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Author SHA1 Message Date
Ricardo Wurmus
e84042fdd4
gnu: cnvkit: Update to 0.9.9. 
* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.9.
[build-system]: Use pyproject-build-system.
[arguments]: Relax restriction on python-joblib.
[propagated-inputs]: Add python-pomegranate and python-scikit-learn.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus
1369b53d49
gnu: seqmagick: Update to 0.8.4. 
* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.4.
[build-system]: Use pyproject-build-system.
[inputs]: Add python-pygtrie.
[native-inputs]: Replace python-nose with python-pytest.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus
9bf2101049
gnu: python-flasgger: Update to 0.9.5. 
* gnu/packages/python-xyz.scm (python-flasgger): Update to 0.9.5.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase; add 'prepare-check phase; disable
"test_swag" test via #:test-flags.
[native-inputs]: Add python-apispec-webframeworks and python-flask-jwt.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus
8c197f990b
gnu: python-pyjwt: Update to 2.6.0. 
* gnu/packages/python-xyz.scm (python-pyjwt): Update to 2.6.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove.
[native-inputs]: Add pytohn-coverage, python-pre-commit, python-sphinx, and
python-sphinx-rtd-theme.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus
99a29b4933
gnu: python-apispec: Update to 6.0.2. 
* gnu/packages/python-xyz.scm (python-apispec): Update to 6.0.2.
[build-system]: Use pyproject-build-system.
[arguments]: Disable test through test-flags, not by replacing the 'check
phase.
[propagated-inputs]: Remove python-pyyaml; add python-packaging.
[native-inputs]: Add python-flake8, python-flake8-bugbear, python-mypy,
python-pre-commit, and python-pyyaml.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus
0fcba8b01c
gnu: python-marshmallow: Update to 3.19.0. 
* gnu/packages/python-xyz.scm (python-marshmallow): Update to 3.19.0.
[build-system]: Use pyproject-build-system.
[propagated-inputs]: Remove python-dateutil and python-simplejson; add
python-packaging.
[native-inputs]: Add python-flake8, python-flake8-bugbear, python-mypy,
python-pre-commit, and python-simplejson.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus
71dc990f22
gnu: python-flask-restful: Update to 0.3.9. 
* gnu/packages/python-web.scm (python-flask-restful): Update to 0.3.9.
[source]: Remove patch.
[build-system]: Use pyproject-build-system.
[arguments]: Disable "test_redirect" test; remove 'fix-imports phase.
[native-inputs]: Replace python-nose with python-pytest.
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/patches/python-flask-restful-werkzeug-compat.patch: Remove file.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus
461dff2651
gnu: python-cgatcore: Update to 0.6.14. 
* gnu/packages/bioinformatics.scm (python-cgatcore): Update to 0.6.14.
[build-system]: Use pyproject-build-system.
[arguments]: Disable broken tests with #:test-flags; do not replace 'check
phase; add phase 'sqlite-compatibility.
[native-inputs]: Drop input labels.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus
2f1d8fb129
gnu: python-apsw: Update to 3.40.0.0. 
* gnu/packages/databases.scm (python-apsw): Update to 3.40.0.0.
[source]: Remove obsolete patch.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-cython.
[arguments]: Move build-extensions phase before build phase.
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/patches/python-apsw-3.39.2.1-test-fix.patch: Remove file.
 2022-12-13 00:08:54 +01:00
Ricardo Wurmus
08b9e29d46
gnu: python-bokeh: Skip failing PIL test. 
The test compares base64-encoded gifs; the gifs look identical but the
base64-encoded data differs.  Since the result seems fine, disabling this PIL
test is probably okay.

* gnu/packages/python-xyz.scm (python-bokeh)[arguments]: Ignore failing
test_transform_PIL test.
 2022-12-13 00:08:13 +01:00
Ricardo Wurmus
b72df3bbb3
gnu: python-dna-features-viewer: Update to 3.1.1. 
