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2026-03-20gnu: Reference the inherited inputs values.Ludovic Courtès
This commit was made by running this command: sed -e's/modify-inputs (package-\([a-z-]*\)inputs [a-zA-Z0-9-]\+)/modify-inputs \1inputs/g' -i gnu/packages/*.scm … and then reverting individual hunks where the change would trigger unbound variable warnings or other issues (such as ‘native-inputs’ is bound in the body of the ‘inputs’ field, but it refers to the ‘native-inputs’ thunk defined just above). Change-Id: I6d94819f2809313fa1fbefc61897502ee7d66fab
2026-03-20gnu: Reference the inherited ‘arguments’ value.Ludovic Courtès
This commit was made by running this command: sed -e's/substitute-keyword-arguments (package-arguments [a-zA-Z0-9-]\+)/substitute-keyword-arguments arguments/g' -i gnu/packages/*.scm … and then: 1. reverting changes from ‘gnu/packages/rust.scm’ and ‘gnu/packages/java.scm’ since they would incur derivation changes and/or breakage; 2. reverting the change for ‘gcc-final’ in ‘gnu/packages/commencement.scm’; 3. reverting the change for ‘onnx-optimizer’, ‘openquest’, and ‘certbot’, which use ‘substitute-keyword-arguments’ for arguments that are not inherited (and thus ‘arguments’ would be unbound); 4. reverting the change for ‘insight-toolkit-legacy’ and ‘wine64-staging’ which make bogus assumptions about inherited arguments. Change-Id: I122a7cf517b6b63cae38944b5d33ade4b1f5a89c
2026-03-05gnu: Pin old pybind11 version.Gabriel Wicki
* gnu/packages/python-xyz.scm (pybind11): Move definition to (pybind11-2). (python-awkward-cpp, python-contourpy, python-hnswlib, python-dm-tree, python-matplotlib, python-pikepdf, python-optree, python-fusepy): Change reference to pybind11-2. * gnu/packages/astronomy.scm (aoflagger, python-galsim, python-pyclp), gnu/packages/bioinformatics.scm (python-metacells, python-strawc, python-coolbox, python-pyspoa, python-scvelo), gnu/packages/chemistry.scm (avogadrolibs), gnu/packages/computer-architecture.scm (gem5), gnu/packages/duckdb.scm (python-duckdb), gnu/packages/electronics.scm (nextpnr, prjtrellis), gnu/packages/engineering.scm (python-orocos-kinematics-dynamics), gnu/packages/geo.scm (ogs-serial), gnu/packages/graphics.scm (openshadinglanguage, openimageio), gnu/packages/image-processing.scm (opencolorio), gnu/packages/machine-learning.scm (python-fasttext, python-ml-dtypes, onnx, onnx-optimizer, onnxruntime, dlib, tensorflow-lite, tensorpipe, python-pytorch, python-torchvision, python-ctranslate2, python-hmmlearn, python-dlib), gnu/packages/maths.scm (python-accupy, python-ducc0), gnu/packages/networking.scm (libcamera), gnu/packages/opencl.scm (python-pyopencl), gnu/packages/package-management.scm (python-libmambapy), gnu/packages/physics.scm (python-brille, python-gofit), gnu/packages/python-check.scm (python-xdoctest), gnu/packages/python-science.scm (pyre, python-boost-histogram, python-cvxpy, python-iminuit, python-osqp, python-pyamg, python-qdldl, python-scikit-build-core, python-scipy, python-vaex-core, python-pyfma), gnu/packages/radio.scm (gnuradio, gr-osmosdr, gr-dsd, gr-iqbal, gr-satellites, limesuite-ng), gnu/packages/simulation.scm (fenics, python-dolfin-adjoint), gnu/packages/statistics.scm (python-diptest, python-george), gnu/packages/syndication.scm (syndication-domination): Change reference to pybind11-2. Change-Id: Ib6abc8580fc2b4c35172f251ff6ba7d80ced4b7b Signed-off-by: Gabriel Wicki <gabriel@erlikon.ch>
