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Author SHA1 Message Date
Sharlatan Hellseher 6896332787 gnu: python-twobitreader: Update to 3.1.9. 
* gnu/packages/bioinformatics.scm (python-twobitreader): Update to 3.1.9.
[build-system]: Switch to pyproject-build-system.
[arguments] <tests?>: Enable.
[native-inputs]: Remove python-sphinx; add python-pytest and
python-setuptools.

Change-Id: I1c8d450611f1a3f3d271606bb744dd24c5f60d4d
 2025-10-30 11:16:21 +00:00
Sharlatan Hellseher 6b6a3c6cba gnu: bwa-meth: Update to 0.2.9. 
* gnu/packages/bioinformatics.scm (bwa-meth): Update to 0.2.9.
[build-system]: Switch to pyproject-build-system.
[arguments] <tests?>: No tests.
[inputs]: Add python-toolshed.
[native-inputs]: Remove python-toolshed; add python-setuptools.

Change-Id: Ib3544054943af904f4acea0a899f86ef66e7a47d
 2025-10-30 11:04:51 +00:00
Sharlatan Hellseher 075dc6ec28 gnu: python-fastalite: Update to 0.4.1. 
* gnu/packages/bioinformatics.scm (python-fastalite): Update to 0.4.1.
[source]: Switch to git-fetch providing test data.
[build-system]: Switch to pyproject-build-system.
[arguments] <tests?>: Enable.
<test-backend>: Use 'unittest.
<phases>: Add set-version.
[native-inputs]: Add python-setuptools.

Change-Id: Ie6659208edb37995303cf332e3b985a89d5e8d39
 2025-10-30 10:52:20 +00:00
Sharlatan Hellseher b68eb98be0 gnu: python-cmseq: Fix build. 
* gnu/packages/bioinformatics.scm (python-bcbio-gff/biopython-1.73):
Rename variable to python-bcbio-gff-for-python-cmseq and pin to 0.6.9
version which is the last one compatible with python-biopython-1.73.
(python-cmseq)[propagated-inputs]: Remove
python-bcbio-gff/biopython-1.73; add python-bcbio-gff-for-python-cmseq.
[native-inputs]: Add python-setuptools.

Change-Id: Id7c37f8f34058648506645ce07c2a89dfcea2067
 2025-10-30 10:25:16 +00:00
Sharlatan Hellseher 898721e174 gnu: python-ega-download-client: Update to 5.2.1. 
* gnu/packages/bioinformatics.scm (python-ega-download-client): Update to 5.2.1.
[arguments]: Use G-Expressions.
<test-flags>: Rework skipped tests and ignored tests files
generating very larg test files (up to 150GiB) which may affect the CI
or user's machine.
[native-inputs]: Remove python-coverage and python-wheel; add
nss-certs-for-test.

Change-Id: Ic91c65e548e27d6c57396000233b6e5f5949554c
 2025-10-30 09:53:54 +00:00
Sharlatan Hellseher cfb5331b36 gnu: python-parabam: Update to 3.0.1-0.be5bd35, fix build. 
* gnu/packages/bioinformatics.scm (python-parabam): Update to
be5bd35012d37df8cfa88771325a0273519c8c98 commit.
[source]: Switch to git-fetch.
[arguments] <tests?>: No tests.
<phases>: Add 'cythonize.
[native-inputs]: Remove python-wheel; add python-cython.

Change-Id: I56e2dbeac106f2942289e2b751520b3bf1abb60f
 2025-10-29 21:44:27 +00:00
Nicolas Graves 389e9019a7 gnu: python-illumina-utils: Update to 2.13. 
* gnu/packages/bioinformatics.scm (python-illumina-utils): Update to 2.13.
<#:phases>: In phase 'adjust-requirements, add python-levenshtein patch.

