gnu: Add samtools-1.14. * gnu/packages/bioinformatics.scm (samtools-1.14): New variable. Change-Id: I0bd35b3865d7a417f55f1f768f7eb0c78a795e0f
gnu: samtools: Update to 1.19. * gnu/packages/bioinformatics.scm (samtools): Update to 1.19. [source]: Simplify snippet. Change-Id: If0e02bbbc8e0443eb418c078dc47525f432d7ebe
gnu: htslib: Update to 1.19. * gnu/packages/bioinformatics.scm (htslib): Update to 1.19. Change-Id: I4d66d8ce37bfd335411a2acc6060f9a8c20c9e4a
gnu: htscodecs: Update to 1.6.0. * gnu/packages/bioinformatics.scm (htscodecs): Update to 1.6.0. Change-Id: Ibd5be30e8fbe7fe5d0ef494c1b1e0cd9ec3333cc
gnu: Add python-prisma. * gnu/packages/databases.scm (python-prisma): New variable. Change-Id: I7df9b5600fb49ef46a73678323bc29993f35fae2
gnu: Add python-strenum. * gnu/packages/python-xyz.scm (python-strenum): New variable. Change-Id: I6b6d64024db9358ea0a65cfd6c7cd6f94747de42
gnu: python-readpaf: Explicitly disable tests. * gnu/packages/bioinformatics.scm (python-readpaf)[arguments]: Disable tests. Change-Id: I28ddfa46675b74bd5073c12e5d33bcbf9dee8252
gnu: python-pyls-black: Fix build. * gnu/packages/patches/python-pyls-black-41.patch: New patch. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/python-xyz.scm (python-pyls-black)[source]: Add patch. [build-system]: Use pyproject-build-system. [arguments]: Disable one failing test. Change-Id: I14b2982644e58c0b43d76838febc6dfceb220b15
gnu: debian-ports-archive-keyring: Update to 2024.01.05. * gnu/packages/debian.scm (debian-ports-archive-keyring): Update to 2024.01.05. Change-Id: Ibaa279a91d9e39804eb5cc1bf759ca3afd69e962
gnu: debootstrap: Update to 1.0.134. * gnu/packages/debian.scm (debootstrap): Update to 1.0.134. [arguments]: Remove obsolete substitution in 'patch-source phase. Change-Id: I2a50ae75a43c0970e3ef866e02c49d87094e14eb
gnu: gourmet: Add missing input. * gnu/packages/nutrition.scm (gourmet)[inputs]: Add python-toml. Change-Id: I53bc9b0247c6dc32c5ec6e3cc518dbc982362bd2
gnu: python-pyrdfa3: Update to 3.6.2. * gnu/packages/rdf.scm (python-pyrdfa3): Update to 3.6.2. [build-system]: Use pyproject-build-system. [arguments]: Remove custom build phases. [propagated-inputs]: Add python-requests. Change-Id: Ie8a1a369a569d29c8f43248d03f024e6cc19c004
gnu: python-clingraph: Update to 1.1.2. * gnu/packages/potassco.scm (python-clingraph): Update to 1.1.2. Change-Id: I5910853d39389ff9ad981543204fd8ef1445e495
gnu: python-astroml: Make compatible with recent Matplot and Scipy. * gnu/packages/astronomy.scm (python-astroml)[arguments]: Add phases 'matplotlib-compatibility and 'scipy-compatibility. Change-Id: Id88cf769f705f9326f41f951403583155bcee58f
gnu: python-bbknn: Update to 1.6.0. * gnu/packages/bioinformatics.scm (python-bbknn): Update to 1.6.0. [arguments]: Remove phase 'do-not-fail-to-find-sklearn. [propagated-inputs]: Add python-pynndescent. [native-inputs]: Add python-flit-core. Change-Id: I5fca2d6ca52e54eb7650b3bb24a34a0aa47b1782
gnu: python-geopandas: Update to 0.14.2. * gnu/packages/geo.scm (python-geopandas): Update to 0.14.2. [arguments]: Disable test_pandas_kind tests. Change-Id: I2a49d6ef73a79b84751ce0225757a2b83019cd42
gnu: python-dask: Propagate click. * gnu/packages/python-xyz.scm (python-dask)[native-inputs]: Move python-click from here... [propagated-inputs]: ...to here. Change-Id: I1a1617d9cb00268d9fc26f4fe6c9ecc6d0a2e375
gnu: python-xarray: Update to 2023.12.0. * gnu/packages/python-science.scm (python-xarray): Update to 2023.12.0. [arguments]: Ignore one test file. [propagated-inputs]: Add python-packaging. Change-Id: I6b70f59670f7bc8b56787fe3436579db8ac113bb
gnu: python-telomerecat: Disable tests. * gnu/packages/bioinformatics.scm (python-telomerecat)[arguments]: Disable tests. Change-Id: I0422ae1e563374a8cc408fc9584cfb7b0e880e95
gnu: python-mysql-connector-python: Defuse time bomb. Additional tests fail due to expired certificates. Disable them. * gnu/packages/python-xyz.scm (python-mysql-connector-python)[arguments]: Disable six additional tests. Change-Id: I99b5f15736af89c0281ab7aca56c1bd3958d1a46