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107 Commits

Author SHA1 Message Date
Antero Mejr
e24b9b42bc
gnu: Add python-pydicom. 
* gnu/packages/python-science.scm (python-pydicom): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2023-01-08 16:11:45 +01:00
Sharlatan Hellseher
7f380a2e26
gnu: python-sgp4: Move to astronomy. 
* gnu/packages/astronomy.scm: (python-sgp4): Move here from python-science.scm.
  [description]: Expand description, annotate acronyms, add link to CelesTrak.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-12-05 22:22:20 +01:00
Sharlatan Hellseher
6468d9c131
gnu: python-sgp4: Update to 2.21. 
The latest version passes build on aarch64-linux system.

* gnu/packages/python-science.scm (python-sgp4): Update to 2.21.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-12-05 22:22:20 +01:00
Navid Afkhami
9ddc4e5b03
gnu: python-msgpack-numpy: Update to 0.4.8. 
* gnu/packages/python-science.scm (python-msgpack-numpy): Update to 0.4.8.
 2022-12-02 15:04:15 +01:00
Navid Afkhami
ba8679fb24
gnu: Add python-tspex. 
* gnu/packages/python-science.scm (python-tspex): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2022-11-11 12:12:04 +01:00
Ricardo Wurmus
b19c12c2d7
gnu: Add python-pyts. 
* gnu/packages/python-science.scm (python-pyts): New variable.
 2022-11-04 19:53:31 +01:00
jgart
70cac2829f
gnu: Add python-simple-pid. 
* gnu/packages/python-science.scm (python-simple-pid): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2022-10-18 14:41:10 +02:00
Marius Bakke
f66067febc
Merge branch 'master' into staging 2022-09-29 07:26:37 +02:00
Guillaume Le Vaillant
05c13b3149
gnu: Add python-simplespectral. 
* gnu/packages/python-science.scm (python-simplespectral): New variable.
 2022-09-28 11:31:49 +02:00
Maxim Cournoyer
3c6e220d81
Merge branch 'master' into staging. 
With resolved conflicts in:
	gnu/local.mk
	gnu/packages/crates-io.scm
 2022-09-27 14:27:28 -04:00
Ricardo Wurmus
ab6931483b
gnu: Add python-vaex-core. 
* gnu/packages/python-science.scm (python-vaex-core): New variable.
 2022-09-25 21:24:34 +02:00
Marius Bakke
2266ec5eb1
gnu: python-cython: Remove duplicate version. 
* gnu/packages/python-xyz.scm (python-cython-0.29.32): Remove variable.
* gnu/packages/python-science.scm (python-pandas)[native-inputs]: Change from
PYTHON-CYTHON-0.29.32 to PYTHON-CYTHON.
 2022-09-18 16:26:18 +02:00
Marius Bakke
ce3b51a4c6
gnu: python-pandas: Update to 1.4.4. 
* gnu/packages/python-science.scm (python-pandas): Update to 1.4.4.
[native-inputs]: Change from PYTHON-CYTHON to PYTHON-CYTHON-0.29.32.
 2022-09-18 16:18:36 +02:00
Marius Bakke
888dfc8eb6
gnu: python-scipy: Update to 1.9.1. 
* gnu/packages/python-science.scm (python-scipy): Update to 1.9.1.
[source]: Switch to GIT-FETCH.
[outputs]: Remove.
[arguments]: Don't disable Pythran.  Don't configure OpenBLAS which is now
discovered by pkg-config.  Do a "manual" PEP 517 style build.  Make
install-doc phase conditional on the presence of Sphinx.  Simplify tests.
[propagated-inputs]: Add PYTHON-PYTHRAN.
[native-inputs]: Remove PERL, WHICH, PYTHON-NUMPYDOC,
PYTHON-PYDATA-SPHINX-THEME, PYTHON-SPHINX, and PYTHON-SPHINX-PANELS.  Add
GCC, PKG-CONFIG, PYTHON-PYPA-BUILD and PYTHON-MESON.
 2022-09-16 18:42:21 +02:00
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