fix merge conflicts #2

* update changelog version * Fix some changelog entries * Rename changelog file for release * Add badges * Add release month * Remove dev tag in directives * Fix sphinx docstring userwarning * [full doc] Request full build

* new changelog * Fix underline * Update release instructions

…ilearn#3648) * apply isort * apply isort * apply pyupgrade * flake8 fix * [DATALAD] Recorded changes * [DATALAD] Recorded changes * [DATALAD] Recorded changes * fix typos * fix fixtures * rename fixture * Update nilearn/plotting/html_stat_map.py Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * Update nilearn/plotting/img_plotting.py Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * Update nilearn/plotting/surf_plotting.py Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * Update nilearn/plotting/img_plotting.py Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * [DATALAD] Recorded changes * [DATALAD] Recorded changes * lint * fix test * fix tests * fix isort * fix catch * move fixtures * revert cfg change * isort * isort * rm old imports * merge lines * try skipping fixture import if matplotlib is missing * keep all fixtures in conftest.py * stringify parameters in error message --------- Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com>

Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

…ist of dicts with different keys (nilearn#3733) * add failing test * fill in missing param_grid entries in _parallel_fit * fix formatting * add entry to changelog

…-> scrubbing) (nilearn#3738)

* [full doc] Fix indent * [full doc] Request full build

…nyu`) (nilearn#3743) * remove cobre and nyu datasets * remove unused NYU dataset references * remove nyu_rest from archive_contents * add changelog entry

…ve Decoder performance (nilearn#3736) * replace LogisticRegression with LogisticRegressionCV * update tests for LogisticRegressionCV * update docstring to use LogisticRegressionCV * fix bad links for SVC * update formatting * add changelog entry * add a comment to clarify how default Cs are chosen * replace "C" with "Cs" in param_grid with warning

…es (nilearn#3746) * Fix test in test_html_report * Fix other test in test_html_report * Remove raise warning since already tested * Fix clipping * Clarify if statement * Improve if statement

Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

* add more info to adhd example * reformat with black * change figsize * Update examples/04_glm_first_level/plot_adhd_dmn.py Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> --------- Co-authored-by: Remi Gau <remi_gau@hotmail.com> Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com>

* improve coverage base masker * isort * lfkae8

* refactor * pep8 * Apply suggestions from code review Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> --------- Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com>

…ilearn#3716) * break test * add monkey patch * flake8 fixes * failing test as the monkeypath version of it works * rm 'created during testing in gitignore' * rm bids_dataset

* Suppress image not readable * Make dummy images * Warnings as errors on partial builds

…est (nilearn#3751) * use list as order matters * simplify regex * use list * prettify error message

…learn#3651) * check all of nilean with isort and flake8 * isort fixes * fix isort and flaek8 issues * update config * isort fixes * update config * pre commit run all * fix remaining isort issues * fix import in examples * fix yaml * fix toml * update examples 1 * silence flaek8 errors about black making changes * flake8 * flake8

…s or den entities (nilearn#3742) * make tests more stringent * fix * flake8 * update changelog * update codespell config to catch more errors via pre-commit * Update doc/changes/latest.rst Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * use private function * flake8 fix * deal with regex --------- Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com>

Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

* update git-blame-ignore * update changelog * fix * update ignore * fix regex escape * flake8 * use list and not set * simplify rev file * rm spaces * pragmatism wins * rm import * reset plotting files

…r` message (nilearn#3763) * Modify ValueError string * Warning based on sklearn version

* apply flynt * apply sourcery * apply sourcery * apply sourcery * apply sourcery * apply sourcery * refactor tests * refactor tests * refactor f strings * avoid casting to string * rm walrus * refactor tests

* add workflow for flynt * configure and run flynt * flake8 * Update .github/workflows/f_strings.yml Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * Update nilearn/_utils/data_gen.py Co-authored-by: bthirion <bertrand.thirion@inria.fr> * pre-commit hooks auto-update (nilearn#3764) Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com> * [DOC] update changelog and git blame ignore (nilearn#3755) * update git-blame-ignore * update changelog * fix * update ignore * fix regex escape * flake8 * use list and not set * simplify rev file * rm spaces * pragmatism wins * rm import * reset plotting files * [FIX] Change error string to match scikit-learn `InvalidParameterError` message (nilearn#3763) * Modify ValueError string * Warning based on sklearn version * relax regex for warning on sanitize reorder error (nilearn#3766) --------- Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> Co-authored-by: bthirion <bertrand.thirion@inria.fr> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

