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4374 Commits

Author SHA1 Message Date
Sharlatan Hellseher
52188611c8 gnu: python-peaks2utr: Update to 1.5.0. 
* gnu/packages/bioinformatics.scm (python-peaks2utr): Update to
1.5.0. Use G-Expressions.
[source]: Switch to git-fetch.
[arguments] <test-flags>: Run all tests.
[phases]{relax-requirements}: Relax upper constrain for NumPy.
[propagated-inputs]: Remove macs, and python-numpy-1; add macs-3, and
python-numpy.
[native-inputs]: Remove python-wheel; add python-pytest.

Change-Id: I7466e00eb99c7fa12263ed8aaedde614c2119d4b
 2026-04-05 20:18:04 +01:00
Sharlatan Hellseher
f4fc7b44e0 gnu: macs-3: Update to 3.0.4. 
* gnu/packages/bioinformatics.scm (macs-3): Update to 3.0.4.
[arguments] <test-flags>: Skip one test.

Change-Id: I7bb990fbaa25bdb3a1f4047cc65a581ffdcd59f7
 2026-04-05 20:18:04 +01:00
Nicolas Graves
93099959cb gnu: packages: Drop python-pytest-runner native-inputs. 
This commit was generated using https://codeberg.org/guix/guix/pulls/5862:

   guix style -S remove-native-inputs --parameter=python-pytest-runner

and adding back python-pytest if necessary.

* gnu/packages/geo.scm (python-pyshp)
* gnu/packages/backup.scm (vorta)
[native-inptus]: Remove python-pytest-runner, add python-pytest.

* gnu/packages/backup.scm (duplicity)
* gnu/packages/linux.scm (python-spython)
* gnu/packages/bioinformatics.scm (python-cwl-utils)
* gnu/packages/databases.scm (python-pyarrow, datasette)
* gnu/packages/fontutils.scm (python-cu2qu)
* gnu/packages/gnome.scm (terminator)
* gnu/packages/music.scm (stargate)
* gnu/packages/python-science.scm (python-upsetplot)
* gnu/packages/python-web.scm (python-falcon, python-cssselect2)
* gnu/packages/python-xyz.scm (python-docrep, python-cairocffi,
  python-entrypoint2)
* gnu/packages/task-management.scm (todoman)
* gnu/packages/video.scm (yle-dl)
* gnu/packages/vpn.scm (sshuttle)
[native-inptus]: Remove python-pytest-runner.

Relates-to: https://codeberg.org/guix/guix/issues/7474
Change-Id: Ia79595309ba8965c4374e7c24a1ef4c3e36fe1ea
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-04-04 22:42:11 +01:00
Nicolas Graves
266d84d922 guix: build-system: Set pypi-uri in pyproject, drop python module. 
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>
 2026-04-04 22:42:07 +01:00
Nicolas Graves
1e099900b2 gnu: python-mysql-connector-python: Relocate and rename. 
* gnu/packages/python-xyz.scm (python-mysql-connector-python): Move from here…
* gnu/packages/databases.scm (mysql-connector-python): …to here.
(python-mysql-connector-python): Deprecate package.

* gnu/packages/bioinformatics.scm (python-genomepy)[propagated-inputs]:
Replace python-mysql-connector-python by mysql-connector-python.

Change-Id: Ib48e3b998d3bf946d03d2c7aaf246a8251776402
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-04-04 22:42:01 +01:00
Nicolas Graves
ea0d6eb43f gnu: python-cooler: Drop phase 'fix-pytest-config. 
* gnu/packages/bioinformatics.scm (python-cooler)[arguments]<#:phases>:
Drop phase 'fix-pytest-config.

Change-Id: Iddad5557655691c11ded0f0a20b1f23b7791b896
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-04-04 22:41:54 +01:00
Nicolas Graves
45b2c1f3f2 gnu: gdc-client: Drop phase 'fix-pytest-config. 
* gnu/packages/bioinformatics.scm (gdc-client)[arguments]<#:phases>:
Drop phase 'fix-pytest-config.

