fix merge conflicts #2
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* 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>
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
* [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 %
* 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
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👋 @Remi-Gau Thanks for creating a PR! Until this PR is ready for review, you can include the [WIP] tag in its title, or leave it as a github draft. Please make sure it is compliant with our contributing guidelines. In particular, be sure it checks the boxes listed below.
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OK let's try that again but with fewer changes... |
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fixes the merge conflicts with upstream for nilearn#3203