Change-Id: I03cafaea1f73206bb5cfc887b9b4d0df7d959fca
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-10-29 00:05:49 +00:00
Nicolas Graves b74285d789 gnu: ciri-long: Adapt to python-levenshtein update. 
* gnu/packages/bioinformatics.scm (ciri-long)[arguments]
<#:phases>: In phase 'relax-requirements, add python-levenshtein
patch.

Change-Id: If16df4f97f42eaf51c3bd73020c5a7c3d0d01b64
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-10-29 00:05:49 +00:00
Nicolas Graves 6f3dc1200d gnu: python-splicekit: Adapt to python-levenshtein update. 
* gnu/packages/bioinformatics.scm (python-splicekit)[arguments]
<#:phases>: In phase 'adjust-requirements, remove python-levenshtein
patch.

Change-Id: I28416ce8456ec69b73e0dbf377cb673b5fa08aa9
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-10-29 00:05:49 +00:00
Nicolas Graves fd2031889c gnu: python-scanrbp: Disable tests. 
* gnu/packages/bioinformatics.scm (python-scanrbp):
[arguments]: Relocate field.
<#:tests?>: Disable them.
[native-inputs]: Remove python-wheel.

Change-Id: If4198e43da472b533ee83c2bbe0ccb9a0bcbf535
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-10-29 00:05:49 +00:00
Sharlatan Hellseher cbad86a985 gnu: python-cython-3: Mark as deprecated. 
This is a followup to 941b6ff1c1 commit.

Replace all python-cython-3 occurrences with python-cython.

* gnu/packages/python-xyz.scm (python-cython-3): Deprecate variable.

* gnu/packages/algebra.scm (python-fpylll, python-flint)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/astronomy.scm (python-astropy, python-astroscrappy,
python-halotools, python-healpy, python-libstempo, python-lofar-h5plot,
python-losoto, python-photutils, python-pyxsim, python-regions,
python-reproject, python-sncosmo, python-sndata, python-stcal,
python-yt)[native-inputs]: Remove python-cython-3; add python-cython.

* gnu/packages/bioinformatics.scm (macs-3, python-pyrodigal):
[native-inputs]: Remove python-cython-3; add python-cython.

* gnu/packages/build-tools.scm (meson-python)[propagated-inputs]: Remove
python-cython-3; add python-cython.
[native-inputs]: Remove python-cython-3; add python-cython.

* gnu/packages/databases.scm: (python-adbc-driver-manager,
python-psycopg, python-pyarrow)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/finance.scm (python-ta-lib)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/game-development.scm (python-pygame-ce)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/geo.scm (python-pyogrio, python-cf-units)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/machine-learning.scm: (python-scikit-learn,
python-opentsne)[native-inputs]: Remove python-cython-3; add
python-cython.

* gnu/packages/maths.scm: (python-cylp, python-petsc4py,
python-primecountpy, python-slepc4py)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/python-check.scm (python-line-profiler)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/python-compression.scm (python-blosc2)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/python-graphics.scm (python-vispy)[native-inputs]:
Remove python-cython-3; add python-cython.

* gnu/packages/python-science.scm: (python-pykdtree, python-qutip,
python-scikit-misc, python-scikit-surprise, python-pandas-2,
python-vaex-core)[native-inputs]: Remove python-cython-3; add
python-cython.

* gnu/packages/python-web.scm: (python-aiohttp, python-falcon,
python-yarl, python-uvloop)[native-inputs]: Remove python-cython-3; add
python-cython.

* gnu/packages/python-xyz.scm: (python-logbook, python-netcdf4,
python-pyyaml, python-propcache, python-pywavelets, python-symengine,
python-cysignals, python-pyemd, python-rbfly)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/sagemath.scm: (python-cypari2, python-pplpy, sage)
[native-inputs]: Remove python-cython-3; add python-cython.

* gnu/packages/sphinx.scm (python-sphinx)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/statistics.scm: (python-statsmodels, python-pyreadstat):
[native-inputs]: Remove python-cython-3; add python-cython.

* gnu/packages/tor.scm (onionshare-cli)[native-inputs]: Remove
python-cython-3; add python-cython.