Change-Id: I12f5dd5306a4c6d562d03b48837bf4bc1ae8ddda
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-04-04 22:41:54 +01:00
Nicolas Graves
9160351b94 build-system/pyproject: Remove python-pytest-cov native-input. 
* gnu/packages/astronomy.scm (python-wiimatch)
* gnu/packages/audio.scm (python-resampy, python-librosa)
* gnu/packages/backup.scm (borgmatic)
* gnu/packages/bioinformatics.scm
(python-bed-reader, python-pysnptool, python-pairtools)
* gnu/packages/check.scm (python-pytest-nunit, python-pytest-perf)
* gnu/packages/dav.scm (vdirsyncer, radicale)
* gnu/packages/django.scm (python-django-redis)
* gnu/packages/engineering.scm (python-scikit-rf)
* gnu/packages/fediverse.scm (python-mastodon-py)
* gnu/packages/fontutils.scm (psautohint)
* gnu/packages/geo.scm (python-pyogrio)
* gnu/packages/graphviz.scm (python-uqbar)
* gnu/packages/jupyter.scm (python-jupyterlab-server python-nbclient,
python-jupyterlite-core, python-ipydatawidgets)
* gnu/packages/machine-learning.scm
(python-pymanopt, python-tensorly, python-torchmetrics)
* gnu/packages/maths.scm (python-libensemble)
* gnu/packages/music.scm (stargate)
* gnu/packages/python-check.scm (python-atpublic, python-vcrpy)
* gnu/packages/python-compression.scm (python-zipstream-ng)
* gnu/packages/python-science.scm (python-plotnine,
python-pandaparallel, python-pyts, python-pingouin)
* gnu/packages/python-web.scm (python-devpi-process, python-cheroot)
(python-jsonpickle, python-flask-babel, python-url-normalize)
(python-elasticsearch, python-hupper, python-simple-websocket)
(python-apiron, python-huggingface-hub, python-aiosignal, python-ovh)
(python-cbor2, python-zeep, hypercorn, python-warcio)
(python-aioftp, python-oauthlib, python-tinycss2, python-cssselect2)
(python-httpcore, python-wsgiprox, python-venusian, gunicorn)
* gnu/packages/python-xyz.scm (python-janus, python-affine)
(python-contourpy, python-echo, python-rasterio, python-rich-tables)
(python-babel, python-pymarshal, python-portalocker)
(python-expandvars, python-mizani, python-cligj, autokey)
(python-robotframework-pythonlibcore, python-lsp-jsonrpc)
(python-numpydoc, python-pillow, python-manimpango)
(python-cairocffi, python-pubmed-parser, python-sentry-sdk)
(python-prettytable, python-sniffio, python-ipywidgets)
(python-pyproject-api, python-pymemcache, python-async-lru)
(python-numcodecs, python-mwclient, python-cmd2, python-pyan3)
(python-platformdirs, python-multipart, python-shtab, python-scooby)
* gnu/packages/rdf.scm (python-rdflib-6)
* gnu/packages/simulation.scm (python-fenics-dijitso)
* gnu/packages/sphinx.scm (python-sphinx-design)
* gnu/packages/statistics.scm (python-patsy, python-rchitect)
* gnu/packages/task-management.scm (todoman)
* gnu/packages/vpn.scm (sshuttle)
* gnu/packages/web.scm (anonip, python-tibanna)
[native-inputs]: Remove python-pytest-cov.

Change-Id: I32f027794e90333c27fdff5871180779f603846c
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-04-04 22:41:51 +01:00
Ricardo Wurmus
10a1b8079d gnu: r-bpcells: Do not build bundled highway library. 
* gnu/packages/bioinformatics.scm (r-bpcells)[source]: Remove bundled highway
sources.
[arguments]: Fix check.
[inputs]: Add google-highway.

Change-Id: Ib70e7f9f64053b9e840c8c5f04e966beb4cf2869
 2026-04-02 07:37:08 +02:00
Nicolas Graves
c8bc423b87 gnu: python-pysam: Update to 0.23.3. 
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.23.3.
[native-inputs]: Replace python-cython-0 by python-cython.  Remove
python-wheel.

Change-Id: I4e93e7ab1a9e763d2d84b6b7601a64e918b0eda8
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-03-28 22:00:01 +00:00
Andreas Enge
6468da288f gnu: cnvkit: Update to 0.9.13. 
* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.13.

Change-Id: I69da49fe80b2e350ff351d39182dcf1e8cf97eb4
 2026-03-25 22:35:13 +01:00
Arun Isaac
7c586f7af8 gnu: cwltool: Update to 3.1.20260315121657. 
* gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20260315121657.

