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Author SHA1 Message Date
Ludovic Courtès
1ae20f03f4 gnu: Reference the inherited inputs values. 
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
 2026-03-20 13:27:16 +01:00
Ludovic Courtès
2a50c9598b gnu: Reference the inherited ‘arguments’ value. 
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
 2026-03-20 13:27:15 +01:00
Gabriel Wicki
f86ff1db98 gnu: Pin old pybind11 version. 
* 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>
 2026-03-05 15:53:36 +01:00
Nicolas Graves
7c9b7b36d2 gnu: ringdecomposerlib: Fix build on python-3.12. 
* 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>
 2026-02-15 21:50:05 +00:00
Nicolas Graves
93b40d330f build-system/pyproject: Remove uneeded use of pyproject-guile-json. 
* 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>
 2026-02-07 12:28:18 +01:00
Danny Milosavljevic
904019a852 gnu: avogadro2: Add Wayland. 
* gnu/packages/chemistry.scm (avogadro2)[inputs]: Add qtwayland-5.
[arguments]<#:phases>{wrap-program}: Add qtwayland-5.

Change-Id: I8d085a782455b6ade8b8d77acd45ee00d9bf4eac
 2026-01-29 20:42:52 +01:00
Nicolas Graves
ef18864eb2 gnu: ringdecomposerlib: Switch to pyproject. 
* 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>
 2026-01-25 21:23:56 +01:00
Nicolas Graves
733ec52b07 gnu: rdkit: Switch to pyproject. 
* 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>
 2026-01-25 21:23:47 +01:00
Nicolas Graves
04365b11c2 gnu: gemmi: Switch to pyproject. 
* 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>
 2026-01-25 21:23:45 +01:00
Sharlatan Hellseher
9b3596ad81 gnu: python-pymol: Use python-numpy@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>
 2026-01-25 21:22:19 +01:00
Sharlatan Hellseher
b54008bb08 gnu: rdkit: Use python-numpy@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>
 2026-01-25 21:21:24 +01:00
David Elsing
ad9d43baa0 gnu: gromacs: Update to 2025.3. 
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>
 2025-10-21 22:18:27 +02:00
Hugo Buddelmeijer
0c3cac7e0e gnu: python-geometric: Fix build. 
* 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>
 2025-09-27 23:45:31 +01:00
Sharlatan Hellseher
08e6a0faba gnu: ringdecomposerlib: Fix tests. 
* gnu/packages/chemistry.scm (ringdecomposerlib)[native-inputs]: Remove
python-cython; add python-cython-0.

Change-Id: Ia63a5bcbc9c1e446cc96948e52645ddfe9e31bb6
 2025-09-25 09:37:02 +01:00
Nicolas Graves
ea4e755f69 gnu: python-pymol: Update to 3.1.0. 
* 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>
 2025-09-25 09:37:01 +01:00
Greg Hogan
364e883298 gnu: Remove #:test-target argument. 
* 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
 2025-08-04 04:10:32 +00:00
David Elsing
5aebea0116 gnu: yaehmop: Fix build with GCC 14. 
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>
 2025-07-31 23:19:38 +01:00
David Elsing
d8d9e51a1f gnu: freesasa: Fix build with newer gemmi. 
* gnu/packages/chemistry.scm (freesasa)[arguments]: Add 'fix-new-gemmi phase.

Change-Id: I78997047eba8245a2d275af5ab18d0d0fe48630f
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-07-31 23:19:34 +01:00
David Elsing
c3e59b2ffa gnu: gemmi: Update to 0.7.3. 
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>
 2025-07-31 23:19:24 +01:00
David Elsing
99fb22110e gnu: openbabel: Fix build and switch to git source. 
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>
 2025-07-31 22:41:38 +02:00
Zheng Junjie
464c3b6340 gnu: qcint: Fix build. 
* gnu/packages/chemistry.scm (qcint)[arguments]: Use G-expression.

Change-Id: I4e26a872b6e78a6ea96d16c661353063b8d3fcd6
 2025-07-13 18:37:56 +08:00
Zheng Junjie
278a80f399 gnu: python-pyscf: Make tune works. 
* gnu/packages/chemistry.scm (python-pyscf)[native-inputs]:
Add (canonical-package gcc).

Change-Id: Ibee49cb64581bd9e6743cdd16aa25739ac53112c
 2025-07-13 18:37:47 +08:00
Sharlatan Hellseher
610af820d4 gnu: packages/chemistry: Sort use-module alphabetically. 
* gnu/packages/chemistry.scm: Sort use-module alphabetically.

Change-Id: Ib6df5e22d91ef443ad57cbb811906ba3bb0644d8
 2025-07-08 12:17:15 +01:00
David Elsing
631a3308f5 gnu: Add python-pyscf-properties. 
* gnu/packages/chemistry.scm (python-pyscf-properties): New variable.

Change-Id: I10823bca5df64a563521bc8f1d28a4a75678ef5d
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-07-08 12:17:15 +01:00
David Elsing
c6f85649b3 gnu: Add python-pyscf-dispersion. 
* gnu/packages/chemistry.scm (python-pyscf-dispersion): New variable.

Change-Id: I1e50ae57c4b79932cab87c16a6f2ab733a5544c0
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-07-08 12:17:15 +01:00
David Elsing
002b62199c gnu: Add python-geometric. 
* gnu/packages/chemistry.scm (python-geometric): New variable.

