fixed code + added test #3137
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fixed code + added test #3137
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Codecov Report
@@ Coverage Diff @@
## main #3137 +/- ##
==========================================
- Coverage 90.18% 90.16% -0.02%
==========================================
Files 119 121 +2
Lines 14442 14445 +3
Branches 2957 2958 +1
==========================================
Hits 13024 13024
- Misses 848 851 +3
Partials 570 570
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NicolasGensollen
approved these changes
Jan 21, 2022
doc/whats_new.rst
Outdated
| @@ -68,6 +68,8 @@ Fixes | |||
| index (See PR `#3078 <https://github.com/nilearn/nilearn/issues/3078>`_). | |||
| - Convert reference in `nilearn/regions/region_extractor.py` to use footcite / footbibliography. | |||
| (See issue `#2787 <https://github.com/nilearn/nilearn/issues/2787>`_ and PR `#3111 <https://github.com/nilearn/nilearn/pull/3111>`_). | |||
| - Computation of Benjamini-Hocheberg threshold fixed in `nilearn/glm/thresholding.py` function (see issue ``#2879 <https://github.com/nilearn/nilearn/issues/2879>`_ and PR `#3137 <https://github.com/nilearn/nilearn/pull/3137>`_`) | |||
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| - Computation of Benjamini-Hocheberg threshold fixed in `nilearn/glm/thresholding.py` function (see issue ``#2879 <https://github.com/nilearn/nilearn/issues/2879>`_ and PR `#3137 <https://github.com/nilearn/nilearn/pull/3137>`_`) | |
| - Computation of Benjamini-Hocheberg threshold fixed in `nilearn/glm/thresholding.py` function (see issue `#2879 <https://github.com/nilearn/nilearn/issues/2879>`_ and PR `#3137 <https://github.com/nilearn/nilearn/pull/3137>`_) |
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Thanks, merging... |
achamma723
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Jan 26, 2022
* fixed code + added test * pep8 * Added to whatsnew * string fix
NicolasGensollen
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Jan 28, 2022
* Repalce numpy with pandas * [MAINT] Fix new typos found by codespell (#3101) Fixes c87847b / #3003. * Fix pep8 + destrieux * Fix pep8 * Merge docs * continue work (unfinished) * Iter * Fix test * Fix other test * Iter * Add warnings * Fix PEP8 * Address Jerome's reviews * Fix PEP8 * convert to lower case in fetch_atlas_difumo * [circle full] Add whatsnew. * Fix * [circle full] remove deprecation warning from example * Fix examples * [ENH] Add `cbar_tick_format` to plotting functions (#2859) * enable cbar_tick_format in BaseSlicer * show in examples * Add whatsnew entry * [circle full] test full build * Fix doctrings and kwarg for colorbar and cbar_tick_format * pep8 * Re-add tests and fix rebase issues * Fix PEP8 * [circle full] request full build * plot_roi cbar tick format defaults to integers * escape % * [circle full] request full build * Rename private functions of `permuted_least_squares` to start with '_' (#3131) * rename functions * update test * Fix PEP8 * [MAINT] Update git protocol in CircleCI fetch step (#3124) * update protocol * try force cleaning * try clearing cache * [MAINT] Scipy deprecation warning in RegionExtractor (#3130) atol='legacy' option in `scipy.sparse.linalg.cg` to avoid deprecation warning * [MAINT] Remove deprecated `sessions` and `sample_mask` attributes of `NiftiMasker` (#3133) * remove deprecated sessions and sample_mask * Update tests * Update doctest * [circle full] add whatsnew entry * [circle full] fix * [MAINT] Remove old workaround (#3092) * [ENH] Move FSL- and BIDS-related functions to interfaces module (#3126) * Move BIDS and FSL-related functions to the interfaces module. * Update associated imports across the library. * Add migrated functions to the reference page. * Add entries to whatsnew page. Will need to update with PR link. * Move tests for new functions into appropriate files. * Update the pull request number. * [FIX] Fix links in whats_new (#3139) * [circle full] fix links * [circle full] fix wrong glossary entry * [FIX] fixed code + added test (#3137) * fixed code + added test * pep8 * Added to whatsnew * string fix * [ENH] Refactor `plot_matrix` (#3001) * Refactor plot_matrix * Improve docstrings * Fix PEP8 * [circle full] request full build * Add tests for plot_matrix and refactor * Fix PEP8 * Add missing test * [circle full] request full build * [circle full] Fix method reference * [circle full] Avoid hardcoded parameters. * Update nilearn/plotting/matrix_plotting.py Co-authored-by: bthirion <bertrand.thirion@inria.fr> Co-authored-by: bthirion <bertrand.thirion@inria.fr> * [FIX] replace interpreter call (#3136) The python command is not guaranteed to exist. On some systems it refers to old python 2. See https://www.python.org/dev/peps/pep-0394/ * [FIX] `FirstLevelModel` signal_scaling (#3135) * Add failing test * get rid of scaling_axis attribute * deprecate scaling_axis * [circle