* gnu/packages/xorg.scm (xpra)[native-inputs]: Remove python-cython-3;
add python-cython.

Change-Id: I38038d2ab18e6a7b549070083d6e4c5beb8b0293
 2025-10-24 11:05:28 +01:00
Andreas Enge 225193d559 gnu: stringtie: Update to 3.0.2. 
* gnu/packages/bioinformatics.scm (stringtie): Update to 3.0.2.

Change-Id: Ie35084c70ad6c91b9e03b09ec6fe4f825bd39dcd
 2025-10-23 21:49:34 +02:00
Andreas Enge 56d3b81e45 gnu: Remove htslib-1.12. 
* gnu/packages/bioinformatics.scm (htslib-1.12): Delete variable.

Change-Id: Id1fd05bddc1b40be0e3186c0e5848a1a0f343ce3
 2025-10-23 21:43:10 +02:00
Andreas Enge ff6b3eb279 gnu: Remove htslib-for-stringtie. 
* gnu/packages/bioinformatics.scm (htslib-for-stringtie): Delete variable.
* gnu/packages/patches/htslib-for-stringtie.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Unregister file.

Change-Id: Idbf3fa982895baed97913e08650cbff6947e8182
 2025-10-23 21:41:51 +02:00
Andreas Enge a3f9fd26bb gnu: stringtie: Update input. 
* gnu/packages/bioinformatics.scm (stringtie)[inputs]:
Replace htslib-for-stringtie by htslib.

Change-Id: I8f197b461ee5f0a0e1b1e1201437d3c7667c2685
 2025-10-23 21:40:47 +02:00
Andreas Enge f8eb0eb0e3 gnu: python-doubletdetection: Corrected deprecated input. 
* gnu/packages/bioinformatics.scm (python-doubletdetection)[inputs]:
Replace python-vtraag-louvain by python-louvain-igraph.

Change-Id: I27c87906c44bd536d67938c0315e40ca7ee82bf5
 2025-10-23 21:36:49 +02:00
Andreas Enge 50591e81be gnu: Remove htslib-1.19. 
* gnu/packages/bioinformatics.scm (htslib-1.19): Delete variable.

Change-Id: I7804d3ae403dbdf149e3012922f7ac9a382288d7
 2025-10-23 21:20:13 +02:00
Andreas Enge 71d60494f5 gnu: Remove samtools-1.14. 
* gnu/packages/bioinformatics.scm (samtools-1.14): Delete variable.

Change-Id: I68e8e3ad05841d300897d830f9bcd7fa73c68adc
 2025-10-23 21:17:47 +02:00
Andreas Enge c5121e088e gnu: Remove bcftools-1.12. 
* gnu/packages/bioinformatics.scm (bcftools-1.12): Delete variable.

Change-Id: I805ec24f6eb47d37b2158b85f9d03d5a36999695
 2025-10-23 21:14:30 +02:00
Andreas Enge cb2dc11bb6 gnu: Remove samtools-1.12. 
* gnu/packages/bioinformatics.scm (samtools-1.12): Delete variable.

Change-Id: Ibd80f3fb79efab17193f82b4f713ff1f2cbd2470
 2025-10-23 21:14:20 +02:00
Andreas Enge 666d490b13 gnu: Remove htslib-1.10. 
* gnu/packages/bioinformatics.scm (htslib-1.10): Delete variable.

Change-Id: I9d1bd86e580de2b9b7fe096e7f86b3a96e6df4d1
 2025-10-23 21:13:31 +02:00
Andreas Enge 00fa458a6c gnu: Remove bcftools-1.10. 
* gnu/packages/bioinformatics.scm (bcftools-1.10): Delete variable.

Change-Id: I41d5a65b6857debf3586b3d3716bb7a2693645cb
 2025-10-23 21:13:13 +02:00
Andreas Enge 44dfc9875e gnu: Remove samtools-1.10. 
* gnu/packages/bioinformatics.scm (samtools-1.10): Delete variable.

