Script 'mail_helper' called by obssrc Hello community, here is the log from the commit of package python-nilearn for openSUSE:Factory checked in at 2022-01-22 08:18:06 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/python-nilearn (Old) and /work/SRC/openSUSE:Factory/.python-nilearn.new.1938 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "python-nilearn" Sat Jan 22 08:18:06 2022 rev:10 rq:947807 version:0.8.1 Changes: -------- --- /work/SRC/openSUSE:Factory/python-nilearn/python-nilearn.changes 2021-04-10 15:28:59.870492833 +0200 +++ /work/SRC/openSUSE:Factory/.python-nilearn.new.1938/python-nilearn.changes 2022-01-22 08:18:40.626704447 +0100 @@ -1,0 +2,37 @@ +Thu Jan 20 21:17:06 UTC 2022 - Ben Greiner <[email protected]> + +- Update to 0.8.1 + * New atlas fetcher nilearn.datasets.fetch_atlas_juelich to + download Juelich atlas from FSL. + * New grey and white-matter template and mask loading functions: + nilearn.datasets.load_mni152_gm_template, + nilearn.datasets.load_mni152_wm_template, + nilearn.datasets.load_mni152_gm_mask, and + nilearn.datasets.load_mni152_wm_mask + * Nilearn development process has been reworked. It now provides + insights on nilearn organization as a project as well as more + explicit Contribution Guidelines. + * nilearn.image.binarize_img binarizes images into 0 and 1. + * nilearn.input_data.NiftiLabelsMasker can now generate HTML + reports in the same way as nilearn.input_data.NiftiMasker. + * nilearn.signal.clean accepts new parameter sample_mask. shape: + (number of scans - number of volumes removed, ) + * All inherent classes of nilearn.input_data.BaseMasker can use + parameter sample_mask for sub-sample masking. + * Fetcher nilearn.datasets.fetch_surf_fsaverage now accepts + fsaverage3, fsaverage4 and fsaverage6 as values for parameter + mesh, so that all resolutions of fsaverage from 3 to 7 are now + available. + * Fetcher nilearn.datasets.fetch_surf_fsaverage now provides + attributes {area, curv, sphere, thick}_{left, right} for all + fsaverage resolutions. + * nilearn.glm.first_level.run_glm now allows auto regressive + noise models of order greater than one. + * Support for Nibabel 2.x is deprecated and will be removed in + the 0.9 release. +- Add nilearn-pr3094-py310.patch -- gh#nilearn/nilearn#3094 +- Add nilearn-pr3136-pythoncall.patch -- gh#nilearn/nilearn#3136 +- Only test on 64-bit platforms + -- http://nilearn.github.io/introduction.html#installation + +------------------------------------------------------------------- Old: ---- nilearn-0.7.1.tar.gz New: ---- nilearn-0.8.1.tar.gz nilearn-pr3094-py310.patch nilearn-pr3136-pythoncall.patch ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ python-nilearn.spec ++++++ --- /var/tmp/diff_new_pack.8yJA8m/_old 2022-01-22 08:18:41.470698759 +0100 +++ /var/tmp/diff_new_pack.8yJA8m/_new 2022-01-22 08:18:41.474698732 +0100 @@ -1,7 +1,7 @@ # # spec file for package python-nilearn # -# Copyright (c) 2021 SUSE LLC +# Copyright (c) 2022 SUSE LLC # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed @@ -16,40 +16,43 @@ # -%{?!python_module:%define python_module() python-%{**} python3-%{**}} +%{?!python_module:%define python_module() python3-%{**}} %define skip_python2 1 -# SciPy 1.6.0 dropped support for Python 3.6 -%define skip_python36 1 Name: python-nilearn -Version: 0.7.1 +Version: 0.8.1 Release: 0 Summary: Statistical learning tool for neuroimaging License: BSD-3-Clause Group: Development/Languages/Python URL: https://github.com/nilearn/nilearn Source: https://github.com/nilearn/nilearn/archive/%{version}.tar.gz#/nilearn-%{version}.tar.gz +# PATCH-FIX-UPSTREAM nilearn-pr3094-py310.patch -- gh#nilearn/nilearn#3094 +Patch0: nilearn-pr3094-py310.patch +# PATCH-FIX-UPSTREAM nilearn-pr3136-pythoncall.patch -- gh#nilearn/nilearn#3136 +Patch1: nilearn-pr3136-pythoncall.patch +BuildRequires: %{python_module base >= 3.6} BuildRequires: %{python_module setuptools} BuildRequires: fdupes BuildRequires: python-rpm-macros Requires: python-joblib >= 0.12 Requires: python-matplotlib >= 2.0 -Requires: python-nibabel >= 2.0.2 -Requires: python-numpy >= 1.11 +Requires: python-nibabel >= 2.5.0 +Requires: python-numpy >= 1.16 Requires: python-requests -Requires: python-scikit-learn >= 0.19 -Requires: python-scipy >= 0.19 +Requires: python-scikit-learn >= 0.21 +Requires: python-scipy >= 1.2.0 BuildArch: noarch # SECTION test requirements BuildRequires: %{python_module joblib >= 0.12} BuildRequires: %{python_module matplotlib >= 2.0} -BuildRequires: %{python_module nibabel >= 2.0.2} -BuildRequires: %{python_module numpy >= 1.11} -BuildRequires: %{python_module pandas} +BuildRequires: %{python_module nibabel >= 2.5.0} +BuildRequires: %{python_module numpy >= 1.16} +BuildRequires: %{python_module pandas >= 0.24} BuildRequires: %{python_module pytest-xdist} BuildRequires: %{python_module pytest} BuildRequires: %{python_module requests} -BuildRequires: %{python_module scikit-learn >= 0.19} -BuildRequires: %{python_module scipy >= 0.19} +BuildRequires: %{python_module scikit-learn >= 0.21} +BuildRequires: %{python_module scipy >= 1.2.0} # /SECTION %python_subpackages @@ -58,7 +61,10 @@ NeuroImaging data. %prep -%setup -q -n nilearn-%{version} +%autosetup -p1 -n nilearn-%{version} +sed -i '/durations/d' setup.cfg +chmod -x nilearn/datasets/tests/data/localizer_index.json +sed -i '1{/env python/d}' nilearn/glm/tests/test_utils.py nilearn/plotting/glass_brain_files/plot_align_svg.py %build %python_build @@ -70,11 +76,18 @@ %check # Test try to build the doc and run examples... rm -rf doc/ examples/ -# Disable tests that require a network connection -# 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 -# https://github.com/nilearn/nilearn/issues/2608 - test_clean_confounds -# https://github.com/nilearn/nilearn/issues/2610 - test_reorder_img_mirror -%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_clean_confounds or test_reorder_img_mirror)' +# sporadic race condition in pytest-xdist +donttest="test_with_globbing_patterns_with_single_subject" +# sporadic unknown failure (on all architectures): https://github.com/nilearn/nilearn/issues/2607 +donttest+=" or test_check_niimg_wildcard" +# https://github.com/nilearn/nilearn/issues/2608 +donttest+=" or test_clean_confounds" +# https://github.com/nilearn/nilearn/issues/2610 +donttest+=" or test_reorder_img_mirror" +if [[ $(getconf LONG_BIT) -eq 64 ]]; then +# this is a noarch rpm package but the pure python code is only intended for 64-bit architectures +%pytest -n auto -k "not ($donttest)" +fi %files %{python_files} %doc AUTHORS.rst README.rst ++++++ nilearn-0.7.1.tar.gz -> nilearn-0.8.1.tar.gz ++++++ /work/SRC/openSUSE:Factory/python-nilearn/nilearn-0.7.1.tar.gz /work/SRC/openSUSE:Factory/.python-nilearn.new.1938/nilearn-0.8.1.tar.gz differ: char 13, line 1 ++++++ nilearn-pr3094-py310.patch ++++++ >From 4d5cf7eef79c5431c478a08209e3c6ad8d0dd421 Mon Sep 17 00:00:00 2001 From: Eric Larson <[email protected]> Date: Tue, 14 Dec 2021 12:41:48 -0500 Subject: [PATCH 1/2] BUG: Import from collections.abc for 3.10 --- nilearn/surface/surface.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) Index: nilearn-0.8.1/nilearn/surface/surface.py =================================================================== --- nilearn-0.8.1.orig/nilearn/surface/surface.py +++ nilearn-0.8.1/nilearn/surface/surface.py @@ -7,7 +7,7 @@ import collections import gzip from distutils.version import LooseVersion from collections import namedtuple - +from collections.abc import Mapping import numpy as np from scipy import sparse, interpolate @@ -960,7 +960,7 @@ def _check_mesh(mesh): """ if isinstance(mesh, str): return datasets.fetch_surf_fsaverage(mesh) - if not isinstance(mesh, collections.Mapping): + if not isinstance(mesh, Mapping): raise TypeError("The mesh should be a str or a dictionary, " "you provided: {}.".format(type(mesh).__name__)) missing = {'pial_left', 'pial_right', 'sulc_left', 'sulc_right', ++++++ nilearn-pr3136-pythoncall.patch ++++++ >From 50a4880a6c71d8bc9a695a14715ad9ae643d1390 Mon Sep 17 00:00:00 2001 From: Ben Greiner <[email protected]> Date: Thu, 20 Jan 2022 22:30:32 +0100 Subject: [PATCH] replace interpreter call The python command is not guaranteed to exist. On some systems it refers to old python 2. See https://www.python.org/dev/peps/pep-0394/ --- nilearn/plotting/html_document.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nilearn/plotting/html_document.py b/nilearn/plotting/html_document.py index f93377cbb2..bfb166af00 100644 --- a/nilearn/plotting/html_document.py +++ b/nilearn/plotting/html_document.py @@ -1,4 +1,5 @@ import os +import sys import weakref import warnings import tempfile @@ -20,7 +21,7 @@ def set_max_img_views_before_warning(new_value): def _remove_after_n_seconds(file_name, n_seconds): script = os.path.join(os.path.dirname(__file__), 'rm_file.py') - subprocess.Popen(['python', script, file_name, str(n_seconds)]) + subprocess.Popen([sys.executable, script, file_name, str(n_seconds)]) class HTMLDocument(object):