full] add whatsnew entry * Fix * [ENH] Include Hierarchical KMeans in regions.Parcellations (#2282) * Including Hierarchical Kmeans in doc and example * Adding hierarchical k_means and make it available in parcellations * test hierarchical_kmeans and test Parcellation using it * fix incompatible apis of fit() and transform() methods * Improve docstring and example layout * "Upgrade to get_data function" * "changing nose function to pytest function as the rest of the library evolved" * "solving sklearn.utils.testing deprecation" * "improve flake8" * "flake8, missing import, adding test exception" * Apply suggestions from code review Including B.T. suggestions Co-authored-by: bthirion <bertrand.thirion@inria.fr> * "adding tests for 'scaling' and warning ; fixed scaling bug" * "test_refactoring" * "flake8 fixes" * "clarify example, fix PEP8" * Apply suggestions from code review Co-authored-by: bthirion <bertrand.thirion@inria.fr> * "apply suggestions from N.G. review" * Apply suggestions from code review Co-authored-by: Gensollen <nicolas.gensollen@gmail.com> * "apply B.T refactoring" * "flake8" * "flake8" * "codespell" * "enforcing final number of clusters is the one asked by the user" * "solving bugging test_case" * "solving edge case" * "missing float casting" * "check that adjusted clusters are int" * "flake8 fix" * Update nilearn/regions/hierarchical_kmeans_clustering.py Co-authored-by: bthirion <bertrand.thirion@inria.fr> * Update examples/03_connectivity/plot_data_driven_parcellations.py Co-authored-by: bthirion <bertrand.thirion@inria.fr> * Update examples/03_connectivity/plot_data_driven_parcellations.py Co-authored-by: bthirion <bertrand.thirion@inria.fr> * "fix code review comments" * 'fix bug introduced by review suggestion' * Update nilearn/regions/hierarchical_kmeans_clustering.py Co-authored-by: Gensollen <nicolas.gensollen@gmail.com> * Update nilearn/regions/hierarchical_kmeans_clustering.py Co-authored-by: Gensollen <nicolas.gensollen@gmail.com> * Update nilearn/regions/hierarchical_kmeans_clustering.py Co-authored-by: Gensollen <nicolas.gensollen@gmail.com> * Update nilearn/regions/hierarchical_kmeans_clustering.py Co-authored-by: Gensollen <nicolas.gensollen@gmail.com> * "apply code review suggestions" * "add whats_new" * fixing docstring * addressing comments of jdockes * trying to fix pep8 violations * simplifying hierarchical k-means avoiding useless checks * pep8 * Addressing other comments by jdockes Co-authored-by: BAZEILLE Thomas <thomas.bazeille@inria.fr> Co-authored-by: bthirion <bertrand.thirion@inria.fr> Co-authored-by: Gensollen <nicolas.gensollen@gmail.com> * [DOC] Fix wrong whats_new entry (#3142) * [FIX] Fix hommel value computation (#3109) * added deploy key * clean deploy key * clean deploy key * clean cricreci.yml * clean circleci.yml * clean circleci.yml * clean circleci.yml * fixed Hommel function + added test * pep8 fixes * pep8 fixes * pep8 fixes * correct use of assert * revert unrelated change * minor fixed on hommel value computation * addedwhatsnew entry Co-authored-by: Gensollen <nicolas.gensollen@gmail.com> * [DOC] Refactor change logs (#3049) * Add gh_substitutions * Add links to contributor profiles (unfinished) * Use contributor links in AUTHORS * Break and refactor changelog (unfinished...) * [circle full] Fix typo and run full build in strict mode. * Add more links * iter * [circle full] request full build * Add more links again * [circle full] Iter. * Update AUTHORS.rst * gh_role --> _gh_role * [circle full] Add fundings. * [circle full] Fix wrong ref. * [circle full] update niconnect link * [circle full] fix ref * fix refs: input_data -> maskers * [circle full] request full build * [circle full] fix old ref to fetch_cobre * [circle full] fix broken ref * [circle full] Fix error in rebase * [circle full] fix whats_new bug * [MAINT] Bump dependencies for release `0.9.0` (#3143) * bump dependencies * [circle full] Add whatsnew. * Jerome's review * remove warning * [INFRA] Add tests min requirements with Matplotlib (#3144) * Add tests min req with matplotlib * remove useless variable * [circle full] update README * 2021 -> 2022 (#3146) * Revert "[MAINT] Bump dependencies for release `0.9.0` (#3143)" This reverts commit 26de3fe. * Revert "[INFRA] Add tests min requirements with Matplotlib (#3144)" This reverts commit 27e00f0. * Revert "2021 -> 2022 (#3146)" This reverts commit 304e782. Co-authored-by: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Co-authored-by: NicolasGensollen <nicolas.gensollen@gmail.com> Co-authored-by: Hao-Ting Wang <htwangtw@gmail.com> Co-authored-by: Taylor Salo <tsalo006@fiu.edu> Co-authored-by: bthirion <bertrand.thirion@inria.fr> Co-authored-by: Ben Greiner <code@bnavigator.de> Co-authored-by: ThomasBaz <6551732+thomasbazeille@users.noreply.github.com> Co-authored-by: BAZEILLE Thomas <thomas.bazeille@inria.fr>
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