Change-Id: If3ef93c3473c4fe9c21f062fe619d883fbafb2ec
 2025-10-23 21:12:28 +02:00
Andreas Enge 87b90f0489 gnu: Remove htslib-for-samtools-1.2. 
* gnu/packages/bioinformatics.scm (htslib-for-samtools-1.2):
Delete variable.

Change-Id: I62c8525d27321acd7fea32e25623e5cbd7e74c33
 2025-10-23 21:10:34 +02:00
Andreas Enge 788513d4e0 gnu: Remove samtools-1.2. 
* gnu/packages/bioinformatics.scm (samtools-1.2): Delete variable.

Change-Id: I38effe41c32349b5b72754da07fe6696d2f21669
 2025-10-23 21:08:49 +02:00
Ludovic Courtès 9fcfb93944 gnu: Use ‘define-deprecated-package’ for deprecated packages. 
Use ‘define-deprecated-package’ instead of (define x (deprecated-package …))
throughout gnu/packages/*.scm.

Change-Id: I4e176da9ac660327489dab256ca4d12c4e78fe8d
 2025-10-23 19:35:06 +02:00
Andreas Enge 7dfdf10fb6 gnu: Remove python-velocyto. 
* gnu/packages/bioinformatics.scm (python-velocyto): Delete variable.

Fixes: guix/guix#2922
Change-Id: Ifcc556de612ee596019b4164e9f5b33e76bf67a3
 2025-10-23 18:02:18 +02:00
Andreas Enge 08392478de gnu: Remove python-plastid. 
* gnu/packages/bioinformatics.scm (python-plastid): Delete variable.

Fixes: guix/guix#2897
Change-Id: I72a38912c7c89997add49d08a01f8522acaa46d1
 2025-10-23 17:57:11 +02:00
Sharlatan Hellseher 5571db7781 gnu: instrain: Update to 1.10.0-0.6180be7. 
* gnu/packages/bioinformatics.scm (instrain): Update to
6180be7b49a61b7e1ffe9f1489da5c6aa2ff9ac3 commit.
[arguments]: Use G-Expressions.
<phases>: Add 'relax-requirements.
[native-inputs]: Remove python-boto3, python-pytest, and python-wheel.

Change-Id: I5cf37e5128a962007aa9d4e8a8ffa3da474e7c6f
 2025-10-23 13:29:24 +01:00
Andreas Enge df7c77aa9f gnu: libsbml: Update to 5.20.5. 
* gnu/packages/bioinformatics.scm (libsbml): Update to 5.20.5.
[source]: Switch to git-fetch.

Change-Id: Idee7f2826c8c863482b048ab5500526e6c10e0f5
 2025-10-22 22:06:49 +02:00
Hartmut Goebel aabdd4f098 gnu: python-pyahocorasick: Update to 2.2.0. 
* gnu/packages/bioinformatics.scm (python-pyahocorasick): Update to 2.2.0.
[native-inputs]: Remove python-twine and python-wheel.

Change-Id: If9901abaae4f52a795d1b9b84f06a3b8cc6fc235
 2025-10-21 00:28:29 +02:00
Hartmut Goebel 7759918c17 gnu: python-ngesh: Remove development inputs. 
* gnu/packages/bioinformatics.scm (python-ngesh): [native-inputs]: Remove
python-black, python-flake8, python-twine, and python-wheel.

Change-Id: Ie401b481f768774732fdf021e52530af644856c7
 2025-10-21 00:28:29 +02:00
Hartmut Goebel 7db8ded42c gnu: python-metacells: Remove development inputs 
* gnu/packages/bioinformatics.scm (python-metacells):
[native-inputs]: Remove python-sphinx and python-sphinx-rtd-theme.

Change-Id: Ifdac5e0a841be105a8e6c82441826d11b2a9031e
 2025-10-21 00:28:29 +02:00
Sharlatan Hellseher 3bbaf5b906 gnu: python-ont-fast5-api: Fix tests. 
* gnu/packages/bioinformatics.scm (python-ont-fast5-api): Use
G-Expressions.
[arguments] <test-backend>: Use 'unittest.