2026-02-15gnu: ringdecomposerlib: Fix build on python-3.12.Nicolas Graves
* gnu/packages/chemistry.scm (ringdecomposerlib)[native-inputs]: Add python-setuptools. Change-Id: I3e8ba8b751c20b36d13c2f0353aeb8c372f8c615 Reviewed-by: Hugo Buddelmeijer <hugo@buddelmeijer.nl> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-02-07build-system/pyproject: Remove uneeded use of pyproject-guile-json.Nicolas Graves
* gnu/packages/bioinformatics.scm (python-bed-reader, python-gseapy) * gnu/packages/chemistry.scm (gemmi, ringdecomposerlib, rdkit) * gnu/packages/cinnamon.scm (libxapp) * gnu/packages/cups.scm (hplip) * gnu/packages/djvu.scm (ocrodjvu) * gnu/packages/finance.scm (electron-cash) * gnu/packages/gnome.scm (terminator) * gnu/packages/image-processing.scm (insight-toolkit) * gnu/packages/machine-learning.scm (onnxruntime, tensorflow-lite, koboldcpp, python-tokenizers) * gnu/packages/maths.scm (gmsh, z3, fp16) * gnu/packages/music.scm (quodlibet) * gnu/packages/photo.scm (lensfun) * gnu/packages/python-science.scm (python-clarabel) * gnu/packages/python-xyz.scm (python-orjson, python-libcst, python-rpds-py, python-streamtracer, python-tiktoken) * gnu/packages/rpm.scm (createrepo-c) * gnu/packages/rust-apps.scm (maturin) * gnu/packages/sugar.scm (sugar, sugar-datastore) * gnu/packages/version-control.scm (mercurial, hg-commitsigs) * gnu/packages/vpn.scm (python-proton-vpn-local-agent) [arguments]<#:phases>: Remove uneeded use of pyproject-guile-json extension. * gnu/packages/python-xyz.scm (python-streamtracer)[arguments] <#:phases>: Also rewrite 'check phase replacement. Change-Id: I779c354120ada3d94f07a127b9ec5011e73254c2 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-01-29gnu: avogadro2: Add Wayland.Danny Milosavljevic
* gnu/packages/chemistry.scm (avogadro2)[inputs]: Add qtwayland-5. [arguments]<#:phases>{wrap-program}: Add qtwayland-5. Change-Id: I8d085a782455b6ade8b8d77acd45ee00d9bf4eac
2026-01-25gnu: ringdecomposerlib: Switch to pyproject.Nicolas Graves
* gnu/packages/chemistry.scm (ringdecomposerlib): [arguments]<#:imported-modules, #:modules, #:phases>: Switch to pyproject-build-system. Change-Id: I3ef172d91c5c7c4a9039ce57be39164af9601e6c Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: rdkit: Switch to pyproject.Nicolas Graves
* gnu/packages/chemistry.scm (rdkit): [arguments]<#:imported-modules, #:modules, #:phases>: Switch to pyproject-build-system. <#:phases>: Take phases 'enable-bytecode-determinism and 'add-install-to-pythonpath from pyproject. Change-Id: If8b134d38b3e23a6974469c1e68b2834219bd67b Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: gemmi: Switch to pyproject.Nicolas Graves
* gnu/packages/chemistry.scm (gemmi): [arguments]<#:imported-modules, #:modules, #:phases>: Switch to pyproject-build-system. Change-Id: Id2bd46050b2820945d5a9d90e17e1c5d1e61c40e Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: python-pymol: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/chemistry.scm (python-pymol): [propagated-inputs]: Remove python-numpy; add python-numpy-1. Change-Id: Icfb0eb4116ecb7b9d34fe13bc8bd81d85a4a64ec Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2026-01-25gnu: rdkit: Use python-numpy@1.Sharlatan Hellseher
* gnu/packages/chemistry.scm (rdkit)[propagated-inputs]: Remove python-numpy; add python-numpy-1. Change-Id: Iab529bb547832bd56040cf4ea1cc414b14c37dd2 Signed-off-by: Rutherther <rutherther@ditigal.xyz>