* gnu/packages/bioinformatics.scm (python-dna-features-viewer):
Update to 3.1.1.
[build-system]: Use pyproject-build-system.
[arguments]: Add build phase to fix a compatibility problem with biopython.
[propagated-inputs]: Add python-packaging.
 2022-12-13 00:07:23 +01:00
Ricardo Wurmus
b66b6bdf70
gnu: python-hicexplorer: Update to 3.7.2. 
* gnu/packages/bioinformatics.scm (python-hicexplorer): Update to 3.7.2.
[build-system]: Use pyproject-build-system.
[arguments]: Use gexp; remove phase "loosen-up-requirements"; add test-flags
to skip some tests; add phase "remove-dependency-on-krbalancing" to remove a
dependency on an unlicensed package; add phase "fix-references"; add phase
"run-only-low-mem-tests".
[propagated-inputs]: Remove python-configparser and python-six; add
python-biopython, python-cleanlab-1, python-fit-nbinom, python-graphviz,
python-hic2cool, python-hicmatrix, python-hyperopt, python-imbalanced-learn,
python-ipykernel, python-psutil, python-pybedtools, python-pygenometracks,
python-scikit-learn, and python-tqdm.
[native-inputs]: Add graphviz.
 2022-12-13 00:07:23 +01:00
Ricardo Wurmus
c3e330cf36
gnu: python-pygenometracks: Update to 3.5. 
* gnu/packages/bioinformatics.scm (python-pygenometracks): Update to 3.5.
[build-system]: Use pyproject-build-system.
[arguments]: Quote phases instead of full list of arguments; remove trailing #T
from build phase.
 2022-12-13 00:07:22 +01:00
Ricardo Wurmus
6e9518e201
gnu: python-hicmatrix: Update to 16. 
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 16.
[build-system]: Use pyproject-build-system.
[arguments]: Shuffle the quote.
 2022-12-13 00:07:22 +01:00
Ricardo Wurmus
5167881a60
gnu: python-biopython: Update to 1.80. 
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.80.
[build-system]: Use pyproject-build-system.
[arguments]: Remove trailing #T from build phase.
 2022-12-13 00:07:22 +01:00
Ricardo Wurmus
de70f957b2
gnu: python-hyperopt: Update to 0.2.7. 
* gnu/packages/machine-learning.scm (python-hyperopt): Update to 0.2.7.
[arguments]: Adjust check phase; disable test_distribution_rvs test.
[build-system]: Use pyproject-build-system.
[propagated-inputs]: Add python-py4j.
[native-inputs]: Remove python-ipython and python-ipyparallel.
 2022-12-13 00:07:22 +01:00
Ricardo Wurmus
3d388fe3d0
gnu: python-graphviz: Update to 0.20.1. 
* gnu/packages/graphviz.scm (python-graphviz): Update to 0.20.1.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom "check" phase; add "prepare-check" phase.
[native-inputs]: Remove python-mock.
 2022-12-13 00:07:22 +01:00
Ricardo Wurmus
75331dc6e6
gnu: python-anndata: Use pyproject-build-system. 
* gnu/packages/python-xyz.scm (python-anndata)[build-system]: Use
pyproject-build-system.
[arguments]: Replace custom 'build phase with 'set-version phase; remove
custom 'install phase; disable doctest via build phase 'disable-doctests and
the #:test-flags property.
[propagated-inputs]: Add python-scikit-learn.
[native-inputs]: Add python-boltons.
 2022-12-12 23:59:39 +01:00
Ricardo Wurmus
2c65106cf5
gnu: python-zarr: Update to 2.13.3. 
* gnu/packages/python-xyz.scm (python-zarr): Update to 2.13.3.
 2022-12-12 23:59:39 +01:00
Ricardo Wurmus
8b9c9051ba
gnu: python-numcodecs: Update to 0.10.2. 
* gnu/packages/python-xyz.scm (python-numcodecs): Update to 0.10.2.
[build-system]: Use pyproject-build-system.