Change-Id: If7058987bdda24345f5a81d29e991764352d03da
 2025-10-20 00:07:52 +01:00
Sharlatan Hellseher 16f158f858 gnu: vbz-compression: Update to 1.0.13. 
* gnu/packages/bioinformatics.scm (vbz-compression): Update to 1.0.13.

Change-Id: I00c8af42bfc10077fbbc6c191b86f67a29e92637
 2025-10-20 00:04:54 +01:00
Hugo Buddelmeijer 317dbfb541 gnu: cwltool: Update to 3.1.20250925164626. 
* gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20250925164626.
[arguments] <#:test-flags>: Update tests to skip.
<#:phases>: Use SETUPTOOLS_SCM_PRETEND_VERSION. Allow tests to multithread.
[inputs]: Remove python-shellescape and python-typing-extensions; add
python-rich-argparse.
[native-inputs]: Remove python-humanfriendly, python-pytest-cov,
python-pytest-runner and python-wheel; add python-pytest-xdist.

Change-Id: I6a224606887346e160b11916ef7b25cb2120bf1d
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-10-18 23:35:53 +01:00
Hugo Buddelmeijer 20b16e2364 gnu: python-schema-salad: Update to 8.9.20250723145140. 
* gnu/packages/bioinformatics.scm (python-schema-salad): Update to 8.9.20250723145140.
[source] <origin>: Switch to git-fetch.
[arguments] <#:test-flags>: Temporarily disable failing test.
<#:phases>: Update 'set-version phase. Add 'relax-requirements phase.
Update 'skip-failing-tests phase.
[native-inputs]: Remove python-mypy, python-pytest-runner,
python-types-dataclasses, python-types-requests,
python-types-setuptools, and python-wheel; add python-pytest-xdist.

Change-Id: I1e5b2b73fb0efaa2e9c2054f949423e04b056c9d
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-10-18 23:35:53 +01:00
Sharlatan Hellseher dbca541c7a gnu: scregseg: Update to 0.1.3-0.78ebff8. 
* gnu/packages/bioinformatics.scm (scregseg): Update to
78ebff8c3507752c3bfbc4db3f72f7e8a733e92f commit.
[arguments] <test-flags>: Provide "--pyargs".
<phases>: Remove 'build-extensions, and 'do-not-fail-to-find-sklearn.
[propagated-inputs]: Remove python-scikit-learn; add
python-scikit-learn-1.6.
[native-inputs]: Remove python-wheel; add python-setuptools.

Change-Id: Ic29e6be3b1fda0d664ed74dfc21da75cb5bcd656
 2025-10-16 13:39:34 +01:00
Jake Forster c3e4224e49 gnu: gdcm: Unbundle some dependencies. 
* gnu/packages/bioinformatics.scm (gdcm)[arguments]<#:configure-flags>: Use
system CharLS, Expat, JSON, OpenSSL, UUID, and zlib.
[inputs]: Add charls, expat, json-c, openssl, util-linux:lib, and zlib.

Change-Id: I3d74ce7efe026ce27986ea3cdaf20c9a372e2ac9
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-10-13 12:16:59 +01:00
Jake Forster 7b2b2ed2f2 gnu: gdcm: Update to 3.2.2. 
* gnu/packages/bioinformatics.scm (gdcm): Update to 3.2.2.
[arguments]<#:test-exclude>: Do not exclude TestFileMetaInformation and
TestElement2; exclude TestImageReaderRandomEmpty and TestTransferSyntax.
<#:configure-flags>: Add "-DGDCM_BUILD_DOCBOOK_MANPAGES=ON".
[home-page]: Update.

Change-Id: I895dea12d4237d29f9f7d826f0a0d65f10f7e116
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-10-13 12:16:53 +01:00
Sharlatan Hellseher ed21c87a71 gnu: python-intervaltree: Move to python-xyz. 
* gnu/packages/bioinformatics.scm (python-intervaltree): Move from here ...
* gnu/packages/python-xyz.scm: ... to here.