2025-10-21gnu: gromacs: Update to 2025.3.David Elsing
Also unbundle libtirpc and muparser. The unbundling is now done in a snippet instead of a build phase. * gnu/packages/chemistry.scm (gromacs): Update to 2025.3. [source]: Switch to git-fetch. Add modules and snippet fields. [arguments]<#:configure-flags>: Add -DGMX_USE_MUPARSER=EXTERNAL and -DCMAKE_CXX_FLAGS. [phases]: Adjust 'fixes phase. Use the package source of googletest-1.13. [inputs]: Add libtirpc and muparser. * gnu/packages/patches/gromacs-tinyxml2.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Deregister patch. Fixes: guix/guix#3584 Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-09-27gnu: python-geometric: Fix build.Hugo Buddelmeijer
* gnu/packages/chemistry.scm (python-geometric): Fix build. [native-inputs]: Remove python-wheel. [arguments] <#:phases>: Remove six dependency. Change-Id: I2dd5191bf2b41719dc3b56c8b914eb090161b090 Reviewed-by: Nicolas Graves <ngraves@ngraves.fr> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-09-25gnu: ringdecomposerlib: Fix tests.Sharlatan Hellseher
* gnu/packages/chemistry.scm (ringdecomposerlib)[native-inputs]: Remove python-cython; add python-cython-0. Change-Id: Ia63a5bcbc9c1e446cc96948e52645ddfe9e31bb6
2025-09-25gnu: python-pymol: Update to 3.1.0.Nicolas Graves
* gnu/packages/chemistry.scm (python-pymol): Update to 3.1.0. [build-system]: Switch to pyproject-build-system. [arguments]<#:tests?>: Disable them. <#:phases>: Refresh them. Delete 'build phase. [native-inputs]: Add cmake-minimal, python-pytest, python-setuptools. [propagated-inputs]: Add python-numpy. [description]: Improve style. Change-Id: Ida6105297f294e3fda060d8c8b938fe743faf6e6 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-08-04gnu: Remove #:test-target argument.Greg Hogan
* gnu/packages/astronomy.scm (libsep), * gnu/packages/bioinformatics.scm (megahit), * gnu/packages/bittorrent.scm (qbittorrent), * gnu/packages/calendar.scm (date), * gnu/packages/check.scm (klee, trompeloeil), * gnu/packages/compression.scm (zziplib), * gnu/packages/cpp.scm (immer, lager, zug), * gnu/packages/databases.scm (timescaledb), * gnu/packages/emulators.scm (dolphin-emu), * gnu/packages/fpga.scm (systemc), * gnu/packages/game-development.scm (box2d), * gnu/packages/games.scm (megaglest, openclonk, teeworld), * gnu/packages/glib.scm (sdbus-c++), * gnu/packages/gnucash.scm (gnucash), * gnu/packages/graph.scm (igraph), * gnu/packages/image.scm (exiv2), * gnu/packages/inkscape.scm (inkscape), * gnu/packages/instrumentation.scm (yactfr), * gnu/packages/kde-multimedia.scm (elisa), * gnu/packages/linux.scm (falcosecurity-libs), * gnu/packages/llvm.scm (libcxx, libomp-15), * gnu/packages/machine-learning.scm (ctranslate2, tvm), * gnu/packages/maths.scm (blitz), * gnu/packages/messaging.scm (libphonenumber), * gnu/packages/music.scm (clementine, libdiscid, opustags, strawberry), * gnu/packages/opencog.scm (atomspace, attention, cogserver, cogutil, opencog), * gnu/packages/python-xyz.scm (pybind11) * gnu/packages/radio.scm (libfec, libcorrect), * gnu/packages/serialization.scm (qtcsv), * gnu/packages/shells.scm (fish), * gnu/packages/tls.scm (aws-lc), * gnu/packages/web.scm (wabt), * gnu/packages/vulkan.com (spirv-llvm-translator) [arguments]: Move #:test-target to ... <#:phases>: ... 