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here is the log from the commit of package python-nilearn for openSUSE:Factory
checked in at 2022-10-12 18:26:59
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/python-nilearn (Old)
and /work/SRC/openSUSE:Factory/.python-nilearn.new.2275 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "python-nilearn"
Wed Oct 12 18:26:59 2022 rev:12 rq:1010211 version:0.9.2
Changes:
--------
--- /work/SRC/openSUSE:Factory/python-nilearn/python-nilearn.changes
2022-07-18 18:34:20.789792397 +0200
+++ /work/SRC/openSUSE:Factory/.python-nilearn.new.2275/python-nilearn.changes
2022-10-12 18:28:32.494198394 +0200
@@ -1,0 +2,101 @@
+Tue Oct 11 22:59:44 UTC 2022 - John Vandenberg <jay...@gmail.com>
+
+- Remove fix-test-decoder.patch merged upstream
+- Remove use of pytest-xdist which makes failures harder to see
+- Update to v0.9.2
+ * save_glm_to_bids has been added, which writes model outputs to
+ disk according to BIDS convention
+ * permuted_ols and non_parametric_inference now support TFCE statistic
+ * permuted_ols and non_parametric_inference now support cluster-level
+ Family-wise error correction
+ * Updated docs with a new theme using furo
+ * Fix _NEUROVAULT_BASE_URL and _NEUROSYNTH_FETCH_WORDS_URL in
+ nilearn/datasets/neurovault.py by using https instead of http
+ * Convert references in nilearn/mass_univariate/permuted_least_squares.py
+ to use bibtex format
+ * Update Craddock 2012 parcellation url in nilearn/datasets/atlas.py
+ * plot_roi failed before when used with the ???contours??? view type
+ and passing a list of cut coordinates in display mode ???x???, ???y??? or
???z???;
+ this has been corrected
+ * plot_markers can now plot a single scatter point
+ * Fix title display for plot_surf_stat_map. The title argument does
+ not set the figure title anymore but the axis title.
+ * load_surf_mesh loaded FreeSurfer specific surface files (e.g. .pial)
+ with a shift in the coordinates. This is fixed by adding the c_ras
+ coordinates to the mesh coordinates
+ * Function nilearn.glm.second_level.second_level._check_second_level_input
+ now raises an error when flm_object argument is False and
+ second_level_input is a list of FirstLevelModel
+ * Function resample_img now warns the user if the provided image has
+ an sform code equal to 0 or None
+ * Fix usage of scipy.stats.gamma.pdf in _gamma_difference_hrf function
+ under nilearn/glm/first_level/hemodynamic_models.py, which resulted
+ in slight distortion of HRF
+ * Fix bug introduced due to a fix in the pre-release version of scipy
+ (1.9.0rc1) which now enforces that elements of a band-pass filter must
+ meet condition Wn[0] < Wn[1]. Now if band-pass elements are equal
+ butterworth returns an unfiltered signal with a warning
+ * The parameter alpha is now correctly passed to plot_glass_brain in
+ plot_connectome
+ * Fix plotting of background image in view_img when the background is
+ not the MNI template
+ * Fix the typographic error on the page Default Mode Network
+ extraction of ADHD dataset
+ * Add sample_masks to fit for censoring time points
+ * Function run_glm and class FirstLevelModel now accept a random_state
+ parameter, which allows users to seed the KMeans cluster model used
+ to estimate AR coefficients
+ * Conform seeding and docstrings in module _utils.data_gen
+ * Docstrings of module second_level were improved
+ * In get_clusters_table, when the center of mass of a binary
+ cluster falls outside the cluster, report the nearest within-cluster
+ voxel instead
+ * Add n_elements_ attribute to masker classes
+ * Functions expecting string filesystem paths now also accept
+ path-like objects
+ * Contributing guidelines now include a recommendation to run flake8
+ locally on the branch diff with main
+ * Improvements to permuted_ols and non_parametric_inference with TFCE
+ statistic runtime
+ * NiftiLabelsMasker now accepts 1-dimensional arrays in its
+ inverse_transform method
+ * Function plot_carpet argument cmap now respects behaviour specified
+ by docs and changes the color of the carpet_plot. Changing the label
+ colors is now delegated to a new variable cmap_labels
+ * Function fetch_surf_fsaverage no longer supports the previously
+ deprecated option fsaverage5_sphere
+ * Classes RegressionResults, SimpleRegressionResults, OLSModel,
+ and LikelihoodModelResults no longer support deprecated shortened
+ attribute names, including df_resid, wdesign, wresid, norm_resid,
+ resid, and wY
+ * Function fetch_openneuro_dataset_index is now deprecated in favor
+ of the new fetch_ds000030_urls function
+ * 64-bit integers in Nifti files: some tools such as FSL, SPM and
+ AFNI cannot handle Nifti images containing 64-bit integers.
