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93 Commits

Author SHA1 Message Date
Marius Bakke
8bd7cd34bf gnu: python-pingouin: Don't pin scikit-learn version. 
* gnu/packages/python-science.scm (python-pingouin)[arguments]: Add phase.
 2022-09-14 21:08:34 +02:00
Marius Bakke
e3ed1d09f9 gnu: python-pingouin: Update to 0.5.2. 
* gnu/packages/python-science.scm (python-pingouin): Update to 0.5.2.
[arguments]: Adjust outdated substitution.
 2022-09-11 23:41:51 +02:00
Christopher Baines
ad1d3f98b1 gnu: 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.
 2022-09-10 10:45:27 +01:00
Paul A. Patience
29491482a1 gnu: 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>
 2022-09-07 22:02:40 +02:00
Paul A. Patience
7e13054373 gnu: 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>
 2022-08-02 20:59:15 +03:00
Ricardo Wurmus
4bc130dcc0 gnu: Add python-geosketch. 
* gnu/packages/python-science.scm (python-geosketch): New variable.
 2022-08-02 14:37:38 +02:00
Ricardo Wurmus
d4b0dc047f gnu: Add python-fbpca. 
* gnu/packages/python-science.scm (python-fbpca): New variable.
 2022-08-02 14:37:38 +02:00
Paul A. Patience
a15b769c2f gnu: 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>
 2022-07-15 09:46:51 +01:00
Ricardo Wurmus
684c718e6a gnu: Add python-opt-einsum. 
* gnu/packages/python-science.scm (python-opt-einsum): New variable.
 2022-07-08 18:41:35 +02:00
Antero Mejr
486251d440 gnu: Add python-deepdish. 
* gnu/packages/python-science.scm (python-deepdish): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-07-03 16:04:23 +02:00
Greg Hogan
e9e05dd129 gnu: 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>
 2022-06-26 01:00:18 +02:00
Vinicius Monego
aa718586fa gnu: python-scikit-image: Update to 0.19.3. 
* gnu/packages/python-science.scm (python-scikit-image): Update to 0.19.3.
 2022-06-18 13:07:09 -03:00
Eric Bavier
b68c87f86a gnu: Add PyGLM. 
* gnu/packages/python-science.scm (python-pyglm): New variable.
 2022-06-08 23:27:47 -05:00
Maxim Cournoyer
30413f1180 gnu: Remove python2-scipy. 
* gnu/packages/python-science.scm (python2-scipy): Delete variable.
(python-scipy)[properties]: Delete field.
 2022-05-31 14:53:35 -04:00
Maxim Cournoyer
b827d0f7b3 gnu: Remove python2-weave. 
* gnu/packages/python-science.scm (python2-weave): Delete variable.
 2022-05-31 14:52:37 -04:00
Maxim Cournoyer
b3c7d69fa0 gnu: Remove python2-pandas. 
* gnu/packages/python-science.scm (python2-pandas): Delete variable.
(python-pandas): Delete related python2-variant property.
 2022-05-31 14:52:25 -04:00
Ricardo Wurmus
07909eb092 gnu: 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.
 2022-05-31 15:18:22 +02:00
Wiktor Zelazny
acb08304c8 gnu: Add python-gpy. 
* gnu/packages/python-science.scm (python-gpy): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-29 23:56:06 +02:00
Wiktor Zelazny
6400f08d07 gnu: Add python-paramz. 
* gnu/packages/python-science.scm (python-paramz): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-29 23:56:05 +02:00
Wiktor Zelazny
6dacd15381 gnu: Add python-climin. 
* gnu/packages/python-science.scm (python-climin): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-29 23:56:05 +02:00
Paul A. Patience
4ab5c8348d gnu: Add python-pyvista. 
* gnu/packages/python-science.scm (python-pyvista): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-23 16:24:47 +02:00
Ricardo Wurmus
d1bdead838 gnu: Add python-aplus. 
* gnu/packages/python-science.scm (python-aplus): New variable.
 2022-05-20 20:42:53 +02:00
Maxim Cournoyer
cecf195347 gnu: python-pingouin: Update to 0.5.1. 
* gnu/packages/python-science.scm (python-pingouin): Update to 0.5.1.
 2022-05-12 12:46:06 -04:00
Maxim Cournoyer
c359a4fabb gnu: python-pandas: Update to 1.4.2. 
* gnu/packages/python-science.scm (python-pandas): Update to 1.4.2.
 2022-05-12 12:45:55 -04:00
Maxim Cournoyer
8b390a8750 gnu: 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.
 2022-05-12 12:45:55 -04:00
Maxim Cournoyer
cddedb9c5b gnu: 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.
 2022-05-12 12:45:37 -04:00
Maxim Cournoyer
5a3634f461 gnu: 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.
 2022-05-12 12:45:36 -04:00
Paul A. Patience
e606e02844 gnu: 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>
 2022-05-06 15:23:06 +02:00
Paul A. Patience
9edc0f3dbb gnu: python-vedo: Disable sanity check. 
* gnu/packages/python-science.scm (python-vedo)[arguments]: Disable
sanity check.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-05-06 15:23:06 +02:00
Paul A. Patience
a5fec06868 gnu: 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>
 2022-05-06 15:23:06 +02:00
Paul A. Patience
34f49d15e6 gnu: 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>
 2022-05-06 15:23:06 +02:00
Ricardo Wurmus
e47b080474 gnu: Add python-traittypes. 
* gnu/packages/python-science.scm (python-traittypes): New variable.
 2022-05-06 13:02:55 +02:00
Malte Frank Gerdes
b4b93035c1 gnu: Add python-trimesh. 
* gnu/packages/python-science.scm (python-trimesh): New variable.

