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127 Commits

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
Andreas Enge
d86bff271a gnu: openfoam-org: Fix build. 
* gnu/packages/simulation.scm (openfoam-org)[inputs]: Replace vtk by
vtk-9.5, which fixes the build; and fmt-11 by fmt, which are the same.

Merges guix/guix!7052
Fixes: guix/guix#3783

Change-Id: Ifac2256ce0f3541fb79a4d89c9affeee22d73fe1
Signed-off-by: Cayetano Santos <csantosb@inventati.org>
 2026-03-13 10:05:40 +01:00
Andreas Enge
ebe4cc6b3b gnu: Remove python-dolfin-adjoint. 
* gnu/packages/simulation.scm (python-dolfin-adjoint): Delete variable.

Fixes: guix/guix#6128
Change-Id: I86bf93403a7cf222b9ae89cb0e786b9b86384d04
 2026-03-06 11:36:48 +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
Andreas Enge
67dc1ca3ec gnu: openfoam-com: Update to 2512. 
* gnu/packages/simulation.scm (openfoam-com): Update to 2512.

Change-Id: Id1961be4899ad5139f33ee59c298085eda25e9ff
 2026-02-14 17:38:28 +01:00
Sharlatan Hellseher
68c057d5d8 gnu: fenics: Fix tests. 
* gnu/packages/simulation.scm (fenics):
  [arguments] <test-flags>: Skip two more tests.
  [native-inputs]: Add pythn-numpy-1.

Change-Id: Ic41cb4f6f92b89cffd87d43b617d34dce756efd9
 2026-02-07 12:28:54 +01:00
Nicolas Graves
fbaf9c22a0 gnu: Remove python-coverage native-input from some packages. 
Remove python-coverage from [native-inputs] in the following packages as
not required for build/tests/install:

* gnu/packages/check.scm: (python-pytest-flakes)
* gnu/packages/cpp.scm: (cpplint)
* gnu/packages/jupyter.scm: (python-nbclassic)
* gnu/packages/machine-learning.scm (onnx,
python-pytorch-lightning) (python-torchmetrics)
* gnu/packages/openstack.scm: (python-hacking)
* gnu/packages/python-xyz.scm: (python-lsp-jsonrpc, python-nodeenv)
* gnu/packages/simulation.scm: (python-dolfin-adjoint)
* gnu/packages/version-control.scm: (pre-commit)

Change-Id: I2c5e14f4aa28906ceee054c857e6abeeb122ad52
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-02-07 12:28:35 +01:00
Nicolas Graves
015bc199ef gnu: Remove python-flake8 native-input from some packages. 
Remove python-flake8 from [native-inputs] in the following packages as
not required for build/tests/install:

* gnu/packages/bioinformatics.scm: (python-doubletdetection)
* gnu/packages/ebook.scm: (calibre)
* gnu/packages/graph.scm: (python-pygsp)
* gnu/packages/machine-learning.scm: (python-pymanopt, python-pyro-api)
* gnu/packages/python-web.scm: (python-furl)
* gnu/packages/python-xyz.scm: (python-jinja2-cli)
* gnu/packages/simulation.scm: (python-dolfin-adjoint)
* gnu/packages/vpn.scm: (sshuttle)

* gnu/packages/music.scm (python-mutagen):
  [arguments]<#:test-flags>: Ignore flake8 quality tests.
  [native-inputs]: Remove python-flake8.

Change-Id: I2789b8711faf3aa60a4bfa2062f95616e216d6c3
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-02-07 12:28:35 +01:00
Sharlatan Hellseher
561736d94d gnu: python-fenics-ffc: Use python-numpy@1. 
* gnu/packages/simulation.scm (python-fenics-ffc):
[propagated-inputs]: Add python-numpy-1.

