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2023-05-05Revert "gnu: Add python-gimmemotifs."Ricardo Wurmus
This reverts commit dc8b3ebe5d4ba2a39c12f62d836963ffee1e4b47. python-gimmemotifs is not usable without proprietary third-party tools.
2023-05-05gnu: gcc-11: Fix patch-hurd-libpthread phase.Christopher Baines
It didn't work when it was introduced in 08acdd0765b5f4fbfafa699a823ea7985d4d35a7. * gnu/packages/gcc.scm (gcc-11)[arguments]: Remove the procedure arguments, and use %build-inputs rather than inputs. * gnu/packages/commencement.scm (gcc-boot0)[native-inputs]: Add hurd-patch, as this package inherits from gcc-11.
2023-05-05gnu: Add python-gimmemotifs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-gimmemotifs): New variable.
2023-05-05gnu: Add python-norns.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-norns): New variable.
2023-05-05gnu: Add python-xdg.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-xdg): New variable.
2023-05-05gnu: Add python-qnorm.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-qnorm): New variable.
2023-05-05gnu: Add python-biofluff.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-biofluff): New variable.
2023-05-05gnu: Add python-genomepy.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-genomepy): New variable.
2023-05-05gnu: Add python-filelock-3.5.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-filelock-3.5): New variable.
2023-05-05gnu: Add python-logomaker.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-logomaker): New variable.
2023-05-05gnu: Add python-mysql-connector-python.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-mysql-connector-python): New variable.
2023-05-05gnu: Add protobuf-3.20.Ricardo Wurmus
* gnu/packages/protobuf.scm (protobuf-3.20): New variable.
2023-05-05gnu: Add python-palettable.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-palettable): New variable.
2023-05-05gnu: python-pyfaidx: Update to 0.7.2.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.7.2.1. [build-system]: Use pyproject-build-system. [arguments]: Ignore tests that require large downloads. [native-inputs]: Remove python-six; add python-fsspec, python-pytest, python-pytest-cov, python-mock, and python-numpy.
2023-05-05gnu: python-sanic: Disable failing SSL tests.Lars-Dominik Braun
Best guess is that they check for broken behavior in one of the dependencies, which has changed. * gnu/packages/python-web.scm (python-sanic)[arguments]: Disable more tests.
2023-05-05gnu: python-gssapi: Update to 1.8.2.Lars-Dominik Braun
* gnu/packages/python-xyz.scm (python-gssapi): Update to 1.8.2. [native-inputs]: Add python-cython.
2023-05-05gnu: python-k5test: Update to 0.10.3.Lars-Dominik Braun
* gnu/packages/python-xyz.scm (python-k5test): Update to 0.10.3.
2023-05-05gnu: python-atpublic: Update to 3.1.1.Lars-Dominik Braun
* gnu/packages/python-check.scm (python-atpublic): Update to 3.1.1. [build-system]: Switch to pyproject-build-system. [arguments]: Remove #:phases, override build backend. [native-inputs]: Replace nose2 with pytest, add python-pdm-backend, python-sybil and python-pytest-cov.
2023-05-05gnu: Add python-pdm-backend.Lars-Dominik Braun
* gnu/packages/python-build.scm (python-pdm-backend): New variable.
2023-05-05gnu: guix: Update to dc5430c.Ludovic Courtès
* gnu/packages/package-management.scm (guix): Update to dc5430c.
2023-05-04gnu: python-fs: Remove indirect dependency on Rust when unsupported.Ludovic Courtès
This allows to build font-abattis-cantarell on aarch64-linux. * gnu/packages/python-xyz.scm (python-fs)[arguments]: Add #:tests?. [native-inputs]: Turn into the empty list when cross-compiling or when PYTHON-PYFTPDLIB is not supported.
2023-05-04gnu: psautohint: Remove unneeded dependencies.Ludovic Courtès
* gnu/packages/fontutils.scm (psautohint)[native-inputs]: Remove PYTHON-FS and PYTHON-PYTEST-RANDOMLY.
2023-05-04services: qemu-binfmt: Add more targets.Efraim Flashner
* gnu/services/virtualization.scm (%i486, %sparc64, %aarch64be, %xtensa, %xtensaeb, %microblaze, %microblazeel, %or1k, %hexagon, %loongson64): New variables. (%armeb): Correct family field. (%qemu-platforms): Add them.
2023-05-04services: earlyoom: Rotate log files.Efraim Flashner
* gnu/services/linux.scm (%earlyoom-log-rotation): New variable. (earlyoom-service-type): Add service-extension for log rotation.
2023-05-04gnu: vifm: Update to 0.13.Efraim Flashner
* gnu/packages/vim.scm (vifm): Update to 0.13. [arguments]: Adjust substitutions in custom 'patch-test-shebangs phase.