* rm license and hide authors * comment more authors * clean up * flake8 fix * rm obsolete addresses

* convert to f strings * use fstrings * fix more f strings * remove last format and %

* try a github workflow to test install * rm test in azure and gh

* fix fstrings in examples * fix more f strings * fix typo * do not use join on int * fix more f strings * fix more f strings * fix format * fix

…s_surf_destrieux (nilearn#3774) * enhancement: [DOC] Inconsistent description of return keys for fetch_atlas_surf_destrieux * updated my contribution info to names.rst and latest.rst file * Update latest.rst * modified the description of changes and placed my info accordingly

* add lint recipe * add flynt to recipe * rm comment

* update black config * apply black * apply black to init files * update config * update config

…rn#3780) * try testing install with gh * try testing on windows * cancel previous test install workflows * rm azure pipeline tests * rm azure badge * update doc

* Fix one example * Fix the rest

…ests (nilearn#3762) * Build individual example commit message * Add make command to build by directory * Add examples base path * Add build directory logic * Add patter * Fix match pattern * Fix directory matching * Limit first 2 digits to match dirs * [examples] plot_nilearn_101.py * [examples] 00 * Correct build command name * [examples] 00 * [examples] 00_tutorials * Build only specific example option * [example] plot_nilearn_101.py * Add to workflows README * Build modified examples plus called one * [example] plot_nilearn_101.py * [example] plot_nilearn_101.py * Improve * [example] plot_nilearn_101.py * [example] plot_nilearn_101.py * [UNDO] test original modified examples trigger still works * [example] plot_python_101.py * Undo change for testing

* f stringify * f strings in examples * f string fix * fix f strings * Update pyproject.toml * [MAINT] test install and run windows tests with github actions (nilearn#3780) * try testing install with gh * try testing on windows * cancel previous test install workflows * rm azure pipeline tests * rm azure badge * update doc * Update examples/04_glm_first_level/plot_localizer_surface_analysis.py Co-authored-by: bthirion <bertrand.thirion@inria.fr> --------- Co-authored-by: bthirion <bertrand.thirion@inria.fr>

* remove duplicate tests * skip test for now * only skip test * silence more tests * ignore all parcellations tests * skip one more test * only run parcellation tests * refactor tests * reintroduce test * reintroduce test * bring yet another test back in * switch ubuntu version for doc * test on all * use latet

* blakc nilearn.plotting.display * Update nilearn/plotting/displays/_figures.py Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * Update nilearn/plotting/displays/_figures.py Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * Update nilearn/plotting/displays/_figures.py Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * Update nilearn/plotting/displays/_slicers.py Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * Update nilearn/plotting/displays/_slicers.py Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * black --------- Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com>

Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

…in hours

* adding keep_masked_labels param * add deprecation warning * add stacklevel to Deprecation warning * improve warning message and docstring * raise a warning when labels are removed * minor update in warning message * make warning shorter * minor change * update doc * run black * update warning message * test new warnings * add new assertions to test_signal_extraction

* apply black * black * black * black * black * black * rm comma

* basic citation file * add other authors * add orcid * add links to doc - [skip ci] * basic script * update citation cff * sort citation authors * add missing authors * fix authors * update AUTHORS.rst * add some affiliations * fix * add workflow to automate file changes * add header * add doc * update doc * fix * update files before doc build * update doc * fix name of lexer

* apply black to plotting * apply black to plotting * apply black to plotting * apply black to plotting * apply black to plotting * apply black to plotting * apply black to plotting * Update nilearn/plotting/html_document.py Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> --------- Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com>

…#3809) * no extra space * fix

* set dual defaults for LinearSVC * silence more warnings * [full doc] request full build * use default * deal with warnings in searchlight * silence more warnings * [full doc] request full build * fix tet * change arg name * rm args to be deprecated

* apply black * apply black * apply black * apply black * Update nilearn/maskers/tests/test_nifti_masker.py * apply black * Apply suggestions from code review Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> --------- Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com>

