gnu: Add ngs-bits. * gnu/packages/bioinformatics.scm (ngs-bits): New variable. Change-Id: I501cc8246aad6876c520d897ab6b9195b449db2a
gnu: Add python-modbedtools. Change-Id: Ia35e2e1640e44766960b28f74786f8371878990e
gnu: Add python-weblogo. * gnu/packages/bioinformatics.scm (python-weblogo): New variable. Change-Id: Ib91f8d04d0df79eeb6039388e7ae6084fa245ad6
gnu: eigensoft: Update to 8.0.0. * gnu/packages/bioinformatics.scm (eigensoft): Update to 8.0.0. Change-Id: Id5d60cc108e1c2114715cce2f17a3a7bca666336
gnu: idr: Switch to pyproject. * gnu/packages/bioinformatics.scm (idr)[build-system]: Switch to pyproject-build-system. [native-inputs]: Add python-setuptools. Change-Id: Ib6811a399b4c531f119bcef23b3216ff70c2d5eb
gnu: python-deeptoolsintervals: Switch to pyproject. * gnu/packages/bioinformatics.scm (python-deeptoolsintervals): [build-system]: Switch to pyproject-build-system. [native-inputs]: Add python-pytest and python-setuptools. Change-Id: I2f95aa4f526f879d9407d7625834f389e384bc39
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
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
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
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
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
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
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>
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>
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>
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>
gnu: python-cython-3: Mark as deprecated. This is a followup to 941b6ff1c11be3ba73e4e67bc661bd0eed3e9d58 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
gnu: stringtie: Update to 3.0.2. * gnu/packages/bioinformatics.scm (stringtie): Update to 3.0.2. Change-Id: Ie35084c70ad6c91b9e03b09ec6fe4f825bd39dcd
gnu: Remove htslib-1.12. * gnu/packages/bioinformatics.scm (htslib-1.12): Delete variable. Change-Id: Id1fd05bddc1b40be0e3186c0e5848a1a0f343ce3
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