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2022-09-15Merge branch 'master' into staging...With resolved conflicts in: gnu/local.mk gnu/packages/freedesktop.scm gnu/packages/gnuzilla.scm Maxim Cournoyer
2022-09-14gnu: python-pingouin: Don't pin scikit-learn version....* gnu/packages/python-science.scm (python-pingouin)[arguments]: Add phase. Marius Bakke
2022-09-11gnu: python-pingouin: Update to 0.5.2....* gnu/packages/python-science.scm (python-pingouin): Update to 0.5.2. [arguments]: Adjust outdated substitution. Marius Bakke
2022-09-10Merge branch 'master' into stagingMarius Bakke
2022-09-10gnu: Add comments to the bottom of a few package modules....This will hopefully discourage patches which add new packages to the bottom of files, as this increases the likelihood of conflicts when applying patches. If there are more specific ways that packages should be arranged in specific modules, this message can be updated accordingly. * gnu/packages/bioconductor.scm: Add comment discouraging adding packages to the bottom of the file. * gnu/packages/bioinformatics.scm: ditto. * gnu/packages/cran.scm: ditto. * gnu/packages/crates-io.scm: ditto. * gnu/packages/emacs-xyz.scm: ditto. * gnu/packages/golang.scm: ditto. * gnu/packages/guile-xyz.scm: ditto. * gnu/packages/haskell-xyz.scm: ditto. * gnu/packages/java.scm: ditto. * gnu/packages/julia-xyz.scm: ditto. * gnu/packages/lisp-xyz.scm: ditto. * gnu/packages/ocaml.scm: ditto. * gnu/packages/perl.scm: ditto. * gnu/packages/python-science.scm: ditto. * gnu/packages/python-xyz.scm: ditto. * gnu/packages/ruby.scm: ditto. * gnu/packages/tex.scm: ditto. Christopher Baines
2022-09-08Merge branch 'master' into stagingMarius Bakke
2022-09-07gnu: python-pyvista: Update to 0.36.1....* gnu/packages/python-science.scm (python-pyvista): Update to 0.36.1. Signed-off-by: Marius Bakke <marius@gnu.org> Paul A. Patience
2022-08-13gnu: python-sphinx-panels: Use python-sphinx@4.......also add deprecation notice, and change its users accordingly. * gnu/packages/sphinx.scm (python-sphinx-panels)[propagated-inputs]: Change from PYTHON-SPHINX to PYTHON-SPHINX-4. [description]: Mention that it is unmaintained. * gnu/packages/python-science.scm (python-scipy)[native-inputs]: Likewise. * gnu/packages/python-xyz.scm (python-numpy-documentation)[native-inputs]: Likewise. Marius Bakke
2022-08-02gnu: python-pyvista: Update to 0.35.2....* gnu/packages/python-science.scm (python-pyvista): Update to 0.35.2. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Paul A. Patience
2022-08-02gnu: Add python-geosketch....* gnu/packages/python-science.scm (python-geosketch): New variable. Ricardo Wurmus
2022-08-02gnu: Add python-fbpca....* gnu/packages/python-science.scm (python-fbpca): New variable. Ricardo Wurmus
2022-07-15gnu: python-pyvista: Update to 0.35.1....* gnu/packages/python-science (python-pyvista): Update to 0.35.1. Signed-off-by: Christopher Baines <mail@cbaines.net> Paul A. Patience
2022-07-08gnu: Add python-opt-einsum....* gnu/packages/python-science.scm (python-opt-einsum): New variable. Ricardo Wurmus
2022-07-03gnu: Add python-deepdish....* gnu/packages/python-science.scm (python-deepdish): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Antero Mejr
2022-06-26gnu: python-modin: Update to 0.15.1....* gnu/packages/python-science.scm (python-modin): Update to 0.15.1. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Greg Hogan
2022-06-18gnu: python-scikit-image: Update to 0.19.3....* gnu/packages/python-science.scm (python-scikit-image): Update to 0.19.3. Vinicius Monego
2022-06-08gnu: Add PyGLM....* gnu/packages/python-science.scm (python-pyglm): New variable. Eric Bavier
