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2024-01-16gnu: python-deepdish: Fix build.Sharlatan Hellseher
* gnu/packages/python-science.scm (python-deepdish): Fix build. [build-system]: Swap to pyproject-build-system. [arguments]<#:test-flags>: Silent failing tests. Change-Id: I4c4df66fc80434aaf5b95a7a62b83e0c1c02a4c6
2024-01-16import/cran: Add more invalid package names and translations.Ricardo Wurmus
These were encountered in a mass import of Bioconductor packages. * guix/import/cran.scm (invalid-packages): Add "rtools". (transform-sysname): Add aliases for Python and bioinformatics packages. Change-Id: I97e13cee10c2ee85d4b9296d91afccbdbcec4946
2024-01-16import/cran: Add more invalid package names and translations.Ricardo Wurmus
* guix/import/cran.scm (invalid-packages): Add "build-essential". (transform-sysname): Add aliases for openssl, libxml2, and zlib. Change-Id: Ia142ebc388dbcd47caf3b2c5165bc21227bc1832
2024-01-16gnu: Add samtools-1.14.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (samtools-1.14): New variable. Change-Id: I0bd35b3865d7a417f55f1f768f7eb0c78a795e0f
2024-01-16gnu: samtools: Update to 1.19.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (samtools): Update to 1.19. [source]: Simplify snippet. Change-Id: If0e02bbbc8e0443eb418c078dc47525f432d7ebe
2024-01-16gnu: htslib: Update to 1.19.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htslib): Update to 1.19. Change-Id: I4d66d8ce37bfd335411a2acc6060f9a8c20c9e4a
2024-01-16gnu: htscodecs: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htscodecs): Update to 1.6.0. Change-Id: Ibd5be30e8fbe7fe5d0ef494c1b1e0cd9ec3333cc
2024-01-16gnu: Add python-prisma.Ricardo Wurmus
* gnu/packages/databases.scm (python-prisma): New variable. Change-Id: I7df9b5600fb49ef46a73678323bc29993f35fae2
2024-01-16gnu: Add python-strenum.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-strenum): New variable. Change-Id: I6b6d64024db9358ea0a65cfd6c7cd6f94747de42
2024-01-16gnu: python-readpaf: Explicitly disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-readpaf)[arguments]: Disable tests. Change-Id: I28ddfa46675b74bd5073c12e5d33bcbf9dee8252
2024-01-16gnu: python-pyls-black: Fix build.Ricardo Wurmus
* 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
2024-01-16import: crate: Simplify find-crate-version.Efraim Flashner
* guix/import/crate.scm (find-crate-version): Reuse nonyanked-crate-versions, max-crate-version-of-semver. Change-Id: I976a3b5a397f0d6a7d723804a98356544bfc7da3
2024-01-16import: crate: Update to latest semver version.Efraim Flashner
* guix/import/crate.scm (min-element, max-crate-version-of-semver, nonyanked-crate-versions): New procedures. (import-release)[version]: Update to the requested version or the newest semver-compatible version. Co-authored by David Elsing <david.elsing@posteo.net> Change-Id: I72b081147c4eb9faf482f159b7145aaaf9f91f29
2024-01-16doc: Fix mistakes in the manual.Efraim Flashner
Recommended by Christian Miller. * doc/guix.texi (Packages with Multiple Outputs): Replace 'a packages' with 'a package'. (Invoking guix time-machine): Don't assume knowledge and give an explicit link to Back to the Future. (Invoking guix pack): Remove doubled word. (Build Systems): Same. (Debugging Build Failures): 'inspect' is not a command to be run. (Invoking guix import): Remove doubled word. (Invoking guix size): Remove stray word. (Invoking guix processes): Replace 'guix environment' with 'guix shell'. (Base Services): Add missing word. (Networking Setup): Adjust a/an usage. (Networking Services): Remove stray symbol. Add space between two words. (Desktop Services): Remove stray symbol from example. (Database Services): Document default postgresql version. (Web Services): Adjust indentation. (Audio Services): Add missing newline. (Miscellaneous Services): Switch 'get' to 'gets'. (Bootloader Configuration): Remove stray symbol. (Secure Shell): Remove marks around accepted values. (Installing Debugging Files): Replace 'is' with 'it'. (Full-Source Bootstrap): Remove doubled word. (Preparing to Use the Bootstrap Binaries): Same. Change-Id: Ifbf2677dff7642c6531384145363d7611286e48b
2024-01-16gnu: debian-ports-archive-keyring: Update to 2024.01.05.Efraim Flashner
* gnu/packages/debian.scm (debian-ports-archive-keyring): Update to 2024.01.05. Change-Id: Ibaa279a91d9e39804eb5cc1bf759ca3afd69e962
2024-01-16gnu: debootstrap: Update to 1.0.134.Efraim Flashner