Change-Id: I57a991c70947babc1734660c1d6723789ef77466
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
 2026-01-25 21:21:17 +01:00
Sharlatan Hellseher
065980a401 gnu: python-fenics-ufl-2019: Use python-numpy@1. 
* gnu/packages/simulation.scm (python-fenics-ufl-2019):
[inputs]: Remove python-numpy.
[propagated-inputs]: Add python-numpy-1

Change-Id: I3171b24924f08a6210504ee03b3726a18609b186
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
 2026-01-25 21:21:16 +01:00
Sharlatan Hellseher
606e072449 gnu: python-meshio: Skip some tests. 
* gnu/packages/simulation.scm (python-meshio)[arguments]<test-flags>:
Skip some NumPy incompatible failing tests.

Change-Id: I48e782b7eb2920c12777bda20a1f3d2753fcf657
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
 2026-01-25 21:19:13 +01:00
Hartmut Goebel
77983185fd gnu: sumo: Update to 1.25.0. 
* gnu/packages/simulation.scm (sumo): Update to 1.25.0.

Change-Id: I6cf32f91ca651784f53477e217e1b901240d2c21
 2026-01-25 18:56:27 +01:00
Francisco-Galindo
303b10692b gnu: Add python-simpy. 
* gnu/packages/simulation.scm (python-simpy): New variable.

Change-Id: Ic95e6b0656dc2e2deffb543491c64ad5ae14632c
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-12-21 22:08:56 +00:00
Reza Housseini
62b90a6569 gnu: openfoam-com: Update to 2506. 
* gnu/packages/simulation.scm (openfoam-com): Update to 2506.
[source]: Switch to git-fetch. Remove snippets.
[arguments]: Add parent variable to replace version for inherited package.

Change-Id: I2c79e98e621516dfe0e950a41b9abb515da43af3
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-12-03 10:47:05 +01:00
Reza Housseini
9938cce4f8 gnu: openfoam-org: Update to 13. 
* gnu/packages/simulation.scm (openfoam-org): Update to 13.
[source]: Switch to git-fetch. Move snippets to phases.
[native-inputs, inputs]: Move runtime dependencies from native-inputs
to inputs. Add dependencies for paraview to build plugin. Switch to Qt6.
[arguments]: Reorder phases, use configure phase for configuration.
Add version suffix to OpenFOAM install folder.
Add phase to patch version. Add phase to patch paraview.
Wrap the binaries with the environment variables sourced from bashrc.

Change-Id: I26a313fa3aab22bff5a743890c6ffb0d56857f0b
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-12-03 10:46:57 +01:00
Greg Hogan
1aebfc74f1 gnu: boost: Update to 1.89.0. 
* gnu/packages/boost.scm (boost-for-source-highlight): Rename this ...
(boost-1.83): ... to this.
(boost-numpy): Inherit from boost-1.83.
* gnu/packages/pretty-print.scm (source-highlight): Update accordingly.

* gnu/packages/boost.scm (boost): Update to 1.89.0.
[source]: Remove patches.

* gnu/packages/boost.scm (mdds)
[propagated-inputs]: Replace boost with boost-1.83.

* gnu/packages/astronomy.scm (aoflagger),
* gnu/packages/embedded.scm (cc-tool),
* gnu/packages/games.scm (0ad, vcmi),
* gnu/packages/image.scm (gpick),
* gnu/packages/maths.scm (highfive),
* gnu/packages/plotutils.scm (asymptote)
[native-inputs]: Replace boost with boost-1.83.