Change-Id: I5d716df3d71a671c334ff2dfd1b44e15e37afc5a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-07-08 12:17:15 +01:00
David Elsing
2f1193181d gnu: Add python-pyscf. 
* gnu/packages/chemistry.scm (python-pyscf): New variable.

Change-Id: I4e265c97644a6f8765c5d509de126de0312a3f98
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-07-08 12:17:15 +01:00
David Elsing
d08c2a882b gnu: Add qcint. 
* gnu/packages/chemistry.scm (qcint): New variable.

Change-Id: Ie32f97a028f847dc401a4b9772df6f0f9a550e97
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-07-08 12:17:14 +01:00
David Elsing
b353e5cb85 gnu: Add libcint. 
* gnu/packages/chemistry.scm (libcint): New variable.

Change-Id: I72da249743392eb8a4be1673b9fc1a7bbbb1c942
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-07-08 12:17:14 +01:00
David Elsing
46cb759a52 gnu: Add xcfun. 
* gnu/packages/chemistry.scm (xcfun): New variable.

Change-Id: Iaf25180a7edafffce1e8eabdbf6a81c289401f2e
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-07-08 12:17:14 +01:00
Sharlatan Hellseher
f9f3fe2082 gnu: packages/chemistry: Add EOF disclaimer. 
* gnu/packages/chemistry.scm: Add a comments to place packages in
alphabetical order.

Change-Id: I2af9eeeb1de77b0420093bf2776b1df7e7bda188
 2025-07-08 12:17:13 +01:00
Jakob Kirsch
a0b0a524aa gnu: avogadro2: Update to 1.100.0. 
* 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>
 2025-06-02 14:52:22 +02:00
Jakob Kirsch
fcee60c803 gnu: avogadrolibs: Update to 1.100.0. 
* 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>
 2025-06-02 14:37:35 +02:00
Jakob Kirsch
c04bb04a39 gnu: spglib: Update to 2.5.0. 
* 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>
 2025-06-02 14:36:49 +02:00
Nicolas Goaziou
1a8b36329f gnu: texlive-libkpathsea: Tweak "texmf.cnf" variables. 
* 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
 2025-05-06 11:25:07 +02:00
Nicolas Goaziou
4df6eda30f gnu: Rename texlive-updmap.cfg' into texlive-local-tree'. 
* 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
 2025-05-06 11:25:06 +02:00
David Elsing
2779928b9c gnu: rdkit: Update to 2024.09.6. 
* 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>
 2025-04-08 13:24:38 +02:00
David Elsing
191b96e7ee gnu: inchi: Update to 1.07.3. 
* 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>
 2025-04-08 13:24:30 +02:00
David Elsing
b2ba3def99 gnu: Add pubchem-align3d. 
* gnu/packages/chemistry.scm (pubchem-align3d): New variable.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-04-07 12:39:28 +02:00
David Elsing
aa55049717 gnu: yaehmop: Update to 2024.03.1. 
* gnu/packages/chemistry.scm (yaehmop): Update to 2024.03.1.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-04-07 12:38:50 +02:00
David Elsing
e5bfc462dd gnu: rdkit: Update to 2023.09.4. 
* 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>
 2024-02-13 11:04:48 +00:00
David Elsing
cc772e7f31 gnu: freesasa: Fix memerr tests. 
* gnu/packages/chemistry.scm (freesasa)[arguments]: Add
"CFLAGS=-fno-builtin-malloc" to #:configure-flags.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2024-02-13 11:04:48 +00:00
David Elsing
52cca41c6f gnu: avalon-toolkit: Update to 2.0.5a. 
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>
 2024-02-13 11:04:48 +00:00
David Elsing
baa711441a gnu: yaehmop: Update to 2023.03.1. 
* gnu/packages/chemistry.scm (yaehmop): Update to 2023.03.1.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2024-02-13 11:04:48 +00:00
David Elsing
805ee72237 gnu: coordgenlibs: Update to 3.0.2. 
* gnu/packages/chemistry.scm (coordgenlibs): Update to 3.0.2.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2024-02-13 11:04:48 +00:00
David Elsing
6ab278b2e7 gnu: maeparser: Update to 1.3.1. 
* gnu/packages/chemistry.scm (maeparser): Update to 1.3.1.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2024-02-13 11:04:47 +00:00
David Elsing
01ec7c3883 gnu: gemmi: Update to 0.6.4. 
* 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>
 2024-02-13 11:04:47 +00:00
Maxim Cournoyer
edb03ceb60 gnu: msgpack: Deprecate with msgpack-c. 
* 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.
 2024-01-09 22:10:12 -05:00
Maxim Cournoyer
8c9f430a05 gnu: python-pymol: Remove msgpack from native-inputs. 
It's now propagated by mmtf-cpp.

* gnu/packages/chemistry.scm (python-pymol)
[native-inputs]: Remove msgpack.

Reviewed-by: Andreas Enge <andreas@enge.fr>
 2023-08-21 14:11:39 -04:00
Maxim Cournoyer
92f3476077 gnu: avogadrolibs: Remove msgpack from native-inputs. 
It's now propagated by mmtf-cpp.

* gnu/packages/chemistry.scm (avogadrolibs)
[native-inputs]: Remove msgpack.

Reviewed-by: Andreas Enge <andreas@enge.fr>
 2023-08-21 14:11:39 -04:00