2022-05-31gnu: Remove python2-scipy....* gnu/packages/python-science.scm (python2-scipy): Delete variable. (python-scipy)[properties]: Delete field. Maxim Cournoyer
2022-05-31gnu: Remove python2-weave....* gnu/packages/python-science.scm (python2-weave): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove python2-pandas....* gnu/packages/python-science.scm (python2-pandas): Delete variable. (python-pandas): Delete related python2-variant property. Maxim Cournoyer
2022-05-31gnu: python-distributed: Update to 2022.05.2....* gnu/packages/python-science.scm (python-distributed): Update to 2022.05.2. [arguments]: Remove 'sanity-check phase; adjust 'check phase. [propagated-inputs]: Add python-urllib3. [native-inputs]: Add python-pytest-timeout and python-flaky. Ricardo Wurmus
2022-05-29gnu: Add python-gpy....* gnu/packages/python-science.scm (python-gpy): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Wiktor Zelazny
2022-05-29gnu: Add python-paramz....* gnu/packages/python-science.scm (python-paramz): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Wiktor Zelazny
2022-05-29gnu: Add python-climin....* gnu/packages/python-science.scm (python-climin): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Wiktor Zelazny
2022-05-23gnu: Add python-pyvista....* gnu/packages/python-science.scm (python-pyvista): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Paul A. Patience
2022-05-20gnu: Add python-aplus....* gnu/packages/python-science.scm (python-aplus): New variable. Ricardo Wurmus
2022-05-12gnu: python-pingouin: Update to 0.5.1....* gnu/packages/python-science.scm (python-pingouin): Update to 0.5.1. Maxim Cournoyer
2022-05-12gnu: python-pandas: Update to 1.4.2....* gnu/packages/python-science.scm (python-pandas): Update to 1.4.2. Maxim Cournoyer
2022-05-12gnu: python-pandas: Build and run tests in parallel....* gnu/packages/python-science.scm (python-pandas) [phases]{enable-parallel-build}: New phase. {check}: Add xdist -n option. Skip test_memory_usage test. [native-inputs]: Add python-pytest-xdist. Maxim Cournoyer
2022-05-12gnu: python-scipy: Update to 1.8.0 and enable parallel build....* gnu/packages/python-science.scm (python-scipy): Update to 1.8.0. [modules]: New argument. [phases]{disable-broken-tests}: Delete phase. {configure-openblas}: Streamline configuration template. {parallelize-build}: New phase. {install-doc}: Move before 'check phase. Remove now extraneous 'add-installed-pythonpath' call. Remove the SPHINXBUILD and PYVER Make variables, as well as conf.py patching. Provide SPHINXOPTS to build doc in parallel. Simply recursively copy the 'html' output directory to install the doc. {check}: Remove extraneous INPUTS and OUTPUTS arguments. Start tests with the 'runtests.py' launcher, which accepts a '-j' argument to run the tests in parallel. [native-inputs]: Sort inputs. Add python-pytest-xdist and python-threadpoolctl. [home-page]: Update. Maxim Cournoyer
2022-05-12gnu: python-scipy: Move input fields below arguments field....* gnu/packages/python-science.scm (python-scipy): Move inputs fields below the arguments field. [phases]: Use gexp. {configure-openblas}: Use this-package-input. {check}: Remove extraneous 'add-installed-pythonpath' call. {install-doc}: Adjust accordingly. Maxim Cournoyer
2022-05-06gnu: python-vedo: Update to 2022.2.0....* gnu/packages/python-science.scm (python-vedo): Update to 2022.2.0. [arguments]: Add 'fix-tests' phase. [inputs]: Move fenics and python-matplotlib to propagated-inputs. Move python-pkgconfig from here... [native-inputs]: ...to here. [propagated-inputs]: Add python-deprecated (and fenics and python-matplotlib). [description]: Make description more accurate. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Paul A. Patience
