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* import: pypi: Honor the 'upstream-name' package property.Xinglu Chen2021-09-30
| | | | | | | | | | | | | | | | | | | | | | | | | | | Previously, when a PyPI package had a “-” followed by one or more digits in its name, e.g., “AV-98”, the importer would interpret “98” as the version of the package and thus mistake the “AV-98” package for the “av” package on PyPI. $ ./pre-inst-env guix refresh av-98 following redirection to `https://pypi.org/pypi/av/json'... /home/yoctocell/src/guix/gnu/packages/web-browsers.scm:914:13: av-98 would be upgraded from 1.0.1 to 8.0.3 Setting the ‘upstream-name’ property to “AV-98” would solve the problem. $ ./pre-inst-env guix refresh av-98 /home/yoctocell/src/guix/gnu/packages/web-browsers.scm:914:13: 1.0.1 is already the latest version of av-98 * guix/import/pypi.scm (guix-package->pypi-name): Honor ‘upstream-name’ property. (make-pypi-sexp): Set ‘upstream-name’ property when appropriate. * tests/pypi.scm (test-json): Rename to ... (test-json-1): ... this. (test-json-2): New variable ("guix-package->pypi-name, honor 'upstream-name'"): New test. ("pypi->guix-package, package name contains \"-\" followed by digits"): Likewise. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Remove python-py-bcrypt.Vinicius Monego2021-09-30
| | | | | | | * gnu/packages/python-crypto.scm (python-py-bcrypt, python2-py-bcrypt): Remove variables. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: python-passlib: Use python-bcrypt.Vinicius Monego2021-09-30
| | | | | | | | | | | py-bcrypt is unmaintained and support will be dropped in passlib 1.8. The recommended option is bcrypt. * gnu/packages/python-crypto.scm (python-passlib)[propagated-inputs]: Remove python-py-bcrypt. Add python-bcrypt. [arguments]<#:phases>: Don't return #t. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Remove python2-passlib.Vinicius Monego2021-09-30
| | | | | | * gnu/packages/python-crypto.scm (python2-passlib): Remove variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: grokmirror: Update to 2.0.11.Xinglu Chen2021-09-30
| | | | | | | * gnu/packages/version-control.scm (grokmirror): Update to 2.0.11. [arguments]<#:phases>: Don’t return #t. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* discovery: Hide Guile warnings when loading modules.Ludovic Courtès2021-09-30
| | | | | | Fixes <https://issues.guix.gnu.org/43747>. * guix/discovery.scm (scheme-modules): Parameterize 'current-warning-port'.
* packages: Factorize and document 'computed-origin-method'.zimoun2021-09-30
| | | | | | | | | | | | The 'computed-origin-method' had been introduced to work around limitations of the 'snippet' mechanism. The procedure was duplicated, which made it hard to automatically detect packages using it. * guix/packages.scm (computed-origin-method): Move procedure from... * gnu/packages/gnuzilla.scm: ...here and... * gnu/packages/gnuzilla.scm: ...there. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: komikku: Update to 0.34.0.Liliana Marie Prikler2021-09-30
| | | | * gnu/packages/gnome.scm (komikku): Update to 0.34.0.
* gnu: Add python-pytest-repeat.Maxim Cournoyer2021-09-30
| | | | * gnu/packages/python-check.scm (python-pytest-repeat): New variable.
* gnu: Add julia-documenter.Efraim Flashner2021-09-30
| | | | | | | | | These four variables are added in the same commit to avoid a cyclic dependency. * gnu/packages/julia-xyz.scm (julia-documenter, julia-documentermarkdown, julia-documentertools): New variables. (julia-documenter-bootstrap): New hidden variable.
* gnu: Add julia-sass.Efraim Flashner2021-09-30
| | | | * gnu/packages/julia-xyz.scm (julia-sass): New variable.
* gnu: Add julia-libsass-jll.Efraim Flashner2021-09-30
| | | | * gnu/packages/julia-jll.scm (julia-libsass-jll): New variable.
* gnu: Add julia-ansicoloredprinters.Efraim Flashner2021-09-30
| | | | * gnu/packages/julia-xyz.scm (julia-ansicoloredprinters): New variable.
* gnu: Add julia-pycall.Efraim Flashner2021-09-30
| | | | * gnu/packages/julia-xyz.scm (julia-pycall): New variable.
* gnu: Add julia-mlstyle.Efraim Flashner2021-09-30
| | | | * gnu/packages/julia-xyz.scm (julia-mlstyle): New variable.
* gnu: Add julia-measurements.Efraim Flashner2021-09-30
| | | | * gnu/packages/julia-xyz.scm (julia-measurements): New variable.
