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2026-06-25gnu: Remove mmtf-cpp.Andreas Enge1-27/+0
* gnu/packages/chemistry.scm (mmtf-cpp): Delete variable. Fixes: guix/guix#4485
2026-06-25gnu: python-pymol: Modernize inputs.Andreas Enge1-2/+1
* gnu/packages/chemistry.scm (python-pymol)[inputs]: Remove mmtf-cpp and python-pyqt; add python-pyqt-6.
2026-06-25gnu: avogadro2: Update to 1.102.1.Laura Kirsch1-26/+31
* gnu/packages/chemistry.scm (avogadro2): Update to 1.102.1. [inputs]: Remove molequeue. Add jkqtplotter and bash-minimal. Replace qtbase-5 by qtbase, qtsvg-5 by qtsvg and qtwayland-5 by qtwayland. [arguments]: Add #:configure-flags. Signed-off-by: Andreas Enge <andreas@enge.fr>
2026-06-25gnu: avogadrolibs: Update to 1.201.1 and switch to Qt6.Laura Kirsch1-58/+79
* gnu/packages/chemistry.scm (avogadrolibs): Update to 1.201.1. [native-inputs]: Replace pybind11-2 by pybind11. Add patchelf. Remove mmtf-cpp. [inputs]: Add hdf5, jkqtplotter and spglib. Remove molequeue. Replace qtbase-5 by qtbase and qtsvg-5 by qtsvg. Update avogadro-molecules, avogadro-crystals and avogadro-fragments. [arguments]<#:configure-flags>: Add -DQT_VERSION=6, -DUSE_HDF5=ON and -DUSE_PYTHON=ON. <#:phases>{extend-python-rpath}: New phase. Co-authored-by: Andreas Enge <andreas@enge.fr>
2026-06-25gnu: rdkit: Update dependency on catch.Cayetano Santos1-2/+3
* gnu/packages/chemistry.scm (rdkit)[native-inputs]: Replace catch2-3.5 with catch2. [arguments]: Update ’check #:phase.
2026-06-21gnu: catch2-3: Rename to catch2-3.5.Andreas Enge1-1/+1
* gnu/packages/check.scm (catch2-3): Rename to and define as deprecated by... (catch2-3.5): ...this. (trompeloeil): Adapt input. * gnu/packages/chemistry.scm (rdkit), * gnu/packages/cpp.scm (immer), * gnu/packages/enchant.scm (nuspell), * gnu/packages/games.scm (fuzzylite, endless-sky) * gnu/packages/gnome.scm (gnome-system-monitor), * gnu/packages/logging.scm (spdlog-1.15), * gnu/packages/luanti.scm (luanti), * gnu/packages/maths.scm (highfive), * gnu/packages/networking.scm (restinio), * gnu/packages/package-management.scm (libmamba), * gnu/packages/physics.scm (python-brille), * gnu/packages/potassco.scm (clingo, clingo-lpx, clingcon), * gnu/packages/xdisorg.scm (j4-dmenu-desktop): Adapt inputs. Change-Id: I69fac4ec6d3914a6dc7d86f2454f410db937a83f
2026-06-21gnu: catch2: Rename to catch2-2.Andreas Enge1-1/+1
* gnu/packages/check.scm (catch2): Rename to... (catch2-2): ...this. (rapidcheck): Adapt inputs. * gnu/packages/animation.scm (pencil2d), * gnu/packages/audio.scm (libkeyfinder), * gnu/packages/chemistry.scm (python-pymol), gnu/packages/cpp.scm (xdgpp, icecream-cpp, span, chaiscript, json-dto, rapidfuzz-cpp, libexpected, zug, lager, cli11, cpp-mustache, tl-optional, type-safe), * gnu/packages/engineering.scm (valeronoi, libigl), * gnu/packages/geo.scm (mapnik), * gnu/packages/maths.scm (osqp), * gnu/packages/networking.scm (cppzmq), * gnu/packages/python-science.scm (python-openpmd-api), * gnu/packages/security-token.scm (libnitrokey): Adapt inputs. Change-Id: Icd92b5aa0491911d5eeb5faf7b1d467e1e85fdc7
2026-06-14gnu: ringdecomposerlib: Bump python-cython.Nicolas Graves1-1/+10
* gnu/packages/chemistry.scm (ringdecomposerlib) [arguments]<#:phases>: Add phase 'patch-cython. [native-inputs]: Replace python-cython-0 by python-cython. Relates-to: guix/guix!9270 Reviewed-by: Cayetano Santos <csantosb@inventati.org> Change-Id: Ie16dc9982390cb3ec910f0a6f9fb3a1260f68277 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-05-29gnu: Remove pending references to deprecated (gnu packages flex).Anderson Torres1-1/+1
