Hello community,
here is the log from the commit of package python-nilearn for
openSUSE:Leap:15.2 checked in at 2020-05-03 14:29:23
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Leap:15.2/python-nilearn (Old)
and /work/SRC/openSUSE:Leap:15.2/.python-nilearn.new.2738 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "python-nilearn"
Sun May 3 14:29:23 2020 rev:2 rq:799677 version:0.6.2
Changes:
--------
--- /work/SRC/openSUSE:Leap:15.2/python-nilearn/python-nilearn.changes
2020-03-27 16:48:04.359931509 +0100
+++
/work/SRC/openSUSE:Leap:15.2/.python-nilearn.new.2738/python-nilearn.changes
2020-05-03 14:30:21.476644063 +0200
@@ -1,0 +2,5 @@
+Wed Apr 29 12:53:13 UTC 2020 - Tomáš Chvátal <tchva...@suse.com>
+
+- Use xdist to speedup the tests to take less than 30 mins
+
+-------------------------------------------------------------------
Old:
----
nilearn-0.6.1.tar.gz
New:
----
nilearn-0.6.2.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ python-nilearn.spec ++++++
--- /var/tmp/diff_new_pack.ThO71y/_old 2020-05-03 14:30:21.952645079 +0200
+++ /var/tmp/diff_new_pack.ThO71y/_new 2020-05-03 14:30:21.956645087 +0200
@@ -19,7 +19,7 @@
%{?!python_module:%define python_module() python-%{**} python3-%{**}}
%define skip_python2 1
Name: python-nilearn
-Version: 0.6.1
+Version: 0.6.2
Release: 0
Summary: Statistical learning tool for neuroimaging
License: BSD-3-Clause
@@ -29,22 +29,23 @@
BuildRequires: %{python_module setuptools}
BuildRequires: fdupes
BuildRequires: python-rpm-macros
+Requires: python-joblib >= 0.11
+Requires: python-matplotlib >= 2.0
+Requires: python-nibabel >= 2.0.2
+Requires: python-numpy >= 0.11
+Requires: python-scikit-learn >= 0.19
+Requires: python-scipy >= 0.19
+BuildArch: noarch
# SECTION test requirements
-BuildRequires: %{python_module joblib}
+BuildRequires: %{python_module joblib >= 0.11}
BuildRequires: %{python_module matplotlib >= 2.0}
BuildRequires: %{python_module nibabel >= 2.0.2}
-BuildRequires: %{python_module nose}
+BuildRequires: %{python_module numpy >= 0.11}
+BuildRequires: %{python_module pytest-xdist}
BuildRequires: %{python_module pytest}
BuildRequires: %{python_module scikit-learn >= 0.19}
BuildRequires: %{python_module scipy >= 0.19}
# /SECTION
-Requires: python-joblib
-Requires: python-matplotlib >= 2.0
-Requires: python-nibabel >= 2.0.2
-Requires: python-scikit-learn >= 0.19
-Requires: python-scipy >= 0.19
-BuildArch: noarch
-
%python_subpackages
%description
@@ -63,7 +64,9 @@
%check
# Disable tests that require a network connection
-%pytest -v -k 'not test_fetch_ and not test_get_batch and not
test_scroll_server_results and not test_simple_download and not
test_fill_html_template and not test_temp_file_removing and not
test_view_img_on_surf and not test_view_surf and not
test_resample_img_segmentation_fault'
+# Disable tests requiring to be executed without xdist (serialization issue):
test_tikhonov_regularization_vs_graph_net or test_connectivity_measure_outputs
or test_canica_square_img or test_with_globbing_patterns_with_single_subject or
test_dict_learning
+# Disable tests failing with new numpy (conversions to float fail):
test_plot_surf_stat_map test_plot_surf_roi
+%pytest -n auto -k 'not (test_fetch_ or test_get_batch or
test_scroll_server_results or test_simple_download or test_fill_html_template
or test_temp_file_removing or test_view_img_on_surf or test_view_surf or
test_resample_img_segmentation_fault or
test_tikhonov_regularization_vs_graph_net or test_connectivity_measure_outputs
or test_canica_square_img or test_with_globbing_patterns_with_single_subject or
test_dict_learning or test_plot_surf_stat_map or test_plot_surf_roi)'