* gnu/packages/audio.scm (guitarix, supercollider),
* gnu/packages/bioconductor.scm (r-mzr),
* gnu/packages/bioinformatics.scm (ataqv, bless, express, isolator,
metabat, r-velocytom, rsem, sailfish, salmon),
* gnu/packages/bittorrent.scm (libtorrent-rasterbar),
* gnu/packages/code.scm (sourcetrail),
* gnu/packages/compression.scm (innoextract),
* gnu/packages/cpp.scm (lager),
* gnu/packages/crypto.scm (cryfs),
* gnu/packages/electronics.scm (nextpnr, prjpeppercorn, prjtrellis,
pulseview),
* gnu/packages/emulators.scm (mupen64plus-video-glide64mk2),
* gnu/packages/engineering.scm (cadabra2, freecad, libigl,
openscad, prusa-slicer),
* gnu/packages/file-systems.scm (snapper),
* gnu/packages/finance.scm (ledger),
* gnu/packages/game-development.scm (dds),
* gnu/packages/games.scm (colobot, fifengine, knightsgame, leela-zero,
pokerth, supertux, wesnoth, wesnoth-server),
* gnu/packages/geo.scm (gplates),
* gnu/packages/gnucash.scm (gnucash),
* gnu/packages/graph.scm (python-graph-tool),
* gnu/packages/graphics.scma (openshadinglanguage),
* gnu/packages/i2p.scm (i2pd),
* gnu/packages/image-viewers.scm (luminance-hdr),
* gnu/packages/kde-graphics.scm (krita),
* gnu/packages/mail.scm (astroid),
* gnu/packages/medical.scm (orthanc, orthanc-mysql,
orthanc-postgresql),
* gnu/packages/messaging.scm (libphonenumber),
* gnu/packages/mpd.scm (ncmpcpp),
* gnu/packages/networking.scm (kismet),
* gnu/packages/opencog.scm (cogutil),
* gnu/packages/photo.scm (hugin),
* gnu/packages/poedit.scm (poedit),
* gnu/packages/radio.scm (gnuradio),
* gnu/packages/rdf.scm (lucene++),
* gnu/packages/serialization.scm (avro-cpp),
* gnu/packages/simulation.scm (fenics-dolfin),
* gnu/packages/version-control.scm (gource),
* gnu/packages/video.scm (aegisub, mkvtoolnix),
* gnu/packages/web.scm (websocketpp)
[inputs]: Replace boost with boost-1.83.

* gnu/packages/libreoffice.scm (libcmis): Update to 0.6.2-00a85bf6.
(librevenge): Update to 0.0.5.
[arguments]<#:configure-flags>: Remove reference to boost system
component for which the compatibility stub has been removed.
* gnu/packages/serialization.scm (msgpack-cxx): Update to 7.0.0.

Change-Id: I247f3eaecde3de3fe227586b840f0312b4797ee1
 2025-11-28 12:26:24 +00:00
Aaron Covrig
97d9c63265 gnu: googletest: Update to 1.17.0. 
* gnu/packages/check.scm (googletest): Update to 1.17.0
(googletest-1.12): Add variable.

* gnu/packages/glib.scm (sdbus-c++)
[native-inputs]: Replace googletest-1.17 with googletest.

* gnu/packages/compression.scm (pzstd)
[native-inputs, inputs]: Replace googletest with googletest-1.8.

* gnu/packages/cpp.scm (c++-gsl),
* gnu/packages/engineering.scm (cura-engine),
* gnu/packages/password-utils.scm (pwsafe)
[native-inputs]: Replace googletest with googletest-1.13.

* gnu/packages/crypto.scm (crc32c),
* gnu/packages/engineering.scm (lib3mf),
* gnu/packages/fontutils.scm (opentype-sanitizer),
* gnu/packages/games.scm (openclonk),
* gnu/packages/gnome.scm (gnome-commander),
* gnu/packages/machine-learning.scm (qnnpack),
* gnu/packages/maths.scm (ruy),
* gnu/packages/serialization.scm (libnop)
[native-inputs]: Replace googletest with googletest-1.12.

* gnu/packages/machine-learning.scm (fann),
* gnu/packages/maths.scm (boolector),
* gnu/packages/parallel.scm (clog),
* gnu/packages/simulation.scm (sumo),
* gnu/packages/telephony.scm (sipp)
[native-inputs]: Replace googletest with googletest-1.8.

* gnu/packages/parallel.scm (cpuinfo)
[inputs]: Replace googletest with googletest-1.13.

* gnu/packages/machine-learning.scm (nnpack, python-pytorch),
* gnu/packages/parallel.scm (pthreadpool)
[inputs]: Replace googletest with googletest-1.12.

* gnu/packages/maths.scm (fp16, fxdiv),
* gnu/packages/serialization.scm (yaml-cpp),
* gnu/packages/web.scm (rapidjson)
[inputs]: Replace googletest with googletest-1.8.