[arguments]: Enable tests; add phase 'build-extensions; remove custom 'check
phase.
[propagated-inputs]: Add python-entrypoints and python-typing-extensions-next.
 2022-12-12 23:59:39 +01:00
Ricardo Wurmus
c4bcb5db49
gnu: python-typer: Simplify by using pyproject-build-system. 
* gnu/packages/python-xyz.scm (python-typer)[build-system]: Use
pyproject-build-system.
[arguments]: Remove extra quoting; remove custom 'build phase; remove custom
'install phase; remove custom 'check phase; add 'pre-check phase.
[synopsis]: Pull onto the same line.
[description]: Reformat.
 2022-12-12 23:59:29 +01:00
jgart
1d160f41f5
gnu: Add erlang-yamerl. 
* gnu/packages/erlang.scm (erlang-yamerl): New variable.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2022-12-12 20:39:41 +00:00
jgart
e4fd04fb92
gnu: Add erlang-jsx. 
* gnu/packages/erlang.scm (erlang-jsx): New variable.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2022-12-12 20:34:57 +00:00
Christopher Baines
d5ad3dd59a
services: guix-build-coordinator: Fix service startup. 
Previously the service would keep starting more and more processes.

* gnu/services/guix.scm (guix-build-coordinator-shepherd-services): Fix how
make-forkexec-constructor is called.
 2022-12-12 19:58:25 +00:00
Marius Bakke
c1695bcadd
gnu: re2: Update to 2022-12-01. 
* gnu/packages/regex.scm (re2): Update to 2022-12-01.
 2022-12-12 20:23:32 +01:00
Marius Bakke
2c1b488d19
tests: Add system tests for each supported kernel version. 
* gnu/tests/base.scm (%test-basic-os): Rename to ...
(test-basic-os): ... this, and turn into procedure that takes optional KERNEL
argument.
(%test-basic-os): Use that procedure.
(%test-linux-libre-5.15, %test-linux-libre-5.10, %test-linux-libre-5.4,
%test-linux-libre-4.19, %test-linux-libre-4.14, %test-linux-libre-4.9): New
tests.
 2022-12-12 20:23:32 +01:00
Marius Bakke
9fc171b62a
gnu: f2fs-tools: Remove obsolete phase. 
* gnu/packages/linux.scm (f2fs-tools)[arguments]: Remove.
(f2fs-tools-1.7)[arguments]: Add #:phases.
 2022-12-12 20:23:31 +01:00
Marius Bakke
a2c6cc4354
gnu: f2fs-tools: Update to 1.15.0. 
* gnu/packages/linux.scm (f2fs-tools): Update to 1.15.0.
(f2fs-tools/static)[arguments]: Add #:make-flags.  Remove make-static phase.
 2022-12-12 20:23:31 +01:00
Marius Bakke
e1fc45b3ea
gnu: f2fs-tools@1.7: Don't fetch autogenerated git snapshot. 
* gnu/packages/linux.scm (f2fs-tools-1.7)[source]: Switch to GIT-FETCH.
 2022-12-12 20:23:31 +01:00
Marius Bakke
61f67290b9
gnu: f2fs-tools: Don't fetch autogenerated git snapshot. 
* gnu/packages/linux.scm (f2fs-tools)[source]: Switch to GIT-FETCH.
 2022-12-12 20:23:31 +01:00
Marius Bakke
58e33da5f5
gnu: f2fs-tools: Reverse inheritance relationship. 
* gnu/packages/linux.scm (f2fs-tools): Update to 1.14.0.
[arguments]: Remove obsolete #:configure-flags and trailing #t in phase.
[inputs]: Remove labels.
(f2fs-tools-1.7): Inherit from above; add #:configure-flags.
[inputs]: Remove labels.
 2022-12-12 20:23:31 +01:00
Marius Bakke
999783b92d
gnu: ungoogled-chromium: Build with ffmpeg@4. 
This is a follow-up to commit 79564bf997.