* gnu/packages/debian.scm (debootstrap): Update to 1.0.134. [arguments]: Remove obsolete substitution in 'patch-source phase. Change-Id: I2a50ae75a43c0970e3ef866e02c49d87094e14eb
2024-01-16gnu: gourmet: Add missing input.Ricardo Wurmus
* gnu/packages/nutrition.scm (gourmet)[inputs]: Add python-toml. Change-Id: I53bc9b0247c6dc32c5ec6e3cc518dbc982362bd2
2024-01-16gnu: python-pyrdfa3: Update to 3.6.2.Ricardo Wurmus
* 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
2024-01-16gnu: python-clingraph: Update to 1.1.2.Ricardo Wurmus
* gnu/packages/potassco.scm (python-clingraph): Update to 1.1.2. Change-Id: I5910853d39389ff9ad981543204fd8ef1445e495
2024-01-16gnu: python-astroml: Make compatible with recent Matplot and Scipy.Ricardo Wurmus
* gnu/packages/astronomy.scm (python-astroml)[arguments]: Add phases 'matplotlib-compatibility and 'scipy-compatibility. Change-Id: Id88cf769f705f9326f41f951403583155bcee58f
2024-01-16gnu: python-bbknn: Update to 1.6.0.Ricardo Wurmus
* 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
2024-01-16gnu: python-geopandas: Update to 0.14.2.Ricardo Wurmus
* gnu/packages/geo.scm (python-geopandas): Update to 0.14.2. [arguments]: Disable test_pandas_kind tests. Change-Id: I2a49d6ef73a79b84751ce0225757a2b83019cd42
2024-01-16gnu: python-dask: Propagate click.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-dask)[native-inputs]: Move python-click from here... [propagated-inputs]: ...to here. Change-Id: I1a1617d9cb00268d9fc26f4fe6c9ecc6d0a2e375
2024-01-16gnu: python-xarray: Update to 2023.12.0.Ricardo Wurmus
* 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
2024-01-16gnu: python-telomerecat: Disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-telomerecat)[arguments]: Disable tests. Change-Id: I0422ae1e563374a8cc408fc9584cfb7b0e880e95
2024-01-16gnu: python-mysql-connector-python: Defuse time bomb.Ricardo Wurmus
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
2024-01-16gnu: python-adjusttext: Disable tests.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-adjusttext)[arguments]: Disable tests. Change-Id: Ib1002de20a6e301f43bb34f64f7299d4316d8a67
2024-01-16gnu: python-scikit-bio: Update to 0.5.9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scikit-bio): Update to 0.5.9. [source]: Add patch. [arguments]: Disable one test via #:test-flags; adjust 'compatibility phase; update 'check phase. [propagated-inputs]: Remove python-cachecontrol, python-lockfile, and python-scikit-learn; add python-requests. * gnu/packages/patches/python-scikit-bio-1887.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Change-Id: Ie57b0256cf695e5ea088545cd2102335303a93e7
2024-01-16gnu: python-pandas: Update to 1.5.3.Ricardo Wurmus
* gnu/packages/python-science.scm (python-pandas): Update to 1.5.3. [build-system]: Use pyproject-build-system. [arguments]: Use G-expression; move test flags to #:test-flags; add phase 'patch-build-system; fix substitution of "which" executable; remove 'enable-parallel-build; remove custom 'check phase; add 'pre-check phase. [propagated-inputs]: Add python-matplotlib. [native-inputs]: Replace python-cython with python-cython-0.29.35. Change-Id: I9d09971f707b925f469e29be67fe040c181314ff
2024-01-16gnu: python-click-default-group: Update to 1.2.4.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-click-default-group): Update to 1.2.4. [build-system]: Use pyproject-build-system. [native-inputs]: Add python-flit-core and python-pytest. Change-Id: I7e617ee57499542b7e832bb5ea24417b70e8cf85
2024-01-16gnu: datasette: Update to 1.0a7.Ricardo Wurmus
* gnu/packages/databases.scm (datasette): Update to 1.0a7. [propagated-inputs]: Add python-asyncinject and python-sqlite-utils. Change-Id: If713cd0f115c8092f9cc200daa850f9a78a20f6b
2024-01-16gnu: Add python-asyncinject.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-asyncinject): New variable. Change-Id: I2647e8340bca2efabc222d19155d330b1a5ff16f
2024-01-16gnu: python-metpy: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/geo.scm (python-metpy): Update to 1.6.0. [arguments]: Add phases 'fix-version-check and 'hide-imp-deprecation-warnings. [native-inputs]: Add python-packaging; remove python-shapely and python-cartopy. Change-Id: I4a46a5e60b1904699475608146f2a09aefc07624
2024-01-16gnu: python-pint: Add missing input.Ricardo Wurmus