Change-Id: I310fb6785d6e19bb8dbf56c25028587573981a0e
 2025-11-28 12:07:09 +00:00
Nicolas Graves
a511728210 gnu: python-meshio: Update to 5.3.5. 
* gnu/packages/simulation.scm (python-meshio): Update to 5.3.5.
[source]: Remove snippet.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools.
[propagated-inputs]: Remove python-importlib-metadata.
[inputs, description]: Improve style.

Change-Id: I9cfe0bdbef3bbb8628e065d523dd65bf1fe388c6
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-11-26 21:22:06 +00:00
Nicolas Graves
c63083b2a1 gnu: fenics: Switch to pyproject. 
* gnu/packages/simulation.scm (fenics):
[build-system]: Switch to pyproject-build-system.
[arguments]: Relocate field, improve style.
<#:test-flags>: Use them, and skip flaky tests.
[native-inputs]: Add python-setuptools.

Change-Id: I85825ec6aa2a68db74cb7b5864103bbf34c33031
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-11-26 21:22:06 +00:00
Nicolas Graves
99e0ae2431 gnu: python-commonroad-route-planner: Switch to pyproject. 
* gnu/packages/simulation.scm (python-commonroad-route-planner):
[build-system]: Switch to pyproject-build-system.
[arguments]: Improve style.
<#:tests?>: Disable them.
[native-inputs]: Add python-setuptools.
[description]: Improve style.

Change-Id: I4df18bbc6bafa2d156e8569646e6b5b1af464714
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-11-26 21:22:06 +00:00
Nicolas Graves
ebf4dccced gnu: python-commonroad-io: Switch to pyproject. 
* gnu/packages/simulation.scm (python-commonroad-io):
[build-system]: Switch to pyproject-build-system.
[arguments]: Improve style.
<#:tests?>: Disable them.
[native-inputs]: Add python-setuptools.  Remove python-pytest.

Change-Id: Ib678e1e41ab51dbfef75fc86dee327c721de5731
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-11-26 21:22:06 +00:00
Nicolas Graves
5cbbbc609f gnu: python-commonroad-vehicle-models: Switch to pyproject. 
* gnu/packages/simulation.scm (python-commonroad-vehicle-models):
[build-system]: Switch to pyproject-build-system.
[arguments]: Improve style.
<#:test-flags>: Ignore failing tests.
[native-inputs]: Add python-matplotlib, python-pytest, python-scipy,
python-setuptools.

Change-Id: If774ec9d9c8185367b2e2360e60e05038b11eca6
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-11-26 21:22:06 +00:00
Nicolas Graves
98d4c1daeb gnu: python-fenics-ffc: Switch to pyproject. 
* gnu/packages/simulation.scm (python-fenics-ffc):
[source, arguments, description]: Improve style.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools.

Change-Id: I311ee58857bb796e6cacece5408a2eb62c754a04
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-11-26 21:22:06 +00:00
Nicolas Graves
a978dc3d3e gnu: Add python-fenics-ufl-2019. 
* gnu/packages/simulation.scm (python-fenics-ufl-2019): New variable.

Change-Id: Ie0dccb8e5500cdaa14b6f32621ce48d1399b9979
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-11-26 21:22:06 +00:00
Nicolas Graves
720b0aa871 gnu: python-fenics-ufl: Update to 2025.2.0. 
* gnu/packages/simulation.scm (python-fenics-ufl): Update to 2025.2.0.
[build-system]: Switch to pyproject-build-system.
[arguments]: Drop them.
[native-inputs]: Add python-setuptools.
[description]: Improve style.

Change-Id: I747c989bd6dbcfa034182523ec6be7976d7f3f33
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-11-26 21:22:06 +00:00
Nicolas Graves
bc4297daa9 gnu: open-simulation-interface: Switch to pyproject. 
* gnu/packages/simulation.scm (open-simulation-interface):
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-pytest, python-setuptools.