…earn#3794) * Make load_confounds more general. * Start working on tests. * Fix f-string. * Run black. * Fix the function. * Expand test cases. * Make test fail with original code. * Fix things more. * Update test_load_confounds_utils.py * Update load_confounds_utils.py * Add whatsnew entry. * Address review. * Update nilearn/interfaces/fmriprep/tests/test_load_confounds_utils.py Co-authored-by: Hao-Ting Wang <haotingwang@pm.me> * Update nilearn/interfaces/fmriprep/tests/test_load_confounds_utils.py * Fix style. * Update nilearn/interfaces/fmriprep/tests/test_load_confounds_utils.py * Fix test. * Update test_load_confounds_utils.py --------- Co-authored-by: Hao-Ting Wang <haotingwang@pm.me> Co-authored-by: Remi Gau <remi_gau@hotmail.com>

* apply black * apply black * Apply suggestions from code review * fixes extra spaces from black * Apply suggestions from code review

* fix warning * rm trailing white space * flake8 * update changelog

* fake bids data creates gifti files * reproduce bug * fix * lint * improve doc * update codespell config * fix doc * update doc string * flake8

…ilearn#3820) * Change nilearn version to textarea * Change example versions to x.y.z

* add keep_masked_maps to NiftiMapsMasker * add stacklevel to deprecation warning * improve warning message and docstring * raise warning when maps are removed * make warning shorter * minor change * minor change * update doc * run black * update warning message * fix isort and flake8 * change the warning message * minor formatting

* apply black * apply black * apply black * fix

* update contributing * multiline docstring * update defaults * flake8 * Apply suggestions from code review * Update CONTRIBUTING.rst Co-authored-by: bthirion <bertrand.thirion@inria.fr> * Apply suggestions from code review Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * fix * move default * add defaults * use single backtick * use single backtick * Update CONTRIBUTING.rst Co-authored-by: bthirion <bertrand.thirion@inria.fr> * sort alphabetically * fix warnings * reorder * move default * fix doc build --------- Co-authored-by: bthirion <bertrand.thirion@inria.fr> Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com>

* apply black * remove extra space

* bg_on_data * rm single occurence from docs.py

* refactor tests * flake8 * refator * rm riles * rm failing tests for now * further refactoring * Apply suggestions from code review Co-authored-by: bthirion <bertrand.thirion@inria.fr> * fix failing test * flake8 --------- Co-authored-by: bthirion <bertrand.thirion@inria.fr>

* apply black * rm extra spaces

Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

* Increase default figsize * [full doc] test plots * [full doc] Increase ortho a bit more * Fix formatting * [full doc] Change default figsize of projectors * [full doc] build examples * [full doc] Increase ortho slicer a bit more * Increase r projector * Add whatsnew

Co-authored-by: ymzayek <ymzayek@users.noreply.github.com>

* Removed all mentions of "License" from header as raised in issue nilearn#3771 * Added entry in doc/changes/latest.rst * Added period at the end of comment that failed flake * Added my name to CITATION.cff --------- Co-authored-by: czarina.sy <czarina.sy@rendernetworks.com>

Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

…learn#3831) * [DATALAD] Recorded changes * refactor * lint * set some defaults * fix * fix name

…strategy to silence warnings (nilearn#3821) * Update more tests * [full doc] Update examples * [full doc] Delete repeated tests * Change almost equal decimal points * Update spheres maskers standardization test * Ignore warning configuration * Revert unnessary changes * Formatting * Change last tests

* FIX allow confound files with no cosine Also some code refectoring - concentrate most of the missing regressor and missing strategy key word catching to `load_confounds_components` - consistency of internal and user facing strategy key for ica-aroma (only using ica_aroma, instead of ica_aroma and aroma) - Add unit test for confound components loading and ensure consistent error catching * apply pre-commit checks.. * Update doc/changes/latest.rst Co-authored-by: Remi Gau <remi_gau@hotmail.com> * TEST `high_pass` should perform differently - `high_pass`: when no cosine regressors presents, don't raise error - everything else should raise error * Update latest.rst PR number --------- Co-authored-by: Remi Gau <remi_gau@hotmail.com>

* update gitblameignore * update contributing * update doc * update changelog * Update CONTRIBUTING.rst Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> --------- Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com>

…are cut off (nilearn#3753) * Test one plot * Apply to second plot * Change y position of title * Change multi line title to one line * Move legend and title too long * Fig sizes for long titles * Fix plot_haxby_different_estimators * Fix y position of titles * Custom figsizes * Update examples/01_plotting/plot_demo_more_plotting.py Co-authored-by: Remi Gau <remi_gau@hotmail.com> * Move import * Add whatsnew --------- Co-authored-by: Remi Gau <remi_gau@hotmail.com>

Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com>

…surface_image

… & drop-in hours" (nilearn#3848)

* replace skipped doctests with default code-blocks * remove ellipses in new code-blocks and tidy spacing * update changelog and add Patrick Sadil to contributors

Co-authored-by: ymzayek <ymzayek@users.noreply.github.com>

* add warning to deprecate darkness * deprecate darkness import isort * Add change to latest.rst * Add name to CITATION.cff * Add name to AUTHORS.rst * deprecate darkness in html_surface.py * Change syntax for reference to functions in doc/changes/latest.rst Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * switch UserWarning to eprecationWarning Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * add comma Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * switch UserWarning to DeprecationWarning Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * add comma Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> --------- Co-authored-by: Alisha Kodibagkar <alishakodibagkar@Alishas-MacBook-Pro.local> Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> Co-authored-by: Remi Gau <remi_gau@hotmail.com>

* refactor test with error raising * undo black formatting on specific files * add changes to latest.rst and author to CITATION.cff * make flake8 happy * make flake8 happier * make flake8 sparkle joy * flake8 I promise I will make you smile again --------- Co-authored-by: Remi Gau <remi_gau@hotmail.com>

Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

… the proper version displayed (nilearn#3851) * update doc * move section * fix indent * fix rst * fixes

* [FIX] transparent vertices in `surf_plotting` function with matplotlib engine. * [ADD] change for PR#3860. * [ADD] infos for citation. * Update doc/changes/latest.rst Fix Sphinx formatting. Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * [FIX] merge conflict. --------- Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com>

Co-authored-by: ymzayek <ymzayek@users.noreply.github.com>

…n#3857) * First pass on adding cross-ref for surface module * Apply suggestions from code review Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * manually fix some flake8 issue * Update nilearn/surface/surface.py Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * Update what's new * FIX long line --------- Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com>

@ymzayek

* Update html_surface.py updated plotting.html_surface.one_mesh_info() and plotting.html_surface.full_brain_info() should be renamed to plotting.html_surface._one_mesh_info() and plotting.html_surface._full_brain_info() based on https://github.com/orgs/nilearn/projects/6/views/2?pane=issue&itemId=31373632 * Update surface.py changed example comment to fit renaming of full_brain_info() to _full_brain_info() * Update html_surface.py Line 301 and 421 called _full_brain_info and _one_mesh_info but I did not update these lines with the new function name * Update html_surface.py updated indenting of new functions to fit style guidelines * Update test_html_surface.py updated code in nilearn/plotting/tests/test_html_surface.py since I did not update the tests. * Update html_surface.py Re-added back public version of one_mesh_info() and full_brain_info() that spit out a warning and call the renamed private method, which is the exact code as the public method * Update html_surface.py Editted error messages in new public method to have full single quotes around method names e.g. ‘full_brain_info()’ has been renamed... ‘_full_brain_info()’ and will be removed in a future version instead of full_brain_info() has been renamed... _full_brain_info() and will be removed in a future version * Update test_html_surface.py added tests to test new error warnings on methods renamed from public to private. new public method calls properly renamed private method and spits out a warning * Update test_html_surface.py in the warnings type, had UserWarning but in my code I have DeprecationWarning * Update test_html_surface.py * Update test_html_surface.py * Update html_surface.py trying to get warning to be the same * Update test_html_surface.py trying to get warning o be the same * Update html_surface.py updated warnigns to remove () since it seems like the regex match was getting stuck on that * Update test_html_surface.py updated the test too to match the right string afterremoving the () from the match phrase * Update test_html_surface.py updated messages to reflect @ymzayek suggestions * Update html_surface.py updated warnings in the code too * Update latest.rst updated changelog with renaming change * Update html_surface.py updated warnings to not extend past 80 characters per line * Update test_html_surface.py updated tests to also not have lines >80 characters * Update CITATION.cff added myself to the CITATION.cff * Update nilearn/plotting/tests/test_html_surface.py Co-authored-by: bthirion <bertrand.thirion@inria.fr> * Fix flake8 and isort --------- Co-authored-by: Remi Gau <remi_gau@hotmail.com> Co-authored-by: bthirion <bertrand.thirion@inria.fr> Co-authored-by: ymzayek <yasmin.mzayek@inria.fr>

Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

* fix flake8 * pacify the linting gods

…rn#3172) * radiological view * add plotting radiological example * Update whats_new.rst * Update nilearn/plotting/displays/_axes.py Co-authored-by: Gensollen <nicolas.gensollen@gmail.com> * Update examples/01_plotting/plot_demo_plotting.py Co-authored-by: Gensollen <nicolas.gensollen@gmail.com> * Update nilearn/plotting/img_plotting.py Co-authored-by: Gensollen <nicolas.gensollen@gmail.com> * Update nilearn/plotting/img_plotting.py Co-authored-by: Gensollen <nicolas.gensollen@gmail.com> * Update nilearn/plotting/img_plotting.py Co-authored-by: Gensollen <nicolas.gensollen@gmail.com> * Update nilearn/plotting/displays/_axes.py Co-authored-by: Gensollen <nicolas.gensollen@gmail.com> * line removed * indent corrected * update latest.rst * Update whats_new.rst * Update nilearn/plotting/displays/_axes.py Co-authored-by: bthirion <bertrand.thirion@inria.fr> * added spaces * update spacing * update formatting * added name * formatting * formatting * formatting fixes * Update _axes.py * Update docs.py * doc string shortcut * Update nilearn/_utils/docs.py Co-authored-by: Gensollen <nicolas.gensollen@gmail.com> * Update nilearn/plotting/img_plotting.py Co-authored-by: Gensollen <nicolas.gensollen@gmail.com> * Update img_plotting.py * Update docs.py * update docs * Fix merge of docs.py * Remove extra default statement * Resolve formatting issues * Add radiological argument to GlassBrainAxes * Add smoke tests for relevant plotting funcs * Remove unneeded argument * Improve testing * Update whatsnew * Change test data --------- Co-authored-by: Gensollen <nicolas.gensollen@gmail.com> Co-authored-by: bthirion <bertrand.thirion@inria.fr> Co-authored-by: ymzayek <yasmin.mzayek@inria.fr>

Co-authored-by: ymzayek <ymzayek@users.noreply.github.com>

* apply toml formatting hook on pyproject.toml * 4 spaces

more of cosmetic change but allows issue number AND name to be rendered directly when viewing the PR top message also removes a space before the # that I am tired of deleting for every PR

…umn "trial_type" (nilearn#3597) * Update first_levels.py Added a non-member function to raise a warning if the events.tsv file doesn't contain a column named "trial_type". The function will be called iteratively on each pandas dataframe corresponding to events.tsv file. * Update first_level.py * Update first_level.py * Update nilearn/glm/first_level/first_level.py Co-authored-by: Remi Gau <remi_gau@hotmail.com> * Update nilearn/glm/first_level/first_level.py Co-authored-by: Remi Gau <remi_gau@hotmail.com> * Update first_level.py * Update nilearn/glm/first_level/first_level.py Co-authored-by: Remi Gau <remi_gau@hotmail.com> * Update nilearn/glm/first_level/first_level.py Co-authored-by: Remi Gau <remi_gau@hotmail.com> * Update nilearn/glm/first_level/first_level.py Co-authored-by: Remi Gau <remi_gau@hotmail.com> * Update nilearn/glm/first_level/first_level.py Co-authored-by: Remi Gau <remi_gau@hotmail.com> * Update nilearn/glm/first_level/first_level.py Co-authored-by: Remi Gau <remi_gau@hotmail.com> * Update nilearn/glm/first_level/first_level.py Co-authored-by: Remi Gau <remi_gau@hotmail.com> * Update nilearn/glm/first_level/first_level.py Co-authored-by: Gensollen <nicolas.gensollen@gmail.com> * Update nilearn/glm/first_level/first_level.py Co-authored-by: Gensollen <nicolas.gensollen@gmail.com> * Update nilearn/glm/first_level/first_level.py Co-authored-by: Gensollen <nicolas.gensollen@gmail.com> * Update nilearn/glm/first_level/first_level.py Co-authored-by: Gensollen <nicolas.gensollen@gmail.com> * Update nilearn/glm/first_level/first_level.py Co-authored-by: Gensollen <nicolas.gensollen@gmail.com> * add test * update changelog * fix linter * fix name * update parameter description * lint --------- Co-authored-by: Remi Gau <remi_gau@hotmail.com> Co-authored-by: Gensollen <nicolas.gensollen@gmail.com>

Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

* apply yml format hook * rm conda env file

* change mni affine in conftest.py: let us see how many things break * change value in tests * fix tests * refactor * fix flake8 * rename function

* add codespell to dev dependencies for linting * add precommit to dev dependencies

…M (estimation and contrast) (nilearn#3879) * regression test and fix * Apply suggestions from code review * update chngelog * fix * rm test files * Apply suggestions from code review Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * use write_fake_bold_img --------- Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com>

… second level (nilearn#3881) * check scd lvl inputs * [DATALAD] Recorded changes * fix test * [DATALAD] Recorded changes * add checks for shape * get shape

* add file path param to write fake fmri data * add parameter in other function

… data generation (nilearn#3893) * remove tmp dir in tests that do not depend on fake fmri data generation * break into smaller tests

* use tmp_path in glm reporter * rm del instances * fix tests * lint * proper silencing of the falke8 errors

* use tmp_path in tests first lvl * refactor tests

…unds.` (nilearn#3863) * Add docstrings for some bigger private functions With the help of copilot. * Apply suggestions from code review Co-authored-by: bthirion <bertrand.thirion@inria.fr> * Add cross-reference links to type definitions * Docstring for compcor related private function * Apply suggestions from code review Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: bthirion <bertrand.thirion@inria.fr> * Simplify docstring - remove outdated one-hot encoder related description - remove options from parameter descriptions, replaced with default option - remove redundant default option descriptions in the docstring * omissed out the default value of scrubbing * Complete all the docstring co-authored by GitHub Co-pilot. * Apply suggestions from code review Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> --------- Co-authored-by: bthirion <bertrand.thirion@inria.fr> Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com>

…ike (nilearn#3723) * Fix pathlib.Path not being counted as Niimg-like * Fix unnecessarily changing mean_img * Change isinstance check to stringify_path * Add unit test for acceptance of pathlib.Path as image * Add name to citation * Update CITATION.cff * Update doc/changes/latest.rst * Update nilearn/image/tests/test_image.py * Fix flake8 --------- Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> Co-authored-by: ymzayek <yasmin.mzayek@inria.fr>

Co-authored-by: ymzayek <ymzayek@users.noreply.github.com>

…earn#3900) * Prevent CI workflows from running on forks * Leave for short workflows * Update .github/workflows/isort.yml * Missed some in testing.yml --------- Co-authored-by: Remi Gau <remi_gau@hotmail.com>

* rm obsolete version comparison * silence warnings for scipy * remove special handling in slicer for old version of matplotlib * more fixes * revert * revert * rm comments * flake8 * add test

) * add LassoCV to DecoderRegressor * update decoder tests * add 'lasso'/'lasso_regressor' to regressor options * update changelog entry * use n_alphas=30 as default instead of 100 * add lasso regression decoding to example * fix formatting in example * add lasso(_regressor) to list of estimators in docs * revert example * fix formatting

…g in matplotlib 3.8.0rc1 (nilearn#3902) * Fix plot_carpet * Add version conditional for new method * isort * Modify test for mpl bug

* Simplify add title * [full doc] build examples * Update test

* use tmp_path in scd lvl tests * refactor * fix

* apply black to masking * update config

* apply black to tests signal * update config * Update nilearn/tests/test_signal.py Co-authored-by: bthirion <bertrand.thirion@inria.fr> --------- Co-authored-by: bthirion <bertrand.thirion@inria.fr>

* Move func _mix_colormaps * Fix isort and black * Add to latest * Clean commit * Fix doc --------- Co-authored-by: achamma <ahmad.chamma@inria.fr>

* apply black to glm * update config * update config * Update nilearn/glm/first_level/first_level.py Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * Update nilearn/glm/first_level/first_level.py Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * Update nilearn/glm/first_level/first_level.py Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> --------- Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com>

* MAINT: Pandas deprecation * STY: Flake

* remove force_min_stat_map_value (not used anywhere) * add vmin to plot_img_on_surf (and _get_colorbar_and_data_ranges) * remove test for error on vmin input * keep old behaviour for plot_stat_map and plot_glass_brain * add check that vmin < vmax * add test cases with vmin * update tests * update docstrings * use different description of symmetric_cbar arg in docstring * add changelog entry * allow vmin == vmax * remove check that vmin <= vmax * add check for "engine" kwarg * clarify error message * try to increase test coverage * fix formatting * revert back to symmetric_cmap=True * remove duplicate test function (bad merge) * remove redundant vmin = -vmax * remove mention of symmetric_data_range in error message * use symmetric_cbar="auto" as default * handle symmetric_cbar == "auto" before filling in vmin/vmax * handle vmax < threshold case