* gnu/packages/c.scm: Remove references to (gnu packages flex). * gnu/packages/video.scm: Likewise. * gnu/packages/web.scm: Likewise. * gnu/packages/admin.scm: Change (gnu packages flex) to (gnu packages compiler-tools). * gnu/packages/algebra.scm: Likewise. * gnu/packages/apparmor.scm: Likewise. * gnu/packages/assembly.scm: Likewise. * gnu/packages/astronomy.scm: Likewise. * gnu/packages/audio.scm: Likewise. * gnu/packages/bioinformatics.scm: Likewise. * gnu/packages/bison.scm: Likewise. * gnu/packages/bootloaders.scm: Likewise. * gnu/packages/cdrom.scm: Likewise. * gnu/packages/chemistry.scm: Likewise. * gnu/packages/cluster.scm: Likewise. * gnu/packages/cobol.scm: Likewise. * gnu/packages/code.scm: Likewise. * gnu/packages/commencement.scm: Likewise. * gnu/packages/coq.scm: Likewise. * gnu/packages/coreboot.scm: Likewise. * gnu/packages/databases.scm: Likewise. * gnu/packages/datalog.scm: Likewise. * gnu/packages/debug.scm: Likewise. * gnu/packages/dictionaries.scm: Likewise. * gnu/packages/dns.scm: Likewise. * gnu/packages/documentation.scm: Likewise. * gnu/packages/dotnet.scm: Likewise. * gnu/packages/education.scm: Likewise. * gnu/packages/electronics.scm: Likewise. * gnu/packages/embedded.scm: Likewise. * gnu/packages/emulators.scm: Likewise. * gnu/packages/engineering.scm: Likewise. * gnu/packages/esolangs.scm: Likewise. * gnu/packages/fabric-management.scm: Likewise. * gnu/packages/file-systems.scm: Likewise. * gnu/packages/finance.scm: Likewise. * gnu/packages/firmware.scm: Likewise. * gnu/packages/flashing-tools.scm: Likewise. * gnu/packages/fontutils.scm: Likewise. * gnu/packages/games.scm: Likewise. * gnu/packages/gcc.scm: Likewise. * gnu/packages/gdb.scm: Likewise. * gnu/packages/geo.scm: Likewise. * gnu/packages/gl.scm: Likewise. * gnu/packages/glib.scm: Likewise. * gnu/packages/gnome.scm: Likewise. * gnu/packages/graph.scm: Likewise. * gnu/packages/graphics.scm: Likewise. * gnu/packages/groff.scm: Likewise. * gnu/packages/gstreamer.scm: Likewise. * gnu/packages/guile.scm: Likewise. * gnu/packages/hardware.scm: Likewise. * gnu/packages/haskell.scm: Likewise. * gnu/packages/heads.scm: Likewise. * gnu/packages/hurd.scm: Likewise. * gnu/packages/image-processing.scm: Likewise. * gnu/packages/instrumentation.scm: Likewise. * gnu/packages/kde-frameworks.scm: Likewise. * gnu/packages/kde-graphics.scm: Likewise. * gnu/packages/kde-pim.scm: Likewise. * gnu/packages/kde-sdk.scm: Likewise. * gnu/packages/kerberos.scm: Likewise. * gnu/packages/lego.scm: Likewise. * gnu/packages/lesstif.scm: Likewise. * gnu/packages/libreoffice.scm: Likewise. * gnu/packages/lighting.scm: Likewise. * gnu/packages/linux.scm: Likewise. * gnu/packages/logging.scm: Likewise. * gnu/packages/mail.scm: Likewise. * gnu/packages/man.scm: Likewise. * gnu/packages/maths.scm: Likewise. * gnu/packages/mpi.scm: Likewise. * gnu/packages/multiprecision.scm: Likewise. * gnu/packages/music.scm: Likewise. * gnu/packages/netpbm.scm: Likewise. * gnu/packages/networking.scm: Likewise. * gnu/packages/nickle.scm: Likewise. * gnu/packages/ocaml.scm: Likewise. * gnu/packages/package-management.scm: Likewise. * gnu/packages/parallel.scm: Likewise. * gnu/packages/plotutils.scm: Likewise. * gnu/packages/pretty-print.scm: Likewise. * gnu/packages/profiling.scm: Likewise. * gnu/packages/qt.scm: Likewise. * gnu/packages/radio.scm: Likewise. * gnu/packages/rdesktop.scm: Likewise. * gnu/packages/rpc.scm: Likewise. * gnu/packages/rust.scm: Likewise. * gnu/packages/security-token.scm: Likewise. * gnu/packages/selinux.scm: Likewise. * gnu/packages/shellutils.scm: Likewise. * gnu/packages/simulation.scm: Likewise. * gnu/packages/statistics.scm: Likewise. * gnu/packages/telephony.scm: Likewise. * gnu/packages/toys.scm: Likewise. * gnu/packages/version-control.scm: Likewise. * gnu/packages/virtualization.scm: Likewise. * gnu/packages/vpn.scm: Likewise. * gnu/packages/vulkan.scm: Likewise. * gnu/packages/webkit.scm: Likewise. * gnu/packages/wine.scm: Likewise. * gnu/packages/wm.scm: Likewise. * gnu/packages/xdisorg.scm: Likewise. * gnu/packages/xorg.scm: Likewise. Merges: https://codeberg.org/guix/guix/pulls/8483 Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
2026-05-24guix: build-system: Set pypi-uri in pyproject, drop python module.Nicolas Graves1-1/+0
