gnu: cwltool: Patch tox.ini. * gnu/packages/bioinformatics.scm (cwltool)[arguments]: Rename 'modify-tests to 'patch-tests; add patch of tox.ini. Change-Id: I2c90a8803e7eb1153cb4c7cc5b683875627c57f1
gnu: cwltool: Use test-flags. * gnu/packages/bioinformatics.scm (cwltool)[arguments]: Use #:test-flags instead of deleting and patching tests in 'modify-tests phase. Change-Id: I0e4f16d48fba23e4197b69bf1c3923828f178cd0
gnu: python-prov: Update to 2.0.1. * gnu/packages/python-xyz.scm (python-prov): Update to 2.0.1. [build-system]: Use pyproject-build-system. [arguments]: Remove 'fix-rdflib-6-compatibility phase; add custom 'check phase. [native-inputs]: Add python-setuptools and python-wheel. Change-Id: Ia5e0ed1ee6e9476f317b345234018f2391cc3e98
gnu: python-rdflib-6: Accept newer isodate. * gnu/packages/rdf.scm (python-rdflib-6)[arguments]: Add phase 'compatibility. Change-Id: I4b4c880b169c6606707c1e973af9488c07d18992
gnu: python-rdflib-6: Disable one test. * gnu/packages/rdf.scm (python-rdflib-6)[arguments]: Disable one additional test. Change-Id: Ifcfe1b11d09299e219499ea77f792ca41aa02d9c
gnu: python-cwl-utils: Add missing inputs. * gnu/packages/bioinformatics.scm (python-cwl-utils)[native-inputs]: Add python-setuptools and python-wheel. Change-Id: I803a68c04923c96f793d508c23bb08069524bc63
gnu: python-cwl-upgrader: Add missing inputs. * gnu/packages/bioinformatics.scm (python-cwl-upgrader)[native-inputs]: Add python-setuptools and python-wheel. Change-Id: I81531d588e6deb8a01c59f2a824b815e8f95e0f0
gnu: python-schema-salad: Update to 8.8.20241206093842. * gnu/packages/bioinformatics.scm (python-schema-salad): Update to 8.8.20241206093842. [arguments]: Patch tox.ini. [propagated-inputs]: Remove python-importlib-resources, python-setuptools, and python-typing-extensions. [native-inputs]: Add python-cachecontrol, python-mypy, python-setuptools, python-setuptools-scm, python-types-dataclasses, python-types-requests, and python-types-setuptools. Change-Id: I22ca7ad772078192117a1139adca410b53844008
gnu: python-isodate: Update to 0.7.2. * gnu/packages/time.scm (python-isodate): Update to 0.7.2. [build-system]: Use pyproject-build-system. [native-inputs]: Remove python-six; add python-pytest, python-setuptools, python-setuptools-scm, and python-wheel. Change-Id: I5ba64eb433e39c0bbb0360273f822d95ea7c63d3
gnu: python-cachecontrol: Update to 0.14.1. * gnu/packages/python-web.scm (python-cachecontrol): Update to 0.14.1. [build-system]: Use pyproject-build-system. [propagated-inputs]: Add python-filelock. [native-inputs]: Add python-flit-core. Change-Id: I61bc38aafe04cf7f11394a654cf28181d39ce355
gnu: python-rdflib-6: Update to 6.3.2. * gnu/packages/rdf.scm (python-rdflib-6): Update to 6.3.2. [build-system]: Use pyproject-build-system. [arguments]: Use #:test-flags instead of a custom build phase; update list of disabled tests. [native-inputs]: Add python-poetry-core and python-pytest-cov. Change-Id: I0dd4ecebdf3ef04562c3a3efb37614bf5eec16f5
gnu: fava: Update to 1.27. * gnu/packages/finance.scm (fava): Update to 1.27. [arguments] <phases>: Remove 'relax-requirements, and 'set-home. [native-inputs]: Remove python-chardet, python-dateutil, and python-setuptootls-scm. Add python-babel, python-mypy, python-pytest-cov, python-setuptootls, python-twine, python-types-setuptootls, python-types-simplejson, and python-wheel. Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Change-Id: Iee27197ece9685c500afe0dedb8ba33e02eb1ea1
gnu: beancount: Fix build. * gnu/packages/finance.scm (beancount) [native-inputs]: Add python-wheel and python-setuptools. Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
gnu: Add python-types-simplejson. * gnu/packages/python-xyz.scm (python-types-simplejson): New variable. Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
gnu: python-pdfminer-six: Update to 20240706. * gnu/packages/python-xyz.scm (python-pdfminer-six): Update to 20240706. Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
gnu: python-markdown2: Update to 2.5.2. * gnu/packages/python-xyz.scm (python-markdown2) [arguments] <phases>: Use default 'check. [native-inputs]: Add python-pytest, python-setuptools and python-wheel. Co-authored-by: Sharlatan Hellseher <sharlatanus@gmail.com> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Change-Id: Ic3df25863bbb37ec6282ec5dcbf815461663f8cd
gnu: python-flask-babel: Update to 4.0.0. * gnu/packages/python-web.scm (python-flask-babel): Update to 4.0.0. [source]: Fetch from git as PyPI release doesn't include tests. [build-system]: Switch to pyproject-build-system. [native-inputs]: Add python-poetry-core, python-pytest, python-pytest-cov, and python-pytest-mock. [propagated-inputs]: Sort. Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Change-Id: I253b88eac7bec8152dc97634059c2402624cb961
gnu: python-babel: Update to 2.16.0. * gnu/packages/python-xyz.scm (python-babel): Update to 2.16.0. [source]: Adjust uri as it's changed in PyPI archive. [build-system]: Swap to pyproject-build-system. [arguments] <phases>: Use default 'check. [native-inputs]: Add python-setuptools and python-wheel. Co-authored-by: Sharlatan Hellseher <sharlatanus@gmail.com> Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com> Change-Id: I32b7c5613e7db2c676745d6621f04b52a1cdf0ba
gnu: pyscenic: Update to 0.12.1-1.eaf23eb. * gnu/packages/bioinformatics.scm (pyscenic): Update to 0.12.1-1.eaf23eb. [arguments]: Update phase 'do-not-reference-deleted-modules. [propagated-inputs]: Add python-numexpr. [native-inputs]: Add python-wheel. Change-Id: Ib1b5a7d36a24b280160befe579057a241d69455d
gnu: python-pydantic-2: Update to 2.7.0. * gnu/packages/python-xyz.scm (python-pydantic-2): Update to 2.7.0. [arguments]: Update tests. [native-inputs]: Add tzdata-for-tests and python-jsonschema; remove python-faker. Change-Id: I8c85598f7603c58108602c6d67aa27314dea285e