Change-Id: Ie27bdc726ee7a943cdb7a59b86595853e78a575e
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-11-26 21:22:05 +00:00
Andreas Enge
4e62f1cc47 Revert "gnu: python-fenics-ufl: Update to 2025.1.0." 
This reverts commit 5c522a1abf.

The update breaks depending packages.
 2025-10-29 21:56:06 +01:00
Andreas Enge
7d6801f5e6 gnu: Remove openfoam. 
* gnu/packages/simulation.scm (openfoam): Delete variable.

Change-Id: I7a15a430e76484ce8e157b55fa90ce271b9372ee
 2025-10-22 23:41:30 +02:00
Maxim Cournoyer
10482f731e Reapply "Update Maxim's email address." 
This reverts commit a7db92d9b3, this time with
the more careful command, to avoid a world rebuild:

grep -rl --exclude-dir=build --exclude-dir=patches --exclude=ld-wrapper.in \
  --exclude=sitecustomize.py --exclude=guix-emacs.el maxim.cournoyer@gmail.com |
  xargs sed -i 's/maxim.cournoyer@gmail.com/maxim@guixotic.coop/g'

Change-Id: I0871f5cf9ace79e34e78e24154d0da6ea95a3a91
 2025-09-18 13:44:12 +09:00
Maxim Cournoyer
a7db92d9b3 Revert "Update Maxim's email address." 
This reverts commit d0d87a744d. Oops! This
caused a world rebuild.

Change-Id: I25fff644b2b61d0ee93d69b457b04c72b5b74d15
 2025-09-18 12:07:31 +09:00
Maxim Cournoyer
d0d87a744d Update Maxim's email address. 
The change was automated via:

  git grep -l maxim.cournoyer@gmail.com |
    xargs sed -i 's/maxim.cournoyer@gmail.com/maxim@guixotic.coop/g'

* .mailmap: New entry.

Change-Id: Iaa88b1e51c94159c49138fb43910badb990eb169
 2025-09-18 08:05:19 +09:00
Nicolas Graves
5c522a1abf gnu: python-fenics-ufl: Update to 2025.1.0. 
* gnu/packages/simulation.scm (python-fenics-ufl): Update to 2025.1.0.
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]: Remove them.
[native-inputs]: Add python-setuptools, python-wheel.
[home-page, description]: Update.

Signed-off-by: jgart <jgart@dismail.de>
 2025-08-26 09:30:00 -05:00
Jake Forster
f30c8b53ea gnu: paraview: Update to 6.0.0. 
* gnu/packages/image-processing.scm (paraview): Update to 6.0.0.
[source]<snippet>: Update list of bundled VTK libraries in comments.  glew is
no longer bundled so do not remove it.
[arguments]<#:configure-flags>: Use a relative directory in
"CMAKE_INSTALL_DOCDIR" and
"PARAVIEW_GENERATED_DOCUMENTATION_OUTPUT_DIRECTORY".  Remove
"-DVTK_MODULE_USE_EXTERNAL_VTK_glew=ON".
[inputs]: Replace fmt with fmt-11.  Remove glew.
* gnu/packages/simulation.scm (openfoam-org)[native-inputs]: Replace fmt with
fmt-11.  Remove glew.

Change-Id: Ifa005f33dd04c0119008726c11f3b32efba28b0d
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2025-08-25 12:17:02 +02:00
Paul Garlick
db2f7f6a76 gnu: fenics-dolfin: Remove support for SUNDIALS. 
The dolfin interface to sundials requires a header file 'cvode_impl.h'
which is not available in sundials v>5.4.0.

