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2021-12-07gnu: python-velocyto: Remove generated C files.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-velocyto)[source]: Remove all generated .c files.
2021-12-07gnu: python-schema-salad: Update to 8.2.20211116214159.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-schema-salad): Update to 8.2.20211116214159. [arguments]: Remove trailing #T. [propagated-inputs]: Replace python-cachecontrol-0.11 with python-cachecontrol. [native-inputs]: Add python-black.
2021-12-07gnu: taxtastic: Update to 0.9.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.9.2. [arguments]: Delete 'sanity-check and 'python37-compatibility phases; adjust 'prepare-directory phase.
2021-12-07gnu: taxtastic: Run tests conditionally.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Respect TESTS? option.
2021-12-07gnu: python-dendropy: Update to 4.5.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.5.1. [arguments]: Skip failing tests.
2021-12-07gnu: make-gccgo: Override empty GOROOT/GCCGOTOOLDIRSarah Morgensen
gnu/packages/gcc.scm (make-gccgo)[arguments]: Set tool paths (GOROOT and GCCGOTOOLDIR) even if they are already set to "". Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-07gnu: python-cooler: Use python-cytoolz-for-cooler.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace python-cytoolz with python-cytoolz-for-cooler.
2021-12-07gnu: Add python-cytoolz-for-cooler.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-cytoolz-for-cooler): New variable.
2021-12-07gnu: python-sparse: Update to 0.13.0.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-sparse): Update to 0.13.0.
2021-12-07gnu: Add diffr.jgart
* gnu/packages/rust-apps.scm (diffr): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-07gnu: python-dask: Update to 2021.11.2.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-dask): Update to 2021.11.2. [source]: Fetch from github. [arguments]: Remove phase 'disable-broken-tests.
2021-12-07gnu: python-dask: Run tests conditionally.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-dask)[arguments]: Respect TESTS? option.
2021-12-07gnu: python-dask: Add missing input for tests.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-dask)[native-inputs]: Add python-pytest-rerunfailures.
2021-12-07gnu: Add rust-diffr-lib-0.1.jgart
* gnu/packages/crates-io.scm (rust-diffr-lib-0.1): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-07gnu: phylip: Update to 3.697.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (phylip): Update to 3.697.
2021-12-07gnu: phylip: Pass -fcommon to compiler.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (phylip)[arguments]: Set CFLAGS.
2021-12-07gnu: phylip: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (phylip)[arguments]: Remove trailing #T from build phases.
2021-12-07gnu: Add dutree.jgart
* gnu/packages/rust-apps.scm (dutree): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-12-07gnu: subread: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (subread)[arguments]: Remove trailing #T from build phases.
2021-12-07gnu: subread: Update to 2.0.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (subread): Update to 2.0.3.
2021-12-07gnu: subread: Update home page..Ricardo Wurmus
* gnu/packages/bioinformatics.scm (subread)[home-page]: Use new home page.
2021-12-07gnu: subread: Pass -fcommon to compiler.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (subread)[arguments]: Add -fcommon to flags.
2021-12-07gnu: python-pytest-console-scripts: Update to 1.2.1.Ricardo Wurmus
* gnu/packages/python-check.scm (python-pytest-console-scripts): Update to 1.2.1.
2021-12-07gnu: Add python-pytest-rerunfailures.Ricardo Wurmus
* gnu/packages/python-check.scm (python-pytest-rerunfailures): New variable.
2021-12-07gnu: mcl: Add -fcommon to compiler flags.Ricardo Wurmus
* gnu/packages/machine-learning.scm (mcl)[arguments]: Set CFLAGS.
2021-12-07gnu: python-cytoolz: Update to 0.11.2.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-cytoolz): Update to 0.11.2. [source]: Add snippet.
2021-12-07gnu: hisat: Update to 0.1.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (hisat): Update to 0.1.6.
2021-12-07gnu: hisat: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove trailing #T from build phase.
2021-12-07gnu: hisat: Remove invalid characters.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove curly quotes.
