[MAINT] sort changelog by labels

doc/changes/0.1.3.rst

@@ -26,9 +26,9 @@ It also includes a full rewamp of the documentation, and support for Python 3.
 Fixes
 -----
 
-- :bdg-dark:`Code` Dealing with ``NaNs`` in function :func:`~plotting.plot_connectome`.
+- :bdg-success:`API` Function :func:`~plotting.plot_connectome` now supports ``vmin`` and ``vmax``.
 
-- :bdg-info:`Plotting` Fix extreme values in colorbar were sometimes brok.
+- :bdg-dark:`Code` Dealing with ``NaNs`` in function :func:`~plotting.plot_connectome`.
 
 - :bdg-dark:`Code` Fix confounds removal with single confounds.
 
@@ -38,10 +38,10 @@ Fixes
 
 - :bdg-dark:`Code` ``add_overlay`` finds ``vmin`` and ``vmax`` automatically.
 
-- :bdg-success:`API` Function :func:`~plotting.plot_connectome` now supports ``vmin`` and ``vmax``.
-
 - :bdg-dark:`Code` Detrending 3D images no longer puts them to zero.
 
+- :bdg-info:`Plotting` Fix extreme values in colorbar were sometimes brok.
+
 
 Contributors (from ``git shortlog -ns 0.1.2..0.1.3``):
 

doc/changes/0.1.4.rst

@@ -13,12 +13,12 @@ Highlights
 
 - :bdg-success:`API` New class :class:`nilearn.maskers.NiftiSpheresMasker` which extracts signals from balls specified by their coordinates.
 
-- :bdg-secondary:`Maint` Obey Debian packaging rules.
-
 - :bdg-dark:`Code` Add the Destrieux 2009 and Power 2011 atlas.
 
 - :bdg-dark:`Code` Better caching in maskers.
 
+- :bdg-secondary:`Maint` Obey Debian packaging rules.
+
 
 Contributors (from ``git shortlog -ns 0.1.3..0.1.4``):
 

doc/changes/0.10.0.rst

@@ -27,59 +27,57 @@ HIGHLIGHTS
 
 - :bdg-success:`API` New classes :class:`~maskers.MultiNiftiLabelsMasker` and :class:`~maskers.MultiNiftiMapsMasker` create maskers to extract signals from a list of subjects with 4D images using parallelization (:gh:`3237` by `Yasmin Mzayek`_).
 
-- :bdg-primary:`Doc` Updated docs with a new theme using `furo <https://github.com/pradyunsg/furo>`_ (:gh:`3125` by `Alexis Thual`_).
-
 - :bdg-success:`API` :func:`~mass_univariate.permuted_ols` and :func:`~glm.second_level.non_parametric_inference` now support :term:`TFCE` statistic (:gh:`3196` by `Taylor Salo`_).
 
 - :bdg-success:`API` :func:`~mass_univariate.permuted_ols` and :func:`~glm.second_level.non_parametric_inference` now support cluster-level Family-wise error correction (:gh:`3181` by `Taylor Salo`_).
 
 - :bdg-success:`API` :func:`~interfaces.bids.save_glm_to_bids` has been added, which writes model outputs to disk according to BIDS convention (:gh:`2715` by `Taylor Salo`_).
 
+- :bdg-primary:`Doc` Updated docs with a new theme using `furo <https://github.com/pradyunsg/furo>`_ (:gh:`3125` by `Alexis Thual`_).
+
 
 NEW
 ---
 
 - :bdg-success:`API` New classes :class:`~maskers.MultiNiftiLabelsMasker` and :class:`~maskers.MultiNiftiMapsMasker` create maskers to extract signals from a list of subjects with 4D images using parallelization (:gh:`3237` by `Yasmin Mzayek`_).
 
-
 Fixes
 -----
 
-- :bdg-dark:`Code` Fix off-by-one error when setting ticks in :func:`~plotting.plot_surf` (:gh:`3105` by `Dimitri Papadopoulos Orfanos`_).
-
 - :bdg-success:`API` Regressor names can now be invalid identifiers but will raise an error with :meth:`~glm.first_level.FirstLevelModel.compute_contrast` if combined to make an invalid expression (:gh:`3374` by `Yasmin Mzayek`_).
 
-- :bdg-info:`Plotting` Fix :func:`~plotting.plot_connectome` which was raising a ``ValueError`` when ``vmax < 0`` (:gh:`3390` by `Paul Bogdan`_).
-
 - :bdg-success:`API` Change the order of applying ``sample_masks`` in :func:`~signal.clean` based on different filtering options (:gh:`3385` by `Hao-Ting Wang`_).
 