This is a follow-up to commit 23b8601cd2cf90ed11a51ca6db133083433e74d8. Without this input the version string will be 0.0.0. * gnu/packages/python-xyz.scm (python-pint)[native-inputs]: Add python-setuptools-scm. Change-Id: Id621e459f119d7268cdcc41ef93bcae135e842d1
2024-01-16gnu: python-hicexplorer: Make compatible with latest scipy.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-hicexplorer)[arguments]: Add 'scipy-compatibility phase. Change-Id: I31e9058b7fd4ff9245837d5f1cd145b569ec35ad
2024-01-16gnu: python-hicmatrix: Update to 17.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 17.1. [arguments]: Remove. Change-Id: I6b1230d703d0dc1a88ee61a84cc6cd95f7eeb6f9
2024-01-16gnu: python-scikit-optimize: Make compatible with latest sklearn.Ricardo Wurmus
* gnu/packages/python-science.scm (python-scikit-optimize)[source]: Add snippet to fix outdated use of "max_features" option. Change-Id: I4272ffc82b4951315b74b4adee27527e8d513fca
2024-01-16gnu: python-fit-nbinom: Disable tests.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-fit-nbinom)[arguments]: Disable tests. Change-Id: I980480a3326dccc67930d34474832712005d1bb2
2024-01-16gnu: scvelo: Make compatible with latest matplotlib.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (scvelo)[arguments]: Add phase 'matplotlib-compatibility. Change-Id: Ia761821c8aa1e516525cff7c680db471a5908e5f
2024-01-16gnu: python-cartopy: Update to 0.22.0.Ricardo Wurmus
* gnu/packages/geo.scm (python-cartopy): Update to 0.22.0. [build-system]: Use pyproject-build-system. [arguments]: Use G-expression; use #:test-flags; update list of disabled tests; add phase 'remove-endpoint. [propagated-inputs]: Add python-packaging; remove python-pykdtree. [native-inputs]: Add python-coveralls and python-pytest-xdist; remove python-flufl-lock. Change-Id: I353fff0ceade648286ef552effdc35671032c62c
2024-01-16gnu: python-demuxem: Disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-demuxem)[arguments]: Disable tests, because there aren't any. Change-Id: I50364ca6744cf9d2704d4b75a8c79c4fdc4ada6e
2024-01-16gnu: python-pint: Update to 0.23.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-pint): Update to 0.23. [arguments]: Disable "test_load_definitions_stage_2" test. [native-inputs]: Remove python-dask, python-distributed, python-importlib-metadata, python-setuptools-scm, python-sparse, python-uncertainties, and python-xarray; add python-pytest-benchmark. [propagated-inputs]: Add python-uncertainties. Change-Id: I98baae3369e5ffeea96355d9509296771c33dc50
2024-01-16gnu: python-cooler: Update to 0.9.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.9.1. [build-system]: Use pyproject-build-system. [arguments]: Remove custom build phases; disable tests via #:test-flags. [propagated-inputs]: Remove python-six and python-sparse. [native-inputs]: Remove python-codecov, python-mock, and python-pytest-flake8; add python-coverage, python-hatchling, and python-isort. Change-Id: I48b6a9c07a2bc1c213971585d7191573fd5d5aca
2024-01-16gnu: python-plastid: Update to 0.6.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.6.1. [arguments]: Disable four tests. Change-Id: If0225f226e702e89d451e2955d0f76691a8816c0
2024-01-16gnu: cnvkit: Update to 0.9.10.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.10. [arguments]: Remove. [inputs]: Add r-minimal. Change-Id: Iaa27fd3dddc507c7a955441f066d4b0e3b8f1757
2024-01-16gnu: python-reportlab: Update to 4.0.8.Ricardo Wurmus
* gnu/packages/pdf.scm (python-reportlab): Update to 4.0.8. [arguments]: Update configure flags and 'find-libraries phase. [inputs]: Remove freetype and libart-lgpl. [propagated-inputs]: Add python-chardet. Change-Id: I626ef4c71a0b867ec4e1c74a71e45843349f46ef
2024-01-16gnu: python-pegasusio: Disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pegasusio)[arguments]: Disable tests. Change-Id: I6b32ed416b562b47088dbc34eb7bcb0b8e2cc414
2024-01-16gnu: python-pyani: Disable tests.Ricardo Wurmus
There are none. * gnu/packages/bioinformatics.scm (python-pyani)[arguments]: Disable tests. Change-Id: I6862082c8335e5d487da6d1705ed094922f14e47
2024-01-16gnu: tadbit: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tadbit)[native-inputs]: Add glib. Change-Id: Ia1f79e2a30f5b57616cf3d1f7b6438f07451fbbf
2024-01-16gnu: python-captum: Update to 0.7.0.Ricardo Wurmus
* gnu/packages/machine-learning.scm (python-captum): Update to 0.7.0. [propagated-inputs]: Add python-tqdm. Change-Id: I8917b6e294fe08077a3af4423deefa9769ba9384
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