%files %{python_files}
%doc AUTHORS.rst README.rst
++++++ nilearn-0.6.1.tar.gz -> nilearn-0.6.2.tar.gz ++++++
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nilearn-0.6.1/PKG-INFO new/nilearn-0.6.2/PKG-INFO
--- old/nilearn-0.6.1/PKG-INFO 2020-01-22 13:52:21.000000000 +0100
+++ new/nilearn-0.6.2/PKG-INFO 2020-02-25 12:03:00.000000000 +0100
@@ -1,13 +1,13 @@
Metadata-Version: 1.2
Name: nilearn
-Version: 0.6.1
+Version: 0.6.2
Summary: Statistical learning for neuroimaging in Python
Home-page: http://nilearn.github.io
Maintainer: Gael Varoquaux
Maintainer-email: gael.varoqu...@normalesup.org
License: new BSD
Download-URL: http://nilearn.github.io
-Description: .. -*- mode: rst -*-
+Description: .. -*- mode: rst -*-
.. image:: https://travis-ci.org/nilearn/nilearn.svg?branch=master
:target: https://travis-ci.org/nilearn/nilearn
@@ -76,7 +76,7 @@
===========
Detailed instructions on how to contribute are available at
- http://nilearn.github.io/contributing.html
+ http://nilearn.github.io/development.html
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nilearn-0.6.1/README.rst new/nilearn-0.6.2/README.rst
--- old/nilearn-0.6.1/README.rst 2020-01-22 11:55:28.000000000 +0100
+++ new/nilearn-0.6.2/README.rst 2020-01-22 17:35:01.000000000 +0100
@@ -1,4 +1,4 @@
-.. -*- mode: rst -*-
+ .. -*- mode: rst -*-
.. image:: https://travis-ci.org/nilearn/nilearn.svg?branch=master
:target: https://travis-ci.org/nilearn/nilearn
@@ -67,4 +67,4 @@
===========
Detailed instructions on how to contribute are available at
-http://nilearn.github.io/contributing.html
+http://nilearn.github.io/development.html
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore'
old/nilearn-0.6.1/nilearn/datasets/description/seitzman_2018.rst
new/nilearn-0.6.2/nilearn/datasets/description/seitzman_2018.rst
--- old/nilearn-0.6.1/nilearn/datasets/description/seitzman_2018.rst
2020-01-22 11:55:28.000000000 +0100
+++ new/nilearn-0.6.2/nilearn/datasets/description/seitzman_2018.rst
2020-02-24 20:26:10.000000000 +0100
@@ -10,7 +10,7 @@
cerebellum. We validate these ROIs in three datasets via several anatomical
and functional criteria, including known
anatomical divisions and functions, as well as agreement with existing
literature.
Further, we demonstrate that combining these ROIs with established cortical
ROIs recapitulates and extends
-previously described functional network organization." (Seitzman et. al, 2018)
+previously described functional network organization." (Seitzman et. al, 2018,
2020)
@@ -29,7 +29,10 @@
ROI coordinates downloaded from:
https://wustl.box.com/s/twpyb1pflj6vrlxgh3rohyqanxbdpelw
-
-Seitzman, B. A., Gratton, C., Marek, S., Raut, R. V., Dosenbach, N. U.,
Schlaggar, B. L., et al. (2018).
+Paper:
+Seitzman, B. A., Gratton, C., Marek, S., Raut, R. V., Dosenbach, N. U. F.,
Schlaggar, B. L., et al. (2020).
A set of functionally-defined brain regions with improved representation of
the subcortex and cerebellum.
-bioRxiv, 450452. http://doi.org/10.1101/450452
\ No newline at end of file
+NeuroImage, 206, 116290. http://doi.org/10.1016/j.neuroimage.2019.116290
+
+Preprint:
+Seitzman et al. (2018). http://doi.org/10.1101/450452
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nilearn-0.6.1/nilearn/datasets/func.py
new/nilearn-0.6.2/nilearn/datasets/func.py
--- old/nilearn-0.6.1/nilearn/datasets/func.py 2020-01-22 11:55:28.000000000
+0100
+++ new/nilearn-0.6.2/nilearn/datasets/func.py 2020-02-24 20:26:10.000000000
+0100
@@ -250,6 +250,9 @@
verbose=1):
"""Download and loads the NYU resting-state test-retest dataset.
+ NOTE: This function is deprecated and will be removed in the 0.8.x
+ release, due to lack of preprocessing.
