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Author SHA1 Message Date
Efraim Flashner dac8d013bd
gnu: python-aiohttp: Remove cythonized files. 
* gnu/packages/python-web.scm (python-aiohttp)[source]: Add snippet to
remove generated cythonized files.
[arguments]: Add phase to generate cythonized files.
[native-inputs]: Add python-cython.
 2021-10-27 23:01:32 +03:00
Efraim Flashner fb995ff510
gnu: python-uvicorn: Update to 0.13.2. 
* gnu/packages/python-web.scm (python-uvicorn): Update to 0.13.2.
[propagated-inputs]: Remove python-wsproto.
[native-inputs]: Remove python-black, python-codecov, python-flake8, python-isort,
python-mypy, and python-pytest-cov; add python-trustme and
python-wsproto.
 2021-10-27 19:48:15 +03:00
Efraim Flashner 013c061ce5
gnu: python-asgiref: Honor #:tests? flag. 
* gnu/packages/python-web.scm (python-asgiref)[arguments]: Adjust custom
'check phase to honor the #:tests? flag.
 2021-10-27 19:40:36 +03:00
Efraim Flashner ee41859cc8
gnu: python-asgiref: Update to 3.4.1. 
* gnu/packages/python-web.scm (python-asgiref): Update to 3.4.1.
 2021-10-27 19:39:20 +03:00
Efraim Flashner 204bac09f9
gnu: python-watchgod: Update to 0.7. 
* gnu/packages/python-xyz.scm (python-watchgod): Update to 0.7.
[native-inputs]: Remove python-docutils, python-flake8, python-isort,
python-pycodestyle, python-pyflakes, and python-pytest-aiohttp; add
python-pytest-asyncio.
 2021-10-27 19:23:09 +03:00
Efraim Flashner ce6b5eb701
gnu: python-aiohttp: Sort inputs alphabetically. 
* gnu/packages/python-web.scm (python-aiohttp)[native-inputs]: Sort
inputs alphabetically.
 2021-10-27 16:00:22 +03:00
Efraim Flashner afbd988dde
gnu: python-aiohttp: Fix test suite. 
* gnu/packages/python-web.scm (python-aiohttp)[arguments]: Adjust custom
'check phase to not load uninstalled code.
[native-inputs]: Replace python-pytest with python-pytest-6.1.
 2021-10-27 15:58:32 +03:00
Efraim Flashner 138c122fef
gnu: Add python-pytest-6.1. 
* gnu/packages/check.scm (python-pytest-6.1): New variable.
 2021-10-27 13:09:57 +03:00
Efraim Flashner 7a0077d7f3
gnu: python-pytest-mock: Adjust package inputs. 
* gnu/packages/check.scm (python-pytest-mock)[propagated-inputs]: Move
python-pytest-asyncio ...
[native-inputs]: ... to here.
(python2-pytest-mock): Adjust to ensure package remains unchanged.
 2021-10-27 13:09:26 +03:00
Efraim Flashner d76e0a36f9
gnu: python-pytest-toolbox: Honor #:tests? flag. 
* gnu/packages/python-check.scm (python-pytest-toolbox)[arguments]:
Adjust custom 'check phase to honor the #:tests? flag.
 2021-10-27 11:01:41 +03:00
Efraim Flashner c2179c27fe
gnu: python-pytest-toolbox: Fix test suite. 
* gnu/packages/python-check.scm (python-pytest-toolbox)[arguments]:
Adjust custom 'check phase to remove obsolete pytest flag.
[native-inputs]: Remove python-coverage, python-docutils, python-flake8,
python-isort, python-pyflakes, python-pygments, python-pytest-cov,
python-pytest-mock, python-pytest-sugar.
 2021-10-27 10:59:33 +03:00
Efraim Flashner a41f93c39d
gnu: python-joblib: Run test suite sequentially. 
* gnu/packages/python-xyz.scm (python-joblib)[arguments]: Adjust custom
'check phase to run the test suite sequentially.
 2021-10-26 09:01:27 +03:00
Efraim Flashner 1aad42e24c
gnu: python-joblib: Honor #:tests? flag. 
* gnu/packages/python-xyz.scm (python-joblib)[arguments]: Adjust custom
'check phase to honor the #:tests? flag.
 2021-10-26 09:00:45 +03:00
Efraim Flashner ffcc5395b7
gnu: mariadb: Only enable parallel tests on x86_64-linux. 
* gnu/packages/databases.scm (mariadb)[arguments]: Only enable parallel
tests when building on x86_64-linux.
 2021-10-26 08:37:17 +03:00
Guillaume Le Vaillant cab17c1c37
gnu: zimg: Update to 3.0.3. 
