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 2024-10-16 23:48:02 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/python-nilearn (Old) and /work/SRC/openSUSE:Factory/.python-nilearn.new.19354 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Package is "python-nilearn" Wed Oct 16 23:48:02 2024 rev:5 rq:1208244 version:0.10.4 Changes: -------- --- /work/SRC/openSUSE:Factory/python-nilearn/python-nilearn.changes 2024-02-22 21:00:41.595939478 +0100 +++ /work/SRC/openSUSE:Factory/.python-nilearn.new.19354/python-nilearn.changes 2024-10-16 23:49:21.287493374 +0200 @@ -1,0 +2,33 @@ +Wed Oct 16 02:30:41 UTC 2024 - Steve Kowalik <steven.kowalik@suse.com> + +- Update to 0.10.4: + ## Highlights + * Use the appropriate HTML templates for nilearn.maskers.MultiNiftiMapsMasker + and nilearn.maskers.MultiNiftiLabelsMasker reports that would lead to + empty reports for MultiNiftiMapsMasker. + * Fix color bar handling with color map with only 1 level. + * Improve colorbar size and labels in mosaic display. + ## Fixes + * Fix plotting of carpet plot due to a change in the coming version of + matplolib (3.9.0). + * Fix errant warning when using stat_type in nilearn.glm.compute_contrast. + * Fix when thresholding is applied to images by GLM reports. + * Make masker report tables horizontally scrollable. + * Masker reports tables do not overlap with report image. + * Ensure that region_names_ can be generated by + nilearn.maskers.NiftiSpheresMasker.transform_single_imgs for deterministic + atlases that use floats or non-consecutive values as region_ids whether + they include background in their labels or not. + * Ensure that nilearn.interfaces.bids.save_glm_to_bids serializes numpy + arrays to list used as GLM parameters before saving them to JSON. + * Check that the view parameter in surface plotting functions is a pair of + int or float when it is not a string. + * Fix positions of the markers on the images on the sphere masker reports. + * Fix cut position in nifti maps maskers to match displayed map maximum. + * Make sure that nilearn.maskers.NiftiSpheresMasker reports displays + properly when it contains only 1 sphere. + ## Enhancements + * Add an avg_method parameter to nilearn.plotting.plot_surf_stat_map. +- Add patch support-new-scipy.patch, support new scipy changes. + +------------------------------------------------------------------- Old: ---- nilearn-0.10.3.tar.gz New: ---- nilearn-0.10.4.tar.gz support-new-scipy.patch BETA DEBUG BEGIN: New: * Add an avg_method parameter to nilearn.plotting.plot_surf_stat_map. - Add patch support-new-scipy.patch, support new scipy changes. BETA DEBUG END: ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ python-nilearn.spec ++++++ --- /var/tmp/diff_new_pack.lZxBGN/_old 2024-10-16 23:49:22.791556101 +0200 +++ /var/tmp/diff_new_pack.lZxBGN/_new 2024-10-16 23:49:22.795556268 +0200 @@ -19,13 +19,14 @@ # Run tests in parallel with pytest-xdist. On by default. %bcond_without pytest_xdist Name: python-nilearn -Version: 0.10.3 +Version: 0.10.4 Release: 0 Summary: Statistical learning tool for neuroimaging License: BSD-3-Clause -Group: Development/Languages/Python URL: https://github.com/nilearn/nilearn Source: https://files.pythonhosted.org/packages/source/n/nilearn/nilearn-%{version}.tar.gz +# PATCH-FIX-UPSTREAM gh#nilearn/nilearn#4394 +Patch0: support-new-scipy.patch BuildRequires: %{python_module base >= 3.8} BuildRequires: %{python_module hatch_vcs} BuildRequires: %{python_module hatchling} @@ -52,6 +53,7 @@ BuildRequires: %{python_module packaging} BuildRequires: %{python_module pandas >= 1.1.5} %{?with_pytest_xdist:BuildRequires: %{python_module pytest-xdist}} +BuildRequires: %{python_module plotly} BuildRequires: %{python_module pytest} BuildRequires: %{python_module requests >= 2.25.0} BuildRequires: %{python_module rich} @@ -91,6 +93,8 @@ # unresolvable documentation package requirement docstring_parser ignorefiles="--ignore maint_tools/check_glossary_term.py" +# ignore cache files too +ignorefiles+=" --ignore nilearn_cache" 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 ++++++ nilearn-0.10.3.tar.gz -> nilearn-0.10.4.tar.gz ++++++ /work/SRC/openSUSE:Factory/python-nilearn/nilearn-0.10.3.tar.gz /work/SRC/openSUSE:Factory/.python-nilearn.new.19354/nilearn-0.10.4.tar.gz differ: char 17, line 1 ++++++ support-new-scipy.patch ++++++ From 5effd2789ed89042a41575fef4a6fc97922b0ac0 Mon Sep 17 00:00:00 2001 From: Remi Gau <remi_gau@hotmail.com> Date: Tue, 23 Apr 2024 13:58:35 +0200 Subject: [PATCH 1/2] changed cg parameters --- nilearn/_utils/segmentation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nilearn/_utils/segmentation.py b/nilearn/_utils/segmentation.py index 8c6367b847..3cc47d87f1 100644 --- a/nilearn/_utils/segmentation.py +++ b/nilearn/_utils/segmentation.py @@ -355,7 +355,7 @@ def _solve_cg(lap_sparse, B, tol): lap_sparse = lap_sparse.tocsc() X = [] for i in range(len(B)): - x0 = cg(lap_sparse, -B[i].todense(), tol=tol, atol="legacy")[0] + x0 = cg(lap_sparse, -B[i].todense(), rtol=tol, atol=0)[0] X.append(x0) X = np.array(X) From 9075d6a15d17cfe9cb684f3a5ac8537af98c3af3 Mon Sep 17 00:00:00 2001 From: Remi Gau <remi_gau@hotmail.com> Date: Wed, 24 Apr 2024 08:38:48 +0200 Subject: [PATCH 2/2] fix compat support scipy < 1.12 [test nightly] --- nilearn/_utils/segmentation.py | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/nilearn/_utils/segmentation.py b/nilearn/_utils/segmentation.py index 3cc47d87f1..844e018807 100644 --- a/nilearn/_utils/segmentation.py +++ b/nilearn/_utils/segmentation.py @@ -11,10 +11,12 @@ import warnings import numpy as np -from scipy import ndimage as ndi, sparse +from scipy import __version__, ndimage as ndi, sparse from scipy.sparse.linalg import cg from sklearn.utils import as_float_array +from nilearn._utils.helpers import compare_version + def _make_graph_edges_3d(n_x, n_y, n_z): """Return a list of edges for a 3D image. @@ -355,7 +357,14 @@ def _solve_cg(lap_sparse, B, tol): lap_sparse = lap_sparse.tocsc() X = [] for i in range(len(B)): - x0 = cg(lap_sparse, -B[i].todense(), rtol=tol, atol=0)[0] + # TODO Python 3.8 + # consider remove if/else block when dropping support for 3.8 + # would require pinning scipy to >= 1.12 + # See https://github.com/nilearn/nilearn/pull/4394 + if compare_version(__version__, ">=", "1.12"): + x0 = cg(lap_sparse, -B[i].todense(), rtol=tol, atol=0)[0] + else: + x0 = cg(lap_sparse, -B[i].todense(), tol=tol, atol="legacy")[0] X.append(x0) X = np.array(X)