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* gnu: python-aiohttp: Remove cythonized files.Efraim Flashner2021-10-271-1/+20
| | | | | | | * 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.
* gnu: python-uvicorn: Update to 0.13.2.Efraim Flashner2021-10-271-12/+7
| | | | | | | | * 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.
* gnu: python-asgiref: Honor #:tests? flag.Efraim Flashner2021-10-271-4/+6
| | | | | * gnu/packages/python-web.scm (python-asgiref)[arguments]: Adjust custom 'check phase to honor the #:tests? flag.
* gnu: python-asgiref: Update to 3.4.1.Efraim Flashner2021-10-271-3/+2
| | | | * gnu/packages/python-web.scm (python-asgiref): Update to 3.4.1.
* gnu: python-watchgod: Update to 0.7.Efraim Flashner2021-10-271-8/+3
| | | | | | | * 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.
* gnu: python-aiohttp: Sort inputs alphabetically.Efraim Flashner2021-10-271-5/+5
| | | | | * gnu/packages/python-web.scm (python-aiohttp)[native-inputs]: Sort inputs alphabetically.
* gnu: python-aiohttp: Fix test suite.Efraim Flashner2021-10-271-2/+2
| | | | | | * 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.
* gnu: Add python-pytest-6.1.Efraim Flashner2021-10-271-0/+11
| | | | * gnu/packages/check.scm (python-pytest-6.1): New variable.
* gnu: python-pytest-mock: Adjust package inputs.Efraim Flashner2021-10-271-3/+5
| | | | | | | * 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.
* gnu: python-pytest-toolbox: Honor #:tests? flag.Efraim Flashner2021-10-271-6/+7
| | | | | * gnu/packages/python-check.scm (python-pytest-toolbox)[arguments]: Adjust custom 'check phase to honor the #:tests? flag.
* gnu: python-pytest-toolbox: Fix test suite.Efraim Flashner2021-10-271-11/+4
| | | | | | | | * 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.
* gnu: python-joblib: Run test suite sequentially.Efraim Flashner2021-10-261-0/+1
| | | | | * gnu/packages/python-xyz.scm (python-joblib)[arguments]: Adjust custom 'check phase to run the test suite sequentially.
* gnu: python-joblib: Honor #:tests? flag.Efraim Flashner2021-10-261-1/+3
| | | | | * gnu/packages/python-xyz.scm (python-joblib)[arguments]: Adjust custom 'check phase to honor the #:tests? flag.
* gnu: mariadb: Only enable parallel tests on x86_64-linux.Efraim Flashner2021-10-261-4/+4
| | | | | * gnu/packages/databases.scm (mariadb)[arguments]: Only enable parallel tests when building on x86_64-linux.
* gnu: zimg: Update to 3.0.3.Guillaume Le Vaillant2021-10-251-2/+2
| | | | * gnu/packages/image.scm (zimg): Update to 3.0.3.
* gnu: mariadb: Don’t run tests in parallel on ppc64le targets.Thiago Jung Bauermann2021-10-251-0/+4
| | | | | | | * gnu/packages/databases.scm (mariadb)[arguments]: Set ‘#:parallel-tests?’ for powerpc64le machines. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: python-pandas: Update to 1.3.4.Efraim Flashner2021-10-251-2/+2
| | | | * gnu/packages/python-science.scm (python-pandas): Update to 1.3.4.
* gnu: python-pandas: Fix building with pytest-6.Efraim Flashner2021-10-251-0/+3
| | | | | * gnu/packages/python-science.scm (python-pandas)[arguments]: In custom 'check phase adjust to not fail tests with missing test data.
* gnu: python-pandas: Honor #:tests? flag.Efraim Flashner2021-10-251-14/+15
| | | | | * gnu/packages/python-science.scm (python-pandas)[arguments]: Adjust custom 'check phase to honor the #:tests? flag.
* gnu: python-cython: Honor #:tests? flag.Efraim Flashner2021-10-251-10/+11
| | | | | * gnu/packages/python-xyz.scm (python-cython)[arguments]: Adjust custom 'check phase to honor the #:tests? flag.
* gnu: python-cython: Update to 0.29.24.Efraim Flashner2021-10-251-5/+7
| | | | | | * 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.
* gnu: gnuradio: Disable a randomly failing test.Guillaume Le Vaillant2021-10-251-1/+4
| | | | | * gnu/packages/radio.scm (gnuradio)[arguments]: Add qa_rotator_cc to the list of disabled tests.
* gnu: python-pyqtgraph: Disable one failing test.Guillaume Le Vaillant2021-10-251-9/+14
| | | | | * gnu/packages/python-xyz.scm (python-pyqtgraph)[arguments]: Add test_reload to list of disabled tests.
* gnu: hexchat: Fix build.Guillaume Le Vaillant2021-10-251-1/+2
| | | | | * gnu/packages/messaging.scm (hexchat)[arguments]: Use GUIX_PYTHONPATH instead of PYTHONPATH in 'wrap-program' phase.
* gnu: java-cisd-args4j: Copy instead of unpacking input.Ricardo Wurmus2021-10-241-5/+3
| | | | | * gnu/packages/java.scm (java-cisd-args4j)[arguments]: Do not unpack build-resources input; just copy the contents.