* gnu/packages/image.scm (zimg): Update to 3.0.3.
 2021-10-25 13:58:57 +02:00
Thiago Jung Bauermann 8e30922767
gnu: mariadb: Don’t run tests in parallel on ppc64le targets. 
* gnu/packages/databases.scm (mariadb)[arguments]: Set ‘#:parallel-tests?’
for powerpc64le machines.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-10-25 14:11:11 +03:00
Efraim Flashner 4e4516599a
gnu: python-pandas: Update to 1.3.4. 
* gnu/packages/python-science.scm (python-pandas): Update to 1.3.4.
 2021-10-25 14:01:32 +03:00
Efraim Flashner c8c35af8ac
gnu: python-pandas: Fix building with pytest-6. 
* gnu/packages/python-science.scm (python-pandas)[arguments]: In custom
'check phase adjust to not fail tests with missing test data.
 2021-10-25 14:01:32 +03:00
Efraim Flashner a0400dc9a5
gnu: python-pandas: Honor #:tests? flag. 
* gnu/packages/python-science.scm (python-pandas)[arguments]: Adjust
custom 'check phase to honor the #:tests? flag.
 2021-10-25 14:01:32 +03:00
Efraim Flashner ab961fe542
gnu: python-cython: Honor #:tests? flag. 
* gnu/packages/python-xyz.scm (python-cython)[arguments]: Adjust custom
'check phase to honor the #:tests? flag.
 2021-10-25 14:01:32 +03:00
Efraim Flashner 2de88bcd7a
gnu: python-cython: Update to 0.29.24. 
* gnu/packages/python-xyz.scm (python-cython): Update to 0.29.24.
[arguments]: Adjust custom 'check phase to skip one test. Remove
trailing #t from phases.
 2021-10-25 14:01:32 +03:00
Guillaume Le Vaillant 988eb73d5b
gnu: gnuradio: Disable a randomly failing test. 
* gnu/packages/radio.scm (gnuradio)[arguments]: Add qa_rotator_cc to the list
  of disabled tests.
 2021-10-25 11:45:53 +02:00
Guillaume Le Vaillant 78a7c7f078
gnu: python-pyqtgraph: Disable one failing test. 
* gnu/packages/python-xyz.scm (python-pyqtgraph)[arguments]: Add test_reload
  to list of disabled tests.
 2021-10-25 11:31:56 +02:00
Guillaume Le Vaillant f3496c2b5c
gnu: hexchat: Fix build. 
* gnu/packages/messaging.scm (hexchat)[arguments]: Use GUIX_PYTHONPATH instead
  of PYTHONPATH in 'wrap-program' phase.
 2021-10-25 11:13:04 +02:00
Ricardo Wurmus 2640da8410
gnu: java-cisd-args4j: Copy instead of unpacking input. 
* gnu/packages/java.scm (java-cisd-args4j)[arguments]: Do not unpack
build-resources input; just copy the contents.
 2021-10-24 23:26:59 +00:00
Ricardo Wurmus 41e5c12c4a
gnu: sailfish: Use TBB 2020. 
* gnu/packages/bioinformatics.scm (sailfish)[inputs]: Replace tbb with
tbb-2020.
 2021-10-24 21:38:25 +00:00
Ricardo Wurmus 1bf55a4850
gnu: sailfish: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Remove trailing #T in
build phases...
[inputs]: ...and in the origin snippet of "rapmap".
 2021-10-24 21:37:39 +00:00
Ricardo Wurmus 4392783232
gnu: sailfish: Do not attempt to unpack a directory. 
patch-and-repack no longer outputs a compressed archive when the input was a
directory.

* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Adjust build phase
'prepare-rapmap.
 2021-10-24 21:35:57 +00:00
Ricardo Wurmus 57c233b37b
gnu: jellyfish: Remove Ruby bindings. 
These bindings no longer build and we have no package that would need them.

* gnu/packages/bioinformatics.scm (jellyfish)[outputs]: Remove "ruby" output.
[arguments]: Remove option for building Ruby bindings.
[native-inputs]: Remove ruby.
 2021-10-24 21:34:26 +00:00
Ricardo Wurmus da526f33f2
gnu: cutadapt: Regenerate Cython files. 
* gnu/packages/bioinformatics.scm (cutadapt)[arguments]: Add phase
'always-cythonize.
 2021-10-24 21:23:20 +00:00
Ricardo Wurmus 3eeae68af1
gnu: python-requests-unixsocket: Fix tests. 
* gnu/packages/python-web.scm (python-requests-unixsocket)[arguments]: Do not
run tests with --pep8 option; only run tests when enabled.