'check phase. * gnu/packages/algebra.scm (xtensor), * gnu/packages/astronomy (stellarium), * gnu/packages/bioinformatics.scm (libsbml), * gnu/packages/chemistry.scm (openbabel), * gnu/packages/cpp.scm (xsimd, xtl), * gnu/packages/documentation.scm (doxygen), * gnu/packages/lua.scm (selene), * gnu/packages/libftdi.scm (libftdi), * gnu/packages/llvm.scm (cling, libomp@12, libomp@13), * gnu/packages/hyperledger.scm (hyperledger-iroha), * gnu/packages/markup.scm (cmark, cmark-gfm), * gnu/packages/maths.scm (cryptominisat, double-conversion), * gnu/packages/mp3.scm (chromaprint), * gnu/packages/qt.scm (qtpromise) * gnu/packages/rdf.scm (clucene), * gnu/packages/sync.scm (lsyncd) [arguments}: Remove #:test-target. * gnu/packages/engineering.scm (libfive), * gnu/packages/game-development.scm (box2d-3) [arguments]: Remove #:test-target and disable tests. Change-Id: I0a82091df1789980bbbac0c334b6f993c36f412a
2025-07-31gnu: yaehmop: Fix build with GCC 14.David Elsing
The C code calls functions from Fortran without declaration. * gnu/packages/chemistry.scm (yaehmop)[arguments]: Add CMAKE_C_FLAGS. Change-Id: Ib115645a414693cd42429d957d746f8435a889a6 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-07-31gnu: freesasa: Fix build with newer gemmi.David Elsing
* gnu/packages/chemistry.scm (freesasa)[arguments]: Add 'fix-new-gemmi phase. Change-Id: I78997047eba8245a2d275af5ab18d0d0fe48630f Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-07-31gnu: gemmi: Update to 0.7.3.David Elsing
Fixes: guix/guix#1567. * gnu/packages/chemistry.scm (gemmi): Update to 0.7.3. [source]: Remove gemmi-fix-sajson-types.patch patch. [arguments]: Adjust 'patch-includes and 'check phases. [native-inputs]: Add python-nanobind and zpp-serializer. Remove pybind11 and tinydir. Change-Id: Ia1a894226d7d0a9536ed0c6646271d475c397ee7 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-07-31gnu: openbabel: Fix build and switch to git source.David Elsing
The git source does not contain the bundled libraries. * gnu/packages/chemistry.scm (openbabel)[source]: Switch to git-fetch. [arguments]<#:configure-flags>: Use search-input-file and search-input-directory. <#:phases>: Add phase 'fix-time-check. [inputs]: Add rapidjson. [home-page]: Update URL. Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-07-13gnu: qcint: Fix build.Zheng Junjie
* gnu/packages/chemistry.scm (qcint)[arguments]: Use G-expression. Change-Id: I4e26a872b6e78a6ea96d16c661353063b8d3fcd6
2025-07-13gnu: python-pyscf: Make tune works.Zheng Junjie
* gnu/packages/chemistry.scm (python-pyscf)[native-inputs]: Add (canonical-package gcc). Change-Id: Ibee49cb64581bd9e6743cdd16aa25739ac53112c
2025-07-08gnu: packages/chemistry: Sort use-module alphabetically.Sharlatan Hellseher
* gnu/packages/chemistry.scm: Sort use-module alphabetically. Change-Id: Ib6df5e22d91ef443ad57cbb811906ba3bb0644d8
2025-07-08gnu: Add python-pyscf-properties.David Elsing
* gnu/packages/chemistry.scm (python-pyscf-properties): New variable. Change-Id: I10823bca5df64a563521bc8f1d28a4a75678ef5d Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-07-08gnu: Add python-pyscf-dispersion.David Elsing
* gnu/packages/chemistry.scm (python-pyscf-dispersion): New variable. Change-Id: I1e50ae57c4b79932cab87c16a6f2ab733a5544c0 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-07-08gnu: Add python-geometric.David Elsing
* gnu/packages/chemistry.scm (python-geometric): New variable. Change-Id: I5d716df3d71a671c334ff2dfd1b44e15e37afc5a Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-07-08gnu: Add python-pyscf.David Elsing
