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2022-08-16gnu: Add go-github-com-biogo-hts-sam.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-sam): New variable.
2022-08-16gnu: Add go-github-com-biogo-hts-bam.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-bam): New variable.
2022-08-16gnu: Add go-github-com-biogo-store-step.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-step): New variable.
2022-08-16gnu: Add go-github-com-biogo-store-llrb.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-llrb): New variable.
2022-08-16gnu: Add go-github-com-biogo-store-kdtree.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-kdtree): New variable.
2022-08-16gnu: Add go-github-com-biogo-store-interval.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-interval): New variable.
2022-08-16gnu: Add go-github-com-biogo-graph.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (go-github-com-biogo-graph): New variable.
2022-08-16gnu: Add stpipeline.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (stpipeline): New variable.
2022-08-16gnu: Add python-taggd.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-taggd): New variable.
2022-08-16gnu: Add python-sqlitedict.Ricardo Wurmus
* gnu/packages/databases.scm (python-sqlitedict): New variable.
2022-08-16gnu: htseq: Update to 2.0.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htseq): Update to 2.0.2. [source]: Fetch from git repository. [arguments]: Delete 'build phase; run tests with pytest in 'check phase. [propagated-inputs]: Add python-matplotlib and python-pysam. [inputs]: Remove python-matplotlib and python-pysam. [native-inputs]: Add python-pandas, python-pytest, python-scipy, and swig. [synopsis]: Update. [description]: Update.
2022-08-16gnu: emacs-geiser-guile: Update guile input to guile-3.0-latest.Andrew Tropin
* gnu/packages/emacs-xyz.scm (emacs-geiser-guile)[inputs]: Update guile to guile-3.0-latest.
2022-08-16gnu: terminals: Deprecate wterm.(
`wterm` no longer works with modern Wayland, and has been unmaintained since early 2021. See issue #52029. * gnu/packages/terminals.scm (wterm): Deprecate in favour of `foot`. Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
2022-08-16gnu: python-daemon: Remove unused input.Marius Bakke
* gnu/packages/python-xyz.scm (python-daemon)[native-inputs]: Remove PYTHON-UNITTEST2.
2022-08-16gnu: python-case: Remove unused input.Marius Bakke
* gnu/packages/python-xyz.scm (python-case)[propagated-inputs]: Remove PYTHON-UNITTEST2.
2022-08-16gnu: python-posix-ipc: Remove unused input.Marius Bakke
* gnu/packages/python-xyz.scm (python-posix-ipc)[native-inputs]: Remove.
2022-08-16gnu: python-pyu2f: Remove unused inputs.Marius Bakke
* gnu/packages/python-crypto.scm (python-pyu2f)[native-inputs]: Remove.
2022-08-16gnu: python-pymysql: Remove unused input.Marius Bakke
* gnu/packages/databases.scm (python-pymysql)[native-inputs]: Remove PYTHON-UNITTEST2.
2022-08-16gnu: python-pyclipper: Update to 1.3.0.post3.Marius Bakke
* gnu/packages/python-xyz.scm (python-pyclipper): Update to 1.3.0.post3. [source](uri): Use tarball instead of zipball. [source](snippet): Adjust for renamed file. [arguments]: Likewise. [propagated-inputs]: Remove. [native-inputs]: Remove PYTHON-UNITTEST2 and UNZIP. Add PYTHON-SETUPTOOLS-SCM.
2022-08-16gnu: python-ufo2ft: Add missing input.Marius Bakke
* gnu/packages/fontutils.scm (python-ufo2ft)[native-inputs]: Add PYTHON-SETUPTOOLS-SCM.
2022-08-16gnu: python-afdko: Add missing input.Marius Bakke
* gnu/packages/fontutils.scm (python-afdko)[native-inputs]: Add PYTHON-SETUPTOOLS-SCM.
2022-08-16gnu: python-ufoprocessor: Add missing input.Marius Bakke
* gnu/packages/fontutils.scm (python-ufoprocessor)[native-inputs]: Add PYTHON-SETUPTOOLS-SCM.
2022-08-16gnu: python-fontparts: Add missing input.Marius Bakke
* gnu/packages/fontutils.scm (python-fontparts-bootstrap)[native-inputs]: Add PYTHON-SETUPTOOLS-SCM.
2022-08-16gnu: python-booleanoperations: Add missing input.Marius Bakke
* gnu/packages/graphics.scm (python-booleanoperations)[native-inputs]: Add PYTHON-SETUPTOOLS-SCM.
2022-08-16gnu: python-mando: Update to 0.7.1.Marius Bakke
* gnu/packages/python-xyz.scm (python-mando): Update to 0.7.1. [arguments]: Override check phase.
2022-08-16gnu: python-radon: Permit newer versions of mando.Marius Bakke
* gnu/packages/python-xyz.scm (python-radon)[arguments]: Add setup.py substitution.
2022-08-16gnu: python-lz4: Update to 4.0.2.Marius Bakke
* gnu/packages/python-compression.scm (python-lz4): Update to 4.0.2. [native-inputs]: Remove PYTHON-NOSE. Add PYTHON-PKGCONFIG and PYTHON-PSUTIL. [arguments]: Override check phase.
2022-08-16gnu: python-mypy: Update to 0.971.Marius Bakke
* gnu/packages/patches/python-mypy-12332.patch, gnu/packages/patches/python-mypy-use-sys-path.patch: Delete files. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/python-check.scm (python-mypy): Update to 0.971. [source](patches): Remove. [arguments]: Skip one test.
