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Author SHA1 Message Date
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
Mădălin Ionel Patrașcu 9c81ab8b39
gnu: Add r-stable. 
* gnu/packages/cran.scm (r-stable): New variable.
 2022-12-12 16:18:17 +01:00
Mădălin Ionel Patrașcu 977a15d8e8
gnu: Add r-rmutil. 
* gnu/packages/cran.scm (r-rmutil): New variable.
 2022-12-12 16:17:39 +01:00
Mădălin Ionel Patrașcu 8d2222fac6
gnu: Add r-statip. 
* gnu/packages/cran.scm (r-statip): New variable.
 2022-12-12 16:17:07 +01:00
Mădălin Ionel Patrașcu 5fb5af5658
gnu: Add r-amplican. 
* gnu/packages/bioconductor.scm (r-amplican): New variable.
 2022-12-12 15:50:28 +01:00
Mădălin Ionel Patrașcu 84392cd024
gnu: Add r-waffle. 
* gnu/packages/cran.scm (r-waffle): New variable.
 2022-12-12 15:48:37 +01:00
Mădălin Ionel Patrașcu ec2388d6b4
gnu: Add r-clustercrit. 
* gnu/packages/cran.scm (r-clustercrit): New variable.
 2022-12-12 15:48:03 +01:00