* gnu/packages/chemistry.scm (python-pyscf): New variable. Change-Id: I4e265c97644a6f8765c5d509de126de0312a3f98 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-07-08gnu: Add qcint.David Elsing
* gnu/packages/chemistry.scm (qcint): New variable. Change-Id: Ie32f97a028f847dc401a4b9772df6f0f9a550e97 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-07-08gnu: Add libcint.David Elsing
* gnu/packages/chemistry.scm (libcint): New variable. Change-Id: I72da249743392eb8a4be1673b9fc1a7bbbb1c942 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-07-08gnu: Add xcfun.David Elsing
* gnu/packages/chemistry.scm (xcfun): New variable. Change-Id: Iaf25180a7edafffce1e8eabdbf6a81c289401f2e Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-07-08gnu: packages/chemistry: Add EOF disclaimer.Sharlatan Hellseher
* gnu/packages/chemistry.scm: Add a comments to place packages in alphabetical order. Change-Id: I2af9eeeb1de77b0420093bf2776b1df7e7bda188
2025-06-02gnu: avogadro2: Update to 1.100.0.Jakob Kirsch
* gnu/packages/chemistry.scm (avogadro2): Update to 1.100.0. [inputs]: Add openbabel and qtsvg-5. [native-inputs]: Add avogadro-i18n. [arguments]<#:phases>{'symlink, 'wrap-program}: New phases. Change-Id: I9577e27021ca449426d7506589939c050a5d0cfb Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-06-02gnu: avogadrolibs: Update to 1.100.0.Jakob Kirsch
* gnu/packages/chemistry.scm (avogadrolibs): Update to 1.100.0. [inputs]: Add qtsvg-5, avogadro-molecules, avogadro-crystals, avogadro-fragments. [arguments]<#:configure-flags>: Drop a flag. <#:phases>{'symlink}: New phase. Change-Id: I67e3c15db14e97394e6ef27a756c2b9dd951ad79 Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-06-02gnu: spglib: Update to 2.5.0.Jakob Kirsch
* gnu/packages/chemistry.scm (spglib): Update to 2.5.0. [arguments]<#:tests?, #:test-target, #:configure-flags>: Disable tests. <#:phases>: Adapt. Change-Id: Ia05bb8e2f012fcf4c576db8a6e5d2f8b153493ff Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-05-06gnu: texlive-libkpathsea: Tweak "texmf.cnf" variables.Nicolas Goaziou
* gnu/packages/tex.scm (texlive-libkpathsea): Use XDG variables instead of HOME for cache and user configuration. Re-instate TEXMFLOCAL, which may be necessary for external TeX installations. (texlive-luatex): Re-instate TEXFLOCAL. * gnu/packages/algebra.scm (gap): * gnu/packages/assembly.scm (asl): (yaehmop): * gnu/packages/bioinformatics.scm (discrover): * gnu/packages/chez.scm (chez-scheme-for-racket): * gnu/packages/engineering.scm (fastcap): * gnu/packages/fsf.scm (book-faif): * gnu/packages/maths.scm (hypre): (stex-boostrap): (suitesparse-amd): (suitesparse-camd): (suitesparse-cholmod): (suitesparse-klu): (suitesparse-ldl): (suitesparse-mongoose): (suitesparse-spex): (suitesparse-spqr): (suitesparse-umfpack): * gnu/packages/ocaml.scm (ocaml-bibtex2html): (unison): * gnu/packages/python-xyz.scm (python-nbconvert): * gnu/packages/statistics.scm (r-with-tests)[arguments]: Set TEXMFVAR to a writable location. Change-Id: I3d2d069cf41a92214d9d6fb7f4d54fc81fe6db7a
2025-05-06gnu: Rename `texlive-updmap.cfg' into `texlive-local-tree'.Nicolas Goaziou