After this commit, when both modules are imported: - if pyproject is imported before, the warning is 'pypi-uri' is deprecated, use '(@ (guix build-system pyproject) pypi-uri)' instead - if python is imported before, the warning is `pypi-uri' imported from both (guix build-system python) and (guix build-system pyproject) This seems convenient enough to warn for deprecation in the short term, while avoiding any breaking changes. * guix/build-system/pyproject.scm (pypi-uri): Move the procedure from (guix build-system python) here. * guix/build-system/python (pypi-uri): Drop definition, import it from (guix build-system pyproject) and deprecate it. * gnu/packages/openldap.scm: Reorder modules to get the right warning. * gnu/packages/pypy.scm: Likewise. * gnu/packages/*.scm : Drop module (guix build-system python). * tests/import/pypi.scm: Likewise. Merges: https://codeberg.org/guix/guix/pulls/7448 Change-Id: Ib42f53bc545052eb7918a25afe9db6d5fc2cb834 Reviewed-by: Nguyễn Gia Phong <cnx@loang.net> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2026-04-20gnu: gromacs: Rewrite input.Andreas Enge1-1/+1
* gnu/packages/chemistry.scm (gromacs)[inputs]: Replace hwloc-2 by the identical hwloc. Change-Id: I5a7f33e12cefff884329a867e05ecef60ce9e1d9
2026-03-20gnu: Reference the inherited inputs values.Ludovic Courtès1-1/+1
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 Courtès1-1/+1
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 Wicki1-1/+1
* 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 Graves1-1/+6
* 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 Graves1-6/+3
* 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 Milosavljevic1-2/+4
* 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 Graves1-47/+46
* 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 Graves1-62/+61
* 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 Graves1-44/+45
* 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 Hellseher1-1/+1
* 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 Hellseher1-1/+1
* 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 Elsing1-29/+54
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 Buddelmeijer1-2/+12
* 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 Hellseher1-1/+1
* 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 Graves1-46/+53
* 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 Hogan1-1/+0
* 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 Elsing1-0/+2
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 Elsing1-0/+6
* 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 Elsing1-10/+14
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 Elsing1-23/+36
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 Junjie1-6/+6
* gnu/packages/chemistry.scm (qcint)[arguments]: Use G-expression. Change-Id: I4e26a872b6e78a6ea96d16c661353063b8d3fcd6
2025-07-13gnu: python-pyscf: Make tune works.Zheng Junjie1-3/+10
* 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 Hellseher1-7/+7
* gnu/packages/chemistry.scm: Sort use-module alphabetically. Change-Id: Ib6df5e22d91ef443ad57cbb811906ba3bb0644d8
2025-07-08gnu: Add python-pyscf-properties.David Elsing1-0/+29
* 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 Elsing1-0/+52
* 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 Elsing1-0/+30
* 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 Elsing1-1/+76
* 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 Elsing1-0/+46
* gnu/packages/chemistry.scm (qcint): New variable. Change-Id: Ie32f97a028f847dc401a4b9772df6f0f9a550e97 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-07-08gnu: Add libcint.David Elsing1-0/+58
* gnu/packages/chemistry.scm (libcint): New variable. Change-Id: I72da249743392eb8a4be1673b9fc1a7bbbb1c942 Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-07-08gnu: Add xcfun.David Elsing1-0/+77
* 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 Hellseher1-0/+8
* 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 Kirsch1-7/+37
* 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 Kirsch1-13/+56
* 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 Kirsch1-18/+33
* 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 Goaziou1-0/+1
* 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 Goaziou1-1/+1
* 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 Elsing1-4/+12
* 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 Elsing1-63/+59
* 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 Elsing1-0/+46
* gnu/packages/chemistry.scm (pubchem-align3d): New variable. Signed-off-by: Andreas Enge <andreas@enge.fr>
generated by cgit v1.2.3 (git 2.25.1) at 2026-09-03 06:56:16 +0000