Change-Id: I1c4503aa65a638a905f8b49235578564fa40802f
 2026-03-24 22:48:07 +00:00
Efraim Flashner
2c52ce2a5f gnu: bpp-core: Build with default gcc. 
* gnu/packages/bioinformatics.scm (bpp-core)[native-inputs]: Remove
gcc-10.
[arguments]: Add a phase to add a missing include statement.

Change-Id: I53cd0c86df7cf5476149c22746c1de971d6770e8
 2026-03-23 13:58:44 +02:00
Efraim Flashner
c7d24e6fbe gnu: skewer: Relabel as version 0.2.2. 
This is the tag for the given commit.

* gnu/packages/bioinformatics.scm (skewer)[version]: Set to 0.2.2.

Change-Id: I7f24b0320b5e20ba36e56c0a0708ea64ec7ba86a
 2026-03-23 13:58:44 +02:00
Efraim Flashner
0bdb5c58cc gnu: skewer: Build with default gcc. 
* gnu/packages/bioinformatics.scm (skewer)[arguments]: Add make-flag to
set the C++ standard used.
[native-inputs]: Remove gcc-10.

Change-Id: I96515ec527cc0e2639def0b9a0b76d2ccb1062b9
 2026-03-23 13:58:44 +02:00
Nicolas Graves
57e76d1e40 gnu: jellyfish: Fix build on python-3.12. 
* gnu/packages/bioinformatics.scm (jellyfish)[native-inputs]: Add
python-setuptools.

Change-Id: I742e32681380277151a0d4b4986d81cc6112c380
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-03-20 14:11:39 +00:00
Nicolas Graves
9e144f00bf gnu: python-schema-salad: Update to 8.9.20251102115403. 
* gnu/packages/bioinformatics.scm (python-schema-salad): Update to 8.9.20251102115403.
[arguments]<#:test-flags>: Update them.
<#:phases>: Drop phase 'skip-failing-tests.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-03-20 14:11:37 +00:00
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
Efraim Flashner
763bd56e64 gnu: plink: Build with gcc-7. 
* gnu/packages/bioinformatics.scm (plink)[native-inputs]: Remove gcc-8,
add gcc-7.

Change-Id: Idd2182ba90509d6bff4fc733e2b6750a210c9dfb
 2026-03-19 15:17:37 +02:00
Efraim Flashner
8b85641253 gnu: plink: Add missing input. 
* gnu/packages/bioinformatics.scm (plink)[inputs]: Add libxcrypt.

Change-Id: I5994c2d02424972f0c1473ea3baf0a496db029bb
 2026-03-19 15:17:32 +02:00
Hugo Buddelmeijer
81cb51f3b7 gnu: python-metacells: Fix build. 
* gnu/packages/bioinformatics.scm (python-metacells): Fix build.
[arguments]<#:phases>: Add pre-sanity-check phase.
[homepage]: Update with redirect.

Change-Id: I9e6c2dfd4d944a589f87716ab8347a161ff630c5
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-03-18 22:39:42 +00:00
Andreas Enge
fbd7a68945 gnu: Remove fastx-toolkit. 
* gnu/packages/bioinformatics.scm (fastx-toolkit): Delete variable.

Change-Id: Ie710da17d23a04cfaafc1de28b2dc6aae23ccfd4
 2026-03-18 18:27:32 +01:00
Spencer King
a58c701785 gnu: deacon: Update to 0.15.0. 
* gnu/packages/bioinformatics.scm (deacon): Update to 0.15.0.
* gnu/packages/rust-crates.scm (lookup-cargo-inputs): Update entry for
deacon.

Change-Id: I6f1a8812d251228e50eabd9f0105c40ed4261a80
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2026-03-18 16:16:20 +02:00
Ricardo Wurmus
60f26275ef gnu: r-voltron: Update to 0.2.5. 
* gnu/packages/bioinformatics.scm (r-voltron): Update to 0.2.5.
[propagated-inputs]: Add r-voltronstore and simpleitk.

Change-Id: I292c4e6b81b23471589c965449766d72d197e200
 2026-03-18 08:11:57 +01:00
Ricardo Wurmus
9b6548fc6e gnu: Add r-voltronstore. 
* gnu/packages/bioinformatics.scm (r-voltronstore): New variable.

Change-Id: Iebeb6fd970aa1dc1a862f4ff4f628b1d8e2fe2d0
 2026-03-18 08:11:57 +01:00
Ricardo Wurmus
8c0aea2fbe gnu: python-decoupler: Update to 2.1.4. 
* gnu/packages/bioinformatics.scm (python-decoupler): Update to 2.1.4.