* doc/build.scm (pdf-manual): * doc/contributing.texi (Submitting Patches): * gnu/packages/algebra.scm (pari-gp): (giac): * gnu/packages/assembly.scm (asl): * gnu/packages/audio.scm (chow-tape-model): * gnu/packages/bioconductor.scm (r-biocstyle): * gnu/packages/bioinformatics.scm (discrover): (phyml): (velvet): * gnu/packages/chemistry.scm (yaehmop): * gnu/packages/chez.scm (chez-scheme-for-racket): (stex-bootstrap): (chez-web): (chez-sockets): * gnu/packages/cran.scm (r-papaja): (r-prereg): * gnu/packages/docbook.scm (dblatex): * gnu/packages/emacs-xyz.scm (emacs-auctex): * gnu/packages/engineering.scm (fastcap): * gnu/packages/finance.scm (optionmatrix): * gnu/packages/fsf.scm (book-faif): * gnu/packages/gettext.scm (po4a): (po4a-minimal): * gnu/packages/graphics.scm (mmg): * gnu/packages/graphviz.scm (dot2tex): * gnu/packages/guile-xyz.scm (emacsy): (guile-cv): * gnu/packages/lisp.scm (sbcl): * gnu/packages/maths.scm (cddlib): (gnuplot): (itpp): (octave): (suitesparse-amd): (suitesparse-camd): (suitesparse-cholmod): (suitesparse-klu): (suitesparse-ldl): (suitesparse-mongoose): (suitesparse-spex): (suitesparse-spqr): (suitesparse-umfpack): (hypre): * gnu/packages/music.scm (lilypond): * gnu/packages/ocaml.scm (unison): (ocaml-bibtex2html): * gnu/packages/pdf.scm (extractpdfmark): * gnu/packages/photo.scm (enblend-enfuse): * gnu/packages/plotutils.scm (asymptote): * gnu/packages/python-xyz.scm (python-numpy-documentation): (python-ipython-documentation): (python-pypandoc): * gnu/packages/radio.scm (gnuradio): (libosmo-dsp): * gnu/packages/scheme.scm (mit-scheme): * gnu/packages/security-token.scm (yubico-piv-tool): * gnu/packages/sphinx.scm (python-sphinx): (python-sphinx-5): * gnu/packages/statistics.scm (r-with-tests): (r-spams): * gnu/packages/tex.scm (texlive-local-tree): Renamed from… (texlive-updmap.cfg): … this. Deprecate the latter. (texlive-biblatex-philosophy): (texlive-bropd): (texlive-fontsize): (texlive-poetrytex): (texlive-reverxii): (texlive-stix): (texlive-suftesi): (texlive-thucoursework): (texlive-ulqda): (texlive-yathesis): (texlive-makecell): (texlive-robotarm): (texlive-bbold): (texlive-babel-romansh): (texlive-polyglossia): (texlive-innerscript): (teximpatient): (texlive-xkeyval): (texlive-arabxetex): (texlive-blox): (texlive-ecgdraw): (texlive-gradientframe): (texlive-everyhook): (texlive-actuarialangle): (texlive-actuarialsymbol): (texlive-autopdf): (texlive-etaremune): (texlive-extract): (texlive-forarray): (texlive-graphicx-psmin): (texlive-ha-prosper): (texlive-namespc): (texlive-newspaper): (texlive-powerdot): (texlive-recipecard): (texlive-show2e): (texlive-tablists): (texlive-ted): (texlive-xargs): (texlive-xpeek): * gnu/packages/xdisorg.scm (xforms): * gnu/packages/algebra.scm (gap): * gnu/packages/cpp.scm (jthread): * guix/lint.scm (check-inputs-should-be-native): Rename `texlive-updmap.cfg' into `texlive-local-tree'. Change-Id: I129280807c418e57acbcbda399545ab27a9e0a33
2025-04-08gnu: rdkit: Update to 2024.09.6.David Elsing
* gnu/packages/chemistry.scm (rdkit): Update to 2024.09.6. [arguments]: Disable more failing tests. [inputs]: Add pubchem-align3d. [native-inputs]: Replace boost with boost-numpy. Add python-pytest. * gnu/packages/patches/rdkit-unbundle-external-dependencies.patch: Adjust patch. Change-Id: I165ebfeaef1f9d4b8c659cfdac65b45b0bc90188 Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-04-08gnu: inchi: Update to 1.07.3.David Elsing
* gnu/packages/chemistry.scm (inchi): Update to 1.07.3. [source]: Switch to git-fetch. [arguments]: Use gexps. Adjust chdir-to-build-directory, build and install phases. Enable parallel building. [native-inputs]: Remove input label. Drop inchi-doc. [license]: Change to Expat license. Change-Id: I50945dc888dd01a6a5f7905874c7d68ecdfd5d4d Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-04-07gnu: Add pubchem-align3d.David Elsing