2022-05-06gnu: python-vedo: Disable sanity check....* gnu/packages/python-science.scm (python-vedo)[arguments]: Disable sanity check. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Paul A. Patience
2022-05-06gnu: python-vedo: Remove input labels....* gnu/packages/python-science.scm (python-vedo)[inputs]: Remove labels and sort the inputs. [propagated-inputs]: Remove labels. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Paul A. Patience
2022-05-06gnu: python-vedo: Honor #:tests? flag....* gnu/packages/python-science.scm (python-vedo)[arguments]: Adjust custom 'check' phase to honor the #:tests? flag. Also remove its trailing boolean. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Paul A. Patience
2022-05-06gnu: Add python-traittypes....* gnu/packages/python-science.scm (python-traittypes): New variable. Ricardo Wurmus
2022-04-07gnu: Add python-trimesh....* gnu/packages/python-science.scm (python-trimesh): New variable. Co-authored-by: Guillaume Le Vaillant <glv@posteo.net> Malte Frank Gerdes
2022-03-31gnu: Add python-numpy-groupies....* gnu/packages/python-science.scm (python-numpy-groupies): New variable. Ricardo Wurmus
2022-03-18gnu: Add python-scikit-allel....* gnu/packages/python-science.scm (python-scikit-allel): New variable. Efraim Flashner
2022-03-17gnu: python-scipy: Adjust phases....* gnu/packages/python-science.scm (python-scipy)[arguments]: Replace 'check with custom 'check phase. Efraim Flashner
2022-03-03gnu: python-scikit-image: Update to 0.19.2....* gnu/packages/python-science.scm (python-scikit-image): Update to 0.19.2. Vinicius Monego
2022-02-19gnu: python-scikit-image: Update to 0.19.1....* gnu/packages/python-science.scm (python-scikit-image): Update to 0.19.1. [propagated-inputs]: Add PYTHON-PYTHRAN. [native-inputs]: Remove PYTHON-CODECOV, PYTHON-FLAKE8, PYTHON-PYTEST-COV, and PYTHON-WHEEL. Marius Bakke
2022-02-19gnu: Add python-pythran....* gnu/packages/python-science.scm (python-pythran): New variable. Marius Bakke
2022-01-22gnu: python-upsetplot: Update to 0.6.0....* gnu/packages/python-science.scm (python-upsetplot): Update to 0.6.0. [source](modules, snippet): New fields. [arguments]: Remove obsolete phase. Respect TESTS? in check phase. Marius Bakke
2022-01-22gnu: python-pandas: Remove old version....* gnu/packages/python-science.scm (python-pandas-0.25): Remove variable. (python2-pandas): Inherit from PYTHON-PANDAS. Marius Bakke
2022-01-17Merge branch 'version-1.4.0'...With resolved conflicts in: gnu/packages/gnome.scm gnu/packages/openstack.scm gnu/packages/python-xyz.scm Maxim Cournoyer
2022-01-10gnu: python-pandas: Update to 1.3.5....* gnu/packages/python-science.scm (python-pandas): Update to 1.3.5. [phases]{check}: Add a reference to the network accessing tests issue, now reported upstream. Reinstate the excelwriter tests. [propagated-inputs]: Add python-xlsxwriter. [native-inputs]: Remove python-nose. Maxim Cournoyer
2022-01-12gnu: python-scikit-fuzzy: Disable tests....* gnu/packages/python-science.scm (python-scikit-fuzzy)[arguments]: Add #:tests?. Remove #:phases. Marius Bakke
2022-01-12gnu: python-modin: Permit newer versions of pandas....* gnu/packages/python-science.scm (python-modin)[arguments]: Add phase. Marius Bakke
2021-12-22gnu: python-scipy: Update to 1.7.3....* gnu/packages/python-science.scm (python-scipy): Update to 1.7.3. [native-inputs]: Add python-pydata-sphinx-theme, python-sphinx-panels. [arguments]: Add phase to build without python-pythran. Remove trailing #t from phases. * gnu/packages/sphinx.scm (python-pydata-sphinx-theme)[native-inputs]: Remove python-plotly. Efraim Flashner
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