Change-Id: I1fdc99e586340ae42530cc209d2e4fe9e22b2292
 2026-03-12 14:51:12 +01:00
Ricardo Wurmus
158098977f gnu: python-cell2cell: Update to 0.8.4. 
* gnu/packages/bioinformatics.scm (python-cell2cell): Update to 0.8.4.

Change-Id: I0210208e0d61f46a707e352d45c9246c473200d0
 2026-03-12 14:51:11 +01:00
Ricardo Wurmus
38917f00de gnu: python-gseapy: Update to 1.1.12. 
* gnu/packages/bioinformatics.scm (python-gseapy): Update to 1.1.12.
* gnu/packages/rust-crates.scm (lookup-cargo-inputs): Update entry for
python-gseapy.

Change-Id: Ia912e4cb5aac93cb2aa523baccd9cc5bfbff6a6a
 2026-03-12 14:51:11 +01:00
Spencer King
51ca2c0da1 gnu: Add deacon. 
* gnu/packages/bioinformatics.scm (deacon): New variable.
* gnu/packages/rust-crates.scm (lookup-cargo-inputs): Add entry for
deacon.

Change-Id: I148a0bdc56abf5dbe68a8cdf81f6fe2944645f4d
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2026-03-12 14:10:13 +02:00
Ricardo Wurmus
e994eb8b64 gnu: r-singlet: Update to 0.99.8-1.ef4a374. 
Yes, this is an update, even though the patch level used to be .26 and now
is .8.  That's post-semantic versioning.

* gnu/packages/bioinformatics.scm (r-singlet): Update to 0.99.8-1.ef4a374.
[propagated-inputs]: Add r-statmod.

Change-Id: I95d1d60966c68cb8f66d79b6af6cab82bcf16a62
 2026-03-07 11:57:38 +01:00
Ricardo Wurmus
0741844d93 gnu: r-voltron: Replace custom phase with #:skipped-tests. 
* gnu/packages/bioinformatics.scm (r-voltron)[arguments]: Remove phase
'skip-bad-tests; provide #:skipped-tests argument.

Change-Id: I00ddc80185972d5bf7e01856b8ab0c47ffcf3fd2
 2026-03-07 11:57:27 +01:00
Spencer King
193b97bd48 gnu: bwa: Update to 0.7.19. 
* gnu/packages/bioinformatics.scm (bwa): Update to 0.7.19.

Merges: https://codeberg.org/guix/guix/pulls/6925
Change-Id: I066277d3746e291426156ae36a70c8a51a59f23f
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-03-06 20:48:39 +00:00
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
Sharlatan Hellseher
5f3cd42859 gnu: Deprecate swig and swig-next in vafor of swig-4.0 and swig-4.4. 
This is a following up change after discussion in
<https://codeberg.org/guix/guix/pulls/3701#issuecomment-11048648>.

* gnu/packages/swig.scm (swig-4.0, swig-4.4): New variables.
(swig, swig-next): Deprecate swig and swig-next in vafor of swig-4.0 and
swig-4.4.

* gnu/packages/accessibility.scm (libbraille)
* gnu/packages/apparmor.scm (libapparmor)
* gnu/packages/bioinformatics.scm (htseq, imp, libsbml)
* gnu/packages/bootloaders.scm (dtc, u-boot)
* gnu/packages/disk.scm (volume-key)
* gnu/packages/dns.scm (ldns, unbound)
* gnu/packages/electronics.scm (opensta, trilinos-serial-xyce, uhdm)
* gnu/packages/embedded.scm (python-libmpsse)
* gnu/packages/engineering.scm (freecad, kicad, meep, mpb)
* gnu/packages/fabric-management.scm (ibutils)
* gnu/packages/game-development.scm (python-pybox2d)
* gnu/packages/games.scm (kiki)
* gnu/packages/geo.scm (saga)
* gnu/packages/gnome.scm (libratbag)
* gnu/packages/gnucash.scm (gnucash)
* gnu/packages/gnupg.scm (python-gpg)
* gnu/packages/graphviz.scm (graphviz)
* gnu/packages/guile-xyz.scm (guile-xapian)
* gnu/packages/image.scm (mypaint)
* gnu/packages/instrumentation.scm (babeltrace, lttng-tools)
* gnu/packages/kodi.scm (kodi)
* gnu/packages/libftdi.scm (libftdi)
* gnu/packages/linux.scm (libnl)
* gnu/packages/llvm.scm (lldb)
* gnu/packages/machine-learning.scm (openmm, tensorflow-lite)
* gnu/packages/maths.scm (nlopt)
* gnu/packages/ncurses.scm (stfl)
* gnu/packages/oneapi.scm (python-onetbb)
* gnu/packages/pretty-print.scm (highlight)
* gnu/packages/python-crypto.scm (python-m2crypto)
* gnu/packages/python-graphics.scm (python-pivy)
* gnu/packages/radio.scm (hamlib, soapysdr)
* gnu/packages/security-token.scm (python-pyscard, python-yubikey-manager)
* gnu/packages/selinux.scm (libselinux, libsemanage, python-setools)
* gnu/packages/speech.scm (pocketsphinx)
* gnu/packages/statistics.scm (python-openturns, r-spams)
* gnu/packages/tbb.scm (python-tbb)
* gnu/packages/version-control.scm (subversion)
* gnu/packages/video.scm (libopenshot, mlt, obs)
[native-inputs]: Remove swig; add swig-4.0.

