Recent Releases of hidimstat

hidimstat - 0.12.1

What's Changed

[MAINT] post release by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5474
chore: update pre-commit hooks by @pre-commit-ci[bot] in https://github.com/nilearn/nilearn/pull/5480
[MAINT] mark slow test by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5479
[MAINT] ensure compliance of GroupSparseCovariance with sklearn guidelines by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5482
[DOC] reduce number of warnings in examples by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5489
[MAINT] improve HierarchicalKMeans sklearn compliance by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5486
[MAINT] add nfeaturesin_ to ConnectivityMeasure by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5483
[MAINT] Unnecessary comprehension by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/5500
[MAINT] check compliance ReNa with sklearn guidelines by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5485
[MAINT] ensure decomposition estimator return self by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5491
[MAINT] silence warnings in test and doc build by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5498
[REF] minor refactor for clustering estimators expected failed checks by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5501
[MAINT] ignore warnings for nilearn check estimators by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5502
[MAINT] homogenize logger calls in maskers by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5496
chore: update pre-commit hooks by @pre-commit-ci[bot] in https://github.com/nilearn/nilearn/pull/5505
[MAINT] ensure img estimators can be pickled by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5499
[FIX] Align symmetric_cmap behavior in plotting package for plotly backend with matplotlib backend by @hndgzkn in https://github.com/nilearn/nilearn/pull/5492
[MAINT] check decoder is fitted by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5490
[MAINT] run doc build on latest python / dependencies by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5462
[MAINT] Unnecessary comprehension by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/5507
[FIX] ensure transform / inverse_transform can be used on decomposition estimators by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5503
[MAINT] reduce warnings and verbosity in doc by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5504
chore: update pre-commit hooks by @pre-commit-ci[bot] in https://github.com/nilearn/nilearn/pull/5514
[MAINT] check all image estimators are unchanged by transform by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5510
[FIX] Update deprecation warning for nilearn.datasets.fetch_neurovault_motor_task by @hndgzkn in https://github.com/nilearn/nilearn/pull/5526
[MAINT] mark slow tests by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5529
[ENH] Refactor plotting to extract engine utils by @hndgzkn in https://github.com/nilearn/nilearn/pull/5521
[STY] fix some ruff issues by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5533
[MAINT] Update pre-commit ruff legacy alias by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/5540
[FIX] change resampling interpolation of maps by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5519
[FIX] avoid darkness deprecation warnings when generating masker reports by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5532
[FIX] do not use setuptools-scm 9... for now by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5549
[REF] speed up some slow tests by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5531
chore: update pre-commit hooks by @pre-commit-ci[bot] in https://github.com/nilearn/nilearn/pull/5541
added my name to citation list by @gurraburra in https://github.com/nilearn/nilearn/pull/5534
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions[bot] in https://github.com/nilearn/nilearn/pull/5552
chore: update pre-commit hooks by @pre-commit-ci[bot] in https://github.com/nilearn/nilearn/pull/5553
[STY] applying some ruff preview rules by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/5546
[FIX] fix type t_r for python < 3.10 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5550
[ENH] Refactor plotting separate image by @hndgzkn in https://github.com/nilearn/nilearn/pull/5481
[FIX] enforce dtype for all parts of SurfaceImage and Polydata by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5530
[MAINT] PEP 639 compliance by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/5543
[DOC] fix bad reference in changelog by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5559
[FIX] ensure better compliance of CacheMixin with sklearn guidelines by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5509
[TEST] check CI runs by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5567
Bump actions/download-artifact from 4 to 5 by @dependabot[bot] in https://github.com/nilearn/nilearn/pull/5571
chore: update pre-commit hooks by @pre-commit-ci[bot] in https://github.com/nilearn/nilearn/pull/5574
[FIX] fix handling of regions names and indices by label maskers by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5551
[DOC] improve doc and test around screening percentile adjustments by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5556
Bump actions/checkout from 4 to 5 by @dependabot[bot] in https://github.com/nilearn/nilearn/pull/5586
chore: update pre-commit hooks by @pre-commit-ci[bot] in https://github.com/nilearn/nilearn/pull/5587
[MAINT] add checkpipelineconsistency for nilearn estimators by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5560
[MAINT] add check that regressor do not have decision function by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5562
[MAINT] run check estimators on other methods by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5563
[MAINT] reduce warnings in doc build by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5520
[MAINT] simplify nilearn.utils.init.py by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5585
[FIX] give a dummy color to background when it needs to be added to LUT by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5582
[REF] turn "isclassification" and "clusteringpercentile" into private properties by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5557
[FIX] check nfeaturesin_ for estimators by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5575
[MAINT] run estimator checks on SpaceNet estimators by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5564
[FIX] check all decoders can work with surfaces by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5569
[FIX] ensure fit and transform takes a y parameter by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5565
[MAINT] check sample order invariance of estimators by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5591
[MAINT] clean up test decoders by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5593
[MAINT] check image estimator idempotence by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5566
[MAINT] fix link redirect by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5602
[MAINT] remove duplicate tests space_net by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5597
chore: update pre-commit hooks by @pre-commit-ci[bot] in https://github.com/nilearn/nilearn/pull/5603
[FIX] ensure consistent signature and documentation of image estimators by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5536
[FIX] remove is_classif (and loss) parameter from SpaceNet classes by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5594
[FIX] set up proper data for a flaky test by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5605
[MAINT] update TODOs to explicitly mention when they become relevant by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5606
[REF] extract _ClassifierMixin and _RegressorMixin by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5595
[DOC] fix doc strings for SpaceNet estimators by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5607
[DEP] start deprecation cycle for default Z threshold by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5601
[REF] refactor spacenet expected fails for sklearn checks by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5612
[FIX] ensure decoders (predict, score, decision_function) work with both image or arrays by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5611
[FIX] handle colorbar plotting for surfaces when vmin == vmax by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5616
[ENH] Refactor nilearn.plotting: extract common code by @hndgzkn in https://github.com/nilearn/nilearn/pull/5608
[MAINT] fix some ruff errors by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5618
[DOC] fix minor rendering issues in the doc by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5617
[FIX] avoid joblib warnings regarding using partial functions by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5613
[FIX] make sure GLM reports plot according to twosided and clusterthreshold parameters by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5578
[FIX] ensure consistent output of surface label masker for output signal, regionid and regionname by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5614
[DOC] minor fixes post #5578 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5639
[FIX] adapt mask_args depending on masking strategy for (Multi)NiftiMasker. by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5637
REL 0.12.1 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5622

New Contributors

@gurraburra made their first contribution in https://github.com/nilearn/nilearn/pull/5534