+
Parameters
----------
n_subjects: int, optional
@@ -325,6 +328,10 @@
F.X. Castellanos, M.P. Milham
"""
+ warnings.warn("fetch_nyu_rest has been deprecated and will "
+ "be removed in the 0.8.x release.",
+ VisibleDeprecationWarning, stacklevel=2)
+
fa1 = 'http://www.nitrc.org/frs/download.php/1071/NYU_TRT_session1a.tar.gz'
fb1 = 'http://www.nitrc.org/frs/download.php/1072/NYU_TRT_session1b.tar.gz'
fa2 = 'http://www.nitrc.org/frs/download.php/1073/NYU_TRT_session2a.tar.gz'
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nilearn-0.6.1/nilearn/datasets/tests/test_func.py
new/nilearn-0.6.2/nilearn/datasets/tests/test_func.py
--- old/nilearn-0.6.1/nilearn/datasets/tests/test_func.py 2020-01-22
11:55:28.000000000 +0100
+++ new/nilearn-0.6.2/nilearn/datasets/tests/test_func.py 2020-02-24
20:26:10.000000000 +0100
@@ -134,7 +134,9 @@
def test_fetch_nyu_rest(tmp_path, request_mocker):
# First session, all subjects
- nyu = func.fetch_nyu_rest(data_dir=str(tmp_path), verbose=0)
+ with pytest.warns(np.VisibleDeprecationWarning,
+ match='fetch_nyu_rest has been deprecated'):
+ nyu = func.fetch_nyu_rest(data_dir=str(tmp_path), verbose=0)
assert len(tst.mock_url_request.urls) == 2
assert len(nyu.func) == 25
assert len(nyu.anat_anon) == 25
@@ -143,8 +145,11 @@
# All sessions, 12 subjects
tst.mock_url_request.reset()
- nyu = func.fetch_nyu_rest(data_dir=str(tmp_path), sessions=[1, 2, 3],
- n_subjects=12, verbose=0)
+ with pytest.warns(np.VisibleDeprecationWarning,
+ match='fetch_nyu_rest has been deprecated'):
+ nyu = func.fetch_nyu_rest(data_dir=str(tmp_path),
+ sessions=[1, 2, 3],
+ n_subjects=12, verbose=0)
# Session 1 has already been downloaded
assert len(tst.mock_url_request.urls) == 2
assert len(nyu.func) == 36
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nilearn-0.6.1/nilearn/plotting/__init__.py
new/nilearn-0.6.2/nilearn/plotting/__init__.py
--- old/nilearn-0.6.1/nilearn/plotting/__init__.py 2020-01-22
11:55:28.000000000 +0100
+++ new/nilearn-0.6.2/nilearn/plotting/__init__.py 2020-02-24
20:26:10.000000000 +0100
@@ -25,10 +25,14 @@
# that the version is greater that the minimum required one
_import_module_with_version_check('matplotlib',
OPTIONAL_MATPLOTLIB_MIN_VERSION)
+ current_backend = matplotlib.get_backend().lower()
+
+ if 'inline' in current_backend or 'nbagg' in current_backend:
+ return
# Set the backend to a non-interactive one for unices without X
if (os.name == 'posix' and 'DISPLAY' not in os.environ
and not (sys.platform == 'darwin'
- and matplotlib.get_backend() == 'MacOSX')
+ and 'macosx' in current_backend)
):
matplotlib.use('Agg')
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nilearn-0.6.1/nilearn/surface/surface.py
new/nilearn-0.6.2/nilearn/surface/surface.py
--- old/nilearn-0.6.1/nilearn/surface/surface.py 2020-01-22
11:55:28.000000000 +0100
+++ new/nilearn-0.6.2/nilearn/surface/surface.py 2020-02-24
20:26:10.000000000 +0100
@@ -470,7 +470,7 @@
You can control how many samples are drawn by setting `n_samples`.
Once the sampling positions are chosen, those that fall outside of the 3d
- image (or ouside of the mask if you provided one) are discarded. If all
+ image (or outside of the mask if you provided one) are discarded. If all
sample positions are discarded (which can happen, for example, if the
vertex itself is outside of the support of the image), the projection at
this vertex will be ``numpy.nan``.
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nilearn-0.6.1/nilearn/version.py
new/nilearn-0.6.2/nilearn/version.py
--- old/nilearn-0.6.1/nilearn/version.py 2020-01-22 13:50:46.000000000
+0100
+++ new/nilearn-0.6.2/nilearn/version.py 2020-02-25 12:00:32.000000000
+0100
@@ -21,7 +21,7 @@
# Dev branch marker is: 'X.Y.dev' or 'X.Y.devN' where N is an integer.
# 'X.Y.dev0' is the canonical version of 'X.Y.dev'
#
-__version__ = '0.6.1'
+__version__ = '0.6.2'
_NILEARN_INSTALL_MSG = 'See %s for installation information.' % (
'http://nilearn.github.io/introduction.html#installation')
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/nilearn-0.6.1/nilearn.egg-info/PKG-INFO
new/nilearn-0.6.2/nilearn.egg-info/PKG-INFO
--- old/nilearn-0.6.1/nilearn.egg-info/PKG-INFO 2020-01-22 13:52:20.000000000
+0100
+++ new/nilearn-0.6.2/nilearn.egg-info/PKG-INFO 2020-02-25 12:02:59.000000000
+0100
@@ -1,13 +1,13 @@
Metadata-Version: 1.2
Name: nilearn
-Version: 0.6.1
+Version: 0.6.2
Summary: Statistical learning for neuroimaging in Python
Home-page: http://nilearn.github.io
Maintainer: Gael Varoquaux
Maintainer-email: gael.varoqu...@normalesup.org
License: new BSD
Download-URL: http://nilearn.github.io
-Description: .. -*- mode: rst -*-
+Description: .. -*- mode: rst -*-
.. image:: https://travis-ci.org/nilearn/nilearn.svg?branch=master
:target: https://travis-ci.org/nilearn/nilearn
@@ -76,7 +76,7 @@
===========
Detailed instructions on how to contribute are available at
- http://nilearn.github.io/contributing.html
+ http://nilearn.github.io/development.html
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
