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Author SHA1 Message Date
Nicolas Goaziou df9d72ddb0
gnu: emacs-org-contrib: Update to 0.2. 
* gnu/packages/emacs-xyz.scm (emacs-org-contrib): Update to 0.2.
 2021-10-01 10:14:52 +02:00
Nicolas Goaziou 88c37b6ac7
gnu: emacs-tramp: Update to 2.5.1.3. 
* gnu/packages/emacs-xyz.scm (emacs-tramp): Update to 2.5.1.3.
 2021-10-01 09:52:30 +02:00
Xinglu Chen 88d26e13fe
gnu: av-98: Set 'upstream-name' property. 
* gnu/packages/web-browsers.scm (av-98)[properties]: Set ‘upstream-name’.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-09-30 23:44:49 +02:00
Xinglu Chen 7b75f90c5b
import: pypi: Honor the 'upstream-name' package property. 
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>
 2021-09-30 23:44:49 +02:00
Vinicius Monego e29c3e1856
gnu: Remove python-py-bcrypt. 
* gnu/packages/python-crypto.scm (python-py-bcrypt, python2-py-bcrypt): Remove
variables.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-09-30 23:44:49 +02:00
Vinicius Monego 6d6b3a0c3c
gnu: python-passlib: Use python-bcrypt. 
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>
 2021-09-30 23:44:49 +02:00
Vinicius Monego fee1a41f95
gnu: Remove python2-passlib. 
* gnu/packages/python-crypto.scm (python2-passlib): Remove variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2021-09-30 23:44:49 +02:00
Xinglu Chen 885c46a7e5
gnu: grokmirror: Update to 2.0.11. 
* 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>
 2021-09-30 23:44:49 +02:00
Ludovic Courtès bedcba8f5c
discovery: Hide Guile warnings when loading modules. 
Fixes <https://issues.guix.gnu.org/43747>.

* guix/discovery.scm (scheme-modules): Parameterize 'current-warning-port'.
 2021-09-30 23:44:49 +02:00
zimoun 270b30705d
packages: Factorize and document 'computed-origin-method'. 
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>
 2021-09-30 23:44:48 +02:00
Liliana Marie Prikler 56b10709ef
gnu: komikku: Update to 0.34.0. 
* gnu/packages/gnome.scm (komikku): Update to 0.34.0.
 2021-09-30 21:46:10 +02:00
Maxim Cournoyer e2c58b9150
gnu: Add python-pytest-repeat. 
* gnu/packages/python-check.scm (python-pytest-repeat): New variable.
 2021-09-30 10:27:55 -04:00
Efraim Flashner 7b59508ca7
gnu: Add julia-documenter. 
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.
 2021-09-30 14:25:48 +03:00
Efraim Flashner 647edfd0d3
gnu: Add julia-sass. 
* gnu/packages/julia-xyz.scm (julia-sass): New variable.
 2021-09-30 14:20:15 +03:00
Efraim Flashner ac1166fbdb
gnu: Add julia-libsass-jll. 
* gnu/packages/julia-jll.scm (julia-libsass-jll): New variable.
 2021-09-30 14:20:15 +03:00
Efraim Flashner 60d3484f7c
gnu: Add julia-ansicoloredprinters. 
* gnu/packages/julia-xyz.scm (julia-ansicoloredprinters): New variable.
 2021-09-30 14:20:14 +03:00
Efraim Flashner 3893f13669
gnu: Add julia-pycall. 
* gnu/packages/julia-xyz.scm (julia-pycall): New variable.
 2021-09-30 14:20:14 +03:00
Efraim Flashner 25bb6f0822
gnu: Add julia-mlstyle. 
* gnu/packages/julia-xyz.scm (julia-mlstyle): New variable.
 2021-09-30 14:20:14 +03:00
Efraim Flashner 55e1fa89f1
gnu: Add julia-measurements. 
* gnu/packages/julia-xyz.scm (julia-measurements): New variable.
 2021-09-30 14:20:14 +03:00
Efraim Flashner 8733d2c235
gnu: Add julia-quadgk. 
* gnu/packages/julia-xyz.scm (julia-quadgk): New variable.
 2021-09-30 14:20:14 +03:00
Ricardo Wurmus b28cd884b8
gnu: r-gdsfmt: Adjust bad substitution. 
* gnu/packages/bioconductor.scm (r-gdsfmt)[source]: Include beginning-of-line
anchor in substitution regular expression.
 2021-09-30 12:39:49 +02:00
Ricardo Wurmus 0398a89fa1
gnu: r-delayedmatrixstats: Update to 1.14.3. 
* gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.14.3.
 2021-09-30 12:39:49 +02:00
Ricardo Wurmus 425c53b568
gnu: r-s4vectors: Update to 0.30.1. 
* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.30.1.
 2021-09-30 12:39:49 +02:00
Ricardo Wurmus c935b25a9e
gnu: r-biocpkgtools: Update to 1.10.2. 
* gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.10.2.
[propagated-inputs]: Remove r-rex.
 2021-09-30 12:39:49 +02:00
Ricardo Wurmus 3683f7f0a8
gnu: r-timeseriesexperiment: Update to 1.10.1. 
* gnu/packages/bioconductor.scm (r-timeseriesexperiment): Update to 1.10.1.
 2021-09-30 12:39:48 +02:00
Ricardo Wurmus 74e2186731
gnu: r-gdsfmt: Update to 1.28.1. 
* gnu/packages/bioconductor.scm (r-gdsfmt): Update to 1.28.1.