* gnu/packages/chemistry.scm (pubchem-align3d): New variable. Signed-off-by: Andreas Enge <andreas@enge.fr>
2025-04-07gnu: yaehmop: Update to 2024.03.1.David Elsing
* gnu/packages/chemistry.scm (yaehmop): Update to 2024.03.1. Signed-off-by: Andreas Enge <andreas@enge.fr>
2024-02-13gnu: rdkit: Update to 2023.09.4.David Elsing
* gnu/packages/chemistry.scm (rdkit): Update to 2023.09.4. [arguments]: Skip testConrec test in check phase. [native-inputs]: Replace catch2 with catch2-3. * gnu/packages/patches/rdkit-unbundle-external-dependencies.patch: Adjust patch. [supported-systems]: New field. Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-02-13gnu: freesasa: Fix memerr tests.David Elsing
* gnu/packages/chemistry.scm (freesasa)[arguments]: Add "CFLAGS=-fno-builtin-malloc" to #:configure-flags. Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-02-13gnu: avalon-toolkit: Update to 2.0.5a.David Elsing
The bug freeing static memory and the makefile have been improved upstream, so we don't have to work around them anymore. Now, two static libraries are built instead. * gnu/packages/chemistry.scm (avalon-toolkit): Update to 2.0.5a. [source]: Switch to git reference from GitHub. Adjust snippet. Add patch from the RDKit fork. [arguments]: Remove 'dont-free-static-memory phase. Use provided makefile. Adjust 'install phase. * gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-02-13gnu: yaehmop: Update to 2023.03.1.David Elsing
* gnu/packages/chemistry.scm (yaehmop): Update to 2023.03.1. Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-02-13gnu: coordgenlibs: Update to 3.0.2.David Elsing
* gnu/packages/chemistry.scm (coordgenlibs): Update to 3.0.2. Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-02-13gnu: maeparser: Update to 1.3.1.David Elsing
* gnu/packages/chemistry.scm (maeparser): Update to 1.3.1. Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-02-13gnu: gemmi: Update to 0.6.4.David Elsing
* gnu/packages/chemistry.scm (gemmi): Update to 0.6.4. [arguments]: Adjust include/gemmi/sprintf.hpp -> src/sprintf.cpp. (freesasa)[arguments]: Link to gemmi_cpp explicitly. Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-01-09gnu: msgpack: Deprecate with msgpack-c.Maxim Cournoyer
* gnu/packages/serialization.scm (msgpack-c): New variable. (msgpack-cxx): New variable. (msgpack): Rename to... (msgpack-3): ... this, and inherit from msgpack-c. * gnu/packages/vim.scm (eovim) [arguments]: Add help-cmake-find-msgpack-c phase. [inputs]: Replace msgpack with msgpack-c. * gnu/packages/terminals.scm (tmate) [inputs]: Replace msgpack with msgpack-3. * gnu/packages/networking.scm (opendht) [propagated-inputs]: Replace msgpack with msgpack-cxx. * gnu/packages/chemistry.scm (mmtf-cpp) [propagated-inputs]: Likewise.
2023-08-21gnu: python-pymol: Remove msgpack from native-inputs.Maxim Cournoyer
It's now propagated by mmtf-cpp. * gnu/packages/chemistry.scm (python-pymol) [native-inputs]: Remove msgpack. Reviewed-by: Andreas Enge <andreas@enge.fr>
2023-08-21gnu: avogadrolibs: Remove msgpack from native-inputs.Maxim Cournoyer
It's now propagated by mmtf-cpp. * gnu/packages/chemistry.scm (avogadrolibs) [native-inputs]: Remove msgpack. Reviewed-by: Andreas Enge <andreas@enge.fr>
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