* gnu/packages/simulation.scm (fenics-dolfin)
[inputs]: Remove SUNDIALS-OPENMPI.
[arguments]<#:configure-flags>: Disable SUNDIALS feature.
<#:phases>: Do not set SUNDIALS_DIR variable.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-08-22 09:38:35 +02:00
Paul Garlick
293cca3324 gnu: fenics-dolfin: Fix build with gcc@14. 
* gnu/packages/patches/fenics-dolfin-integer-types.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register new patch.
* gnu/packages/simulation.scm (fenics-dolfin)[source]: Use new patch.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-07-28 22:30:03 +02:00
宋文武
c31c4522ad gnu: qtxmlpatterns: Rename to qtxmlpatterns-5. 
* gnu/packages/qt.scm (qtxmlpatterns): Rename to qtxmlpatterns-5.
(qtspeech-5) [native-inputs]: Adjust accordingly.
(python-pyqt) [inputs]: Likewise.
(python-shiboken-2) [inputs]: Likewise.
(python-pyside-2) [inputs]: Likewise.
* gnu/packages/animation.scm (pencil2d) [inputs]: Likewise.
* gnu/packages/education.scm (openboard) [inputs]: Likewise.
(ktouch) [inputs]: Likewise.
* gnu/packages/engineering.scm (freecad) [inputs]: Likewise.
* gnu/packages/finance.scm (monero-gui) [inputs]: Likewise.
* gnu/packages/geo.scm (gplates) [inputs]: Likewise.
* gnu/packages/image-processing.scm (paraview) [inputs]: Likewise.
* gnu/packages/kde-frameworks.scm (ktexteditor-5) [inputs]: Likewise.
(ksyntaxhighlighting-5) [native-inputs]: Likewise.
* gnu/packages/messaging.scm (kaidan) [inputs]: Likewise.
* gnu/packages/music.scm (hydrogen) [inputs]: Likewise.
* gnu/packages/simulation.scm (openfoam-org) [inputs]: Likewise.

Change-Id: Ic260988913600dee261bd138efc6a830bc45d057
Signed-off-by: Zheng Junjie <z572@z572.online>
 2025-07-21 19:41:24 +08:00
Paul Garlick
0d8a0acc53 gnu: python-dolfin-adjoint: Fix build. 
* gnu/packages/simulation.scm (python-dolfin-adjoint): Fix build.
[arguments]: Set pytest import mode. Update list of failing tests.
[native-inputs]: Add python-setuptools and python-wheel, needed by
pyproject-build-system.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-07-10 12:07:22 +02:00
Paul Garlick
a8769dddaa gnu: fenics: Fix build. 
* gnu/packages/simulation.scm (fenics): Run guix style, improve
formatting.
[arguments] <phases>: Remove test module references to expired numpy
aliases in the 'pre-check' phase.  Use '--deselect' instead of '--ignore'
to skip a test in the 'check' phase.  Add a FIXME note to enable reading
and writing files in the binary HDF5 format.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-07-05 16:47:08 +02:00
Paul Garlick
4b2f52e998 gnu:fenics-dolfin: Fix build with hdf5@1.14. 
* gnu/packages/patches/fenics-dolfin-hdf5-version-check.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Register new patch.
* gnu/packages/simulation.scm (fenics-dolfin): Run guix style.
[source]: Use new patch.
[arguments] <phases>: Update 'pre-check' comment.
Add 'demo_stokes-iterative_mpi' test to list of skipped tests.

Change-Id: I8ec4534d96af6726fcfd3a601d34b109d06c4ca6
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-06-28 16:33:42 +02:00
Sharlatan Hellseher
8f17262ceb gnu: python-fenics-fiat: Refresh package, fix build. 
This package is quite dated and upstream no longer maintains it: "This
repository was archived by the owner on Feb 21, 2022. It is now
read-only." <https://bitbucket.org/fenics-project/fiat> ->
<https://github.com/FEniCS/fiat> while providing a new refactored
fork <https://github.com/firedrakeproject/fiat>.

* gnu/packages/simulation.scm (python-fenics-fiat)
[build-system]: Swap to pyproject-build-system.
[arguments] <test-flags>: Move tests skip logic here.
<phases>: Use default 'check.
[native-inputs]: Add python-setuptools and python-wheel.
[description]: Adjust fill column indentation.