 2021-09-30 12:39:48 +02:00
Ricardo Wurmus 494b7c4eca
gnu: r-cicero: Update to 1.10.1. 
* gnu/packages/bioconductor.scm (r-cicero): Update to 1.10.1.
 2021-09-30 12:39:48 +02:00
Ricardo Wurmus 3278daa726
gnu: r-zinbwave: Update to 1.14.2. 
* gnu/packages/bioconductor.scm (r-zinbwave): Update to 1.14.2.
 2021-09-30 12:39:48 +02:00
Ricardo Wurmus a88e7abf2f
gnu: r-clusterprofiler: Update to 4.0.5. 
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.0.5.
[propagated-inputs]: Remove r-rvcheck; add r-yulab-utils.
 2021-09-30 12:39:48 +02:00
Ricardo Wurmus 1359fc7fbd
gnu: r-ggtree: Update to 3.0.4. 
* gnu/packages/bioconductor.scm (r-ggtree): Update to 3.0.4.
[propagated-inputs]: Remove r-rvcheck; add r-ggfun and r-yulab-utils.
 2021-09-30 12:39:48 +02:00
Ricardo Wurmus 538618552b
gnu: r-matrixgenerics: Update to 1.4.3. 
* gnu/packages/bioconductor.scm (r-matrixgenerics): Update to 1.4.3.
 2021-09-30 12:39:48 +02:00
Ricardo Wurmus ce23a074f0
gnu: r-chippeakanno: Update to 3.26.4. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.26.4.
 2021-09-30 12:39:48 +02:00
Ricardo Wurmus 4fb187b79e
gnu: r-diffbind: Update to 3.2.7. 
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.2.7.
 2021-09-30 12:39:47 +02:00
Ricardo Wurmus 43ac163bdf
gnu: r-genomicfeatures: Update to 1.44.2. 
* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.44.2.
 2021-09-30 12:39:47 +02:00
Ricardo Wurmus 7c6046a6db
gnu: r-genomeinfodb: Update to 1.28.4. 
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.28.4.
 2021-09-30 12:39:47 +02:00
Ricardo Wurmus 0ac7b8b6ad
gnu: r-edger: Update to 3.34.1. 
* gnu/packages/bioconductor.scm (r-edger): Update to 3.34.1.
 2021-09-30 12:39:47 +02:00
Ricardo Wurmus 77a5fdd51c
gnu: r-biocparallel: Update to 1.26.2. 
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.26.2.
 2021-09-30 12:39:47 +02:00
Ricardo Wurmus e8aab58d0c
gnu: r-affxparser: Update to 1.64.1. 
* gnu/packages/bioconductor.scm (r-affxparser): Update to 1.64.1.
 2021-09-30 12:39:47 +02:00
Ricardo Wurmus 74717852d4
gnu: r-r-filesets: Fix build by setting HOME. 
* gnu/packages/cran.scm (r-r-filesets)[arguments]: Add build phase to set HOME
variable.
 2021-09-30 12:39:47 +02:00
Ricardo Wurmus 655a23fa8b
gnu: r-glinternet: Update to 1.0.12. 
* gnu/packages/statistics.scm (r-glinternet): Update to 1.0.12.
 2021-09-30 12:39:47 +02:00
Ricardo Wurmus 1322fe25a6
gnu: r-pbapply: Update to 1.5-0. 
* gnu/packages/statistics.scm (r-pbapply): Update to 1.5-0.
 2021-09-30 12:39:46 +02:00
Ricardo Wurmus 8170baded5
gnu: r-rrcov: Update to 1.6-0. 
* gnu/packages/statistics.scm (r-rrcov): Update to 1.6-0.
 2021-09-30 12:39:46 +02:00
Ricardo Wurmus 849d0f0f63
gnu: r-fastica: Update to 1.2-3. 
* gnu/packages/statistics.scm (r-fastica): Update to 1.2-3.
 2021-09-30 12:39:46 +02:00
Ricardo Wurmus f5cfcd0110
gnu: r-sfsmisc: Update to 1.1-12. 
* gnu/packages/statistics.scm (r-sfsmisc): Update to 1.1-12.
 2021-09-30 12:39:46 +02:00
Ricardo Wurmus 745e373982
gnu: r-matrixstats: Update to 0.61.0. 
* gnu/packages/statistics.scm (r-matrixstats): Update to 0.61.0.
 2021-09-30 12:39:46 +02:00
Ricardo Wurmus a94068188c
gnu: r-r-utils: Update to 2.11.0. 
* gnu/packages/statistics.scm (r-r-utils): Update to 2.11.0.
 2021-09-30 12:39:46 +02:00
Ricardo Wurmus 295b984fbc
gnu: r-e1071: Update to 1.7-9. 
* gnu/packages/statistics.scm (r-e1071): Update to 1.7-9.
 2021-09-30 12:39:46 +02:00
Ricardo Wurmus 031c6f65a2
gnu: r-rngtools: Update to 1.5.2. 
* gnu/packages/statistics.scm (r-rngtools): Update to 1.5.2.
 2021-09-30 12:39:46 +02:00
Ricardo Wurmus 0ac0dfdf7b
gnu: r-xml: Update to 3.99-0.8. 
* gnu/packages/statistics.scm (r-xml): Update to 3.99-0.8.
 2021-09-30 12:39:46 +02:00
Ricardo Wurmus d866a9c829
gnu: r-rmarkdown: Update to 2.11. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 2.11.
[propagated-inputs]: Add r-jquerylib.
 2021-09-30 12:39:45 +02:00