Hello community, here is the log from the commit of package python-nilearn for openSUSE:Factory checked in at 2020-04-29 20:53:40 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/python-nilearn (Old) and /work/SRC/openSUSE:Factory/.python-nilearn.new.2738 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Package is "python-nilearn" Wed Apr 29 20:53:40 2020 rev:4 rq:798921 version:0.6.2 Changes: -------- --- /work/SRC/openSUSE:Factory/python-nilearn/python-nilearn.changes 2020-01-31 23:57:55.655671391 +0100 +++ /work/SRC/openSUSE:Factory/.python-nilearn.new.2738/python-nilearn.changes 2020-04-29 20:54:48.353330960 +0200 @@ -1,0 +2,5 @@ +Wed Apr 29 12:53:13 UTC 2020 - Tomáš Chvátal <tchvatal@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.APbcTp/_old 2020-04-29 20:54:49.093332655 +0200 +++ /var/tmp/diff_new_pack.APbcTp/_new 2020-04-29 20:54:49.097332664 +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.varoquaux@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.varoquaux@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