 - :bdg-success:`API` When using cosine filter and ``sample_masks`` is used, :func:`~signal.clean` generates the cosine discrete regressors using the full time series (:gh:`3385` by `Hao-Ting Wang`_).
 
+- :bdg-success:`API` Pass values with correct type to scikit-learn estimator parameters and remove deprecated parameter (:gh:`3430` by `Yasmin Mzayek`_).
+
+- :bdg-dark:`Code` Fix off-by-one error when setting ticks in :func:`~plotting.plot_surf` (:gh:`3105` by `Dimitri Papadopoulos Orfanos`_).
+
+- :bdg-dark:`Code` Fix cluster labeling for two-sided cluster level permutation tests in :func:`~mass_univariate.permuted_ols` and associated function test ``test_cluster_level_parameters_smoke`` (:gh:`3436` by `Jelle Roelof Dalenberg`_).
+
 - :bdg-primary:`Doc` Description of the ``opening`` parameter added to ``compute_multi_epi_mask`` docs (:gh:`3412` by `Natasha Clarke`_).
 
 - :bdg-info:`Plotting` Fix display of colorbar in matrix plots. Colorbar was overlapping in :func:`~matplotlib.pyplot.subplots` due to a hardcoded adjustment value in the subplot (:gh:`3403` by `Raphael Meudec`_).
 
-- :bdg-success:`API` Pass values with correct type to scikit-learn estimator parameters and remove deprecated parameter (:gh:`3430` by `Yasmin Mzayek`_).
-
-- :bdg-dark:`Code` Fix cluster labeling for two-sided cluster level permutation tests in :func:`~mass_univariate.permuted_ols` and associated function test ``test_cluster_level_parameters_smoke`` (:gh:`3436` by `Jelle Roelof Dalenberg`_).
+- :bdg-info:`Plotting` Fix :func:`~plotting.plot_connectome` which was raising a ``ValueError`` when ``vmax < 0`` (:gh:`3390` by `Paul Bogdan`_).
 
 - :bdg-warning:`Test` Fix failing CanICA test by adding noise to the data creation step (:gh:`3453` by `Yasmin Mzayek`_).
 
-
 Enhancements
 ------------
 
 - :bdg-success:`API` :func:`~signal.clean` imputes scrubbed volumes (defined through ``sample_masks``) with cubic spline function before applying butterworth filter (:gh:`3385` by `Hao-Ting Wang`_).
 
-- :bdg-primary:`Doc` As part of making the User Guide more user-friendly, the introduction was reworked (:gh:`3380` by `Alexis Thual`_)
-
-- :bdg-primary:`Doc` Added instructions for maintainers to make sure LaTeX dependencies are installed before building and deploying the stable docs (:gh:`3426` by `Yasmin Mzayek`_).
+- :bdg-success:`API` Add parameter ``cut_coords`` in :func:`~reporting.make_glm_report` (:gh:`3452` by `Audrey Duran`_).
 
 - :bdg-success:`API` Parameter ``sample_masks`` in :func:`~signal.clean` and masker functions accept binary mask (:gh:`3439` by `Hao-Ting Wang`_).
 
+- :bdg-primary:`Doc` As part of making the User Guide more user-friendly, the introduction was reworked (:gh:`3380` by `Alexis Thual`_)
+
 - :bdg-primary:`Doc` Contributing docs were improved by adding clear guidelines for users about changelog/whatsnew entries (:gh:`3446` by `Robert Williamson`_).
 
-- :bdg-success:`API` Add parameter ``cut_coords`` in :func:`~reporting.make_glm_report` (:gh:`3452` by `Audrey Duran`_).
+- :bdg-primary:`Doc` Added instructions for maintainers to make sure LaTeX dependencies are installed before building and deploying the stable docs (:gh:`3426` by `Yasmin Mzayek`_).
 
 
 Changes
@@ -91,12 +89,8 @@ Changes
 
 - :bdg-danger:`Deprecation` Function ``nilearn.masking.compute_multi_gray_matter_mask`` has been removed since it has been deprecated and replaced by :func:`~masking.compute_multi_brain_mask` (:gh:`3427` by `Yasmin Mzayek`_).
 
-- :bdg-primary:`Doc` :mod:`~nilearn.glm` will no longer warn that the module is experimental (:gh:`3424` by `Yasmin Mzayek`_).
-
 - :bdg-danger:`Deprecation` Python ``3.6`` is no longer supported. Support for Python ``3.7`` is deprecated and will be removed in release ``0.12`` (:gh:`3429` by `Yasmin Mzayek`_).
 