2021-12-07gnu: crossmap: Update to 0.6.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (crossmap): Update to 0.6.1. [source]: Add snippet to remove generated files.
2021-12-07gnu: Remove python2-bx-python.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python2-bx-python): Delete variable.
2021-12-07gnu: python-bx-python: Update to 0.8.12.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.8.12. [propagated-inputs]: Remove python-six. [arguments]: Remove. Tests are still not run, though.
2021-12-07gnu: Remove pbtranscript-tofu.Ricardo Wurmus
Upstream has disappeared and it depends on Python 2, which is no longer supported. * gnu/packages/bioinformatics.scm (pbtranscript-tofu): Remove variable.
2021-12-07gnu: python-pyfit-sne: Update to 1.2.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pyfit-sne): Update to 1.2.1. [arguments]: Disable tests explicitly.
2021-12-07gnu: guile-netlink: Update to 1.1.1.Julien Lepiller
* gnu/packages/guile.scm (guile-netlink): Update to 1.1.1.
2021-12-06gnu: emacs-csv-mode: Update to 1.17.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-csv-mode): Update to 1.17.
2021-12-06gnu: helm: Fix build with GCC 9 and later.Pierre Langlois
* gnu/packages/music.scm (helm)[origin]: Add patch. * gnu/packages/patches/helm-fix-gcc-9-build.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
2021-12-06gnu: patchwork: Adjust for python-build-system change.Marius Bakke
This is a follow-up to commit db5646d957895944007c1bb44fcd998ea392f168, et.al. * gnu/packages/patchutils.scm (patchwork)[arguments]: Adapt one more site-packages call.
2021-12-06gnu: f-seq: Update name of commons-cli JAR.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Use new name of commons-cli JAR.
2021-12-06gnu: f-seq: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Remove trailing #T from build phase.
2021-12-06gnu: f-seq: Simplify snippet.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (f-seq)[source]: Simplify snippet.
2021-12-06gnu: Go 1.17: Update to 1.17.4.Leo Famulari
* gnu/packages/golang.scm (go-1.17): Update to 1.17.4.
2021-12-06gnu: Go 1.16: Update to 1.16.11.Leo Famulari
* gnu/packages/golang.scm (go-1.16): Update to 1.16.11.
2021-12-06gnu: Syncthing: Update to 1.18.4.Leo Famulari
* gnu/packages/syncthing.scm (syncthing): Update to 1.18.4. [arguments]: Build with Go 1.17.
2021-12-06gnu: osinfo-db-next: Fix uri.Mathieu Othacehe
* gnu/packages/virtualization.scm (osinfo-db-next)[source]: Fix URI.
2021-12-06gnu: go-gopkg-in-yaml-v2: Update to 2.4.0.Efraim Flashner
* gnu/packages/golang.scm (go-gopkg-in-yaml-v2): Update to 2.4.0.
2021-12-06gnu: go-gopkg-in-yaml-v2: Fix test suite on 32-bit systems.Efraim Flashner
* gnu/packages/golamg.scm (go-gopkg-in-yaml-v2)[source]: Add snippet to no longer cause integer overflow on 32-bit systems during test suite.
2021-12-06gnu: go-github-com-golang-snappy: Adjust test-suite on 32-bit systems.Efraim Flashner
* gnu/packages/syncthing.scm (go-github-com-golang-snappy)[source]: Add patch to skip a test on 32-bit systems. * gnu/packages/patches/go-github-com-golang-snappy-32bit-test.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
2021-12-06gnu: python-kivy: Add missing dependencies.Ludovic Courtès
* gnu/packages/python-xyz.scm (python-kivy)[arguments]: Add 'set-home' phase. [inputs]: Add PYTHON-DOCUTILS, PYTHON-KIVY-GARDEN, and PYTHON-PYGMENTS. [synopsis, description]: Tweak.
2021-12-06gnu: Add python-kivy-garden.Ludovic Courtès
* gnu/packages/python-xyz.scm (python-kivy-garden): New variable.
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