Full Changelog: https://github.com/nilearn/nilearn/compare/0.12.0...0.12.1

- Python
Published by Remi-Gau 9 months ago

hidimstat - 0.12.0

What's Changed

[MAINT] post release 0.11.1 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4982
[MAINT] only run link checks on full build of the doc by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4969
[STY] Apply assorted ruff preview rules by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4977
[ENH] rename parameter: version -> atlas_type by @hndgzkn in https://github.com/nilearn/nilearn/pull/4929
[FIX] fix rendering unordered list in doc by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4979
[STY] add doc strings in classes in test by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4970
[MAINT] use UV to install in CI by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4964
[REF] refactor test surface plotting by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4966
[DOC] fix citations by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4981
[DOC] fix figures stacking in doc by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4980
[STY] remove code block wrapping by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4973
[TEST] do not install latex for doc build by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4976
[FIX] Use figure_to_svg_base64 instead of figure_to_png_base64 by @man-shu in https://github.com/nilearn/nilearn/pull/4985
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/4987
[MAINT] remove .nojekyll handling by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4992
[DOC] add page for older doc versions by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4989
[REF] refactor test plotting by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4986
[MAINT] fix dead link flagged by linkcheck by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4993
[DOC] fix references by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4994
[FIX] fix deploy on release by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4988
Revert "[FIX] fix deploy on release" by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4995
[REF] move surface utility functions by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4956
[FIX] fix deploy on release by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4996
Revert "[FIX] fix deploy on release" by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4997
[FIX] fix deploy on release by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4998
Bump astral-sh/setup-uv from 4 to 5 by @dependabot in https://github.com/nilearn/nilearn/pull/5000
[FIX] set git username / mail for dev doc deploy by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5001
[ENH] Allow plotting hemi="both" by @man-shu in https://github.com/nilearn/nilearn/pull/4991
[ENH] update default colors by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4959
[MAINT] Remove legacy format for dataset fetchers by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5004
[MAINT] optional import of getclustertable by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4881
[FIX] Fix two-sided image thresholding by @hndgzkn in https://github.com/nilearn/nilearn/pull/4951
[FIX] minor fixes in examples by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5007
[MAINT] remove if block for unsupported sklearn version by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5009
[REF] extract check doc build type by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4984
[FIX] convert labels to string in labels in dataset fetchers by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5006
[DOC] update labels in plotsurfaceimage_maskers by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5011
[FIX] skip failing tests on "windows & matplotlib==3.3.0" by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5010
[FIX] Convert Schaeffer atlas labels to list of strings by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5013
[FIX] build examples in PR by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5017
[STY] add mising stacklevel in warnings in in nilearn.image by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5005
[DOC] refactor description datasets functional derivatives by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5015
[REF] extract niftimapsmasker_ into property by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5008
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5025
[DOC] update colormaps and doc strings by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5021
[MAINT] update badges by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5026
[MISC] update doc strings types by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5023
[ENH] Standardize atlases: add look up tables for deterministic atlases by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4820
[DOC] update documentation for look up tables of atlases by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5019
[FIX] validate meshes by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5036
[DOC] add links to more older doc versions by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5033
[DOC] add ':obj:' link in doc strings by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5012
[MAINT] pacify mypy by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5022
Revert "[MAINT] pacify mypy" by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5040
[DOC] refactor description templates by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5014
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5046
[MAINT] remove dead code by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5038
[MAINT] Make functions used outside of their module public by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5037
[FIX] updates to fix some tests failures with sklearn 1.6.1 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5044
[MAINT] Add docstrings to test mass_univariate by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5032
[DOC] update defaults in doc strings by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5024
[DOC] update description nki by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5031
[REF] refactor tests nifti maps masker by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5027
[DOC] use matplolib by default in plot3dmaptosurface_projection.py by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5020
[REF] refactor atlas by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5041
[MAINT] use tag for commit message of release by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5034
[MAINT] fix doc build in main by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5047
[ENH] add report to surface based GLMs by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4442
[MAINT] add nilearn estimator checks by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5029
[MAINT] fix check CFF workflows by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5048
[MAINT] NiftiSphereMasker: comply with checkparametersdefault_constructible by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4914
[ENH] Plot PNG instead of SVG in surface masker reports by @man-shu in https://github.com/nilearn/nilearn/pull/5052
[MAINT] ruff formatter now compatible with ISC001/ISCO02 by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/5054
[STY] Multiple imports for an import name by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/5055
[REF] reuse fixtures in testregionextractor by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5051
[MAINT] Fix check_docstrings not checking any files and not catching unneeded fill_doc by @michellewang in https://github.com/nilearn/nilearn/pull/5049
MAINTNiftiLabelsMasker: comply with checkparametersdefault_constructible by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4916
[REF] change order of input checks in fit of nifti label masker by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5056
[REF] refactor test nifti maskers with masks by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5058
MAINTNiftiMapsMasker: comply with checkparametersdefault_constructible by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4917
[DOC] add docstrings to some tests for maskers by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5057
[MAINT] refactor import in maskers by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5060
[MAINT] remove old 'tags' in nilearn/decoding by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5065
[MAINT] remove valid checks duplicate by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5066
[MAINT] add transformer checks for all estimators by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5067
[MAINT] Improve test of cleaning in maskers by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5059
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5072
[DOC][FIX] Interacting buttons and navbar across different reports by @man-shu in https://github.com/nilearn/nilearn/pull/5071
[MAINT] refactor checks nifti maskers by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5068
[REF] refactor permuted_ols by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5077
[FIX] improve compliance with sklearn checks by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5061
[DOC] Add documentation about CI and doc build by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5073
[MAINT] make sure surf_mesh fixture returns a polymesh by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5083
[REF] refactor plotsurfcontours by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5076
[MAINT] add check dtype for all nifti maskers by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5069
[FIX] adapt surf_mesh fixture by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5087
[FIX] Pin Kaleido to 0.2.1 by @man-shu in https://github.com/nilearn/nilearn/pull/5089
[DOC] add docstrings to all masker tests by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5079
[ENH] Add reports for SurfaceMapsMasker by @man-shu in https://github.com/nilearn/nilearn/pull/4968
[ENH] Use pandas to create parameter HTML tables in masker reports by @man-shu in https://github.com/nilearn/nilearn/pull/5084
[MAINT] pacify mypy by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5045
[REF] refactor resample_img by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5075
Check that sample_mask ends up as array of signed integers by @psadil in https://github.com/nilearn/nilearn/pull/5030
[ENH] standardize yeo atlas fetcher by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5085
[TEST] skip test on windows, old mpl, new np by @man-shu in https://github.com/nilearn/nilearn/pull/5098
[FIX] Introduce clean_args for nifti maskers to replace paramaters passed via kwargs by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5082
[MAINT] check maskers fit return self by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5099
[ENH] Move js out of HTML report templates by @man-shu in https://github.com/nilearn/nilearn/pull/5090
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5102
[MAINT] skip check estimators for estimators with image input by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5100
[FIX] fix typo that prevents doc build on main by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5104
[MAINT] run linkcheck only on main by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5103
[FIX] fix issues regarding using two_sided and negative plotting threshold during plotting by @hndgzkn in https://github.com/nilearn/nilearn/pull/5088
[REF] centralize test maskers smoothing by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5094
[REF] refactor test to check 5D input to nifti masker transform by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5107
[ENH] Use look up table in surface label masker by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5086
[FIX] ensure datasets do not contain bytes or numpy arrays by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5109
[FIX] Do not set score=0 if all decoder.coef_ ==0 by @man-shu in https://github.com/nilearn/nilearn/pull/5097
[FIX] pass correct image to build surface masker report by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5111
[DOC] Add link to older doc versions by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5115
[FIX] update thresolding in paired / unpaired t-test example by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5116
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5118
[ENH] Add thresholding examples by @hndgzkn in https://github.com/nilearn/nilearn/pull/5108
[ENH] add surface support for nonparametricinference by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5078
[MAINT] remove obsolete check to skip by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5119
[ENH] add plotblandaltman function by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5112
[ENH] implement strategy for surface label masker by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4809
[MAINT] centralize image comparison functions into a separate module by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5120
[ENH] improve nilearn check is fitted by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5105
[FIX] Specify output dtype of SurfaceLabelsMasker.transform by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5123
[MAINT] add type checking for parameters listed in nilearn_utils.docs by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5117
[MAINT] apply checkestimatorsunfitted to all estimators by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5122
[REF] refactor groupsparsecovariance by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5126
[REF] refactor test label maskers by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5127
[FIX] ensure all nifti maskers throw warning when dealing with non finite mask by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5070
[MAINT] expand type checking at run time by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5125
[REF] refactor test masking by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5131
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5139
[ENH] allow numpy equivalent to int and float for several common parameters by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5135
[ENH] extend type checking at run time by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5133
[REF] extract function to save figure by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5136
[REF] refactor tests signals by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5140
[FIX] return design matrices of FIAC as dataframes by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5142
[DOC] mention atlasreader package to locate clusters by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5143
[REF] remove unnecessary memory handling by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5147
[FIX] Update parameters to comply with run time checks by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5146
[ENH] improve sulci and subcortical schema for glass brain sagittal plots by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5141
[REF] extract reporting functions that do not depend on matplotlib by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5145
[REF] refactor example thresolding by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5153
[REF] refactor resampling by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5156
[DOC] Masking huge fMRI images efficiently by @man-shu in https://github.com/nilearn/nilearn/pull/5113
[REF] refactor test interfaces by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5157
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5158
[ENH] add vmax to example plotresampleto_template.py by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5155
[REF] add doc strings to tests in for datasets/_utils by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5159
[DOC] Leave twitter by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5163
[MAINT] remove authors from modules by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5164
[ENH] add function to threshold surface image by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4999
[DOC] update colormap example by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4851
[FIX] improve bg_map checks by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5167
[REF] simplify complex tests by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5162
[REF] refactor test maskers generate_report by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5129
[MAINT] Add pytest-mpl unit tests to check ouput changes in plots by @ymzayek in https://github.com/nilearn/nilearn/pull/4123
[REF] fix simple issues flagged by sourcery by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5170
[ENH] add surface image support to plotimgcomparison by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5132
[ENH] add possibility to use atlas look-up table as cmap by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5160
[REF] move estimator checks in their own module by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5173
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5177
[ENH] make colorbar=True the default for plotting functions by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5172
DOC Fix binder notebook generation by @lesteve in https://github.com/nilearn/nilearn/pull/5187
[MAINT] skip compare figures tests for windows + matplotlib 3.3.0 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5182
[MAINT] check coverage of tests file by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5189
[MAINT] track and plot tests duration by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5188
[REF] refactor fixtures by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5190
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5193
[FIX][DOC] Load images once in parallel function instead of single function by @man-shu in https://github.com/nilearn/nilearn/pull/5185
[DOC] Add license for Yeo 2011 Atlas by @psadil in https://github.com/nilearn/nilearn/pull/5195
[ENH] Refactor plotting imports by @hndgzkn in https://github.com/nilearn/nilearn/pull/5194
[DOC] show API main modules in doc by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5196
[MAINT] speed up slow tests by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5191
[REF] apply sourcery refactoring by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5176
[MAINT] up timeout of test by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5198
[MAINT] set license for documentation by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5165
[REF] Create single variable to set default colormaps by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5200
[MAINT] use same variable name for write_fake_fmri_data_and_design and generate_fake_fmri_data_and_design by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5197
[FIX] Assign most frequent value in the neighborhood for atlases via vol_to_surf with method='nearest_most_frequent' by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5169
[DOC] add summary table for atlases by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5174
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5205
[FIX] prevent range overrun by @Leengit in https://github.com/nilearn/nilearn/pull/5179
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/5206
[MAINT] only run some workflows on upstream by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5204
[FIX] set xlim for plot events by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5208
[FIX] fix layout and ui issues in the report by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5201
[ENH] add transparency to overlays for volume based plots by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5151
[FIX] tweak latex image to render better by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5213
[FIX] fix headings in plotting API page by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5217
[REF] refactor GLM reports by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5202
[MAINT] use proper sklearn 1.6 functions and methods in tests by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5212
[FIX] ensure maskers can be refitted by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5225
[REF] refactor valid check_estimators by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5229
[REF] refactor generating report warnings when no matplotlib is present by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5221
[STY] fix some image resizing on mobile by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5230
[ENH] generate method section in GLM reports by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5226
[MAINT] add glm estimator checks by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5227
[MAINT] add check_transformers replacement for instead of using sklearn one by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5228
[DOC] Add future deprecation directive for 'nearest' interpolation in vol_to_surf by @man-shu in https://github.com/nilearn/nilearn/pull/5238
[REF] refactor more extravalidchecks into expectedfailedchecks by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5236
[REF] hoist imports by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5239
[FIX] reduce number of warning during searchligh by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5242
[REF] rename getvoxelwisemodelattribute by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5241
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5245
[ENH] Refactor nilearn.plotting - create plotting.matrix package by @hndgzkn in https://github.com/nilearn/nilearn/pull/5240
[FIX][DOC] make sure figure in plotsurfaceimageandmaskers is created and shown in same cell by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5248
[MAINT] drop using extra allow list for estimator checks by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5246
[ENH] Refactor nilearn.plotting - create plotting.surface package by @hndgzkn in https://github.com/nilearn/nilearn/pull/5234
[REF] refactor reports carousel by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5252
[ENH] add surface support to thresholdstatsimg by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5222
[ENH] use saved GLM output to generate report by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5231
[ENH] make surface utility functions public by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5224
[REF] refactor code checking compatibility betwen mask and images by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5254
ENH Refactor plotting to separate surface related util functions by @hndgzkn in https://github.com/nilearn/nilearn/pull/5253
[FIX] update test threshold surface image copy by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5258
[ENH] check compatibily of inputs to fit and transform for maskers by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5259
[MAINT] start deprecation of fetchneurovaultmotor_task by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5266
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5270
[MAINT] adjust stacklevel for several warnings by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5265
[ENH] add timeout parameter to neurovault API by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5268
[REF] use checkembeddedmasker in GLM fit by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5263
[ENH] Refactor plotting.surface package to extract backend utility functions for plotly and matplotlib by @hndgzkn in https://github.com/nilearn/nilearn/pull/5276
[REF] use NiimgLike typing where possible by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5273
[MAINT] remove dead code by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5274
[ENH] infer bids name from input files when saving by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5256
[FIX] update docstrings by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5278
[FIX] improve display of reports in notebooks by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4453
[ENH] save GLM mask with saveglmto_bids by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5279
[FIX] stacklevel maskers by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5287
[DOC] improve doc nilearn.image by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5290
[ENH] use dynamic stacklevel finding for warnings by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5295
[ENH] add surface suport to nilearn.image.highvarianceconfounds by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5277
[MAINT] use more stringent check on meshes by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5296
[MAINT] run doc qc scripts in CI by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5285
[ENH] use findstacklevel for nilearn logger by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5297
[ENH] save GLM results table by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5281
[ENH] compute mean of means for list of surface images by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5301
[FIX] changelog entry by @man-shu in https://github.com/nilearn/nilearn/pull/5307
[FIX] throw warning when meshes are unequal but have compatible number of vertices by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5304
[MAINT] implement transformsingleimgs for surface masker by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5291
[ENH] run tests with free threaded python by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5284
[FIX] create report html for tests with minimum dependencies by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5315
[FIX] fix filenames when saving GLM to BIDS by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5311
[ENH] upload HTML report of code coverage by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5316
[ENH] Refactor nilearn.plotting move nilearn.plotting.edge_detect by @hndgzkn in https://github.com/nilearn/nilearn/pull/5306
[ENH] Refactor plotting.surface.plot_surf function to separate backend code for matplotlib and plotly by @hndgzkn in https://github.com/nilearn/nilearn/pull/5282
[REF] refactor doc strings for sample_mask and confounds for maskers by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5314
[ENH] Refactor nilearn.plotting.matrix to separate utility and backend functions by @hndgzkn in https://github.com/nilearn/nilearn/pull/5305
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5321
[ENH] Setup performance benchmarks using asv by @man-shu in https://github.com/nilearn/nilearn/pull/5280
[FIX] plotmasklarge_fmri.py oversubscribing threads by @man-shu in https://github.com/nilearn/nilearn/pull/5323
[FIX] linkcheck failures on the main by @man-shu in https://github.com/nilearn/nilearn/pull/5324
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/5326
[FIX] update API by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5327
Bump actions/setup-python from 3 to 5 by @dependabot in https://github.com/nilearn/nilearn/pull/5331
Bump actions/checkout from 3 to 4 by @dependabot in https://github.com/nilearn/nilearn/pull/5330
[FIX] allow generation of glm report with no contrasts by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5332
[ENH] use bids terminology in output of parsebidsfilename by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5320
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5333
[FIX] Github action for running benchmarks by @man-shu in https://github.com/nilearn/nilearn/pull/5329
[FIX] failing benchmark github action attempt 2 by @man-shu in https://github.com/nilearn/nilearn/pull/5336
[FIX] failing benchmark github action attempt 3 by @man-shu in https://github.com/nilearn/nilearn/pull/5338
[ENH] use imgs instead of img / X for fit, transform, fit_transform by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5262
[REF] refactor mask loading and validation in maskers by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5317
[FIX] use legacy=False to parse FLM filenames inputs as bids files by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5339
[ENH] add coverage information to reports for NiftiMasker, SurfaceMasker, GLM by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5337
[FIX] fetch full history to append new results to older results by @man-shu in https://github.com/nilearn/nilearn/pull/5343
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5344
[ENH] Refine nilearn.plotting.surface by @hndgzkn in https://github.com/nilearn/nilearn/pull/5322
[DOC] misc doc improvements related to handling surface by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5345
[ENH] add support for look-up-table to nifti label masker by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5342
[ENH] ensure estimators have a y parameter by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5351
[ENH] standardize content of maskimg after fit for all maskers by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5347
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5355
FIX] cast surface image to float before create a mask from them in surface masker by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5356
[ENH] ensure that all atlases are usable by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5350
[REF] standardize how n_elements is handled across maskers by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5353
[MAINT] check estimator fitting on different dtypes by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5358
[ENH] Radiological Viewer and Left Right labels Added, for interactive HTML brain viewer (view_img function) by @rohan3412 in https://github.com/nilearn/nilearn/pull/5346
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/5360
[ENH] Revisit example plotmasklarge_fmri by @man-shu in https://github.com/nilearn/nilearn/pull/5352
[FIX] use property regionnames in surface label examples by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5362
[MAINT] Bump to Brainsprite 0.15.0 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5363
[FIX] Failing benchmark workflow on schedule by @man-shu in https://github.com/nilearn/nilearn/pull/5367
[FIX] Failing script for plotting test timing on windows python 3.10 by @man-shu in https://github.com/nilearn/nilearn/pull/5369
Bump astral-sh/setup-uv from 5 to 6 by @dependabot in https://github.com/nilearn/nilearn/pull/5368
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5370
[REF] create large 3D shape fixture by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5365
[FIX] rely in __sklearn_tags__ for sklearn > 1.5.2 and on _more_tags otherwise by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5374
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5375
[MAINT] only test label maskers on real atlases on main by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5372
[DOC][FIX] fix figure / plotting function in doc table by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5366
[FIX] Fixes extra resampling when plotting with transparency by @hndgzkn in https://github.com/nilearn/nilearn/pull/5371
[ENH] generate report for second level model when inputs are first level models or dataframe by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5357
[MAINT] estimators dict should be unchanged after transform by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5124
[ENH] update spm multimodal description and its example by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5154
[ENH] Refactor plotting.surface.plot_surf_contours by @hndgzkn in https://github.com/nilearn/nilearn/pull/5349
[DOC] use template doc string for dummy y by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5383
[ENH] Simplify nilearn image code. by @hndgzkn in https://github.com/nilearn/nilearn/pull/5378
[FIX] skip plotly 6.1.0 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5387
[FIX] add stacklevel to warnings in plotting by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5385
[ENH] Refactor to separate backends for plotsurfstat_map by @hndgzkn in https://github.com/nilearn/nilearn/pull/5389
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5393
[FIX] hide set_output from doc and raise not implemeted error if called by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4902
[DEP] change default of slicetimeref in firstlevelfrom_bids by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5382
[FIX] ensure that multi maskers can clean with confounds and high variance confounds by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5379
[MAINT] ensure transform on 3D volume (1D surface) images returns 1D arrays by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5381
[FIX] avoid masking out vertices with zero-valued timepoints by @man-shu in https://github.com/nilearn/nilearn/pull/5392
[ENH] Refactor to separate backends for plotsurfroi by @hndgzkn in https://github.com/nilearn/nilearn/pull/5391
[REF] sort estimator checks by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5397
[ENH] add surface support to mathimg and binarizeimg by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5396
[REF] extract nilearn check_estimators by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5400
[MAINT] avoid extra warning when computing fixed effects by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5399
[FIX] ensure consistent output dimension for inverse_transform of NiftiMapsMasker and NiftiLabelsMasker by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5398
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5405
[REF] run of sklearn checks to check for expected failures by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5402
[DOC] add log 5398 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5406
[ENH] Refactor nilearn.plotting.surface.plot_img_on_surf to separate backends by @hndgzkn in https://github.com/nilearn/nilearn/pull/5401
[ENH] Refactor plotting surface - use modules as backend by @hndgzkn in https://github.com/nilearn/nilearn/pull/5407
[MAINT] Ensure decoders return self on fit and fail with invalid Y (none or contains non finite values) by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5403
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5412
[FIX] incorrect dtype.itemsize check in _ensure_float by @const7 in https://github.com/nilearn/nilearn/pull/5416
[FIX] fix tests failures on main by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5418
[FIX] labels do not need to be numeric for searlight by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5420
[MAINT] add tests glm affine shape by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5422
[ENH] add support for SurfaceImage to image.clean_img by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5425
[FIX] prevent negative threshold for surface plots by @hndgzkn in https://github.com/nilearn/nilearn/pull/5413
[MAINT] ensure estimators (maskers / glm / decoders) do not change public parameters passed at init during fit by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5404
[ENH] Refactor nilearn.plotting.surface.html_surface to separate backend by @hndgzkn in https://github.com/nilearn/nilearn/pull/5426
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5428
[MAINT] update list of core devs by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5429
[ENH] allow ConnectivityMeasure to accept arrays as input by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5424
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/5430
[MAINT] identify slow tests by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5427
[MAINT] Multiple imports for an import name by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/5432
[MAINT] Implicit enumerate call by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/5431
[FIX] turn sanitizecleaning_parameters into a private method by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5435
[FIX] less warning when using symmetric_cmap with matplotlib engine and warn to use the proper 'hemi' when plotting surfaces by @hndgzkn in https://github.com/nilearn/nilearn/pull/5421
[MAINT] Unassigned string statement by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/5438
[MAINT] do not test all minimum dependencies on PR by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5440
[MAINT] Fix typos and apply Sourcery suggestions by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/5439
[MAINT] check empty images by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5293
[MAINT] part revert of check empty image by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5454
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/5455
[ENH] have GLM report "no supra-threshold found" in GLM report when relevant by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5448
[MAINT] run some more sklearn checks on HierarchicalKMeans by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5453
[ENH] Improve user experience of multi runs GLM reports by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5450
[FIX] warn when some attributes passed at first level model init will be ignored at fit time by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5437
[ENH] Refactor nilearn.plotting.matrix, partially reverting previous refactoring by @hndgzkn in https://github.com/nilearn/nilearn/pull/5457
[MAINT] Apply new ruff rules by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/5464
[MAINT] Consistency between ruff and pre-commit by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/5465
[MAINT] Apply ruff rule RUF012 by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/5466
[DOC] measure and reduce number of warnings in doc build by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5459
[REF] refactor suggested by sourcery by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5376
[MAINT] fix links by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5463
[ENH] Make all decomposition methods work with surface data by @man-shu in https://github.com/nilearn/nilearn/pull/5377
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/5467
[ENH] save surface GLM output to disk by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5309
[FIX] fix input connectivity matrices by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5469
[FIX] nilearn.plotting.surface function params by @hndgzkn in https://github.com/nilearn/nilearn/pull/5470
REL 0.12.0 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/5456