* gnu: Add julia-quadgk.Efraim Flashner2021-09-30
| | | | * gnu/packages/julia-xyz.scm (julia-quadgk): New variable.
* gnu: r-gdsfmt: Adjust bad substitution.Ricardo Wurmus2021-09-30
| | | | | * gnu/packages/bioconductor.scm (r-gdsfmt)[source]: Include beginning-of-line anchor in substitution regular expression.
* gnu: r-delayedmatrixstats: Update to 1.14.3.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.14.3.
* gnu: r-s4vectors: Update to 0.30.1.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.30.1.
* gnu: r-biocpkgtools: Update to 1.10.2.Ricardo Wurmus2021-09-30
| | | | | * gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.10.2. [propagated-inputs]: Remove r-rex.
* gnu: r-timeseriesexperiment: Update to 1.10.1.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/bioconductor.scm (r-timeseriesexperiment): Update to 1.10.1.
* gnu: r-gdsfmt: Update to 1.28.1.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/bioconductor.scm (r-gdsfmt): Update to 1.28.1.
* gnu: r-cicero: Update to 1.10.1.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/bioconductor.scm (r-cicero): Update to 1.10.1.
* gnu: r-zinbwave: Update to 1.14.2.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/bioconductor.scm (r-zinbwave): Update to 1.14.2.
* gnu: r-clusterprofiler: Update to 4.0.5.Ricardo Wurmus2021-09-30
| | | | | * gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.0.5. [propagated-inputs]: Remove r-rvcheck; add r-yulab-utils.
* gnu: r-ggtree: Update to 3.0.4.Ricardo Wurmus2021-09-30
| | | | | * gnu/packages/bioconductor.scm (r-ggtree): Update to 3.0.4. [propagated-inputs]: Remove r-rvcheck; add r-ggfun and r-yulab-utils.
* gnu: r-matrixgenerics: Update to 1.4.3.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/bioconductor.scm (r-matrixgenerics): Update to 1.4.3.
* gnu: r-chippeakanno: Update to 3.26.4.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.26.4.
* gnu: r-diffbind: Update to 3.2.7.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/bioconductor.scm (r-diffbind): Update to 3.2.7.
* gnu: r-genomicfeatures: Update to 1.44.2.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.44.2.
* gnu: r-genomeinfodb: Update to 1.28.4.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.28.4.
* gnu: r-edger: Update to 3.34.1.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/bioconductor.scm (r-edger): Update to 3.34.1.
* gnu: r-biocparallel: Update to 1.26.2.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.26.2.
* gnu: r-affxparser: Update to 1.64.1.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/bioconductor.scm (r-affxparser): Update to 1.64.1.
* gnu: r-r-filesets: Fix build by setting HOME.Ricardo Wurmus2021-09-30
| | | | | * gnu/packages/cran.scm (r-r-filesets)[arguments]: Add build phase to set HOME variable.
* gnu: r-glinternet: Update to 1.0.12.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/statistics.scm (r-glinternet): Update to 1.0.12.
* gnu: r-pbapply: Update to 1.5-0.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/statistics.scm (r-pbapply): Update to 1.5-0.
* gnu: r-rrcov: Update to 1.6-0.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/statistics.scm (r-rrcov): Update to 1.6-0.
* gnu: r-fastica: Update to 1.2-3.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/statistics.scm (r-fastica): Update to 1.2-3.
* gnu: r-sfsmisc: Update to 1.1-12.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/statistics.scm (r-sfsmisc): Update to 1.1-12.
* gnu: r-matrixstats: Update to 0.61.0.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/statistics.scm (r-matrixstats): Update to 0.61.0.
* gnu: r-r-utils: Update to 2.11.0.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/statistics.scm (r-r-utils): Update to 2.11.0.
* gnu: r-e1071: Update to 1.7-9.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/statistics.scm (r-e1071): Update to 1.7-9.
* gnu: r-rngtools: Update to 1.5.2.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/statistics.scm (r-rngtools): Update to 1.5.2.
* gnu: r-xml: Update to 3.99-0.8.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/statistics.scm (r-xml): Update to 3.99-0.8.
* gnu: r-rmarkdown: Update to 2.11.Ricardo Wurmus2021-09-30
| | | | | * gnu/packages/statistics.scm (r-rmarkdown): Update to 2.11. [propagated-inputs]: Add r-jquerylib.
* gnu: r-plotrix: Update to 3.8-2.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/statistics.scm (r-plotrix): Update to 3.8-2.
* gnu: r-hms: Update to 1.1.1.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/statistics.scm (r-hms): Update to 1.1.1.
* gnu: r-openssl: Update to 1.4.5.Ricardo Wurmus2021-09-30
| | | | * gnu/packages/statistics.scm (r-openssl): Update to 1.4.5.
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