Fix spelling of "highlighting". * gnu/packages/scheme.scm (owl)[description]: Fix spelling of "support". * gnu/packages/statistics.scm (r-mixedpower)[description]: Fix spelling of "separate". * gnu/packages/sugar.scm (sugar-commander-activity)[description]: Fix spelling of "removable".
2025-02-17gnu: Add openblas-0.3.29.Ricardo Wurmus
* gnu/packages/maths.scm (openblas-0.3.29): New variable. Change-Id: I8727a024db201cda8360a656bc525b0b1e572452
2025-02-15gnu: Add maxima-ecl.Andreas Enge
* gnu/packages/maths.scm (maxima-ecl): New variable. Change-Id: I71a14d064e67aa34fdd7f6eb8499dfbd1dea11b9
2025-02-14gnu: gmsh: Update to 4.13.1.Lars Bilke
* gnu/packages/maths.scm (gmsh): Update to 4.13.1. Change-Id: Iee56d09055f0803c4f4bc432402dadb3d34bc107 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-02-10gnu: Add glucose.Vinicius Monego
* gnu/packages/maths.scm (glucose): New variable. Change-Id: I8e9031db55aa98ddde82ea676d3287656f7c4288 Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-02-10gnu: Add hpcombi.Vinicius Monego
* gnu/packages/maths.scm (hpcombi): New variable. Change-Id: I64eb46aa4002a2291ae59122e083998a9c846eaf Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-02-10gnu: Add python-cylp.Vinicius Monego
* gnu/packages/maths.scm (python-cylp): New variable. Change-Id: Id3467bc34833472aa7fca3416801a5fbf5c033e6 Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-02-10gnu: python-cvxopt: Update to 1.3.2.Vinicius Monego
* gnu/packages/maths.scm (python-cvxopt): Update to 1.3.2. Change-Id: I7924821a69e092da529a5188df3d1b2e3f4eed49 Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-02-07gnu: python-mathics-core: Update to 8.0.0.Danny Milosavljevic
* gnu/packages/maths.scm (python-mathics-core): Update to 8.0.0. [arguments]<#:phases>[patch-bugs]: Modify. [propagated-inputs]: Add python-pympler, python-stopit. Change-Id: Ia0f7be188fcbbaa46de9222eed95e5c47ab056aa
2025-02-07gnu: python-mathics-django: Update to 8.0.0.Danny Milosavljevic
* gnu/packages/maths.scm (python-mathics-django): Update to 8.0.0. Change-Id: Ie23035a9fdd2f17318a5df8b8d3d7b83bc271e4b
2025-02-07gnu: python-mathicsscript: Update to 8.0.0.Danny Milosavljevic
* gnu/packages/maths.scm (python-mathicsscript): Update to 8.0.0. Change-Id: Ic417f421bb175f19d93803635bf61fb824a52a34
2025-02-07gnu: python-mathics-pygments: Update to 1.0.4.Danny Milosavljevic
* gnu/packages/maths.scm (python-mathics-pygments): Update to 1.0.4. Change-Id: I831b34d05eae73cad88277443f9f4e374df257b9
2025-02-07gnu: python-mathics-scanner: Update to 1.4.1.Danny Milosavljevic
* gnu/packages/maths.scm (python-mathics-scanner): Update to 1.4.1. [arguments]<#:phases>[prepare]: New phase. Change-Id: Iab614a14365e42588635ef9b3ee71426b93cbca1
2025-01-29gnu: Add python-ducc0.Sharlatan Hellseher
* gnu/packages/maths.scm (python-ducc0): New variable. Change-Id: Icb8990b32d25f4ad9bd2391f7745b6c298758efa
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