New Contributors

@Leengit made their first contribution in https://github.com/nilearn/nilearn/pull/5179
@rohan3412 made their first contribution in https://github.com/nilearn/nilearn/pull/5346

Full Changelog: https://github.com/nilearn/nilearn/compare/0.11.1...0.12.0

- Python
Published by Remi-Gau 11 months ago

hidimstat - 0.11.1

List of pull requests

Bump actions/checkout from 3 to 4 by @dependabot in https://github.com/nilearn/nilearn/pull/4850
[REF] use underscore for unused variable in loop by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4846
[REF] simplify empty collection comparison by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4845
[REF] use join by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4844
[REF] avoid not any() or not all() by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4843
[FIX] rendering version changed by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4842
[REF] use dict comprehension by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4833
[REF] refactor unnecessary else block by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4826
[REF] apply sourcery suggestions to use comprehension by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4822
[REF] apply use-fstring suggested by sourcery by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4819
[REF] remove redundant slice index by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4825
[FIX] use linebreaks in doc to avoid noqa by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4815
[STY] apply US spelling by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4707
[REF] move assign variable within the if block where they are needed by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4823
[REF] Apply de Morgan's law for conditional by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4831
[REF] simplify-len-comparison by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4821
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/4858
[FIX] release_docs workflow by @man-shu in https://github.com/nilearn/nilearn/pull/4854
[STY] run style checks on doc by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4818
[MAINT] Post-release 0.11.0 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4861
[REF] use get item where possible by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4832
[DOC] use higher contrast pygment style for dark mode by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4847
[MAINT] add pyarrow dependencies for some test and doc build by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4863
[REF] use list extend instead of append by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4827
[REF] minor refactor of example by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4867
[REF] Do simple refactor on resample_img by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4864
[REF] refactor maint tools by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4866
[REF] simplify assignement by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4824
[REF] Simple refactor of permuted_ols by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4865
[FIX][ENH][DOC] allow events and design matrices inputs to be pathlike by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4807
[FIX] Fix dead links by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4814
[DOC] add min and max for plot_matrix in examples by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4882
[REF] refactor permute_ols by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4875
[FIX] Save gifti with datatype None by @man-shu in https://github.com/nilearn/nilearn/pull/4857
[REF] refactor groupsparsecovariance by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4899
[FIX] ignore link that gives 403 Client Error: Forbidden for url by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4901
[FIX] simplify table loading by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4895
[FIX] update tag checks for sklearn 1.7 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4903
[REF] further refactor of permuted_ols by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4905
[REF] fix last-if-guard and lift-return-into-if by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4909
[REF] refactor 1D and 2D surface fixtures by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4897
[FIX] update estimator checks for sklearn 1.6 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4925
[MAINT] check constructors compatibility with scikitlearn in nilearn.decomposition by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4918
[REF] merge duplicate blocks by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4908
[MAINT] update constructors of estimators in nilearn.connectome for sklearn compliance by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4915
[MAINT] check compatibility of FirstLevelModel with scikitlearn by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4912
[FIX] Properly set number fo permutation chunks when njobs > nperm by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4911
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/4923
[REF] refactor long tests in nilearn/tests/test_signal.py by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4919
[MAINT] Fail fast for test matrix by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4927
[MAINT] remove pre-commit related workflows by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4775
[FIX] fix dead link by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4933
[MAINT] remove some checks for matplotlib we no longer support by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4936
[FIX] change stacklevel warning label masker by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4938
[ENH] Do sklearn checks on SurfaceLabelsMasker by @man-shu in https://github.com/nilearn/nilearn/pull/4921
[ENH] allow using confounds via fit_transform in SurfaceLabelsMasker by @man-shu in https://github.com/nilearn/nilearn/pull/4926
[ENH] Refactor surf_mask fixture to be 1D by @man-shu in https://github.com/nilearn/nilearn/pull/4930
[MAINT] remove deprecation warning session -> run by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4940
[ENH] Accept mask_img in SurfaceLabelsMasker by @man-shu in https://github.com/nilearn/nilearn/pull/4937
[FIX] rename parameter for inverse_transform of SurfaceMasker by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4941
[STY] apply US spelling by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4944
[STY] Apply a couple preview ruff rules by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4943
[DOC] Add comparison of meaning differences of GLM between different libraries by @tpremrud in https://github.com/nilearn/nilearn/pull/4287
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/4945
[ENH] add bluesky and youtube badge to readme by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4946
[FIX] add some stacklevel in warnings by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4947
[REF] refactor long tests testfindcuts by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4920
[FIX] add nilearn tags to estimators by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4935
[ENH] Implement surface maps masker by @man-shu in https://github.com/nilearn/nilearn/pull/4830
[DOC] use short ref to nilearn functions and classes in the examples by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4892
[FIX] allow use of small alpha value for plotimgon_surf by @paulcbogdan in https://github.com/nilearn/nilearn/pull/4906
[FIX] fix expand user path when passing niimg filename by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4948
[MAINT] Refactor tags surface masker by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4950
[REF] refactor fetch localizer contrasts by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4928
[MAINT] version checks clean up by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4949
[FIX] add two_sided parameter to RegionExtractor by @hndgzkn in https://github.com/nilearn/nilearn/pull/4849
chore: update pre-commit hooks by @pre-commit-ci in https://github.com/nilearn/nilearn/pull/4957
[REF] refactor surface fixtures by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4955
[MAINT] use UV to install in CI by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4958
[FIX] Add ClassVar type to mutable class defaults by @badrinini in https://github.com/nilearn/nilearn/pull/4954
Revert "[MAINT] use UV to install in CI" by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4963
[FIX] Change link to TFCE tutorial by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4962
[MAINT] check compatibility of (multi)nifti masker with scikitlearn by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4913
[FIX] make HierarchicalKMeans.fit() takes X as array of shape [nsamples, nfeatures] by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4939
[FIX] allow support for confounds as numpy arrays in FirstLevelModel by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4967
[ENH] Allow Parcellations to work with Surface API by @man-shu in https://github.com/nilearn/nilearn/pull/4756
REL 0.11.1 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4971
[FIX] ensure list of images can be fitted by a SurfaceMasker instance even if it has a mask by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4975

New Contributors

@pre-commit-ci made their first contribution in https://github.com/nilearn/nilearn/pull/4858
@tpremrud made their first contribution in https://github.com/nilearn/nilearn/pull/4287
@badrinini made their first contribution in https://github.com/nilearn/nilearn/pull/4954

