ryan77627/guix
1
0
Fork 0
mirror of https://git.in.rschanz.org/ryan77627/guix.git synced 2024-11-19 05:07:11 -05:00
Code Issues Projects Releases Packages Wiki Activity Actions
89723 commits 1 branch 0 tags 448 MiB
Commit graph

89723 commits

This branch
This branch
All branches
Author SHA1 Message Date
Ricardo Wurmus
6e67cda755
gnu: python-schema-salad: Update to 8.2.20211116214159. 
* 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.
 2021-12-07 15:28:13 +01:00
Ricardo Wurmus
16474f85cf
gnu: taxtastic: Update to 0.9.2. 
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.9.2.
[arguments]: Delete 'sanity-check and 'python37-compatibility phases;  adjust
'prepare-directory phase.
 2021-12-07 15:13:06 +01:00
Ricardo Wurmus
00ba04020e
gnu: taxtastic: Run tests conditionally. 
* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Respect TESTS?
option.
 2021-12-07 15:12:15 +01:00
Ricardo Wurmus
58fecfd18e
gnu: python-dendropy: Update to 4.5.1. 
* gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.5.1.
[arguments]: Skip failing tests.
 2021-12-07 14:53:37 +01:00
Sarah Morgensen
68d15fcf20
gnu: make-gccgo: Override empty GOROOT/GCCGOTOOLDIR 
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>
 2021-12-07 15:25:54 +02:00
Ricardo Wurmus
2da567d137
gnu: python-cooler: Use python-cytoolz-for-cooler. 
* gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace
python-cytoolz with python-cytoolz-for-cooler.
 2021-12-07 13:24:58 +01:00
Ricardo Wurmus
92a2f55cf9
gnu: Add python-cytoolz-for-cooler. 
* gnu/packages/python-xyz.scm (python-cytoolz-for-cooler): New variable.
 2021-12-07 13:24:49 +01:00
Ricardo Wurmus
c08d6e63a0
gnu: python-sparse: Update to 0.13.0. 
* gnu/packages/python-xyz.scm (python-sparse): Update to 0.13.0.
 2021-12-07 13:16:47 +01:00
jgart
51bf893e53
gnu: Add diffr. 
* gnu/packages/rust-apps.scm (diffr): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-07 14:15:28 +02:00
Ricardo Wurmus
224d1c5818
gnu: python-dask: Update to 2021.11.2. 
* gnu/packages/python-xyz.scm (python-dask): Update to 2021.11.2.
[source]: Fetch from github.
[arguments]: Remove phase 'disable-broken-tests.
 2021-12-07 13:07:46 +01:00
Ricardo Wurmus
ed15986a32
gnu: python-dask: Run tests conditionally. 
* gnu/packages/python-xyz.scm (python-dask)[arguments]: Respect TESTS? option.
 2021-12-07 13:07:23 +01:00
Ricardo Wurmus
ad17046040
gnu: python-dask: Add missing input for tests. 
* gnu/packages/python-xyz.scm (python-dask)[native-inputs]: Add
python-pytest-rerunfailures.
 2021-12-07 13:06:37 +01:00
jgart
f36f58a564
gnu: Add rust-diffr-lib-0.1. 
* gnu/packages/crates-io.scm (rust-diffr-lib-0.1): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-07 14:05:54 +02:00
Ricardo Wurmus
899121f4d6
gnu: phylip: Update to 3.697. 
* gnu/packages/bioinformatics.scm (phylip): Update to 3.697.
 2021-12-07 13:05:53 +01:00
Ricardo Wurmus
e86fe9801e
gnu: phylip: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (phylip)[arguments]: Set CFLAGS.
 2021-12-07 13:05:35 +01:00
Ricardo Wurmus
125fdc3ba4
gnu: phylip: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (phylip)[arguments]: Remove trailing #T from
build phases.
 2021-12-07 13:05:15 +01:00
jgart
72dbf04b55
gnu: Add dutree. 
* gnu/packages/rust-apps.scm (dutree): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-12-07 14:01:42 +02:00
Ricardo Wurmus
4561ca7f4e
gnu: subread: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (subread)[arguments]: Remove trailing #T
from build phases.
 2021-12-07 12:59:51 +01:00
Ricardo Wurmus
96b2be833d
gnu: subread: Update to 2.0.3. 
* gnu/packages/bioinformatics.scm (subread): Update to 2.0.3.
 2021-12-07 12:59:36 +01:00
Ricardo Wurmus
9a03587b62
gnu: subread: Update home page.. 
* gnu/packages/bioinformatics.scm (subread)[home-page]: Use new home page.
 2021-12-07 12:55:08 +01:00
Ricardo Wurmus
aa25c9b1a4
gnu: subread: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (subread)[arguments]: Add -fcommon to flags.
 2021-12-07 12:54:48 +01:00
Ricardo Wurmus
417299f004
gnu: python-pytest-console-scripts: Update to 1.2.1. 
* gnu/packages/python-check.scm (python-pytest-console-scripts): Update to
1.2.1.
 2021-12-07 12:41:14 +01:00
Ricardo Wurmus
6874994fa9
gnu: Add python-pytest-rerunfailures. 
* gnu/packages/python-check.scm (python-pytest-rerunfailures): New variable.
 2021-12-07 12:35:00 +01:00
Ricardo Wurmus
c25a6d39f3
gnu: mcl: Add -fcommon to compiler flags. 
* gnu/packages/machine-learning.scm (mcl)[arguments]: Set CFLAGS.
 2021-12-07 12:34:34 +01:00
Ricardo Wurmus
b214034109
gnu: python-cytoolz: Update to 0.11.2. 
* gnu/packages/python-xyz.scm (python-cytoolz): Update to 0.11.2.
[source]: Add snippet.
 2021-12-07 12:34:22 +01:00
Ricardo Wurmus
06fca01968
gnu: hisat: Update to 0.1.6. 
* gnu/packages/bioinformatics.scm (hisat): Update to 0.1.6.
 2021-12-07 11:51:10 +01:00
Ricardo Wurmus
2f7287b3a7
gnu: hisat: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove trailing #T from
build phase.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
9dc727f827
gnu: hisat: Remove invalid characters. 
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove curly quotes.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
478e3e714a
gnu: crossmap: Update to 0.6.1. 
* gnu/packages/bioinformatics.scm (crossmap): Update to 0.6.1.
[source]: Add snippet to remove generated files.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
b5c9afb7c5
gnu: Remove python2-bx-python. 
* gnu/packages/bioinformatics.scm (python2-bx-python): Delete variable.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
699b443c86
gnu: python-bx-python: Update to 0.8.12. 
* 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.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
4b4ab4ce4d
gnu: Remove pbtranscript-tofu. 
Upstream has disappeared and it depends on Python 2, which is no longer
supported.

* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Remove variable.
 2021-12-07 11:51:09 +01:00
Ricardo Wurmus
b452d7c2cf
gnu: python-pyfit-sne: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (python-pyfit-sne): Update to 1.2.1.
[arguments]: Disable tests explicitly.
 2021-12-07 11:51:09 +01:00
Julien Lepiller
05deb26be9
gnu: guile-netlink: Update to 1.1.1. 
* gnu/packages/guile.scm (guile-netlink): Update to 1.1.1.
 2021-12-07 00:09:35 +01:00
Nicolas Goaziou
e21b422f7f
gnu: emacs-csv-mode: Update to 1.17. 
* gnu/packages/emacs-xyz.scm (emacs-csv-mode): Update to 1.17.
 2021-12-06 22:01:31 +01:00
Pierre Langlois
4afacd4546
gnu: helm: Fix build with GCC 9 and later. 
* 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.
 2021-12-06 20:41:18 +00:00
Marius Bakke
757a2eb970
tests: patchwork: Use the default PostgreSQL. 
* gnu/tests/web.scm (patchwork-os)[services]: Change from POSTGRESQL-10 to
POSTGRESQL.
 2021-12-06 21:17:31 +01:00
Marius Bakke
8662057130
gnu: patchwork: Adjust for python-build-system change. 
This is a follow-up to commit db5646d957, et.al.

* gnu/packages/patchutils.scm (patchwork)[arguments]: Adapt one more
site-packages call.
 2021-12-06 21:15:42 +01:00
Ricardo Wurmus
ca2f851da1
gnu: f-seq: Update name of commons-cli JAR. 
* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Use new name of
commons-cli JAR.
 2021-12-06 18:48:01 +01:00
Ricardo Wurmus
f0763fba5c
gnu: f-seq: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Remove trailing #T from
build phase.
 2021-12-06 18:48:01 +01:00
Ricardo Wurmus
1310879fb0
gnu: f-seq: Simplify snippet. 
* gnu/packages/bioinformatics.scm (f-seq)[source]: Simplify snippet.
 2021-12-06 18:48:01 +01:00
Leo Famulari
404f695385
gnu: Go 1.17: Update to 1.17.4. 
* gnu/packages/golang.scm (go-1.17): Update to 1.17.4.
 2021-12-06 12:40:38 -05:00
Leo Famulari
e4d8f2fe31
gnu: Go 1.16: Update to 1.16.11. 
* gnu/packages/golang.scm (go-1.16): Update to 1.16.11.
 2021-12-06 12:40:38 -05:00
Leo Famulari
4e282bc934
gnu: Syncthing: Update to 1.18.4. 
* gnu/packages/syncthing.scm (syncthing): Update to 1.18.4.
[arguments]: Build with Go 1.17.
 2021-12-06 12:10:12 -05:00
Mathieu Othacehe
3b6a7693fa
gnu: osinfo-db-next: Fix uri. 
* gnu/packages/virtualization.scm (osinfo-db-next)[source]: Fix URI.
 2021-12-06 17:28:22 +01:00
Efraim Flashner
30c776a6a8
gnu: go-gopkg-in-yaml-v2: Update to 2.4.0. 
* gnu/packages/golang.scm (go-gopkg-in-yaml-v2): Update to 2.4.0.
 2021-12-06 14:45:50 +02:00
Efraim Flashner
c569430b6c
gnu: go-gopkg-in-yaml-v2: Fix test suite on 32-bit systems. 
* 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.
 2021-12-06 14:43:17 +02:00
Efraim Flashner
b6a726222a
gnu: go-github-com-golang-snappy: Adjust test-suite on 32-bit systems. 
* 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.
 2021-12-06 14:04:30 +02:00
Ludovic Courtès
f4d4c40500
gnu: python-kivy: Add missing dependencies. 
* 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.
 2021-12-06 11:49:06 +01:00
Ludovic Courtès
7e40d0ee90
gnu: Add python-kivy-garden. 
* gnu/packages/python-xyz.scm (python-kivy-garden): New variable.
 2021-12-06 11:48:47 +01:00