2023-05-04gnu: python-screed: Update to 1.1.2.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (python-screed): Update to 1.1.2. [build-system]: Use pyproject-build-system. [native-inputs]: Remove python-pytest. [inputs]: Remove python-bz2file. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-05-04gnu: Add python-goatools.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-goatools): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2023-05-04gnu: Add r-rcircos.Navid Afkhami
* gnu/packages/cran.scm (r-rcircos): New variable.
2023-05-04gnu: Add python-diff-cover.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-diff-cover): New variable.
2023-05-04gnu: Add python-loguru.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-loguru): New variable.
2023-05-04gnu: Add python-pytest-mypy-plugins.Ricardo Wurmus
* gnu/packages/check.scm (python-pytest-mypy-plugins): New variable.
2023-05-04gnu: Add python-chevron.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-chevron): New variable.
2023-05-04gnu: Add python-iteround.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-iteround): New variable.
2023-05-04gnu: airspyhf: Update to 1.6.8-1.40836c5.Guillaume Le Vaillant
* gnu/packages/radio.scm (airspyhf): Update to 1.6.8-1.40836c5.
2023-05-04gnu: linux-libre 5.15: Update to 5.15.110.Leo Famulari
* gnu/packages/linux.scm (linux-libre-5.15-version): Update to 5.15.110. (linux-libre-5.15-pristine-source): Update hash.
2023-05-04gnu: linux-libre 6.1: Update to 6.1.27.Leo Famulari
* gnu/packages/linux.scm (linux-libre-6.1-version): Update to 6.1.27. (linux-libre-6.1-pristine-source): Update hash.
2023-05-04gnu: linux-libre: Update to 6.2.14.Leo Famulari
* gnu/packages/linux.scm (linux-libre-6.2-version): Update to 6.2.14. (linux-libre-6.2-pristine-source): Update hash.
2023-05-04gnu: sakura: Remove input labels.Ludovic Courtès
* gnu/packages/terminals.scm (sakura)[native-inputs]: Remove input labels.
2023-05-04gnu: peek: Remove input labels.Ludovic Courtès
* gnu/packages/video.scm (peek)[inputs, native-inputs]: Remove labels.
2023-05-04gnu: tint2: Remove input labels.Ludovic Courtès
* gnu/packages/xdisorg.scm (tint2)[native-inputs]: Remove input labels.
2023-05-04gnu: maim: Remove input labels.Ludovic Courtès
* gnu/packages/xdisorg.scm (maim)[inputs]: Remove labels.
2023-05-04gnu: armadillo: Remove input labels.Ludovic Courtès
* gnu/packages/maths.scm (armadillo)[inputs]: Remove labels.
2023-05-04gnu: vulkan-loader: Skip tests on riscv64-linux.Efraim Flashner
* gnu/packages/vulkan.scm (vulkan-loader)[arguments]: Skip tests when building on riscv64-linux.
2023-05-04gnu: exiv2: Adjust tests on riscv64-linux.Efraim Flashner
* gnu/packages/image.scm (exiv2)[arguments]: Also use the custom 'adjust-tests phase when building for riscv64-linux.
2023-05-04gnu: r-bigmemory: Remove several supported systems.Christopher Baines
Where the package consistently fails to build. * gnu/packages/statistics.scm (r-bigmemory)[supported-systems]: Remove armhf-linux, aarch64-linux and powerpc64le-linux.
2023-05-04gnu: gcc-11: Adapt patching for hurd to not use gexp's.Christopher Baines
As this causes issues with gcc-cross-boot0, since it doesn't use gexp's and that means the builder script ends up broken. I'm not testing this properly, I've only confirmed that with this change, you can generate a derivation for hello for i586-gnu where that derivation and all inputs don't have broken builder scripts. Plus the output for hello on x86_64-linux is unchanged. * gnu/packages/gcc.scm (gcc-11)[arguments]: Rewrite to not use gexps. [native-inputs]: Add a patch for the hurd if that's the target.
2023-05-04gnu: dune-common: Skip tests that fail on aarch64-linux.Felix Gruber
* gnu/packages/patches/dune-common-skip-failing-tests.patch: New file. * gnu/packages/maths.scm (dune-common)[source]: Add it * gnu/local.mk (dist_patch_DATA): Register it. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2023-05-03gnu: rdiff-backup: Update to 2.2.4.Eric Bavier
* gnu/packages/backup.scm (rdiff-backup): Update to 2.2.4. [inputs]: Add python-pyaml.
2023-05-03gnu: pinball: Update to 0.3.20230219.Eric Bavier
* gnu/packages/games.scm (pinball): Update to 0.3.20230219. [inputs]: Use sdl-union. [arguments]: Adjust configure flags. Use gexps. Remove debug outpu.
2023-05-03gnu: python-wxpython: Add a debug outputMaxim Cournoyer
* gnu/packages/wxwidgets.scm (python-wxpython) [outputs]: New field. [arguments]: Provide the '--debug' build option in the configure phase.