Full Changelog: https://github.com/nilearn/nilearn/compare/0.11.0...0.11.1

- Python
Published by Remi-Gau over 1 year ago

hidimstat - 0.11.0

List of pull requests

[MAINT] Post release 0.10.4 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4366
[MAINT] clean up makefiles and allow color in CLI in github workflows by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4370
[DOC] update release procotol by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4371
Change "resting state" to "movie watching" in compare means example by @man-shu in https://github.com/nilearn/nilearn/pull/4373
[DOC] Mention in style guide the meaning of trailing underscore for attributes by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4374
[REF] Refactor CSS and html masker reports by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4372
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/4381
[FIX] skip problematic plotting in doc build by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4383
[ENH] enhance save_glm_to_bids outputs by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4375
[MAINT] change schedule of GH workflows by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4386
[MAINT] monitor duration of doc build by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4387
[MAINT] pre-download data on full doc build by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4390
[FIX] fix flake8 bugbear errors by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4384
[MAINT] improve workflow to test on nightly dependencies by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4364
[MAINT] update precommit configuration by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4391
[MAINT] update parameters for scipy.sparse.linalg.cg by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4394
[FIX] remove, implement or better document "unused" arguments by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4273
[MAINT] Update circle-ci trigger-hosting by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4402
[REF] refactor style checks in CI by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4406
[MAINT] test on several macos versions by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4405
[DOC] Fix typos found by codespell by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4410
FIX failing load_confound test related to standardisation by @htwangtw in https://github.com/nilearn/nilearn/pull/4411
add width input to view_img() by @alexsayal in https://github.com/nilearn/nilearn/pull/4416
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/4418
[FIX] Raise error if unknown kwargs are given to first_level_from_bids by @michellewang in https://github.com/nilearn/nilearn/pull/4414
[FIX] Refactor design matrix and contrast formula for the two-sample T-test example by @YCHuang0610 in https://github.com/nilearn/nilearn/pull/4407
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/4422
[MAINT] only on use macOS-latest by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4424
[MAINT] pacify codepspell by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4430
[ENH] add plotting functions to the experimental surface module by @jeromedockes in https://github.com/nilearn/nilearn/pull/4235
[ENH] Adapt FirstLevelModel to work with surface data objects from new API by @ymzayek in https://github.com/nilearn/nilearn/pull/4126
Copy input image header to the output by default by @man-shu in https://github.com/nilearn/nilearn/pull/4397
Example to demonstrate copy_header_from in math_img by @man-shu in https://github.com/nilearn/nilearn/pull/4392
[STY] apply black to files no longer invovled in other pull requests by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4433
[ENH] Add warning for future change of the default of force_resample to True by @ajoshiusc in https://github.com/nilearn/nilearn/pull/4412
[MAINT] remove some try/except on imports by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4440
[ENH] add footer to all masker reports by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4307
[ENH] expand surface plotting with new surface object by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4431
[ENH] update example to show parametric modulation by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4436
[MAINT] add force_resample where missing by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4441
[DOC] add ...CV in logistic estimator name by @man-shu in https://github.com/nilearn/nilearn/pull/4438
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/4447
[REF] add force_resample default to cached calls by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4450
[ENH] add report for SurfaceMasker by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4432
[MAINT] remove duplicate code by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4449
[DOC] Fix deploy doc on main by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4455
[REF] minor refactor of get_cmap and matplotlib version-handling by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4458
[REF] refactor report templates by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4460
[FIX] throw warning a masker generate_report is called without matplotlib by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4457
[FIX] use string as label names in example involving the new surface based destrieux atlas by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4462
[REF] refactor FLM fitting by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4461
[MAINT] for monitoring of duration of CI only plot doc build on main (full builds) by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4463
[MAINT] rename tr variable - private occurences by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4468
[ENH] Replace tr by t_r in HRF generating functions and examples by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4470
[FIX] pacify ruff warning about numpy 2 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4477
[FIX] coerce loaded data from NKI to float in examples by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4475
[ENH] add function to plot regressor correlation matrix by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4467
[ENH] use nilearn logger.log function instead of print or sys.stderr.write by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4469
[FIX] change creation of region_names and add test by @mtorabi59 in https://github.com/nilearn/nilearn/pull/4360
[FIX] fix trigger hosting of doc of PR on circle-ci by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4481
[FIX] Change default ratio value in glover to fit canonical Glover HRF (1999) by @const7 in https://github.com/nilearn/nilearn/pull/4452
Update second_level.py by @arovai in https://github.com/nilearn/nilearn/pull/4483
[MAINT] use pytest-reporter-html1 to create test reports by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4444
Revert "[MAINT] use pytest-reporter-html1 to create test reports" by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4485
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/4487
[FIX] host doc from PR on Circle-CI by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4494
Explain Decoder's default cross-validation scheme by @man-shu in https://github.com/nilearn/nilearn/pull/4491
Change default clustering_percentile in _BaseDecoder docstring by @man-shu in https://github.com/nilearn/nilearn/pull/4489
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/4499
[DOC] Small correction on instructions for setting up environment by @kimsin98 in https://github.com/nilearn/nilearn/pull/4459
[API] renamed ax parameter for consistency by @muddi900 in https://github.com/nilearn/nilearn/pull/4476
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/4504
[FIX] Reduce dtype of mask from int64 to int8 in image.binarize_img by @psadil in https://github.com/nilearn/nilearn/pull/4502
[FIX] force np.float64 format for second level matrix dataframe by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4503
[MAINT] Finish adding tests for _utils.data_gen by @kimsin98 in https://github.com/nilearn/nilearn/pull/4465
[REF] refactor nibabel import by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4506
[ENH] improve I/O for SurfaceImage by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4446
[FIX] revert save analyze for SPM auditory data by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4508
[MAINT] use pytest-reporter-html1 to create test reports by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4486
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/4514
[ENH] Change Butterworth filtering in nilearn.signal.clean to use 'sos' output by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4510
[STY] apply black to remaining example by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4518
[STY] apply black to remaining files in plotting subpackage by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4520
[STY] apply black to surface subpackage by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4519
[REF] remove obsolete try import by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4528
[MAINT] Handle 2 numpy and matplolib deprecation warnings by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4522
[MAINT] raise stacklevel of copy_header warning by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4530
[MAINT] remove flynt config by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4532
[MAINT] Clean up some warnings from the tests by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4529
[FIX] return 3D effect maps for t contrasts by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4439
Bump peter-evans/create-pull-request from 6 to 7 by @dependabot in https://github.com/nilearn/nilearn/pull/4537
[MAINT] reduce occurence of resampling related warnings by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4531
[MAINT] simplify dependencies of dev and style installs by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4541
[FIX] update scikit-learn decoder tags by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4535
[FIX] remove several typos or double space by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4545
[FIX] fix version to check for scikit learn for new decoder tags by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4546
[MAINT] replace nb by n by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4548
[FIX] fix sklearn version check by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4550
[REF] refactor nifti maskers tests by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4388
[ENH] add optional pretty printing with rich for logging by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4544
[FIX] only use tight_layout when figure is owned by @larsoner in https://github.com/nilearn/nilearn/pull/4542
[ENH] Add last version of the AAL atlas to its fetcher by @JLefortBesnard in https://github.com/nilearn/nilearn/pull/4554
[FIX] fix radiological view by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4556
[FIX] fix name of parameter in the "extract_type" definition by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4559
[FIX] load_confounds: Raise an exception when all volumes are scrubbed by @victoris93 in https://github.com/nilearn/nilearn/pull/4558
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/4564
[MAINT] Optimize _resample_one_img logic check for nearest interpolation by @kaitj in https://github.com/nilearn/nilearn/pull/4571
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/4572
[FIX] avoid warning when creating int64 images by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4555
[MAINT] drop python 3.8 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4516
[STY] Start using and configuring ruff by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4574
[STY] run ruff on extra files excluded from previous PR by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4578
[DOC] add youtube channel in the doc footer by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4580
[FIX] first_level_from_bids will now return subjects in order by @tharun634 in https://github.com/nilearn/nilearn/pull/4582
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/4584
[ENH] use BIDS version of the SPM auditory dataset by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4515
[STY] fix error D209 from ruff by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4583
[DOC] Explaining how Decoder works by @man-shu in https://github.com/nilearn/nilearn/pull/4437
[DOC] Demonstrate how to compute & plot functional connectivity for each hemisphere separately with Yeo 17 networks by @victoris93 in https://github.com/nilearn/nilearn/pull/4585
[STY] fix ruff pandas error by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4597
[FIX] fix error PTH122 from by @hndgzkn in https://github.com/nilearn/nilearn/pull/4590
[STY] fix simplify ruff errors by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4599
[STY] fix numpy ruff error by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4598
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/4609
[REF] fix ruff 'errors' by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4602
[REF] fix refactor 'errors' flagged by ruff by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4600
[REF] fix comprehension 'errors' flagged by ruff by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4601
[STY] fix fly and up errors flagged by ruff by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4611
[FIX] fix error PTH106 by @hndgzkn in https://github.com/nilearn/nilearn/pull/4607
[STY] fixes several PERF error flagged by ruff by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4614
[FIX] fix several errors (PTH112, PTH114, PTH117) by @hndgzkn in https://github.com/nilearn/nilearn/pull/4612
[STY] Fix PTH118 for all files except in nilearn.datasets by @michellewang in https://github.com/nilearn/nilearn/pull/4606
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/4621
[STY] fixes simplify error flagged by ruff by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4616
[FIX] check type compatibility of GLM mask and input data by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4603
[FIX] fix several errors (PTH202, PTH203, PTH204) by @hndgzkn in https://github.com/nilearn/nilearn/pull/4618
[FIX] Fix doc strings for path by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4623
[REF] refactor check matplotlib and plotly by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4527
[ENH] Add SurfaceImage.from_volume by @jeromedockes in https://github.com/nilearn/nilearn/pull/4593
[STY] Fix some naming errors flagged by ruff by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4624
[STY] Resolve several PTH issues by @PrakharJain1509 in https://github.com/nilearn/nilearn/pull/4620
[ENH] Allow Decoder to work with surface objects by @ymzayek in https://github.com/nilearn/nilearn/pull/4205
[MAINT] support for python 3.13 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4513
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/4632
Return signals if standardisation was not applied, and change the condition when adding signal mean back for psc method by @htwangtw in https://github.com/nilearn/nilearn/pull/4604
[MAINT] Replace tempfile in tests with proper pytest fixtures by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4631
[STY] Fix ruff errors RUF002-3 and RUF005 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4627
[ENH] Improve plotting contours for PlotlySurfaceFigure objects by adding add_contours method by @psadil in https://github.com/nilearn/nilearn/pull/3949
[MAINT] Replace pytest.warns(DeprecationWarning, match = pattern) with pytest.deprecated_call(match = pattern) by @victoris93 in https://github.com/nilearn/nilearn/pull/4637
Test for screening adjustment by @man-shu in https://github.com/nilearn/nilearn/pull/4630
[ENH] Allow saving SurfaceImage data to Gifti files by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4589
[STY] Fix or silence ARG001-3 error (unused argument) by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4641
[STY] Fix or silence ruff error PD901 - use more meaningful variable name than df for pandas dataframe by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4646
[REF] Rename get_mask_volume by @man-shu in https://github.com/nilearn/nilearn/pull/4640
[MAINT] remove some unecessary warning filters by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4649
[STY] fix PLR1704 (redefined-argument-from-local) by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4644
[DOC] minor changes to examples for better rendering by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4651
[STY] fix or silence N802 error related to name of functions (only use lower case) by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4643
[STY] fix ruff error PD011 - use .to_numpy() instead of .values for pandas dataframe by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4645
[MAINT] always run tests in random order by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4653
[DOC] Add missing default values to the docstrings in 'nilearn/glm' - part 1 by @anupriyakkumari in https://github.com/nilearn/nilearn/pull/4656
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/4667
[FIX] Fix several errors (PTH100, PTH103, PTH119, PTH120) by @hndgzkn in https://github.com/nilearn/nilearn/pull/4648
[DOC] Add missing default values to the docstrings in 'nilearn/glm' - part 2 by @anupriyakkumari in https://github.com/nilearn/nilearn/pull/4659
[DOC] Add missing default values to the docstrings in 'nilearn/plotting' by @anupriyakkumari in https://github.com/nilearn/nilearn/pull/4660
[FIX] Warn if smoothing_fwhm parameter passed to FLM for surface data by @emdupre in https://github.com/nilearn/nilearn/pull/4666
[MAINT] minor fixes on maintenance scripts by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4655
[STY] fix SIM117 error by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4670
[FIX] Fix several errors (PTH101, PTH102, PTH107, PTH110, PTH111, PTH113, PTH201) in nilearn.datasets package by @hndgzkn in https://github.com/nilearn/nilearn/pull/4671
[DOC][MAINT] build doc with minimum version of python and dependencies by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4650
[DOC] use new surface API in plotsurfacebids_analysis by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4682
[DOC] use new surface API in plotlocalizersurface_analysis by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4681
[DOC] use new surface API in plotsurfstat_map by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4683
[TEST] Clean surface fixtures by @man-shu in https://github.com/nilearn/nilearn/pull/4657
[STY] Fix PTH123 by @hndgzkn in https://github.com/nilearn/nilearn/pull/4677
[MAINT] move surface report tests by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4687
[FIX] Make load_confounds return None for confounds if no cleaning strategy is provided by @mibur1 in https://github.com/nilearn/nilearn/pull/4636
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/4690
[FIX] Silence B018 errors by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4675
[MAINT] speed up some tests for first level GLM and interface/bids by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4629
[STY] Fix remaining PTH118 errors in nilearn.datasets by @michellewang in https://github.com/nilearn/nilearn/pull/4676
[MAINT] enact deprecations due for 0.11.0 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4517
[ENH] add a function to help reporting post-masking atlas in LabelsMaskers by @mtorabi59 in https://github.com/nilearn/nilearn/pull/4500
[DOC] use new surface API in plot3dmaptosurface_projection by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4674
[ENH] move experimental surface plotting into the stable API by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4688
[FIX] do not use scaling_axis in example by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4694
[STY] Fix PTH123 in nilearn.datasets by @michellewang in https://github.com/nilearn/nilearn/pull/4696
[MAINT] move surface IO module to stable surface API by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4685
[DOC] use new surface API in plotsurfatlas by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4678
[MAINT] remove useles test line by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4699
[ENH] Improved SearchLight with NIfTI Support, Mask Handling, and Reusable Transform Method by @PrakharJain1509 in https://github.com/nilearn/nilearn/pull/4652
[REF] Refactor function 'addgraph' in nilearn/plotting/displays/projectors.py by @anupriyakkumari in https://github.com/nilearn/nilearn/pull/4635
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/4705
[DOC] Apply codespell by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4703
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/4706
[FIX] Fix bug in fetch_single_file with resume=True and improve tests by @michellewang in https://github.com/nilearn/nilearn/pull/4701
Maint/refactor old numpy by @hndgzkn in https://github.com/nilearn/nilearn/pull/4689
[MAINT] check estimators compliance with the scikit-learn recommendations by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4547
[REF] use path for resolve globbing by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4658
[MAINT] remove dependency on matplotlib to filter packages to be tested by @hndgzkn in https://github.com/nilearn/nilearn/pull/4709
[DOC] Surface API explainer by @man-shu in https://github.com/nilearn/nilearn/pull/4665
[DOC] move example for surface API plotsurfaceimageandmaskers by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4684
[ENH] Add plotting contours using SurfaceImage with plotly by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4713
[DOC] Use SurfaceImage object for the Searchlight surface example by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4711
[ENH] Handling of SurfaceData in compute_contrast by @bthirion in https://github.com/nilearn/nilearn/pull/4610
[DOC] add link to masking functions by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4718
[FIX] GitHub workflow script injection by @joycebrum in https://github.com/nilearn/nilearn/pull/4722
[STY] Apply assorted ruff rules by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4704
[MAINT] run tests in parallel by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4673
[ENH] move SurfaceMasker to stable part of the code base by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4692
[DOC] minor RST fixes to improve doc rendering by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4726
[ENH] Move experimental surface classes to the stable API by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4723
[MAINT] fix failure windows with Python 3.9 and matplotlib==3.3.0 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4721
[MAINT] use pathlib.Path more systematically in nilearn.datasets by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4725
[DOC] update internal references to SurfaceImage classes in doc strings by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4727
[STY] Enforce ruff/flake8-pie rules (PIE) by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4732
[STY] Enforce ruff/pygrep-hooks rules (PGH) by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4731
[STY] Apply ruff/flake8-implicit-str-concat rules (ISC) by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4730
[STY] Enforce ruff/refurb rules (FURB) by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4752
[MAINT] Expression not assigned by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4751
[MAINT] String statement has no effect by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4750
[MAINT] Pythagorean calculation with sub-optimal numerics by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4748
[STY] Appending to list following its definition by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4747
[STY] Unnecessary use of json.loads() for file data by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4746
[STY] Simplify chained comparison by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4745
[MAINT] Exception arguments suggest string formatting by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4744
[MAINT] Undefined name in __all__ by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4734
[STY] Multiple imports for an import name by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4735
[STY] Comparison with callable by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4737
[STY] np.testing.assert_ → assert by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4738
[STY] Unnecessary None provided as default by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4741
[STY] Use of an unneeded not by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4742
Bump codecov/codecov-action from 4 to 5 by @dependabot in https://github.com/nilearn/nilearn/pull/4757
[ENH] move SurfaceLabelMasker to stable API by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4714
[ENH] Allow to run clustering on SurfaceImage by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4577
[ENH] move experimental datasets into stable API by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4693
[ENH] run fit and transform of SurfaceMasker on list of Surface images by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4719
[FIX][DOC] fix doc build by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4763
[FIX] update checks estimators - fix compatibibility issues with scikit-learn >1.5.2 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4724
[DOC] reorder classes and functions in doc by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4766
Use the estimator type tags as required by scikit-learn 1.6.0 by @man-shu in https://github.com/nilearn/nilearn/pull/4774
[STY] Appending to dictionary following its definition by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4740
[MAINT] Special method should return NotImplemented by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4749
[FIX] add version added in the new classes and functions by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4772
[STY] Explicit exception raised in the assert message by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4733
[FIX] Force the parts of PolyData to be 2D by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4771
[MAINT] Sequence value overwritten unconditionally by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4743
[ENH] Allow SurfaceLabelsMasker to work with a list of Surface images by @man-shu in https://github.com/nilearn/nilearn/pull/4770
[MAINT] Disable ruff rules conflicting with the formatter by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4753
[MAINT] Apply repo-review rules by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4754
[MAINT] Make sure only changed examples are rebuilt on PR by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4780
Module imports itself by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4778
[DOC] fix doc string to remove warning in doc build by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4782
[DOC] split atlases section by probabilistic and deterministic by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4779
[STY] Implicit enumerate calls by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4785
[DOC] fix rendering hrf list by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4784
[MAINT] Update ruff to 0.8.0 by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4786
[DOC] improve doc regarding events with 0 duration by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4776
[FIX] create parent doc for .nojekyll by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4788
[MAINT] allow possiblity to skip doc build or test in CI via specific commit message by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4783
[DOC] Fix rendering of attributes by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4787
[ENH] make the number of vertices the first dimension of image data by @jeromedockes in https://github.com/nilearn/nilearn/pull/4591
[DOC] Fix render of lists, notes and code blocks in 'template' parameters by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4790
[ENH] run GLM on surface data on BIDS datasets by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4507
[MAINT] increase coverage by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4794
[STY] Use .items() to iterate over the dictionary by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4798
[MAINT] update checks scikit learn >= 1.7 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4796
[DOC] move doc string for classes out of constructor by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4795
[STY] Implicit enumerate calls by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4799
[DOC] add bluesky to footer by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4800
[FIX] allow tr, highpass, low_pass to be int in signal.clean by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4804
[FIX] Allow single 4D nifti as input for SecondLevelModel by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4806
[STY] Unused import by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4812
[ENH] Remove old surface by @man-shu in https://github.com/nilearn/nilearn/pull/4791
[ENH] revert coercing surface data to 2D by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4793
[ENH] allow to ignore certain BIDS entities when using query_bids by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4802
[DOC][FIX] update number of participants loaded in load_nki by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4817
[ENH] fit second level model on surface by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4715
[REL] 0.11.0 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4813
[FIX] rework plotsurfatlas example by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4836
[FIX] update plotsurfacebids_analysis by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4841
[FIX] update plot3dmaptosurface_projection by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4837
[FIX] update plotsurfstat_map to properly use surface api by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4838
[FIX] update plotsurface101 example by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4834
[FIX] update plotsurfaceimageandmaskers.py by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4835
[FIX] update plotlocalizersurface_analysis by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4840