-- :bdg-secondary:`Maint` The function ``_safe_cache`` is removed because it was deemed outdated and not necessary anymore (:gh:`3375` by `Yasmin Mzayek`_).
-
 - :bdg-danger:`Deprecation` Minimum supported versions of packages have been bumped up:
 
     * Numpy -- v1.19.0
@@ -110,4 +104,8 @@ Changes
 
 - :bdg-danger:`Deprecation` In release ``0.10.0`` the default resolution for loaded MNI152 templates will be 1mm instead of 2mm (:gh:`3433` by `Yasmin Mzayek`_).
 
+- :bdg-primary:`Doc` :mod:`~nilearn.glm` will no longer warn that the module is experimental (:gh:`3424` by `Yasmin Mzayek`_).
+
 - :bdg-primary:`Doc` Remove all docstring mentions of GLM module being experimental and any references to nistats migration. ``doc/nistats_migration.rst`` is also removed (:gh:`3449` by `Yasmin Mzayek`_).
+
+- :bdg-secondary:`Maint` The function ``_safe_cache`` is removed because it was deemed outdated and not necessary anymore (:gh:`3375` by `Yasmin Mzayek`_).

doc/changes/0.10.1.rst

@@ -19,20 +19,20 @@ NEW
 Fixes
 -----
 
-- :bdg-danger:`Deprecation` Improve how :func:`~.glm.first_level.first_level_from_bids` handles fetching slice timing metadata and add additional input validation. In release ``0.12`` the default ``slice_time_ref`` will be ``None`` instead of ``0`` (:gh:`3605` by `Rémi Gau`_).
+- :bdg-success:`API` :func:`~nilearn.interfaces.fmriprep.load_confounds` can support searching preprocessed data in native space. (:gh:`3531` by `Hao-Ting Wang`_)
+
+- :bdg-success:`API` :func:`~glm.second_level.non_parametric_inference` can accept first level model as input without failing. (:gh:`3600` by `Rémi Gau`_)
+
+- :bdg-success:`API` The label of the clusters in the label maps returned by :func:`~nilearn.reporting.get_clusters_table` now matches the Cluster IDs in the clusters table (:gh:`3563` by `Julio A Peraza`_).
 
 - :bdg-dark:`Code` Fixes several bugs in :func:`~glm.first_level.first_level_from_bids`. Refactors :func:`~glm.first_level.first_level_from_bids` and ``nilearn._utils.data_gen.create_fake_bids_dataset``. (:gh:`3525` by `Rémi Gau`_).
 
 - :bdg-dark:`Code` Change calculation of TR in :func:`~.glm.first_level.compute_regressor` to be more precise (:gh:`3362` by `Anne-Sophie Kieslinger`_)
 
-- :bdg-success:`API` :func:`~nilearn.interfaces.fmriprep.load_confounds` can support searching preprocessed data in native space. (:gh:`3531` by `Hao-Ting Wang`_)
-
-- :bdg-success:`API` :func:`~glm.second_level.non_parametric_inference` can accept first level model as input without failing. (:gh:`3600` by `Rémi Gau`_)
+- :bdg-danger:`Deprecation` Improve how :func:`~.glm.first_level.first_level_from_bids` handles fetching slice timing metadata and add additional input validation. In release ``0.12`` the default ``slice_time_ref`` will be ``None`` instead of ``0`` (:gh:`3605` by `Rémi Gau`_).
 
 - :bdg-danger:`Deprecation` Add correct "zscore_sample" strategy to ``signal.standardize_signal`` which will replace the default "zscore" strategy in release 0.13  (:gh:`3474` by `Yasmin Mzayek`_).
 
-- :bdg-success:`API` The label of the clusters in the label maps returned by :func:`~nilearn.reporting.get_clusters_table` now matches the Cluster IDs in the clusters table (:gh:`3563` by `Julio A Peraza`_).
-
 Enhancements
 ------------
 
@@ -53,18 +53,18 @@ Changes
 
 - :bdg-success:`API` The behavior of :func:`~nilearn.datasets.fetch_atlas_craddock_2012`, :func:`~nilearn.datasets.fetch_atlas_smith_2009` and :func:`~nilearn.datasets.fetch_atlas_basc_multiscale_2015` is updated with their new parameters to return one map along with a deprecation cycle (:gh:`3353` by `Ahmad Chamma`_).
 