* gnu/packages/chromium.scm (ungoogled-chromium)[inputs]: Change from FFMPEG
to FFFMPEG-4.
 2022-12-12 20:23:31 +01:00
Mădălin Ionel Patrașcu
3640310d69
gnu: Add r-golem. 
* gnu/packages/cran.scm (r-golem): New variable.
 2022-12-12 19:01:21 +01:00
Mădălin Ionel Patrașcu
79ecb5f35f
gnu: Add r-attempt. 
* gnu/packages/cran.scm (r-attempt): New variable.
 2022-12-12 19:01:21 +01:00
Mădălin Ionel Patrașcu
75a9ee5b8e
gnu: Add r-anytime. 
* gnu/packages/cran.scm (r-anytime): New variable.
 2022-12-12 18:45:32 +01:00
Mădălin Ionel Patrașcu
61124bc7b0
gnu: Add r-shinycustomloader. 
* gnu/packages/cran.scm (r-shinycustomloader): New variable.
 2022-12-12 18:45:31 +01:00
Mădălin Ionel Patrașcu
ca7141234d
gnu: Add r-logging. 
* gnu/packages/cran.scm (r-logging): New variable.
 2022-12-12 18:45:31 +01:00
Mădălin Ionel Patrașcu
b9014985be
gnu: Add r-asics. 
* gnu/packages/bioconductor.scm (r-asics): New variable.
 2022-12-12 18:41:13 +01:00
Mădălin Ionel Patrașcu
061ce5500a
gnu: Add r-pepsnmr. 
* gnu/packages/bioconductor.scm (r-pepsnmr): New variable.
 2022-12-12 18:40:46 +01:00
Mădălin Ionel Patrașcu
1e5c9bb0d2
gnu: Add r-ptw. 
* gnu/packages/cran.scm (r-ptw): New variable.
 2022-12-12 18:40:11 +01:00
Mădălin Ionel Patrașcu
c2d25c7b5e
gnu: Add r-rcppde. 
* gnu/packages/cran.scm (r-rcppde): New variable.
 2022-12-12 18:39:26 +01:00
Mădălin Ionel Patrașcu
e0746ee4c4
gnu: Add r-animalcules. 
* gnu/packages/bioconductor.scm (r-animalcules): New variable.
 2022-12-12 17:30:05 +01:00
Mădălin Ionel Patrașcu
8f80c99e2b
gnu: Add r-plotroc. 
* gnu/packages/cran.scm (r-plotroc): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2022-12-12 17:24:07 +01:00
Mădălin Ionel Patrașcu
b6873a836c
gnu: Add r-gridsvg. 
* gnu/packages/cran.scm (r-gridsvg): New variable.
 2022-12-12 16:22:28 +01:00
Mădălin Ionel Patrașcu
5154e76a2e
gnu: Add r-gunifrac. 
* gnu/packages/cran.scm (r-gunifrac): New variable.
 2022-12-12 16:21:50 +01:00
Mădălin Ionel Patrașcu
48e6e67990
gnu: Add r-dirmult. 
* gnu/packages/cran.scm (r-dirmult): New variable.
 2022-12-12 16:20:36 +01:00
Mădălin Ionel Patrașcu
e99b3c0d25
gnu: Add r-modeest. 
* gnu/packages/cran.scm (r-modeest): New variable.
 2022-12-12 16:19:49 +01:00
Mădălin Ionel Patrașcu
7ec230fe12
gnu: Add r-fbasics. 
* gnu/packages/cran.scm (r-fbasics): New variable.
 2022-12-12 16:19:49 +01:00
Mădălin Ionel Patrașcu
3e6e0696cc
gnu: Add r-timeseries. 
* gnu/packages/cran.scm (r-timeseries): New variable.
 2022-12-12 16:19:18 +01:00
Mădălin Ionel Patrașcu
9e03e01aae
gnu: Add r-gss. 
* gnu/packages/cran.scm (r-gss): New variable.
 2022-12-12 16:18:43 +01:00