Change-Id: I49d3e4959f2aff99fc3faf42b3f5dae60622ef47
 2025-10-11 08:37:55 +01:00
Nicolas Graves d71d054b9c gnu: python-metacells: Remove development native-inputs. 
* gnu/packages/bioinformatics.scm (python-metacells)[native-inputs]:
Remove python-black, python-bumpversion, python-flake8, python-isort,
python-mypy, python-mypy-extensions, python-pandas-stub,
python-pylint, python-pytest-cov, python-tox, python-twine,
python-wheel.

Change-Id: Ife79f40723d704ad6b47fc49640a059f6597901e
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-10-09 11:34:28 +01:00
Nicolas Graves 9b96e4d74e gnu: python-pybiomart: Remove development native-inputs. 
* gnu/packages/bioinformatics.scm (python-pybiomart)[native-inputs]:
Remove python-bumpversion, python-pytest-cov, python-coveralls and
python-wheel.
[source]: Switch to git-fetch.
[arguments]: Relocate field.

Change-Id: I60065f76d561c53bd34832f88fea05ac6b58f24f
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-10-09 11:34:28 +01:00
Sharlatan Hellseher d805203f8b gnu: macs: Fix build. 
* gnu/packages/bioinformatics.scm (macs)[propagated-inputs]: Remove
python-cython; add python-cython-0.

Change-Id: I417d42d05758bc69534d9b3de623ab4ca11abe90
 2025-10-07 11:38:12 +01:00
Anderson Torres 3f738d5709 gnu: Remove fast5. 
* gnu/packages/bioinformatics.scm (fast5): Remove variable.

Fixes: guix/guix#2340
Change-Id: I2d1a121e2338944ab52bba59fe1600d2b7f4d84f
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-10-06 16:03:39 +02:00
Sharlatan Hellseher c0d172278b gnu: python-logomaker: Update to 0.8.7. 
* gnu/packages/bioinformatics.scm (python-logomaker): Update to 0.8.7.
[native-inputs]: Remove python-setuptools and python-wheel; add
python-hatchling.
[home-page]: Fixed as seen on <https://pypi.org/project/logomaker/>.

Change-Id: I530664f48fee31e52c31e4ec7d27a7580c6c8fc9
 2025-10-06 12:16:01 +01:00
Sharlatan Hellseher 09b2af5140 gnu: python-htsget: Disable tests. 
* gnu/packages/bioinformatics.scm (python-htsget)[arguments] <tests?>:
They depend on Nose test runner, which is deprecated upstream.
[native-inputs]: Remove python-wheel.

Change-Id: I9876ff1846c1475e9ad50679ad5beca53e252471
 2025-10-06 12:16:01 +01:00
Sharlatan Hellseher 671090cd83 gnu: python-gffutils: Fix tests. 
* gnu/packages/bioinformatics.scm (python-gffutils)[arguments]
<test-flags>: Ignore one not compatible test file.

Change-Id: I30c6abc726ba58a3ce3a08ad36cd48a6573efc29
 2025-10-06 01:29:30 +01:00
Sharlatan Hellseher 5aa8ab38b1 gnu: python-episcanpy: Fix sanity check. 
* gnu/packages/bioinformatics.scm (python-episcanpy):
[propagated-inputs]: Remove python-anndata; add python-anndata-0.11.

Change-Id: I8f6889b3fcce6c5c9f1eac27d45f49a81e815dcf
 2025-10-06 01:29:29 +01:00
Sharlatan Hellseher 7c9e322594 gnu: python-cyvcf2: Update to 0.31.2. 
* gnu/packages/bioinformatics.scm (python-cyvcf2): Update to 0.31.2.
[native-inputs]: Remove python-wheel.

Change-Id: Ieba07d46864472b2c7d6a3f7936f1d225c174825
 2025-10-06 01:29:29 +01:00