2022-08-16gnu: libreoffice: Remove obsolete workaround.Marius Bakke
* gnu/packages/libreoffice.scm (libreoffice)[arguments]: Don't pass LDFLAGS.
2022-08-14gnu: encodings: Update to 1.0.6.Tobias Geerinckx-Rice
* gnu/packages/xorg.scm (encodings): Update to 1.0.6.
2022-08-14gnu: mu: Update to 1.8.9.Tobias Geerinckx-Rice
* gnu/packages/mail.scm (mu): Update to 1.8.9. [arguments]: Adjust the 'patch-bin-references phase accordingly.
2022-08-15gnu: plink-ng: Build sources from 2.0 directoryRicardo Wurmus
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Disable tests; adjust make flags; enter 2.0 directory in 'chdir phase; replace 'install phase. [inputs]: Add zstd:lib.
2022-08-14gnu: rnnoise: Remove input labels.Tobias Geerinckx-Rice
* gnu/packages/xiph.scm (rnnoise)[native-inputs]: Remove input labels.
2022-08-14gnu: rnnoise: Unhide and rename variable.Tobias Geerinckx-Rice
* gnu/packages/xiph.scm (xiph-rnnoise): Rename to… (rnnoise): …this. Adjust all users. [properties]: Remove HIDDEN? property as it is no longer ambiguous.
2022-08-14gnu: noise-suppression-for-voice: Rename from ‘rnnoise’.Tobias Geerinckx-Rice
This is a set of plug-ins *based on* Xiph's rnnoise package (also in Guix). * gnu/packages/pulseaudio.scm (rnnoise): Rename this variable… (noise-suppression-for-voice): …to this. [noisetorch](inputs): Adjust its only user.
2022-08-14gnu: noisetorch: Update to 0.12.2.Tobias Geerinckx-Rice
* gnu/packages/pulseaudio.scm (noisetorch): Update to 0.12.2. [source]: Switch to maintained fork. [arguments]: Update all ‘paths’ accordingly. Rename 'symlink-rnnoise phase to 'copy-rnnoise-library and do so. Remove 'gen-version.go phase. Don't explicitly return #f from phases. [home-page]: Update to match SOURCE.
2022-08-14gnu: openvpn: Update to 2.5.7.Tobias Geerinckx-Rice
* gnu/packages/vpn.scm (openvpn): Update to 2.5.7.
2022-08-14gnu: nftables: Update to 1.0.5.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (nftables): Update to 1.0.5.
2022-08-14gnu: libnftnl: Update to 1.2.3.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (libnftnl): Update to 1.2.3.
2022-08-14gnu: bird: Update to 2.0.10.Tobias Geerinckx-Rice
* gnu/packages/networking.scm (bird): Update to 2.0.10.
2022-08-14gnu: catfish: Update to 4.16.4.Tobias Geerinckx-Rice
* gnu/packages/xfce.scm (catfish): Update to 4.16.4.
2022-08-14gnu: libupnp: Update to 1.14.13.Tobias Geerinckx-Rice
* gnu/packages/upnp.scm (libupnp): Update to 1.14.13.
2022-08-14gnu: os-prober: Update to 1.81.Tobias Geerinckx-Rice
* gnu/packages/bootloaders.scm (os-prober): Update to 1.81.
2022-08-15guile-fibers: Backport the ‘epoll instance is dead’ bugfix.Maxime Devos
This fixes some indeterministic test failures for gnunet-scheme observed while developing gnunet-scheme. The following checks were made: All dependents compile for x86_64: $ ./pre-inst-env guix build shepherd gnunet-scheme guix-build-coordinator nar-herder guix-data-service guile-fibers --system=x86_64-linux Everything except guix-build-coordinator (which depends on the non-cross-compilable sqitch) cross-compile from x86_64 to aarch64-linux-gnu: $ ./pre-inst-env guix build shepherd gnunet-scheme nar-herder guile-fibers --system=x86_64-linux --target=aarch64-linux-gnu I tried testing for reproducibility but the check phase took to long. However, you can compare the hash you get against the hash I got: $ ./pre-inst-env guix hash --serializer=nar $(./pre-inst-env guix build guile-fibers --no-grafts --system=x86_64-linux) 0qsaqx27b6q2s22h7y93417ijpkwl6gc1fhhck8aha6bvmawk5h0 I tried an emulated build for another architecture, but there the tests took overly long. There were no lint warnings for guile-fibers. * gnu/packages/patches/guile-fibers-epoll-instance-is-dead.patch: New patch. * gnu/local.mk (dist_patch_DATA): Register the patch. * gnu/packages/guile-xyz.scm (guile-fibers)[source]{patches}: Use the patch. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
2022-08-15Revert "gnu: python-lxml: Update to 4.6.5."Mathieu Othacehe
This reverts commit 2365e8435a13c3aa4308e88773de0a0e7b9ffef9 as it triggers >15k rebuilds: https://ci.guix.gnu.org/eval/543158.
2022-08-15gnu: Add kissat.Maximilian Heisinger
* gnu/packages/maths.scm (kissat): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2022-08-15gnu: python-lxml: Update to 4.6.5.Danny Milosavljevic
* gnu/packages/xml.scm (python-lxml): Update to 4.6.5.
2022-08-15gnu: Add python-robotframework-sshtunnellibrary.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-robotframework-sshtunnellibrary): New variable.
2022-08-15gnu: Add python-sshtunnel.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-sshtunnel): New variable.
2022-08-15gnu: torsocks: Wrap lines.Mathieu Othacehe
* gnu/packages/tor.scm (torsocks)[source, arguments]: Wrap long lines and remove a trailing #t.
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