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2022-01-10build/python: Improve error output in sanity check.Hartmut Goebel
Instead of printing the "str()" representation of the excaption, print the "repr()" representation. This will print the name of the exception and thus ease understanding the actual error. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: rust: Use rust-1.57.0.Maxim Cournoyer
* gnu/packages/rust.scm (rust-1.54): Make it a private variable. Move definition to... (rust-1.57): ... here. (rust-1.55, rust-1.56): Make private. * gnu/packages/shells.scm (nushell)[rust]: Remove argument.
2022-01-10gnu: simple-scan: Add python to native inputs.Maxim Cournoyer
* gnu/packages/gnome.scm (simple-scan)[native-inputs]: Add python.
2022-01-10gnu: gnome-calculator: Add python to native inputs.Maxim Cournoyer
* gnu/packages/gnome.scm (gnome-calculator)[native-inputs]: Add python.
2022-01-10gnu: gnome-screenshot: Add python to native inputs.Maxim Cournoyer
* gnu/packages/gnome.scm (gnome-screenshot)[native-inputs]: Add python.
2022-01-10gnu: file-roller: Add python to native inputs.Maxim Cournoyer
* gnu/packages/gnome.scm (file-roller)[native-inputs]: Add python.
2022-01-10gnu: python-pandas: Update to 1.3.5.Maxim Cournoyer
* gnu/packages/python-science.scm (python-pandas): Update to 1.3.5. [phases]{check}: Add a reference to the network accessing tests issue, now reported upstream. Reinstate the excelwriter tests. [propagated-inputs]: Add python-xlsxwriter. [native-inputs]: Remove python-nose.
2022-01-10gnu: python-xlwt: Add comment about maintainership of the package.Maxim Cournoyer
The package appears to be abandoned. * gnu/packages/python-xyz.scm (python-xlwt): Add comment.
2022-01-10gnu: python-openpyxl: Update to 3.0.9.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-openpyxl): Update to 3.0.9.
2022-01-10gnu: python-xlrd: Update to 2.0.1.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-xlrd): Update to 2.0.1. [source]: Use git-fetch. [arguments]: Delete field. [native-inputs]: Add python-pytest.
2022-01-10gnu: mutter: Add python to native inputs.Maxim Cournoyer
* gnu/packages/gnome.scm (mutter)[native-inputs]: Add python.
2022-01-10gnu: libgweather: Add python to native inputs.Maxim Cournoyer
* gnu/packages/gnome.scm (libgweather)[native-inputs]: Add python.
2022-01-10gnu: baobab: Add python to native inputs.Maxim Cournoyer
* gnu/packages/gnome.scm (baobab)[native-inputs]: Add python.
2022-01-10gnu: python-pytest-timeout: Update to 2.0.2.Maxim Cournoyer
* gnu/packages/check.scm (python-pytest-timeout): Update to 2.0.2.
2022-01-10gnu: binutils: Fix CVE-2021-45078.Leo Famulari
This is for the release branch. Should we also use a graft for the master branch? It would be even better if we could add a binutils-next package that users could install, in my opinion. * gnu/packages/patches/binutils-CVE-2021-45078.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/base.scm (binutils)[source]: Use it. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: glib: Update to 2.70.2.Maxim Cournoyer
* gnu/packages/glib.scm (glib): Update to 2.70.2.
2022-01-10gnu: meson: Update to 0.60.3.Maxim Cournoyer
* gnu/packages/build-tools.scm (gn): Update to 0.60.3.
2022-01-10gnu: glibmm: Update to 2.70.0 and apply guix style.Maxim Cournoyer
* gnu/packages/glib.scm (glibmm): Update to 2.70.0. [native-inputs]: Use new style.
2022-01-10gnu: cpuid: Remove obsolete file permissions change.Sarah Morgensen
* gnu/packages/linux.scm (cpuid)[arguments]<#:phases>{fix-makefile}: Remove Makefile gzip permissions patch. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: pre-commit: Remove obsolete phase.Sarah Morgensen
* gnu/packages/version-control.scm (pre-commit)[arguments]<#:phases>: Remove 'make-gz-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: go-github-com-prometheus-common: Remove obsolete phase.Sarah Morgensen
* gnu/packages/syncthing.scm (go-github-com-prometheus-common) [arguments]<#:phases>: Remove 'make-gzip-archive-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: python-pdfminer-six: Remove obsolete phase.Sarah Morgensen
* gnu/packages/python-xyz.scm (python-pdfminer-six)[arguments] <#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: arcanist: Remove obsolete phase.Sarah Morgensen
* gnu/packages/phabricator.scm (arcanist)[arguments]<#:phases>: Remove 'make-compressed-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: helm: Remove obsolete phase.Sarah Morgensen
* gnu/packages/music.scm (helm)[arguments]<#:phases>: Remove 'make-gz-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: lmms: Remove obsolete phase.Sarah Morgensen
* gnu/packages/music.scm (lmms)[arguments]<#:phases>: Remove 'make-manpages-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: jalv-select: Remove obsolete phase.Sarah Morgensen
* gnu/packages/music.scm (jalv-select)[arguments]<#:phases>: Remove 'make-manpages-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: python-scikit-learn: Remove obsolete phase.Sarah Morgensen
* gnu/packages/machine-learning.scm (python-scikit-learn)[arguments] <#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: go-ipfs: Remove obsolete phase.Sarah Morgensen
* gnu/packages/ipfs.scm (go-ipfs)[arguments]<#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: python-plotly: Remove obsolete phase.Sarah Morgensen