* gnu: sailfish: Use TBB 2020.Ricardo Wurmus2021-10-241-1/+1
| | | | | * gnu/packages/bioinformatics.scm (sailfish)[inputs]: Replace tbb with tbb-2020.
* gnu: sailfish: Remove trailing #T.Ricardo Wurmus2021-10-241-6/+3
| | | | | | * gnu/packages/bioinformatics.scm (sailfish)[arguments]: Remove trailing #T in build phases... [inputs]: ...and in the origin snippet of "rapmap".
* gnu: sailfish: Do not attempt to unpack a directory.Ricardo Wurmus2021-10-241-8/+2
| | | | | | | | 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.
* gnu: jellyfish: Remove Ruby bindings.Ricardo Wurmus2021-10-241-4/+0
| | | | | | | | 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.
* gnu: cutadapt: Regenerate Cython files.Ricardo Wurmus2021-10-241-0/+10
| | | | | * gnu/packages/bioinformatics.scm (cutadapt)[arguments]: Add phase 'always-cythonize.
* gnu: python-requests-unixsocket: Fix tests.Ricardo Wurmus2021-10-241-3/+7
| | | | | * gnu/packages/python-web.scm (python-requests-unixsocket)[arguments]: Do not run tests with --pep8 option; only run tests when enabled.
* gnu: python-mpmath: Update to 1.2.1.Ricardo Wurmus2021-10-241-23/+33
| | | | | | | * 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.
* gnu: java-commons-io: Replace %build-inputs with gexp.Ricardo Wurmus2021-10-241-3/+3
| | | | | * gnu/packages/java.scm (java-commons-io)[arguments]: Do not use %build-inputs; use gexp with this-package-native-inputs instead.
* gnu: python-dnaio: Update to 0.6.0.Ricardo Wurmus2021-10-241-2/+2
| | | | * gnu/packages/bioinformatics.scm (python-dnaio): Update to 0.6.0.
* gnu: python-xopen: Update to 0.8.2.Ricardo Wurmus2021-10-241-7/+7
| | | | * gnu/packages/python-xyz.scm (python-xopen): Update to 0.8.2.
* gnu: macs: Fix build by setting HOME.Ricardo Wurmus2021-10-241-0/+2
| | | | | * gnu/packages/bioinformatics.scm (macs)[arguments]: Add build phase to set HOME variable.
* gnu: methyldackel: Remove trailing #T.Ricardo Wurmus2021-10-241-2/+1
| | | | | * gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Remove trailing #T from build phase.
* gnu: methyldackel: Pass -fcommon to compiler.Ricardo Wurmus2021-10-241-0/+1
| | | | | * gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Add -fcommon to CFLAGS.
* gnu: flexbar: Use TBB 2020.Ricardo Wurmus2021-10-241-1/+1
| | | | | * gnu/packages/bioinformatics.scm (flexbar)[inputs]: Replace tbb with tbb-2020.
* gnu: flexbar: Remove trailing #T.Ricardo Wurmus2021-10-241-6/+3
| | | | | * gnu/packages/bioinformatics.scm (flexbar)[arguments]: Remove trailing #T from all build phases.
* gnu: bwa: Remove trailing #T.Ricardo Wurmus2021-10-241-2/+1
| | | | | * gnu/packages/bioinformatics.scm (bwa)[arguments]: Remove trailing #T in build phase.
* gnu: bwa: Pass -fcommon to compiler.Ricardo Wurmus2021-10-241-0/+1
| | | | | * gnu/packages/bioinformatics.scm (bwa)[arguments]: Add -fcommon option to CFLAGS.
* gnu: bowtie1: Use TBB 2020.Ricardo Wurmus2021-10-241-1/+1
| | | | | * gnu/packages/bioinformatics.scm (bowtie1)[inputs]: Replace tbb with tbb-2020.
* gnu: bowtie: Replace invalid characters.Ricardo Wurmus2021-10-241-1/+6
| | | | | * gnu/packages/bioinformatics.scm (bowtie)[arguments]: Replace invalid quotes with straight quotes in the 'configure phase.
* gnu: bowtie: Remove trailing #T.Ricardo Wurmus2021-10-241-4/+2
| | | | | | * gnu/packages/bioinformatics.scm (bowtie)[arguments]: Remove trailing #T from build phases... [source]: ...and from the snippet.
* gnu: bowtie: Use TBB 2020.Ricardo Wurmus2021-10-241-1/+1
| | | | * gnu/packages/bioinformatics.scm (bowtie)[inputs]: Replace tbb with tbb-2020.
* gnu: diffoscope: Update to 188.Ricardo Wurmus2021-10-241-2/+2
| | | | * gnu/packages/diffoscope.scm (diffoscope): Update to 188.
* gnu: diffoscope: Disable another broken libfile test.Ricardo Wurmus2021-10-241-5/+6
| | | | | | * 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.
* gnu: python-magic: Update to 0.4.24.Ricardo Wurmus2021-10-241-3/+3
| | | | * gnu/packages/python-xyz.scm (python-magic): Update to 0.4.24.
* gnu: blender: Use older TBB and update header variables.Ricardo Wurmus2021-10-241-8/+14
| | | | | * 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.
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