* gnu/packages/geo.scm (gdal)
* gnu/packages/graph.scm (python-faiss)
[inputs]: Remove swig; add swig-4.0.

* gnu/packages/games.scm (fifengine): Update to 0.4.2.
[inputs]: Remove swig; add swig-4.0.
[native-inputs]: Likewise.

* gnu/packages/image-processing.scm (insight-toolkit, simpleitk)
* gnu/packages/pdf.scm (mupdf, python-pymupdf)
[native-inputs]: Remove swig-next; add swig-4.4.

Change-Id: I544bef0a0b1a81004596fad9f116610ef5cb52ae
 2026-02-27 14:07:00 +00:00
Arun Isaac
99556e7724 gnu: wfmash: Install split_approx_mappings_in_chunks script. 
* gnu/packages/bioinformatics.scm (wfmash)[arguments]: Add install-scripts
phase.
[inputs]: Add python-wrapper.

Change-Id: I1a68399d1b14e9783a2a2c2fe8d65fc777de18b6
 2026-02-25 00:50:49 +00:00
Leo Orveillon
e44f96cbfd gnu: lammps-serial: Finalize update to 250722.3. 
* gnu/packages/bioinformatics.scm (lammps-serial): Adapt to updated lammps.
[configure-flags]: Same as lammps, but remove MPI and openMP related ones.
[phases]{link-lammps-so}: Change binary names due to LAMMPS_MACHINE flag
removal.
[inputs]: Remove pnetcdf. Replace hdf5-parallel-openmpi with hdf5.

Change-Id: I585e75fc7894c3e38f7b144f400193c9a767741a
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2026-02-24 16:06:46 +01:00
Leo Orveillon
3327e22c3e gnu: lammps: Update to 250722.3 and refacto. 
* gnu/packages/bioinformatics.scm (lammps): Update to 250722.3.
[build-system]: Switch from gnu to cmake.
[configure-flags]: Add more packages.
[phases]{link-lammps-so}: Link lammps libraries to the main binary.
[inputs]: Add fftw, n2p2, gsl, hdf5-parallel-openmpi, openblas, libomp,
eigen, netcdf, pnetcdf, python-numpy. Remove gfortran.
[native-inputs]: Add pkg-config, python-cython, patchelf, gfortran.

Change-Id: I65f0739c1df11981691aa54868e5dbf69ac29496
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2026-02-24 16:06:38 +01:00
Andreas Enge
12f5bf16e1 gnu: Remove wfa2-lib. 
* gnu/packages/bioinformatics.scm (wfa2-lib): Delete variable.

Fixes: guix/guix#3705
Change-Id: Ib19e25a84c982ab7a6403a9578adf2ecbaa46b9b
 2026-02-23 17:39:47 +01:00
Andreas Enge
1a9576ab21 gnu: Remove vcflib. 
* gnu/packages/bioinformatics.scm (vcflib): Delete variable.

Change-Id: I3ffdcfdbd8a3bb9d573fc0d5dc03da59acdd482e
 2026-02-23 17:39:07 +01:00
Andreas Enge
209a8025f8 gnu: Remove freebayes. 
* gnu/packages/bioinformatics.scm (freebayes): Delete variable.