* Remove decorator * Add whatsnew * Fix flake8 * Remove changes in first_level --------- Co-authored-by: achamma <ahmad.chamma@inria.fr>

* Revert behavior of vmin being ignored * Add smoke test for passing vmin and vmax * [example] plot_second_level_two_sample_test.py * Just being

* rename mni affine fixture * further fixture refactroring * refactor fixtures in nilearn/regions * refactor fixtures in decomposition * fix test pollution * try to get around the global var problem * add some doc in fixtures * rm constants * add rng fixture * add doc about fixture * Apply suggestions from code review Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com> * update contributing * fix tests --------- Co-authored-by: Yasmin <63292494+ymzayek@users.noreply.github.com>

* rm extra fixture calls * rm duplicate test * refactor test get datadir * refactor test_func * refactor tests atlas * test neurovault * Apply suggestions from code review Co-authored-by: bthirion <bertrand.thirion@inria.fr> * rm one extra reuest mocker * refactor tests * refactor and add comment * use fixtures * capture and test error message --------- Co-authored-by: bthirion <bertrand.thirion@inria.fr>

…or the maskers (nilearn#3897) * Pass imgs to fit in fit_transform * Change colormap * Improve docstrings * Remove unused import * Store 1 timepoint * Revert "Store 1 timepoint" This reverts commit 8d6d427. * Allow users to pass cmap * Add whatsnew

* refactor tests * refactor * refactor * fix * use fixtures * update code doc * refactor * use testing.write_tmp_imgs * Revert "use testing.write_tmp_imgs" This reverts commit 244f0f3.

* replace tmpdir with tmp_path * rm extra import

* refactort tests deprecation warning * add restriction function length * test functions lenght in CI * config

…w handling of deprecation (nilearn#3927) * Add standardize to address deprecation * Update examples * [full doc] build examples * Handle RegionExtractor case * [example] plot_extract_regions_dictlearning_maps.py * Handle last case * Add doctstring * [full doc] build examples * Add test for plot_carpet * Add test for connectivity measure * Add whatsnew

* refactor test paradigm * refactor glm test utils * fixturize * add fxitures * use fixtures * use more fixtures * fix

* refactor design matrix related tests * rm extra n_frames * parametrize tests and add error match * fix

* Plot only one atlas * Plot 3 atlases according to display type * Improve rendering * Add missed atlas * Add whatsnew

* fix nilearn#3941 * fix kwargs * implement test for matplotlib * update changelog * flake 8 * fix failed ref * simplify * simplify * flake8 * fix other argument * rename test * update changelog * flake8

…tting functions using `colorscale` (nilearn#3945) * Allow both vmin and threshold to be passed * Add whatsnew * Add test * Add reference

…#3943) * manual "rebase" * make functions public * throw errors for nan values * refactor * plot null duration events * fix link in doc * update example * ignore results * revert useless change * rm useless code * update changelog * rm :func: from changelog

* improve section on private functions * fix

* add :bdg-secondary:`Maint` badges * mooorrreee baaaadges

Co-authored-by: Remi-Gau <Remi-Gau@users.noreply.github.com>

Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

…es (nilearn#3961) * Change block splitters format * Fix pattern not found

* update citation.cff * get affiliations from github * manual claeaning * update citation.cff * rm tsv * add affiliations to AUTHORS.rst * rm utility scripts * update affiliations after manual lookup * Apply suggestions from code review Co-authored-by: bthirion <bertrand.thirion@inria.fr> * Apply suggestions from code review Co-authored-by: bthirion <bertrand.thirion@inria.fr> * uniformize changes into citation.cff * update affiliations * update some affiliations that only had countries * update some orcid * update more orcid and affiliations --------- Co-authored-by: bthirion <bertrand.thirion@inria.fr>

* add links and edit buttons to doc * update year in doc * add discord and mastodon * add badges * update

fix merge conflicts #2

fix merge conflicts #2

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