Co-authored-by: Guillaume Le Vaillant <glv@posteo.net>
 2022-04-07 18:35:38 +02:00
Ricardo Wurmus
38b2026515 gnu: Add python-numpy-groupies. 
* gnu/packages/python-science.scm (python-numpy-groupies): New variable.
 2022-03-31 14:37:58 +02:00
Efraim Flashner
3e34b01b70 gnu: Add python-scikit-allel. 
* gnu/packages/python-science.scm (python-scikit-allel): New variable.
 2022-03-18 15:58:23 +02:00
Efraim Flashner
e4b91f10c8 gnu: python-scipy: Adjust phases. 
* gnu/packages/python-science.scm (python-scipy)[arguments]: Replace
'check with custom 'check phase.
 2022-03-17 14:51:38 +02:00
Vinicius Monego
2907c700eb gnu: python-scikit-image: Update to 0.19.2. 
* gnu/packages/python-science.scm (python-scikit-image): Update to 0.19.2.
 2022-03-03 22:27:48 -03:00
Marius Bakke
2f6f9f2e54 gnu: 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.
 2022-02-19 10:43:23 +01:00
Marius Bakke
fb84285b7a gnu: Add python-pythran. 
* gnu/packages/python-science.scm (python-pythran): New variable.
 2022-02-19 10:43:23 +01:00
Marius Bakke
b2faad4bd0 gnu: 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.
 2022-01-22 10:23:00 +01:00
Marius Bakke
4f6cbc0aee gnu: python-pandas: Remove old version. 
* gnu/packages/python-science.scm (python-pandas-0.25): Remove variable.
(python2-pandas): Inherit from PYTHON-PANDAS.
 2022-01-22 10:23:00 +01:00
Maxim Cournoyer
276f40fdc3 Merge branch 'version-1.4.0' 
With resolved conflicts in:
	gnu/packages/gnome.scm
	gnu/packages/openstack.scm
	gnu/packages/python-xyz.scm
 2022-01-17 11:47:09 -05:00
Maxim Cournoyer
836daaf8f6 gnu: 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.
 2022-01-10 11:47:02 -05:00
Marius Bakke
cdd0fcee8c gnu: python-scikit-fuzzy: Disable tests. 
* gnu/packages/python-science.scm (python-scikit-fuzzy)[arguments]: Add
 #:tests?.  Remove #:phases.
 2022-01-12 23:50:17 +01:00
Marius Bakke
8622e0a721 gnu: python-modin: Permit newer versions of pandas. 
* gnu/packages/python-science.scm (python-modin)[arguments]: Add phase.
 2022-01-12 23:50:15 +01:00
Efraim Flashner
e8c1562599 gnu: 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.
 2021-12-22 21:17:19 +02:00
Arun Isaac
e97197cccb gnu: python-pingouin: Update to 0.5.0. 
* gnu/packages/python-science.scm (python-pingouin): Update to 0.5.0.
 2021-12-22 21:17:16 +02:00
Efraim Flashner
8e213a15d3 Revert "gnu: python-pingouin: Update to 0.5.0." 
This reverts commit f2ad33bc39.

python-pingouin after 0.3.12 needs newer versions of all the python
science libraries.
 2021-12-21 16:22:50 +02:00
Lars-Dominik Braun
08218fd7a4 gnu: python-pyflow: Rename to python2-pyflow. 
The package was never compatible with Python 3. Not adding a deprecated
package variant, because going from Python 3 to Python 2 is a breaking
change and it’s unlikely anyone ever used the package anyway (it was
likely broken).

* gnu/packages/python-science.scm (python-pyflow): Move…
(python2-pyflow): …here.
[arguments]: Use Python 2.
 2021-12-16 09:48:02 +01:00
Marius Bakke
95447b293d gnu: python-distributed: Update to 2021.11.2. 
* gnu/packages/python-science.scm (python-distributed): Update to 2021.11.2.
[source](snippet): New field.
[arguments]: Add versioneer phase.
[native-inputs]: Add PYTHON-VERSIONEER.
 2021-12-13 23:28:58 +01:00