 2021-10-24 20:49:46 +00:00
Ricardo Wurmus b67013c8ca
gnu: python-mpmath: Update to 1.2.1. 
* gnu/packages/python-xyz.scm (python-mpmath): Update to 1.2.1.
[source]: Fetch from git.
[arguments]: Run tests directly with pytest; set the version with setuptools.
[native-inputs]: Add python-setuptools-scm.
 2021-10-24 20:10:26 +00:00
Ricardo Wurmus 722c4685f0
gnu: java-commons-io: Replace %build-inputs with gexp. 
* gnu/packages/java.scm (java-commons-io)[arguments]: Do not use
%build-inputs; use gexp with this-package-native-inputs instead.
 2021-10-24 20:02:54 +00:00
Ricardo Wurmus 4faca03bed
gnu: python-dnaio: Update to 0.6.0. 
* gnu/packages/bioinformatics.scm (python-dnaio): Update to 0.6.0.
 2021-10-24 19:47:20 +00:00
Ricardo Wurmus 88919aa8a2
gnu: python-xopen: Update to 0.8.2. 
* gnu/packages/python-xyz.scm (python-xopen): Update to 0.8.2.
 2021-10-24 19:47:02 +00:00
Ricardo Wurmus 238f47c76f
gnu: macs: Fix build by setting HOME. 
* gnu/packages/bioinformatics.scm (macs)[arguments]: Add build phase to set
HOME variable.
 2021-10-24 19:09:35 +00:00
Ricardo Wurmus 1d01043a4f
gnu: methyldackel: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Remove trailing #T
from build phase.
 2021-10-24 19:01:22 +00:00
Ricardo Wurmus 2820b03509
gnu: methyldackel: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Add -fcommon to
CFLAGS.
 2021-10-24 19:00:53 +00:00
Ricardo Wurmus cc331ad7eb
gnu: flexbar: Use TBB 2020. 
* gnu/packages/bioinformatics.scm (flexbar)[inputs]: Replace tbb with
tbb-2020.
 2021-10-24 18:50:09 +00:00
Ricardo Wurmus 084bdf9d69
gnu: flexbar: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (flexbar)[arguments]: Remove trailing #T
from all build phases.
 2021-10-24 18:49:43 +00:00
Ricardo Wurmus d0a1d798ee
gnu: bwa: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Remove trailing #T in
build phase.
 2021-10-24 18:48:53 +00:00
Ricardo Wurmus 2da99b671e
gnu: bwa: Pass -fcommon to compiler. 
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Add -fcommon option to
CFLAGS.
 2021-10-24 18:48:20 +00:00
Ricardo Wurmus 724972bcca
gnu: bowtie1: Use TBB 2020. 
* gnu/packages/bioinformatics.scm (bowtie1)[inputs]: Replace tbb with
tbb-2020.
 2021-10-24 18:47:45 +00:00
Ricardo Wurmus f336cc4fe7
gnu: bowtie: Replace invalid characters. 
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Replace invalid quotes
with straight quotes in the 'configure phase.
 2021-10-24 18:44:57 +00:00
Ricardo Wurmus e5a26a1f02
gnu: bowtie: Remove trailing #T. 
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Remove trailing #T from
build phases...
[source]: ...and from the snippet.
 2021-10-24 16:59:39 +00:00
Ricardo Wurmus 2ec601580b
gnu: bowtie: Use TBB 2020. 
* gnu/packages/bioinformatics.scm (bowtie)[inputs]: Replace tbb with tbb-2020.
 2021-10-24 16:58:58 +00:00
Ricardo Wurmus 7f151c9bd8
gnu: diffoscope: Update to 188. 
* gnu/packages/diffoscope.scm (diffoscope): Update to 188.
 2021-10-24 15:09:31 +00:00
Ricardo Wurmus b142611b36
gnu: diffoscope: Disable another broken libfile test. 
* gnu/packages/diffoscope.scm (diffoscope)[arguments]: Rename build phase
'remove-berkeley-test to 'remove-broken-file-type-detection-test and delete
another test that is broken due to our `file' package.
 2021-10-24 15:09:30 +00:00
Ricardo Wurmus 1d9cf387b3
gnu: python-magic: Update to 0.4.24. 
* gnu/packages/python-xyz.scm (python-magic): Update to 0.4.24.
 2021-10-24 15:09:18 +00:00
Ricardo Wurmus b3ac826e18
gnu: blender: Use older TBB and update header variables. 
* gnu/packages/graphics.scm (blender)[inputs]: Replace tbb with tbb-2020.
[arguments]: Don't set CPATH; set C_INCLUDE_PATH and CPLUS_INCLUDE_PATH instead.
 2021-10-24 13:28:05 +00:00