Change-Id: I19fadd85a384cb4520160cfab04b114e5ca47cec
 2026-02-23 17:38:24 +01:00
Ricardo Wurmus
1b17e46a9b gnu: r-voltron: Skip bad tests. 
* gnu/packages/bioinformatics.scm (r-voltron)[arguments]: Add phase
'skip-bad-tests.

Change-Id: I51b33fd613f9eb744b4fd51400cad55e5b2c65ef
 2026-02-20 14:15:00 +01:00
Ricardo Wurmus
ce7b0bd514 gnu: r-giotto: Update to 4.2.2-1.7988300. 
* gnu/packages/bioinformatics.scm (r-giotto): Update to 4.2.2-1.7988300.
[source]: Fetch from true upstream.
[arguments]: Disable tests.
[propagated-inputs]: Add r-arrow, r-biocparallel, r-biocsingular, r-bluster,
r-checkmate, r-future-apply, r-giottoclass, r-giottoutils, r-giottovisuals,
r-limma, r-matrixgenerics, r-sparsematrixstats, r-terra, and r-uwot; remove
r-cowplot, r-deldir, r-farver, r-ggrepel, r-irlba, r-lfa, r-magick,
r-magrittr, r-matrixstats, r-qvalue, r-rcolorbrewer, r-rcpp, r-reshape2, and
r-rtsne.
[native-inputs]: Add r-testthat.
[home-page]: Update to true upstream.

Change-Id: I938e0c19fcc68fe4b100646fe051ff1a42411092
 2026-02-20 14:15:00 +01:00
Ricardo Wurmus
5437b46262 gnu: Add r-giottovisuals. 
* gnu/packages/bioinformatics.scm (r-giottovisuals): New variable.

Change-Id: I403d712ac4ce99cd5c08215ea83d5bf3cf2dd50a
 2026-02-20 14:15:00 +01:00
Ricardo Wurmus
2da36d46a8 gnu: Add r-giottodata. 
* gnu/packages/bioinformatics.scm (r-giottodata): New variable.

Change-Id: Icaed4b19a20e866523703e2241025943096954ba
 2026-02-20 14:15:00 +01:00
Ricardo Wurmus
f53a46f660 gnu: Add r-giottoutils. 
* gnu/packages/bioinformatics.scm (r-giottoutils): New variable.

Change-Id: Ia7acb1fc364f7076cf73f08d9335cd05a23b5f43
 2026-02-20 14:15:00 +01:00
Ricardo Wurmus
07eae7c915 gnu: Add r-giottoclass. 
* gnu/packages/bioinformatics.scm (r-giottoclass): New variable.

Change-Id: Icf95b3fd1f6dd4f14a13bc71d52a6febf6713b3e
 2026-02-20 14:15:00 +01:00
Ricardo Wurmus
e817a66e7b gnu: r-anndatar: Update to 1.0.1. 
anndataR is now on Bioconductor.

* gnu/packages/bioinformatics.scm (r-anndatar): Move from here...
* gnu/packages/bioconductor.scm (r-anndatar): ...to here; update to 1.0.1.
[properties]: Remove updater-extra-native-inputs.
[inputs]: Add python-wrapper and python-anndata.
[native-inputs]: Add r-processx, r-s4vectors, r-seurat, r-spelling, and
r-withr; remove r-vctrs.
[propagated-inputs]: Add r-cli, r-lifecycle, r-purrr, r-reticulate, and
r-rlang.

Change-Id: I2410f00b33451c60d8b1657ac30a6c1b014e260d
 2026-02-20 14:15:00 +01:00
Ricardo Wurmus
0ab540eb28 gnu: r-voltron: Update to 0.2.3. 
* gnu/packages/bioinformatics.scm (r-voltron): Update to 0.2.3.
[inputs]: Replace python with python-wrapper.

Change-Id: I180622af927e2386d45a4dadad4ebdad6e7ab6ac
 2026-02-20 14:15:00 +01:00
Ricardo Wurmus
6d327699d8 gnu: r-imagearray: Update to 0.99.6-1.2f90694. 
* gnu/packages/bioinformatics.scm (r-imagearray): Update to 0.99.6-1.2f90694.
[propagated-inputs]: Add r-ebimage, r-rarr, r-rhdf5, and r-s4vectors; remove
r-zarrarray.
[native-inputs]: Add r-knitr and r-testthat.
[synopsis]: Update.
[description]: Update.

Change-Id: Ife5670dacaad9c5b737ab282e7fc939126e845d8
 2026-02-20 14:14:59 +01:00