* gnu/packages/graph.scm (python-plotly)[arguments]<#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: go-github-com-gdamore-tcell: Remove obsolete phase.Sarah Morgensen
* gnu/packages/golang.scm (go-github-com-gdamore-tcell)[arguments] <#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: go-github-com-docker-distribution: Remove obsolete phase.Sarah Morgensen
* gnu/packages/golang.scm (go-github-com-docker-distribution)[arguments] <#:phases>: Remove 'make-gzip-archive-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: go-golang-org-x-crypto: Remove obsolete phase.Sarah Morgensen
* gnu/packages/golang.scm (go-golang-org-x-crypto)[arguments]<#:phases>: Remove 'make-gzip-archive-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: po4a: Remove obsolete phase.Sarah Morgensen
* gnu/packages/gettext.scm (po4a)[arguments]<#:phases>: Remove 'make-compressed-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: emacs: Remove obsolete phase.Sarah Morgensen
* gnu/packages/emacs.scm (emacs)[arguments]<#:phases>: Remove 'make-compressed-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: cups-minimal: Remove obsolete phase.Sarah Morgensen
* gnu/packages/cups.scm (cups-minimal)[arguments]<#:phases>: Remove 'make-manpages-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: clipper: Remove obsolete phase.Sarah Morgensen
* gnu/packages/bioinformatics.scm (clipper)[arguments]<#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: python-biom-format: Remove obsolete phase.Sarah Morgensen
* gnu/packages/bioinformatics.scm (python-biom-format)[arguments] <#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10build-system/gnu: Make gzip files writable before resetting timestamps.Sarah Morgensen
guix/build/gnu-build-system.scm (reset-gzip-timestamps): Ensure gzip files are writable before resetting their timestamps. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2022-01-10gnu: tbb-2020: Use ld.gold to work around segfaults in check phase.Maxim Cournoyer
* gnu/packages/tbb.scm (tbb-2020) [configure-flags]: Use -fuse-ld=gold in CFLAGS. [native-inputs]: Add ld-gold-wrapper.
2022-01-10gnu: python-igraph: Update to 0.9.8.Maxim Cournoyer
* gnu/packages/graph.scm (python-igraph): Update to 0.9.8. [origin]: Fetch from git. [configure-flags]: Delete argument. [phases]{build}: No longer override phase. {check}: Preserve ordering and streamline. {specify-libigraph-location}: New phase. [native-inputs]: Remove pkg-config. [home-page]: Update.
2022-01-10gnu: igraph: Update to 0.9.5.Maxim Cournoyer
* gnu/packages/graph.scm (igraph): Update to 0.9.5. [source]: Add snippet to fully unbundle. [build-system]: Use cmake-build-system. [configure-flags]: Replace all by just '-DBUILD_SHARED_LIBS=ON'. [native-inputs]: Add pkg-config. [inputs]{zlib}: Delete input. {arpack-ng, plfit, suitesparse}: New inputs.
2022-01-10gnu: Add plfit.Maxim Cournoyer
* gnu/packages/graph.scm (plfit): New variable.
2022-01-10gnu: python-pysam: Update to 0.18.0.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.18.0. [source]: Add FIXME to clarify bundled libraries in use. [phases]{check}: Streamline. [propagated-inputs]: Use latest htslib (1.14). [native-inputs]: Use latest samtools and bcftools (1.14). Remove python-nose.
2022-01-10gnu: bcftools: Update to 1.14.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.14. (bcftools-1.12): New variable. (bcftools-1.10): Use package/inherit and delete trailing #t. [name]: Delete field.
2022-01-10gnu: samtools: Update to 1.14.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (samtools): Update to 1.14. [modules]: Delete argument. [phases]{install-library, install-headers}: Delete phases. This version no longer includes the legacy library (it links to htslib directly). (samtools-1.12): New variable.
2022-01-10gnu: htslib: Update to 1.14.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (htslib): Update to 1.14. (htslib-1.12): New variable. (htslib-1.10, htslib-1.9, htslib-1.3) (htslib-for-samtools-1.2): Normalize style.
2022-01-10gnu: python-beautifulsoup4: Update to 4.10.0.Maxim Cournoyer
* gnu/packages/python-xyz.scm (python-beautifulsoup4): Update to 4.10.0. [propagated-inputs]{python-html5lib, python-lxml}: New inputs. [arguments]: Delete field. (python2-beautifulsoup4): Peg at version 4.9.3.
2022-01-10gnu: poetry: Update to 1.1.12.Maxim Cournoyer
* gnu/packages/python-xyz.scm (poetry): Update to 1.1.12. [phases]{patch-setup-py}: Relax packaging version requirement. [propagated-inputs]{python-msgpack-transitional}: Replace with... {python-msgpack}: ... this. {python-requests-toolbelt-0.9.1}: Replace with... {python-requests-toolbelt}: ... this. {python-msgpack-transitional}: Delete variable.
2022-01-10gnu: python-requests-toolbelt: Update to 0.9.1 and enable tests.Maxim Cournoyer
* gnu/packages/python-web.scm (pyhton-requests-toolbelt): Update to 0.9.1. [phases]{delete-problematic-tests}: New phase. (python-requests-toolbelt-0.9.1): Delete variable. (python2-requests-toolbelt): Likewise. (python-cloudscraper): Adjust accordingly.
2022-01-10gnu: python-cachecontrol: Update to 0.12.10.Maxim Cournoyer
* gnu/packages/python-web.scm (python-cachecontrol): Update to 0.12.10.
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