Change-Id: Ifea4430b1e49491f1b145702ec6df58153a9c809
 2025-03-23 00:12:27 +00:00
Sharlatan Hellseher
f2b3c36bee gnu: python-fenics-dijitso: Fix build. 
* gnu/packages/simulation.scm (python-fenics-dijitso): Improve style,
fix build, use G-Expressions.
[phases] {check}: Respect tests? flag.
[native-inputs]: Add python-pytest-cov.

Change-Id: I4032735228d36366a7014b48e9d21606628c56a6
 2025-01-27 21:22:32 +00:00
Nicolas Graves
3c2943b621 gnu: build-system/pyproject: Add missing native-inputs. 
* gnu/packages/bioinformatics.scm (python-ega-download-client)
[native-inputs]: Add python-setuptools and python-wheel.

* gnu/packages/databases.scm (datasette)[native-inputs]: Add
python-pip.

* gnu/packages/django.scm (python-django-localflavor,
python-django-contact-form)[native-inputs]: Add python-setuptools and
python-wheel.

* gnu/packages/graphviz.scm (python-uqbar)[native-inputs]: Add
python-setuptools and python-wheel.

* gnu/packages/jupyter.scm (python-jupyterlab-server)[native-inputs]:
Add python-wheel.
(python-nbstripout)[native-inputs]: Add python-setuptools and
python-wheel.

* gnu/packages/machine-learning.scm (python-captum,
python-linear-operator, python-gpytorch)[native-inputs]: Add
python-setuptools.

* gnu/packages/music.scm (abjad, abjad-ext-rmarkers,
abjed-ext-nauert, python-mutagen)[native-inputs]: Add
python-setuptools and python-wheel.

* gnu/packages/package-management.scm
(python-conda-package-handling)[native-inputs]: Add python-setuptools
and python-wheel.
(conda)[native-inputs]: Add python-wheel.

* gnu/packages/python-check.scm (python-pyinstrument,
python-pytest-testmon, python-pytest-trio, python-nbval,
python-pytest-toolbox)[native-inputs]: Add python-setuptools and
python-wheel.
(python-nptyping)[native-inputs]: Add python-setuptools.

* gnu/packages/python-check.scm (python-dask-expr)[native-inputs]:
Add python-setuptools and python-wheel.

* gnu/packages/python-web.scm (parfive, python-aioftp, python-hupper,
python-sanic, python-mechanicalsoup, python-tinycss, python-aiostream,
python-cbor2, gunicorn)[native-inputs]: Add python-setuptools and
python-wheel.

* gnu/packages/python-xyz.scm (python-apprise, python-jaraco-classes,
python-sparse, python-shtab, python-pyan3)[native-inputs]: Add
python-setuptools.
(python-jupytext, python-orderedmultidict, python-identify, python-nodeenv,
python-cfgv, python-zarr, python-multipart, python-nbconvert, python-cram,
python-immutables, python-numpydoc, python-cairosvg, python-unidecode,
python-black, python-multidict, python-mpv-jsonipc, python-humanize,
python-cmd2)[native-inputs]: Add python-setuptools and python-wheel.
(python-partd, python-dask, python-zarr)[native-inputs]: Add
python-wheel.
(python-nbconvert)[propagated-inputs]: Add texlive-etoolbox. Remove
duplicate textlive-jknapltx.
(python-isort)[native-inputs]: Add python-pip.

* gnu/packages/simulation.scm (python-fenics-dijitso)[native-inputs]:
Add python-setuptools and python-wheel.

* gnu/packages/sphinx.scm (python-pydata-sphinx-theme,
python-sphinx-autodoc-typehints)[native-inputs]: Add
python-setuptools.

* gnu/packages/syndication.scm (tuir)[native-inputs]: Add
python-setuptools and python-wheel.

* gnu/packages/terminals.scm (python-halo)[native-inputs]: Add
python-setuptools and python-wheel.

* gnu/packages/time.scm (python-arrow, python-dateutil)
[native-inputs]: Add python-setuptools and python-wheel.

* gnu/packages/version-control.scm (pre-commit)[native-inputs]: Add
python-setuptools and python-wheel.  Remove input labels.