New Contributors

@alexsayal made their first contribution in https://github.com/nilearn/nilearn/pull/4416
@YCHuang0610 made their first contribution in https://github.com/nilearn/nilearn/pull/4407
@ajoshiusc made their first contribution in https://github.com/nilearn/nilearn/pull/4412
@arovai made their first contribution in https://github.com/nilearn/nilearn/pull/4483
@muddi900 made their first contribution in https://github.com/nilearn/nilearn/pull/4476
@victoris93 made their first contribution in https://github.com/nilearn/nilearn/pull/4558
@kaitj made their first contribution in https://github.com/nilearn/nilearn/pull/4571
@tharun634 made their first contribution in https://github.com/nilearn/nilearn/pull/4582
@hndgzkn made their first contribution in https://github.com/nilearn/nilearn/pull/4590
@PrakharJain1509 made their first contribution in https://github.com/nilearn/nilearn/pull/4620
@anupriyakkumari made their first contribution in https://github.com/nilearn/nilearn/pull/4656
@mibur1 made their first contribution in https://github.com/nilearn/nilearn/pull/4636
@joycebrum made their first contribution in https://github.com/nilearn/nilearn/pull/4722

Full Changelog: https://github.com/nilearn/nilearn/compare/0.10.4...0.11.0

- Python
Published by Remi-Gau over 1 year ago

hidimstat - 0.10.4

Released April 2024

HIGHLIGHTS

Use the appropriate HTML templates for nilearn.maskers.MultiNiftiMapsMasker and nilearn.maskers.MultiNiftiLabelsMasker reports that would lead to empty reports for MultiNiftiMapsMasker (#4310 by Rémi Gau).
Fix color bar handling with color map with only 1 level (#4255 by Rémi Gau).
Improve colorbar size and labels in mosaic display (#4284 by Rémi Gau).
Remove unused **kwargs from nilearn.plotting.view_img and nilearn.plotting.plot_surf (#4270 by Rémi Gau).

Fixes

Fix plotting of carpet plot due to a change in the coming version of matplolib (3.9.0) (#4279 by Rémi Gau).
Fix errant warning when using stat_type in nilearn.glm.compute_contrast (#4257 by Eric Larson).
Fix when thresholding is applied to images by GLM reports (#4258 by Rémi Gau).
Use the appropriate HTML templates for nilearn.maskers.MultiNiftiMapsMasker and nilearn.maskers.MultiNiftiLabelsMasker reports that would lead to empty reports for MultiNiftiMapsMasker (#4310 by Rémi Gau).
Make masker report tables horizontally scrollable (#4308 by Rémi Gau).-
Masker reports tables do not overlap with report image (#4308 by Rémi Gau).
Fix color bar handling with color map with only 1 level (#4255 by Rémi Gau).
Ensure that regionnames can be generated by nilearn.maskers.NiftiSpheresMasker.transformsingleimgs for deterministic atlases that use floats or non-consecutive values as region_ids whether they include background in their labels or not (#4274 by Rémi Gau).
Ensure that nilearn.interfaces.bids.saveglmto_bids serializes numpy arrays to list used as GLM parameters before saving them to JSON (#4325 by Rémi Gau).
Check that the view parameter in surface plotting functions is a pair of int or float when it is not a string (#4297 by Rémi Gau).
Fix positions of the markers on the images on the sphere masker reports (#4285 by Rémi Gau).
Fix cut position in nifti maps maskers to match displayed map maximum (#4304 by Rémi Gau).
Make sure that nilearn.maskers.NiftiSpheresMasker reports displays properly when it contains only 1 sphere (#4269 by Rémi Gau).
Miscellaneous fixes in GLM reports (only display FIR delay if FIR is used, display color bar “Z score” legend…) (#4266 by Rémi Gau).
Fix minor typos in documentation (glossary and connectivity/parcellating) (#4343 by Florent Pollet).
Update minor information on the Code of Conduct page (#4318 and #4320 by Himanshu Aggarwal).

Enhancements

Add an avg_method parameter to nilearn.plotting.plotsurfstat_map (#4298 by Rémi Gau).
Advertise nilearn’s in built globbing capability in an example (#4334 by Himanshu Aggarwal).

Changes

Throw warnings when passing parameters to surface plotting functions that are not used by the plotly engine (#4298 by Rémi Gau).
Improve colorbar size and labels in mosaic display (#4284 by Rémi Gau).
Change the colormap to gray for the background image in the nilearn.maskers.NiftiSpheresMasker (#4269 by Rémi Gau).
Remove unused **kwargs from nilearn.plotting.view_img and nilearn.plotting.plot_surf (#4270 by Rémi Gau).
Use red to blue color map in the GLM reports (#4266 by Rémi Gau).
nilearn.maskers.NiftiSpheresMasker will throw warnings if the labels passed to it is not a list of str, or if the number of items in the list of labels does not match the number of regions in the label image (#4274 by Rémi Gau).
Copy headers from user-specified image to the result of nilearn.image.math_img (#4337 by Himanshu Aggarwal).
Render the description of the templates, atlases and datasets of the nilearn.datasets as part of the documentation (#4232 by Rémi Gau).
Render examples of GLM and masker reports as part of the documentation (#4267 and #4295 by Rémi Gau).
HTML, CSS are now linted using prettier. (#4302, by Rémi Gau).

List of pull requests

[MAINT] Post release 0.10.3 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4246
[MAINT] Refactor test reporting by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4247
[MAINT] remove date from copyright by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4249
[FIX] numpy 2 compatibility by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4251
[DOC] Add datasets description to the documentation by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4232
[FIX] Replace remaining contrast_type by stat_type by @larsoner in https://github.com/nilearn/nilearn/pull/4257
[DOC] Add versionadded directive to two_sided parameter of binarize_img function by @NicolasGensollen in https://github.com/nilearn/nilearn/pull/4262
[DOC] Improve warnings for BIDS folders by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4253
[DOC] clean citation and bibliography in the documentation by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4254
[STY] fix doc strings flake8 errors that were ignored until now by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4264
[FIX] read only problem with numpy 2 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4265
[FIX] threshold images right before ploting in GLM reports by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4258
[FIX] Make sure that NiftiSphereMaskers reports display properly for only 1 sphere by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4269
[FIX] use proper grid spec when plotting carpet plots by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4279
[FIX] fix positions markers on images on sphere masker reports by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4285
[DOC] add documentation about kwargs in nilearn.plotting by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4270
[DOC] update doc strings of the maskers by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4286
[FIX] improve colorbar in mosaic display by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4284
[FIX] Fix color bar handling with color map with only 1 level by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4256
[DOC] render reports in the documentation by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4267
[FIX] fixes several plotting details in glm reports by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4266
[FIX] force views in surface plotting to be pairs of int or float when not a string by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4297
[FIX] fix cut position in nifti maps maskers by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4304
[FIX] remove conftest for externals by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4306
[MAINT] add script to check duration of test suite by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4231
[DOC] display all masker reports in the doc by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4295
Revert "[FIX] remove conftest for externals" by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4311
[ENH] Add avg_method to plot_surf_stat_map by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4298
[FIX] make masker report tables horizontally scrollable and not overlap with masker report images by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4308
[FIX] use the proper html template for mutli maps and label masker by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4310
[DOC] Update drop-in hour information on contributing page by @man-shu in https://github.com/nilearn/nilearn/pull/4318
[MAINT] Use prettier to format HTML and CSS by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4302
[DOC] Refer to nilearn datasets module by @man-shu in https://github.com/nilearn/nilearn/pull/4320
[DOC] Adding Himanshu to authors by @man-shu in https://github.com/nilearn/nilearn/pull/4322
[FIX] check data format passed to surface plotting functions by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4323
[FIX] serialize numpy arrays to list before saving to json by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4325
[FIX] make identifying region names more robust by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4289
[DOC] Advertise nilearn's in built globbing by @man-shu in https://github.com/nilearn/nilearn/pull/4334
[MAINT] Refactor test nifti label maskers by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4333
[MAINT] add test to resampling_target = None for nifti label maskers by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4336
[DOC] Fix typos doc by @florian6973 in https://github.com/nilearn/nilearn/pull/4343
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/4348
[ENH] relax requirements for testsamplingaffine by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4349
[DOC] Fix typo and docstring formatting in glm.first_level.first_level_from_bids by @michellewang in https://github.com/nilearn/nilearn/pull/4352
[FIX] change "grey" to "gray" in doc/visual_testing/reporter_visual_inspection_suite.py for older Matplotlib versions by @michellewang in https://github.com/nilearn/nilearn/pull/4353
[DOC] Update release section of maintainence page by @man-shu in https://github.com/nilearn/nilearn/pull/4356
[FIX] resolve numpy2 compatibility related to ambiguity when broadcasting in np.solve by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4350
[FIX] Headers not carried over by math_img by @man-shu in https://github.com/nilearn/nilearn/pull/4337
REL 0.10.4 by @man-shu in https://github.com/nilearn/nilearn/pull/4354
[MAINT] Post release 0.10.4 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4366

New Contributors

@man-shu made their first contribution in https://github.com/nilearn/nilearn/pull/4318
@florian6973 made their first contribution in https://github.com/nilearn/nilearn/pull/4343

Full Changelog: https://github.com/nilearn/nilearn/compare/0.10.3...0.10.4

- Python
Published by Remi-Gau about 2 years ago

hidimstat - 0.10.3

Released January 2024

HIGHLIGHTS

[!WARNING]

Support for python 3.7 has been dropped. We recommend moving to python >= 3.11.

Minimum supported versions of packages have been bumped up:

Numpy – v1.19.0

SciPy – v1.8.0

Scikit-learn – v1.0.0

Nibabel – v4.0.0

Pandas – v1.1.5

Joblib – v1.0.0

API Allow passing arguments to firstlevelfrom_bids to build first level models that include specific set of confounds by relying on the strategies from load_confounds (#4103 by Rémi Gau).
Support passing t and F contrasts to compute_contrast that that have fewer columns than the number of estimated parameters. Remaining columns are padded with zero (#4067 by Rémi Gau).
NiftiSpheresMasker now has generate_report method (#3102 by Yasmin Mzayek and Nicolas Gensollen).
Update the CompCor strategy in load_confounds and loadconfoundsstrategy to support fmriprep 21.x series and above. (#3285 by Hao-Ting Wang).
Allow setting vmin in plotglassbrain and plotstatmap (#3993 by Michelle Wang).
When plotting thresholded statistical maps with a colorbar, the threshold value(s) will now be displayed as tick labels on the colorbar (##2833 by Nicolas Gensollen).
Combine GLM examples plotfixedeffect and plotfiacanalysis into a a single example plottworuns_model (#3191 by Taylor Salo and Rémi Gau).

