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
gnu: stringtie: Update input. * gnu/packages/bioinformatics.scm (stringtie)[inputs]: Replace htslib-for-stringtie by htslib. Change-Id: I8f197b461ee5f0a0e1b1e1201437d3c7667c2685
gnu: python-doubletdetection: Corrected deprecated input. * gnu/packages/bioinformatics.scm (python-doubletdetection)[inputs]: Replace python-vtraag-louvain by python-louvain-igraph. Change-Id: I27c87906c44bd536d67938c0315e40ca7ee82bf5
gnu: Remove htslib-1.19. * gnu/packages/bioinformatics.scm (htslib-1.19): Delete variable. Change-Id: I7804d3ae403dbdf149e3012922f7ac9a382288d7
gnu: Remove samtools-1.14. * gnu/packages/bioinformatics.scm (samtools-1.14): Delete variable. Change-Id: I68e8e3ad05841d300897d830f9bcd7fa73c68adc
gnu: Remove bcftools-1.12. * gnu/packages/bioinformatics.scm (bcftools-1.12): Delete variable. Change-Id: I805ec24f6eb47d37b2158b85f9d03d5a36999695
gnu: Remove samtools-1.12. * gnu/packages/bioinformatics.scm (samtools-1.12): Delete variable. Change-Id: Ibd80f3fb79efab17193f82b4f713ff1f2cbd2470
gnu: Remove htslib-1.10. * gnu/packages/bioinformatics.scm (htslib-1.10): Delete variable. Change-Id: I9d1bd86e580de2b9b7fe096e7f86b3a96e6df4d1
gnu: Remove bcftools-1.10. * gnu/packages/bioinformatics.scm (bcftools-1.10): Delete variable. Change-Id: I41d5a65b6857debf3586b3d3716bb7a2693645cb
gnu: Remove samtools-1.10. * gnu/packages/bioinformatics.scm (samtools-1.10): Delete variable. Change-Id: If3ef93c3473c4fe9c21f062fe619d883fbafb2ec
gnu: Remove htslib-for-samtools-1.2. * gnu/packages/bioinformatics.scm (htslib-for-samtools-1.2): Delete variable. Change-Id: I62c8525d27321acd7fea32e25623e5cbd7e74c33
gnu: Remove samtools-1.2. * gnu/packages/bioinformatics.scm (samtools-1.2): Delete variable. Change-Id: I38effe41c32349b5b72754da07fe6696d2f21669