* gnu/packages/virtualization.scm (python-qemu-qmp,
python-transient)[native-inputs]: Add python-setuptools and
python-wheel.

* gnu/packages/xorg.scm (python-xcffib)[native-inputs]: Add
python-setuptools and python-wheel.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

Change-Id: Id61cf8cdc47bd4c2871c0a9c8e9a5bfd51157df0
 2024-12-13 20:18:58 +00:00
Nicolas Graves
b3435d3ed1 gnu: python-fenics-dijitso: Move to pyproject-build-system. 
* gnu/packages/simulation.scm (python-fenics-dijitso):
  [build-system]: Move to pyproject-build-system.
  [arguments]<#:phases>: Rewrite check phase replacement to care about
  .guix-pytest.

Change-Id: I3383f4078fbb0100e6d8257d7d84785b953ab0cf
Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
 2024-12-13 20:18:57 +00:00
Gabriel Wicki
8d05f0c8db gnu: Fix synopsis in various python packages. 
* gnu/packages/python-compression.scm (python-inflate64): Fix synopsis.
* gnu/packages/python-science.scm (python-xarray-dataclasses): Fix synopsis.
* gnu/packages/python-web.scm (python-waybackpack): Fix synopsis.
* gnu/packages/python-xyz.scm (python-mir-eval): Fix synopsis.
(python-restructuredtext-lint): Fix synopsis.  (python-pixelmatch): Fix
synopsis.  (python-google-pasta): Fix synopsis.  (python-xmp-toolkit): Fix
synopsis.
* gnu/packages/bioinformatics.scm (python-mgatk): Fix synopsis.
* gnu/packages/rpc.scm (python-grpc-stubs): Fix synopsis.
* gnu/packages/simulation.scm (python-commonroad-io): Fix synopsis.

Signed-off-by: Vagrant Cascadian <vagrant@debian.org>
 2024-12-10 22:35:06 -08:00
Sharlatan Hellseher
a1e6ac72fd gnu: packages/simulation: Add self to copyright header. 
* gnu/packages/simulation.scm: Add Sharlatan Hellseher
<sharlatanus@gmail.com> to copyright header.

Change-Id: I18e82c7344cfa206ff8f82dfa963b7d8b026dcf0
 2024-07-11 19:15:10 +01:00
Sharlatan Hellseher
a54f6f1c87 gnu: python-dolfin-adjoint: Disable failing tests, fix build. 
* gnu/packages/simulation.scm (python-dolfin-adjoint) [arguments]:
<#:test-flags>: Explicitly ignore failing tests during collection phase
and some tests during runt test phase.
<#:phases>: Change HOME env to GETCWD in 'set-environment-variable phase.

Change-Id: Ibee5e45052a3828b4522752a87c97367d7caec65
 2024-07-11 19:15:10 +01:00
Sharlatan Hellseher
72024ae490 gnu: python-dolfin-adjoint: Swap to pyproject-build-system. 
* gnu/packages/simulation.scm (python-dolfin-adjoint) [source]: Remove
trailing #t from snippet.
[build-system]: Swap to pyproject-build-system.
[arguments]: Apply G-expressions. <#:phases>: Swap back to defaul 'check
phase.

python-dolfin-adjoint

Change-Id: Idf100b718b44d9d6695e598c434fbbac55a38845
 2024-07-11 19:15:10 +01:00
Sharlatan Hellseher
9da142540e gnu: python-dolfin-adjoint: Adjust package style. 
* gnu/packages/simulation.scm (python-dolfin-adjoint): Move inputs after
arguments.
[description]: Place it on a new line, fix indentation.

Change-Id: I3d971e48b4072258ed0b41af5c202e64af9de8f3
 2024-07-11 19:15:10 +01:00
Sharlatan Hellseher
5a33a71e67 gnu: python-dolfin-adjoint: Fix indentation. 
* gnu/packages/simulation.scm (python-dolfin-adjoint): Fix indentation.

Change-Id: I457639a98f1ae49d43042e557352d390afc9419d
 2024-07-11 19:15:09 +01:00