NEW

The tempfilelifetime parameter of interactive plots’ openinbrowser method is deprecated and has no effect (#4180 by Jerome Dockes)..

Fixes

MultiNiftiMasker can now call generate_report which will generate a report for the first subject in the list of subjects (#4001 by Yasmin Mzayek).
Make sure that all atlases and datasets fetchers return a description (#4215 Rémi Gau).
Update the CompCor strategy in load_confounds and loadconfoundsstrategy to support fmriprep 21.x series and above. (#3285 by Hao-Ting Wang).
Fix SimpleRegressionResults to accommodate for the lack of a model attribute (#4071 Rémi Gau)
clean_img can now use kwargs clean_samplemask argument to correctly reshape the nifti image to the dimensions of the mask in the output (#4051 by Mia Zwally).
Fix plotting of an image with color bar when maximum value is exactly zero (#4204 by Rémi Gau).
Code Fix PSC normalisation method applied by standardize_signal in signal (#4116 by Hao-Ting Wang and Yasmin Mzayek).
Fixed inheritance of decoder classes to keep compatibility with scikit-learn>v1.3 (#4188 by Yasmin Mzayek).
Make sure that all the fetchers for atlas and func from nilearn.datasets return a sklearn.utils.Bunch. Add new behavior to fetchlanguagelocalizerdemodataset to return output as Bunch. This behavior will become the default in version 0.13.0 (#4233 by Rémi Gau).

Enhancements

NiftiSpheresMasker now has generate_report method (#3102 by Yasmin Mzayek and Nicolas Gensollen).
Allow passing Pandas Series of image filenames to SecondLevelModel (#4070 by Rémi Gau).
Allow passing arguments to firstlevelfrom_bids to build first level models that include specific set of confounds by relying on the strategies from load_confounds (#4103 by Rémi Gau).
Support passing t and F contrasts to compute_contrast that that have fewer columns than the number of estimated parameters. Remaining columns are padded with zero (#4067 by Rémi Gau).
Multi-subject maskers’ generate_report method no longer fails with 5D data but instead shows report of first subject. User can index input list to show report for different subjects (#3935 by Yasmin Mzayek).
Allow globalsignal parameter in loadconfoundsstrategy in denoisestrategy='compcor' (#4225 by Hao-Ting Wang).
Add two_sided option for binarize_img (#4121 by Steven Meisler).
generate_report now uses appropriate cut coordinates when functional image is provided (#4099 by Yasmin Mzayek and Nicolas Gensollen).
Mention the classification type (all-vs-one) in Decoding of a dataset after GLM fit for signal extraction (#4122 by Tamer Gezici).
Add backslash to homogenize Parcellations documentation (#4042 by Nikhil Krish).
Specify full form of LSS in Beta-Series Modeling for Task-Based Functional Connectivity and Decoding (#4141 by Tamer Gezici).
Don’t fetch tmaps in examples if tmaps aren’t used in the example. (#4136 by Christina Roßmanith).
Describe the return value in fetchabidepcp documentation (#4159 by Suramya Pokharel).
Allow setting vmin in plotglassbrain and plotstatmap (#3993 by Michelle Wang).
When plotting thresholded statistical maps with a colorbar, the threshold value(s) will now be displayed as tick labels on the colorbar (##2833 by Nicolas Gensollen).

Changes

Expose scipy CubicSpline extrapolate parameter in clean to control the interpolation of censored volumes in both ends of the BOLD signal data (#4028 by Jordi Huguet).
Make nilearn.reporting.getclusterstable module public and move copyimg out of nilearn._utils.niimg (#4166 by Rémi Gau).
Private utility context manager writetmpimgs is refactored into function writeimgsto_path (#4094 by Yasmin Mzayek).
Move user facing function concatniimgs out of private module nilearn.utils.niimg_conversions (#4167 by Rémi Gau).
Remove leading underscore from non private functions to align with PEP8 (#4086 by Rémi Gau).
Make decoding/proximal_operator explicitly private to align with PEP8 (#4153 by Rémi Gau).
Make private functions public when used outside of their module nilearn.interface to align with PEP8 (#4168 by Rémi Gau).
imgtosignals_labels will also return maskedatlas in release 0.15. Meanwhile, use returnmasked_atlas parameter to enable/disable this behavior. (#3761 by Mohammad Torabi).
cation Rename the parameter contrasttype in compute_contrast and attribute contrasttype in Contrast to stat_type (#4191 by Rémi Gau).
plotsurfroi will raise a warning if roi_map contains negative or non-integer values; in version 0.13 this will be a ValueError (#4131 by Michelle Wang).
nilearn.datasets.fetchbidslangloc_dataset will be deprecated in release 0.13 as it returns data simuilar to fetchlanguagelocalizerdemodataset (#4219 by Rémi Gau).
the default parameter of fdthreshold and stddvars_threshold in load_confounds with be updated to match fmriprep default in version 0.13 (#4225 by Hao-Ting Wang).
Combine GLM examples plotfixedeffect and plotfiacanalysis into a a single example plottworuns_model (#3191 by Taylor Salo and Rémi Gau).
Switch to using tox to manage environments during development and testing. All plotting python dependencies (matplotlib AND plotly) are now installed when running pip install nilearnplotting.

List of pull requests

[MAINT] Post release 0.10.2 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4022
[FIX] fix spelling by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4026
[MAINT] Add python 3.12 to CI by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4023
[FIX] Allow MultiNiftiMasker to use generate_report method by @ymzayek in https://github.com/nilearn/nilearn/pull/4001
[MAINT] Implement deprecation warnings-as-errors in prerelease test using pytest fixture by @ymzayek in https://github.com/nilearn/nilearn/pull/3936
[MAINT] Ignore private visual testing file when running pytest by @ymzayek in https://github.com/nilearn/nilearn/pull/4030
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/4041
[DOC] Change all block splitters in examples to use short syntax by @ymzayek in https://github.com/nilearn/nilearn/pull/4031
[MAINT] Update issue labels by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4036
[MAINT] Add partial build specific to CI doc build workflow by @ymzayek in https://github.com/nilearn/nilearn/pull/4044
[ENH] Allow setting vmin in plot_glass_brain and plot_stat_map by @michellewang in https://github.com/nilearn/nilearn/pull/3993
[MAINT] Use correct target name for Makefile recipe by @ymzayek in https://github.com/nilearn/nilearn/pull/4045
[MAINT] Rename and move testing utilities under tests directory in each module by @ymzayek in https://github.com/nilearn/nilearn/pull/4047
[MAINT] refactor is plotly installed by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4034
[FIX] fix typos in Harvard Oxford atlas labels by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4035
[ENH] add readme to default data locations by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4037
[DOC] link terms to glossary by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4038
[DOC] update URLs with http:// to https:// by @DimitriPapadopoulos in https://github.com/nilearn/nilearn/pull/4050
[DOC] Fix wrong indentation of example code by @ymzayek in https://github.com/nilearn/nilearn/pull/4053
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/4058
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/4059
[MAINT] Use rng fixture for setting up np.random.RandomState() - part 2 by @ymzayek in https://github.com/nilearn/nilearn/pull/4054
[MAINT] use affine_eye fixture by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4056
[MAINT] Refactor fixture for plotting by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4057
[DOC] move default from end of argument description to type name by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4040
[MAINT fix typo in fixture name by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4062
[MAINT] Pytest fixture to ignore internal deprecation warnings by @ymzayek in https://github.com/nilearn/nilearn/pull/4043
[MAINT] change function privacy in _utils by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4061
[MAINT] change future warning to deprecation warning by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4060
[MAINT] Use rng fixture for setting up np.random.RandomState() - part 1 by @ymzayek in https://github.com/nilearn/nilearn/pull/4052
[FIX] fix experimental example private function in monkeypatch by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4065
[DOC] Formatting of docstring in regions.Parcellations by @NIkhilgKrish in https://github.com/nilearn/nilearn/pull/4042
[MAINT] Use rng fixture instead of checkrandomstate by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4063
[STY] Minor doc formatting by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4072
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/4075
[ENH] Allow pandas.Series as valid input for secondlevelinput by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4070
[ENH] pad t and F 'short' contrasts with zeros by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4067
[DOC] Fix failing docs on main by @ymzayek in https://github.com/nilearn/nilearn/pull/4079
[MAINT] refactor of tests and code in GLM module by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4066
[MAINT] drop python 3.7 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4033
[DOC] Make scope limit more obvious regarding accepting new downloaders by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4080
[DOC][MAINT] Remove restriction on Sphinx version by @ymzayek in https://github.com/nilearn/nilearn/pull/4081
[FIX] image.clean_img() kwargs integration by @MIZwally in https://github.com/nilearn/nilearn/pull/4051
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/4083
[FIX] fix typo by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4091
[MAINT] update DOI and add RRID by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4032
[DOC] mention checking badges during release by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4085
[MAINT] Fix Zenodo DOI badge by @ymzayek in https://github.com/nilearn/nilearn/pull/4093
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/4097
[DOC] Remove extraneous hash symbols for examples' section splitters by @ymzayek in https://github.com/nilearn/nilearn/pull/4096
[DOC] Improve docstring rendering for typed experimental surface module by @ymzayek in https://github.com/nilearn/nilearn/pull/4049
[DOC] Add tagging of release version to stable doc build by @ymzayek in https://github.com/nilearn/nilearn/pull/4100
[FIX] Disable extrapolation of out-of-bounds volumes by @jhuguetn in https://github.com/nilearn/nilearn/pull/4028
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/4102
[MAINT] Add listing utilities by @NicolasGensollen in https://github.com/nilearn/nilearn/pull/2991
[MAINT] Pin kaleido version to 0.1.0.post1 for windows by @ymzayek in https://github.com/nilearn/nilearn/pull/4101
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/4105
[MAINT] Rewrite write_tmp_imgs function and use it with pytest's tmp_path by @ymzayek in https://github.com/nilearn/nilearn/pull/4094
[MAINT] Use Numpy Random Generator to replace legacy RandomState by @ymzayek in https://github.com/nilearn/nilearn/pull/4084
[MAINT] Store 1 timepoint for 4D generating a report with the maskers by @ymzayek in https://github.com/nilearn/nilearn/pull/3935
[DOC] Speed up fit computation with parallel processing by @ymzayek in https://github.com/nilearn/nilearn/pull/4108
[REF] Clarify code in find_parcellation_cut_coords function by @ymzayek in https://github.com/nilearn/nilearn/pull/4107
[MAINT] using tox to test in different environments by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4029
[DOC] Fix label in changelog by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4114
[DOC] Clarify docstrings of plotting functions in img_plotting by @ymzayek in https://github.com/nilearn/nilearn/pull/4115
[EHN] Implement signal.clean to SurfaceMasker by @htwangtw in https://github.com/nilearn/nilearn/pull/4117
[ENH] Update binarize_img for negative value handling by @smeisler in https://github.com/nilearn/nilearn/pull/4121
[ENH] Colorbar ticks at threshold values by @NicolasGensollen in https://github.com/nilearn/nilearn/pull/2887
[ENH] Add new returns to NiftiLabelsMasker's transform output by @mtorabi59 in https://github.com/nilearn/nilearn/pull/3761
[ENH] Set appropriate cut coordinates for NiftiLabelsMasker reports by @ymzayek in https://github.com/nilearn/nilearn/pull/4099
[MAINT] minor pre-commit fix by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4125
[ENH] Let checkembeddedniftimasker work with surface masker by @ymzayek in https://github.com/nilearn/nilearn/pull/4120
[MAINT] Test against Numpy 2.0 nightly releases by @ymzayek in https://github.com/nilearn/nilearn/pull/4130
[MAINT] Remove trigger on PR for numpy2 test by @ymzayek in https://github.com/nilearn/nilearn/pull/4133
[DOC] Mention classification type in plothaxbyglm_decoding.py by @TamerGezici in https://github.com/nilearn/nilearn/pull/4122
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/4134
[MAINT] remove leading underscore from non private functions by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4086
[ENH] NiftiSpheresMasker reports by @NicolasGensollen in https://github.com/nilearn/nilearn/pull/3102
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/4142
Bump actions/setup-python from 4 to 5 by @dependabot in https://github.com/nilearn/nilearn/pull/4143
Don't use get_tmaps=True if tmaps aren't used by @crossmanith in https://github.com/nilearn/nilearn/pull/4136
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/4148
[ENH] Raise error when negative or non-integer ROI values are passed to plot_surf_roi by @michellewang in https://github.com/nilearn/nilearn/pull/4131
[DOC] Specify full form of LSS in beta series tutorial by @TamerGezici in https://github.com/nilearn/nilearn/pull/4141
[MAINT] Apply Black to niftilabelsmasker.py by @ymzayek in https://github.com/nilearn/nilearn/pull/4146
[MAINT] Apply Black to reporting files by @ymzayek in https://github.com/nilearn/nilearn/pull/4145
[MAINT] Apply Black img_plotting.py by @ymzayek in https://github.com/nilearn/nilearn/pull/4147
[INFRA] Remove CI workflow to error on DeprecationWarnings of dependencies by @ymzayek in https://github.com/nilearn/nilearn/pull/4149
[MAINT] Apply Black to niftispheresmasker.py by @ymzayek in https://github.com/nilearn/nilearn/pull/4144
[MAINT] Improve error for nifti masker when fit is called without imgs or mask_img by @ymzayek in https://github.com/nilearn/nilearn/pull/4151
[MAINT] make proximal_operator a private module by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4153
[ENH] rename nilearn.datasets._utils.fetch_file to nilearn.datasets._utils.fetch_single_file by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4156
[MAINT] make __all__ and API doc more consistent by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4157
[MAINT] relocate functions from nilearn.datasets.utils by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4154
[FIX] Load compcor related confounds generated from fmriprep 21.x series by @htwangtw in https://github.com/nilearn/nilearn/pull/3285
[STY] run black on nilearn/interfaces/fmriprep by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4163
[FIX] Adjust figure size to display title for functions calling plot_surf by @ymzayek in https://github.com/nilearn/nilearn/pull/4164
[FIX] fix SimpleRegressionResults by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4071
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/4169
[ENH] integrate loadconfounds into firstlevelfrombids by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4103
Bump actions/upload-artifact from 3 to 4 by @dependabot in https://github.com/nilearn/nilearn/pull/4170
Updated docs for fetchabidepcp by @SuramyaP in https://github.com/nilearn/nilearn/pull/4159
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/4174
[MAINT] nilearn.interface: make private functions used outside of their module public by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4168
[DOC] link surface terms to glossary by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4161
[STY] apply black to nilearn._utils.data_gen by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4171
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/4179
[INFRA] Proposal for building stable docs in remote runner for releases by @ymzayek in https://github.com/nilearn/nilearn/pull/4160
[INFRA] Quick fix for automated stable doc build by @ymzayek in https://github.com/nilearn/nilearn/pull/4181
[INFRA] Fix auto trigger for release doc build in Actions workflow by @ymzayek in https://github.com/nilearn/nilearn/pull/4182
[FIX] use a local server rather than temp file to open plots in a browser by @jeromedockes in https://github.com/nilearn/nilearn/pull/4180
[FIX] rich display in jupyter notebook/lab by @jeromedockes in https://github.com/nilearn/nilearn/pull/4183
[MAINT] move user facing functions out of private modules by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4166
[MAINT] move user facing functions out of private modules - part 2 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4167
[FIX] use parameter deprecation decorator by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4189
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/4193
[STY] deal with private functions in nilearn.glm that do not coform to PEP8 naming by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4190
[ENH] Allow string expressions for second_level_contrast of non_parametric_inference by @ymzayek in https://github.com/nilearn/nilearn/pull/4150
[FIX] rename contrast_type to stat_type by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4191
[DOC] fix edit button for examples by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4196
[MAINT] remove duplicate dependency by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4199
[MAINT] remove some old mention of nistats by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4200
[MAINT] make private functions in nilearn.plotting used outside of their module public by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4197
[MAINT] testing minimal version of dependencies by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4068
[MAINT] sort changelog by labels by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4201
[MAINT] Remove unnecessary lines describe in test_clean_psc by @paul-reiners in https://github.com/nilearn/nilearn/pull/4208
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/4213
[DOC] format citation by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4212
[DOC] replace session by run to align with BIDS terminology by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4214
Bump actions/setup-python from 4 to 5 by @dependabot in https://github.com/nilearn/nilearn/pull/4217
[FIX] fix plotting of an image with color bar when maximum value is exactly zero by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4204
[FIX] Fix PSC normalization when a high-pass filter is applied by @ymzayek in https://github.com/nilearn/nilearn/pull/4116
[MAINT] Adapt decoder for scikit-learn > 1.3 by @ymzayek in https://github.com/nilearn/nilearn/pull/4188
[DOC] update dataset descriptions by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4215
[DOC] Combine similar two-runs GLM examples by @tsalo in https://github.com/nilearn/nilearn/pull/3191
[MAINT] speed up tests for html reports by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4221
[DEP] deprecate bids_langloc fetcher by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4219
FIX/EHN update loadconfoundstrategy defaults by @htwangtw in https://github.com/nilearn/nilearn/pull/4225
[FIX] Let decoder accept list of paths as input by @ymzayek in https://github.com/nilearn/nilearn/pull/4227
[FIX] Ensure that fetchers for atlas and func return a Bunch by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4233
[MAINT] Examples output all their results in a single main directory by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4230
Bump actions/cache from 3 to 4 by @dependabot in https://github.com/nilearn/nilearn/pull/4234
[DOC] update version in sphinx directives by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4238
[DOC] sort changelog and add highlights by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4237
[STY] apply black 24.1.0 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4162
[DOC] remove warning from experimental module and add it as doc string by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4240
[STY] re apply black by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4241
Release 0.10.3 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4242