-- :bdg-secondary:`Maint` Modules :mod:`~nilearn.image` code and docstrings have been reformatted using black. Changes resulted in improved readability overall and increased consistency (:gh:`3548` by `Rémi Gau`_).
-
-- :bdg-secondary:`Maint` Examples have been made PEP8 compliant and reformatted using black. (:gh:`3549`, :gh:`3550`, :gh:`3551`, :gh:`3552`, :gh:`3553`, :gh:`3554`, :gh:`3555`,  by `Rémi Gau`_).
-
 - :bdg-dark:`Code` Extract helper-functions for input-image validation from :func:`~regions.img_to_signals_labels`, :func:`~regions.signals_to_img_labels`, :func:`~regions.img_to_signals_maps` :func:`~regions.signals_to_img_maps` (:gh:`3523` by `Rémi Gau`_ and `Christian Gerloff`_).
 
-- :bdg-secondary:`Maint` Moved packaging from ``setup.py`` and setuptools build backend to ``pyproject.toml`` and hatchling backend. This change comes about as new standards are defined for Python packaging that are better met by the new configuration (:gh:`3635` by `Yasmin Mzayek`_).
-
 - :bdg-primary:`Doc` Examples are updated with the new atlas API :ref:`sphx_glr_auto_examples_00_tutorials_plot_3d_and_4d_niimg.py`, :ref:`sphx_glr_auto_examples_01_plotting_plot_multiscale_parcellations.py` and :ref:`sphx_glr_auto_examples_01_plotting_plot_prob_atlas.py` (:gh:`3557` by `Ahmad Chamma`_).
 
 - :bdg-primary:`Doc` Update the references format of the functions :func:`~nilearn.decomposition.CanICA` and :func:`~nilearn.decomposition.DictLearning` with bibtex (:gh:`3558` by `Ahmad Chamma`_)
 
+- :bdg-secondary:`Maint` Modules :mod:`~nilearn.image` code and docstrings have been reformatted using black. Changes resulted in improved readability overall and increased consistency (:gh:`3548` by `Rémi Gau`_).
+
+- :bdg-secondary:`Maint` Examples have been made PEP8 compliant and reformatted using black. (:gh:`3549`, :gh:`3550`, :gh:`3551`, :gh:`3552`, :gh:`3553`, :gh:`3554`, :gh:`3555`,  by `Rémi Gau`_).
+
+- :bdg-secondary:`Maint` Moved packaging from ``setup.py`` and setuptools build backend to ``pyproject.toml`` and hatchling backend. This change comes about as new standards are defined for Python packaging that are better met by the new configuration (:gh:`3635` by `Yasmin Mzayek`_).
+
 
 0.10.1rc1
 =========
@@ -77,21 +77,21 @@ This is a pre-release.
 Fixes
 -----
 
-- :bdg-dark:`Code` Restore :func:`~image.resample_img` compatibility with all :class:`nibabel.spatialimages.SpatialImage` objects (:gh:`3462` by `Mathias Goncalves`_).
-
 - :bdg-success:`API` :func:`~nilearn.glm.second_level.non_parametric_inference` now supports confounding variates when they are available in the input design matrix :func:`~nilearn.mass_univariate.permuted_ols` (:gh:`3465` by `Jelle Roelof Dalenberg`_).
 
 - :bdg-success:`API` :func:`~nilearn.mass_univariate.permuted_ols` now checks if confounding variates contain a intercept and raises an warning when multiple intercepts are defined across target and confounding variates (:gh:`3465` by `Jelle Roelof Dalenberg`_).
 
+- :bdg-dark:`Code` Restore :func:`~image.resample_img` compatibility with all :class:`nibabel.spatialimages.SpatialImage` objects (:gh:`3462` by `Mathias Goncalves`_).
+
 Enhancements
 ------------
 
-- :bdg-primary:`Doc` Addition to docs to note that :meth:`~maskers.BaseMasker.inverse_transform` only performs spatial unmasking (:gh:`3445` by `Robert Williamson`_).
-
 - :bdg-success:`API` Give users control over Butterworth filter (:func:`~signal.butterworth`) parameters in :func:`~signal.clean` and Masker objects as kwargs (:gh:`3478` by `Taylor Salo`_).
 
 - :bdg-success:`API` Allow users to output label maps from :func:`~reporting.get_clusters_table` (:gh:`3477` by `Steven Meisler`_).
 
+- :bdg-primary:`Doc` Addition to docs to note that :meth:`~maskers.BaseMasker.inverse_transform` only performs spatial unmasking (:gh:`3445` by `Robert Williamson`_).
+
 Changes
 -------