+ To avoid compatibility issues, it is best to avoid writing such
+ images and in the future trying to create them with nibabel
+ without explicitly specifying a data type will result in an error.
+ To avoid this, new_img_like now warns when given int64 arrays
+ and converts them to int32 when possible (ie when it would not
+ result in an overflow). Moreover, any atlas fetcher that returned
+ int64 images now produces images containing smaller ints.
+ * Refactors fmriprep confound loading such that that the parsing
+ of the relevant image file and the loading of the confounds are
+ done in separate steps
+ * Private submodules, functions, and classes from the decomposition
+ module now start with a ???_??? character to make it clear that they
+ are not part of the public API
+ * Convert references in nilearn/glm/regression.py and
+ nilearn/glm/thresholding.py to use footcite/footbibliography
+ * Boolean input data in new_img_like now defaults to np.uint8
+ instead of np.int8
+ * The current behavior of maskers??? transform on 3D niimg inputs,
+ in which a 2D array is returned, is deprecated, and 1D arrays
+ will be returned starting in version 0.12
+
+-------------------------------------------------------------------
+Fri Sep 16 12:01:19 UTC 2022 - Guillaume GARDET <guillaume.gar...@opensuse.org>
+
+- Disable multi-thread tests until fixed upstream -- gh#nilearn/nilearn#3359
+
+-------------------------------------------------------------------
Old:
----
fix-test-decoder.patch
nilearn-0.9.1.tar.gz
New:
----
nilearn-0.9.2.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ python-nilearn.spec ++++++
--- /var/tmp/diff_new_pack.hZtWue/_old 2022-10-12 18:28:32.950199396 +0200
+++ /var/tmp/diff_new_pack.hZtWue/_new 2022-10-12 18:28:32.954199406 +0200
@@ -19,15 +19,13 @@
%{?!python_module:%define python_module() python3-%{**}}
%define skip_python2 1
Name: python-nilearn
-Version: 0.9.1
+Version: 0.9.2
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
https://github.com/nilearn/nilearn/commit/4242c0d03e3fc790b17a1d88ce5a4140633c6b6f
fix test decoder (#3252)
-Patch0: fix-test-decoder.patch
BuildRequires: %{python_module base >= 3.6}
BuildRequires: %{python_module setuptools}
BuildRequires: fdupes
@@ -46,7 +44,6 @@
BuildRequires: %{python_module nibabel >= 3.0}
BuildRequires: %{python_module numpy >= 1.18}
BuildRequires: %{python_module pandas >= 1.0}
-BuildRequires: %{python_module pytest-xdist}
BuildRequires: %{python_module pytest}
BuildRequires: %{python_module requests >= 2}
BuildRequires: %{python_module scikit-learn >= 0.22}
@@ -59,7 +56,7 @@
NeuroImaging data.
%prep
-%autosetup -p1 -n nilearn-%{version}
+%setup -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
@@ -82,11 +79,14 @@
donttest+=" or test_clean_confounds"
# https://github.com/nilearn/nilearn/issues/2610
donttest+=" or test_reorder_img_mirror"
-# https://github.com/nilearn/nilearn/issues/3309
-donttest+=" or test_with_globbing_patterns_with_multiple_images"
+# ppc64 https://github.com/nilearn/nilearn/issues/3363
+donttest+=" or (test_load_confounds and test_nilearn_standardize)"
+# x86_64 https://github.com/nilearn/nilearn/issues/3382
+donttest+=" or test_tfce_smoke"
+
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)"
+ # this is a noarch rpm package but the pure python code is only intended
for 64-bit architectures
+%pytest -k "not ($donttest)"
fi
%files %{python_files}
++++++ nilearn-0.9.1.tar.gz -> nilearn-0.9.2.tar.gz ++++++
/work/SRC/openSUSE:Factory/python-nilearn/nilearn-0.9.1.tar.gz
/work/SRC/openSUSE:Factory/.python-nilearn.new.2275/nilearn-0.9.2.tar.gz
differ: char 13, line 1