New Contributors

@NIkhilgKrish made their first contribution in https://github.com/nilearn/nilearn/pull/4042
@MIZwally made their first contribution in https://github.com/nilearn/nilearn/pull/4051
@jhuguetn made their first contribution in https://github.com/nilearn/nilearn/pull/4028
@TamerGezici made their first contribution in https://github.com/nilearn/nilearn/pull/4122
@crossmanith made their first contribution in https://github.com/nilearn/nilearn/pull/4136
@SuramyaP made their first contribution in https://github.com/nilearn/nilearn/pull/4159
@paul-reiners made their first contribution in https://github.com/nilearn/nilearn/pull/4208

Full Changelog: https://github.com/nilearn/nilearn/compare/0.10.2...0.10.3

- Python
Published by Remi-Gau over 2 years ago

hidimstat - 0.10.2

Released September 2023

HIGHLIGHTS

Volume plotting functions like plotting.plot_img now have an optional radiological parameter, defaulting to False. If True, this will invert the x-axis and L and R annotations to confirm to radiological conventional view..
Update Decoder objects to use the more efficient LogisticRegressionCV.
Add LassoCV as a new estimator option for Decoder objects
Add vmin and symmetric_cbar arguments to nilearn.plotting.plot_img_on_surf.
Improve contrasts allowing fixed effects on F contrasts
New experimental surface API to facilitate working with surface data in downstream surface-based analyses. We provide this API as a nilearn.experimental.surface module as it is still incomplete and subject to change without a deprecation cycle..

NEW

Volume plotting functions like plotting.plot_img now have an optional radiological parameter, defaulting to False. If True, this will invert the x-axis and L and R annotations to confirm to radiological conventional view..
New experimental surface API to facilitate working with surface data in downstream surface-based analyses. We provide this API as a nilearn.experimental.surface module as it is still incomplete and subject to change without a deprecation cycle..

Fixes

Fix bug in method transform_imgs of maskers.MultiNiftiMapsMasker and maskers.MultiNiftiLabelsMasker that would raise an error if a list of sample_mask was specified to fit_transform.
Fix bug in nilearn.plotting.surf_plotting._plot_surf_matplotlib that would make vertices transparent when saving in PDF or SVG format.
Fix bug that would prevent using symmetric_cmap=True or the avg_method argument with plotting.plot_surf_roi.
Fixes a bug that would lead to an error when loading a fsaverage surface while relying on numpy >= 1.24.x.
Fix bug that would prevent loading the confounds of a gifti file in actual fmriprep datasets.
Fix bug that prevented using dataframes as input for second level GLM when computing contrasts.
Fix bug in glm.first_level.first_level_from_bids that returned no confound files if the corresponding bold files contained derivatives BIDS entities.
Fix bug in glm.first_level.first_level_from_bids that would throw a warning about slice_time_ref not being provided even when it was.
Fix bug where the cv_params_ attribute of fitter Decoder objects sometimes had missing entries if grid_param is a sequence of dicts with different keys.
Make the nilearn.interfaces.fmriprep.load_confounds confounds file selection more generic.
Change default figure sizes to prevent titles from overlapping figure content
Relax the nilearn.interfaces.fmriprep.load_confounds confounds selection on cosine as not all confound files contained the variables.
Fix pathlib.Path not being counted as Niimg-like object in image.new_img_like.
Fix fit_transform behavior to match when fit method is passed image data
Allow using both vmin and threshold with "plotly" engine to be consistent with "matplotlib" behavior
Set edgecolors to be the same as facecolors in plotting.plot_surf_contours so that ROI contours are rendered clearly
Refactor deprecation of behavior of datasets.fetch_atlas_craddock_2012, datasets.fetch_atlas_smith_2009 and datasets.fetch_atlas_basc_multiscale_2015 fetchers including using API consistent maps key

Enhancements

Add cross-reference links to type definitions in public surface functions.
Update Decoder objects to use the more efficient LogisticRegressionCV.
Throw warning in glm.first_level.first_level_from_bids when using event.tsv files with no trial type column.
Make return key names in the description file of destrieux surface consistent with datasets.fetch_atlas_surf_destrieux.
Add LassoCV as a new estimator option for Decoder objects
Add vmin and symmetric_cbar arguments to nilearn.plotting.plot_img_on_surf.
Improve generate_report method of maskers by allowing users to pass a cmap argument for plotting image
Improve contrasts allowing fixed effects on F contrasts

Changes

Validate the content of events files before plotting them.
nilearn.glm.first_level.experimental_paradigm.check_events will now throw a warning if some events have a 0 second duration and will throw an error if an event has NaN onset or duration.
Removed old files and test code from deprecated datasets COBRE and NYU resting state.
PEP8 and isort compliance extended to the whole nilearn codebase..
Finish applying black formatting to most of the codebase..
Empty region signals resulting from applying mask_img in maskers.NiftiLabelsMasker will no longer be kept in release 0.15. Meanwhile, use keep_masked_labels parameter when initializing the maskers.NiftiLabelsMasker object to enable/disable this behavior..
Empty region signals resulting from applying mask_img in maskers.NiftiMapsMasker will no longer be kept in release 0.15. Meanwhile, use keep_masked_maps parameter when initializing the maskers.NiftiMapsMasker object to enable/disable this behavior..
Removed mention of license in "header".
Configure plots in example gallery for better rendering
Make onemeshinfo and fullbraininfo into private functions onemeshinfo and _fullbrain_info
Refactor error raising tests using context managers
Added warning to deprecate darkness in surf_plotting._compute_facecolors_matplotlib and html_surface._get_vertexcolor
Replace skipped doctests with default code-blocks
Move the ~nilearn.plotting.html_surface._mix_colormaps to cm.py in nilearn.plotting
Remove deprecation decorator from ~nilearn.glm.regression
Expose standardize in plotting.plot_carpet and connectome.ConnectivityMeasure to handle "zscore" deprecation.
Example :ref:sphx_glr_auto_examples_01_plotting_plot_prob_atlas.py is shortened to speed up build time

List of pull requests

Post release 0.10.1 by @ymzayek in https://github.com/nilearn/nilearn/pull/3730
[MAINT] Format nilearn/plotting: apply isort and fix flake8 errors by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3648
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/3731
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/3734
[FIX] Missing values in Decoder.cv_params_ when param_grid is a list of dicts with different keys by @michellewang in https://github.com/nilearn/nilearn/pull/3733
Correcting typo in the "loadconfoundsstrategy" function ("scrubbing") by @jonasmago in https://github.com/nilearn/nilearn/pull/3738
[DOC] Fix broken doc build by @ymzayek in https://github.com/nilearn/nilearn/pull/3744
[MAINT] Clean up remaining files from deprecated datasets (cobre, nyu) by @michellewang in https://github.com/nilearn/nilearn/pull/3743
[ENH] Use LogisticRegressionCV instead of LogisticRegression to improve Decoder performance by @michellewang in https://github.com/nilearn/nilearn/pull/3736
[FIX] Fix tests failing due to deprecations in pre-release dependencies by @ymzayek in https://github.com/nilearn/nilearn/pull/3746
[INFRA] Add timeout setting in Azure Pipelines CI by @ymzayek in https://github.com/nilearn/nilearn/pull/3747
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/3748
add more info to adhd example by @mtorabi59 in https://github.com/nilearn/nilearn/pull/3739
[MAINT] improve test coverage BaseMasker by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3721
[MAINT] refactor nilearn/maskers (sourcery, f-strings) by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3685
[MAINT] avoid creating files during testing: testinfereffect_maps by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3716
[MAINT] Catch warnings as errors on partial doc builds by @ymzayek in https://github.com/nilearn/nilearn/pull/3749
[FIX] force ordered output of _sanitize_reorder to match regex in test by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3751
[MAINT] run isort and flake8 on the whole nilearn code base in CI by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3651
[FIX] find confounds even when BIDS derivatives bold files contain res or den entities by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3742
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/3764
[DOC] update changelog and git blame ignore by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3755
[FIX] Change error string to match scikit-learn InvalidParameterError message by @ymzayek in https://github.com/nilearn/nilearn/pull/3763
[MAINT] relax regex for warning on sanitize reorder error by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3766
[DOC] fix duplicate entry in examples dropdown by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3760
[MAINT] refactor nilearn/datasets (sourcery, f-strings) by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3727
[MAINT] add workflow to check for f strings by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3759
[DOC] Remove license and hide authors in examples by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3765
[MAINT] refactor nilearn/plotting (f-strings) by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3757
[MAINT] remove test install with python 2.7 workflow by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3768
[REF] fix f strings by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3770
[ENH][DOC] Fix inconsistent description of return keys for fetchatlassurf_destrieux by @tarunsamanta2k20 in https://github.com/nilearn/nilearn/pull/3774
[MAINT] add lint recipe to make file by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3758
[MAINT] Update config black and pre-commit by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3777
[MAINT] test install and run windows tests with github actions by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3780
[FIX] Fix test assertion to not always be true by @ymzayek in https://github.com/nilearn/nilearn/pull/3786
[DOC] Better print output in example output block by @ymzayek in https://github.com/nilearn/nilearn/pull/3787
[REF] Apply black to nilearn.interface by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3783
[DOC] Fix position of plots in relation to code blocks by @ymzayek in https://github.com/nilearn/nilearn/pull/3788
[INFRA] Add trigger to build specific examples on a push in pull requests by @ymzayek in https://github.com/nilearn/nilearn/pull/3762
[REF] Fix more f strings by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3776
[FIX] address flaky tests in CI by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3785
[FMT] apply black nilearn.plotting.display by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3790
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/3798
Adding keepmaskedlabels parameter to Labels_masker by @mtorabi59 in https://github.com/nilearn/nilearn/pull/3722
[FMT] apply black to maskers - part 1 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3795
[ENH] use citation.cff to store affiliations of authors by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3754
[FMT] apply black to plotting - part 1 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3802
[FIX] prevent extra line with spaces at the end of names.rst by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3809
[DOC] Workaround for sphinx warning reference target not found for 2 scikit-learn (v1.3) classes by @ymzayek in https://github.com/nilearn/nilearn/pull/3804
[MAINT] deal with new warnings related to sklearn 1.3 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3801
[FMT] apply black to maskers - part 2 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3803
[FIX] Make load_confounds' confounds file selection more generic by @tsalo in https://github.com/nilearn/nilearn/pull/3794
[FMT] apply black to plotting - part 2 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3810
[FIX] improve warnings in building glm from BIDS by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3811
[FIX] fix loading of confounds for giftis by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3819
[INFRA] move validation of citation.cff in doc build workflow by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3823
[MAINT] Set nilearn version input in bug issue template to text area by @ymzayek in https://github.com/nilearn/nilearn/pull/3820
add keepmaskedmaps to NiftiMapsMasker by @mtorabi59 in https://github.com/nilearn/nilearn/pull/3732
[FMT] apply black to plotting - part 3 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3827
[DOC] move defaults in docs.py by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3621
[FMT] apply black to plotting - part 4 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3833
[DOC] remove single occurence from docs.py by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3834
[FIX] refactor second-level tests by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3814
[FMT] apply black by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3836
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/3837
[MAINT] remove old check for unsupported scipy versions by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3835
[FIX] Fix long titles overlapping plot contents by @ymzayek in https://github.com/nilearn/nilearn/pull/3797
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/3840
[MAINT] Removed all mentions of "License" from headers by @czarinasy in https://github.com/nilearn/nilearn/pull/3838
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/3841
[REF] refactor filename building in tests for interfaces/fmriprep by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3831
[MAINT] Update some missed tests and examples to use new standardize strategy to silence warnings by @ymzayek in https://github.com/nilearn/nilearn/pull/3821
FIX allow confound files with no cosine by @htwangtw in https://github.com/nilearn/nilearn/pull/3816
[MAINT] update gitblame ignore and contributing by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3842
[DOC] Fix rendering of plots in some examples where titles or images are cut off by @ymzayek in https://github.com/nilearn/nilearn/pull/3753
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/3843
First draft of surface stuff after discussion during meetings & drop-in hours by @jeromedockes in https://github.com/nilearn/nilearn/pull/3799
Revert "First draft of surface stuff after discussion during meetings & drop-in hours" by @ymzayek in https://github.com/nilearn/nilearn/pull/3848
[DOC] replace skipped doctests with default code-blocks by @psadil in https://github.com/nilearn/nilearn/pull/3858
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/3862
[MAINT] add warning to deprecate darkness by @alishakodibagkar in https://github.com/nilearn/nilearn/pull/3855
[REF] refactor test with error raising by @FrancoisPgm in https://github.com/nilearn/nilearn/pull/3854
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/3864
[DOC] update doc to mention how get all the tags from upstream to get the proper version displayed by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3851
[FIX] transparent vertices in surf_plotting function by @mathdugre in https://github.com/nilearn/nilearn/pull/3860
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/3866
[DOC] First pass on adding cross-refence links surface module by @htwangtw in https://github.com/nilearn/nilearn/pull/3857
[REF] Rename html surface func to make them private by @Rahul-Brito in https://github.com/nilearn/nilearn/pull/3847
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/3867
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/3868
[MAINT] fix flake8 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3869
[MRG] [ENH] Radiological view for cross-sectional MRI plotting by @kwagstyl in https://github.com/nilearn/nilearn/pull/3172
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/3876
[FMT] apply toml formatting hook on pyproject.toml by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3872
[DOC] apply badges for plotting to changelog by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3885
[INFRA] Update pullrequesttemplate.md by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3880
[ENH] Raise a warning if the bids events.tsv file doesn't contain column "trial_type" by @vaswin0 in https://github.com/nilearn/nilearn/pull/3597
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/3887
[FMT] apply yml format pre commit hook by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3877
[MAINT] uniformize value of MNI affine used in tests by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3882
[MAINT] add missing dev dependencies for linting by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3888
[DOC] add badge for deprecation by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3889
[FIX] ensure that dataframes can be used as input for second level GLM (estimation and contrast) by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3879
[ENH] check affine and shape of first level models when passed at the second level by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3881
[MAINT] extract dataset ids and file lists by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3890
[MAINT] add file path param to write fake fmri data by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3892
[MAINT] use tmp_path fixture in tests that do not depend on fake fmri data generation by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3893
[MAINT] use tmp_path in glm reporter by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3895
[MAINT] use tmp_path in tests for first lvl GLM by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3894
[DOC] Add docstrings for some bigger private functions in load_confounds. by @htwangtw in https://github.com/nilearn/nilearn/pull/3863
[Fix] Fix pathlib.Path not being counted as Niimg-like in newimagelike by @mcsitter in https://github.com/nilearn/nilearn/pull/3723
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/3901
[INFRA] Prevent Actions workflows from running on people's forks by @ymzayek in https://github.com/nilearn/nilearn/pull/3900
[MAINT] remove obsolete version comparison by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3883
[ENH] Add LassoCV to nilearn.decoding.DecoderRegressor by @michellewang in https://github.com/nilearn/nilearn/pull/3781
[MAINT] Fix failing tests in prerelease job due to deprecation and bug in matplotlib 3.8.0rc1 by @ymzayek in https://github.com/nilearn/nilearn/pull/3902
[FIX][DOC][MAINT] pin sphinx version by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3918
[FIX] Fix overlapping titles for plot_matrix function by @ymzayek in https://github.com/nilearn/nilearn/pull/3899
[MAINT] apply black to utils.doc by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3917
[MAINT] use tmp_path in scd lvl tests by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3896
[MAINT] apply black and pre-commit hooks to files not in PRs by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3906
[MAINT] apply black to nilearn.masking.py by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3907
[MAINT] apply black to tests nilean.signal.py by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3908
[ENH]: Move func mixcolormaps by @achamma723 in https://github.com/nilearn/nilearn/pull/3919
[MAINT] Remove MKL dependency for the documentation build dependencies by @ymzayek in https://github.com/nilearn/nilearn/pull/3920
[MAINT] apply black to glm.firstlevel.firstlevel by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3909
MAINT: Pandas deprecation by @larsoner in https://github.com/nilearn/nilearn/pull/3922
[ENH] add vmin argument to plotting.plot_img_on_surf by @michellewang in https://github.com/nilearn/nilearn/pull/3873
[ENH]: Remove decorator from glm/regression by @achamma723 in https://github.com/nilearn/nilearn/pull/3921
Revert breaking behavior in plot_glass_brain by @ymzayek in https://github.com/nilearn/nilearn/pull/3924
[MAINT] Refactor fixtures by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3905
[MAINT] refactor tests datasets by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3912
[FIX/ENH] Improve generatereport method to work with fittransform for the maskers by @ymzayek in https://github.com/nilearn/nilearn/pull/3897
[MAINT] Refactor/test utils by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3910
[MAINT] remove long decription from pyproject.toml by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3930
[MAINT] replace tmpdir with tmp_path in tests by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3929
[MAINT] refactor tests regions extractions by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3931
[MAINT] Expose standardize parameter in function signatures to allow handling of deprecation by @ymzayek in https://github.com/nilearn/nilearn/pull/3927
[MAINT] refactor tests glm by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3915
[MAINT] refactor design matrix tests by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3939
[DOC] Plot only a few examples of probabilistic atlases by @ymzayek in https://github.com/nilearn/nilearn/pull/3934
[DOC] Include guidelines for private functions in contributing docs by @ymzayek in https://github.com/nilearn/nilearn/pull/3946
[FIX] allow using symmetric maps with plotly by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3942
Fix typo in tutorial by @paulcbogdan in https://github.com/nilearn/nilearn/pull/3950
[FIX] Allow both vmin and threshold argument values to be used in plotting functions using colorscale by @ymzayek in https://github.com/nilearn/nilearn/pull/3945
[ENH] Handle GLM designs with null or nan durations / onsets by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3943
[DOC] improve section on private functions by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3952
[MAINT] simplify flake8 config by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3953
[MAINT] add more badges to changelog by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3955
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/3957
Bump actions/checkout from 3 to 4 by @dependabot in https://github.com/nilearn/nilearn/pull/3958
[MAINT] Update dependabot label by @ymzayek in https://github.com/nilearn/nilearn/pull/3959
[INFRA] Reorganize some optional dependencies under doc by @ymzayek in https://github.com/nilearn/nilearn/pull/3962
[DOC] Use code cell syntax for splitting blocks in 00_tutorial examples by @ymzayek in https://github.com/nilearn/nilearn/pull/3961
[MAINT] Add affiliations by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3956
[MAINT] Update handling of matplotlib ax overwrite deprecation by @ymzayek in https://github.com/nilearn/nilearn/pull/3965
[DOC] add links and edit buttons to doc by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3964
[MAINT] add consortium authorship by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3969
[FIX] allow using a list of sample_mask in MultiNiftiMapsMasker.fit_transform by @acionca in https://github.com/nilearn/nilearn/pull/3971
[BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in https://github.com/nilearn/nilearn/pull/3975
[MAINT] update ORCID by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3970
[DOC] Finish adding badges to changelog by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3968
[DOC] Fix rendering of explanatory text by @ymzayek in https://github.com/nilearn/nilearn/pull/3972
[FIX] Set edgecolors when plotting contours so that they are rendered by @ymzayek in https://github.com/nilearn/nilearn/pull/3973
[DOC] reduce font size for headings by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3978
[INFRA] Use latest Ubuntu machines for CI by @ymzayek in https://github.com/nilearn/nilearn/pull/3981
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/3984
[INFRA] Test minimum supported version of matplotlib for min_requirements testing by @ymzayek in https://github.com/nilearn/nilearn/pull/3976
[DOC] fix doc that mentioned event_type instead of trial_type by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3986
[MAINT] Fix comment in test by @ymzayek in https://github.com/nilearn/nilearn/pull/3989
[FIX] specify dtype when loading gifti by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3644
[MAINT] check events before plotting them by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3994
[FIX] Use maps key for API consistency and improve deprecation for new behavior of some atlas fetchers by @ymzayek in https://github.com/nilearn/nilearn/pull/3987
[INFRA] Configure doc build CI to always host artifacts by @ymzayek in https://github.com/nilearn/nilearn/pull/3990
[MAINT] Deal with Numpy alltrue deprecation by @ymzayek in https://github.com/nilearn/nilearn/pull/3996
[DOC] Workaround for sphinx reference target not found for scikit-learn 1.3.1 by @ymzayek in https://github.com/nilearn/nilearn/pull/3998
[DOC] fix missing @fill_doc by @Remi-Gau in https://github.com/nilearn/nilearn/pull/3992
[DOC] Use code cell syntax for splitting blocks in 01_plotting examples by @ymzayek in https://github.com/nilearn/nilearn/pull/4000
[INFRA/FIX] Minimum testing with minimum matplotlib is not installing matplotlib by @ymzayek in https://github.com/nilearn/nilearn/pull/4002
[BOT] update pre-commit hooks by @github-actions in https://github.com/nilearn/nilearn/pull/4007
[MAINT] Make black CI more verbose by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4008
[DOC] use double backticks in rst files by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4010
[FIX] improve support for F statistics in compute_fixed_effects by @bthirion in https://github.com/nilearn/nilearn/pull/3203
[REL] remove dev in sphinx directives related to version by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4013
[MAINT] add names to all steps in all GHA workflows by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4006
[WIP] apply black to docs by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4005
[REL] add tags to changelog by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4012
[MAINT] update pytest config by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4009
SurfaceImage and maskers by @jeromedockes in https://github.com/nilearn/nilearn/pull/3856
[DOC] Set up experimental module and surface API for docs by @ymzayek in https://github.com/nilearn/nilearn/pull/4017
Release 0.10.2 by @Remi-Gau in https://github.com/nilearn/nilearn/pull/4014

New Contributors

@jonasmago made their first contribution in https://github.com/nilearn/nilearn/pull/3738
@tarunsamanta2k20 made their first contribution in https://github.com/nilearn/nilearn/pull/3774
@czarinasy made their first contribution in https://github.com/nilearn/nilearn/pull/3838
@alishakodibagkar made their first contribution in https://github.com/nilearn/nilearn/pull/3855
@FrancoisPgm made their first contribution in https://github.com/nilearn/nilearn/pull/3854
@mathdugre made their first contribution in https://github.com/nilearn/nilearn/pull/3860
@Rahul-Brito made their first contribution in https://github.com/nilearn/nilearn/pull/3847
@kwagstyl made their first contribution in https://github.com/nilearn/nilearn/pull/3172
@vaswin0 made their first contribution in https://github.com/nilearn/nilearn/pull/3597
@mcsitter made their first contribution in https://github.com/nilearn/nilearn/pull/3723
@acionca made their first contribution in https://github.com/nilearn/nilearn/pull/3971