Release 0.10.0 (#3454)

doc/changes/latest.rst → doc/changes/0.10.0.rst

@@ -2,48 +2,101 @@
 
 .. include:: names.rst
 
-0.9.3.dev
-=========
+0.10.0
+======
+
+**Released January 2023**
+
+
+HIGHLIGHTS
+----------
+
+.. warning::
+
+ | **Python 3.7 is deprecated and will be removed in release 0.12.**
+ | **We recommend upgrading to Python 3.10.**
+ |
+ | **Minimum supported versions of packages have been bumped up:**
+ | - Numpy -- v1.19.0
+ | - SciPy -- v1.6.0
+ | - Scikit-learn -- v1.0.0
+ | - Nibabel -- v3.2.0
+ | - Pandas -- v1.1.5
+ | - Joblib -- v1.0.0
+
+
+- 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`_).
+
+- Updated docs with a new theme using `furo <https://github.com/pradyunsg/furo>`_ (:gh:`3125` by `Alexis Thual`_).
+
+- :func:`~mass_univariate.permuted_ols` and :func:`~glm.second_level.non_parametric_inference` now support :term:`TFCE` statistic (:gh:`3196` by `Taylor Salo`_).
+
+- :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`_).
+
+- :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`_).
+
 
 NEW
 ---
 
 - 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
 -----
 
 - Fix off-by-one error when setting ticks in :func:`~plotting.plot_surf` (:gh:`3105` by `Dimitri Papadopoulos Orfanos`_).
+
 - 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`_).
+
 - Fix :func:`~plotting.plot_connectome` which was raising a ``ValueError`` when ``vmax < 0`` (:gh:`3390` by `Paul Bogdan`_).
+
 - Change the order of applying ``sample_masks`` in :func:`~signal.clean` based on different filtering options (:gh:`3385` by `Hao-Ting Wang`_).
+
 - 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`_).
+
 - Description of the ``opening`` parameter added to ``compute_multi_epi_mask`` docs (:gh:`3412` by `Natasha Clarke`_).
+
 - 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`_).
+
 - Pass values with correct type to scikit-learn estimator parameters and remove deprecated parameter (:gh:`3430` by `Yasmin Mzayek`_).
+
 - 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`_).
+
 - Fix failing CanICA test by adding noise to the data creation step (:gh:`3453` by `Yasmin Mzayek`_).
 
+
 Enhancements
 ------------
 
 - :func:`~signal.clean` imputes scrubbed volumes (defined through ``sample_masks``) with cubic spline function before applying butterworth filter (:gh:`3385` by `Hao-Ting Wang`_). 
+
 - As part of making the User Guide more user-friendly, the introduction was reworked (:gh:`3380` by `Alexis Thual`_)
+
 - Added instructions for maintainers to make sure LaTeX dependencies are installed before building and deploying the stable docs (:gh:`3426` by `Yasmin Mzayek`_).
-- Parameter ``sample_masks`` in :func:`~signal.clean` and masker functions accept binary mask (:gh:`3439` by `Hao-Ting Wang`_). 
+
+- Parameter ``sample_masks`` in :func:`~signal.clean` and masker functions accept binary mask (:gh:`3439` by `Hao-Ting Wang`_).
+
 - Contributing docs were improved by adding clear guidelines for users about changelog/whatsnew entries (:gh:`3446` by `Robert Williamson`_).
+
 - Add parameter ``cut_coords`` in :func:`~reporting.make_glm_report` (:gh:`3452` by `Audrey Duran`_).
 
+
 Changes
 -------
 
 - Private functions ``nilearn.regions.rena_clustering.weighted_connectivity_graph`` and ``nilearn.regions.rena_clustering.nearest_neighbor_grouping`` have been renamed with a leading "_", while function :func:`~regions.recursive_neighbor_agglomeration` has been added to the public API (:gh:`3347` by `Ahmad Chamma`_).
+
 - Numpy deprecated type aliases are replaced by equivalent builtin types (:gh:`3422` by `Yasmin Mzayek`_).
-- 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`_).
+
+- 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`_).
+
 - :mod:`~nilearn.glm` will no longer warn that the module is experimental (:gh:`3424` by `Yasmin Mzayek`_).
+
 - 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`_).
+
 - The function ``_safe_cache`` is removed because it was deemed outdated and not necessary anymore (:gh:`3375` by `Yasmin Mzayek`_).
+
 - Minimum supported versions of packages have been bumped up:
 
     * Numpy -- v1.19.0
@@ -54,5 +107,7 @@ Changes
     * Joblib -- v1.0.0
 
   (:gh:`3440` by `Yasmin Mzayek`_).
+
 - In release ``0.10.0`` the default resolution for loaded MNI152 templates will be 1mm instead of 2mm (:gh:`3433` by `Yasmin Mzayek`_).
+
 - 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`_).

doc/changes/whats_new.rst

@@ -5,8 +5,8 @@
 What's new
 ==========
 
-.. _latest:
-.. include:: latest.rst
+.. _v0.10.0:
+.. include:: 0.10.0.rst
 .. _v0.9.2:
 .. include:: 0.9.2.rst
 .. _v0.9.1:

nilearn/image/image.py

@@ -717,7 +717,7 @@ def new_img_like(ref_niimg, data, affine=None, copy_header=False):
         Data to be stored in the image. If data dtype is a boolean, then data
         is cast to 'uint8' by default.
 
-    .. versionchanged:: 0.9.2dev
+    .. versionchanged:: 0.9.2
         Changed default dtype casting of booleans from 'int8' to 'uint8'.
 
     affine : 4x4 :class:`numpy.ndarray`, optional

nilearn/interfaces/bids/_utils.py

@@ -8,7 +8,7 @@
 def _clean_contrast_name(contrast_name):
     """Remove prohibited characters from name and convert to camelCase.
 
-    .. versionadded:: 0.9.2dev
+    .. versionadded:: 0.9.2
 
     BIDS filenames, in which the contrast name will appear as a
     contrast-<name> key/value pair, must be alphanumeric strings.
@@ -54,7 +54,7 @@ def _clean_contrast_name(contrast_name):
 def _generate_model_metadata(out_file, model):
     """Generate a sidecar JSON file containing model metadata.
 
-    .. versionadded:: 0.9.2dev
+    .. versionadded:: 0.9.2
 
     Parameters
     ----------
@@ -123,7 +123,7 @@ def _generate_model_metadata(out_file, model):
 def _generate_dataset_description(out_file, model_level):
     """Generate a BIDS dataset_description.json file with relevant metadata.
 
-    .. versionadded:: 0.9.2dev
+    .. versionadded:: 0.9.2
 
     Parameters
     ----------

nilearn/interfaces/bids/glm.py

@@ -19,7 +19,7 @@ def save_glm_to_bids(
 ):
     """Save GLM results to BIDS-like files.
 
-    .. versionadded:: 0.9.2dev
+    .. versionadded:: 0.9.2
 
     Parameters
     ----------

nilearn/maskers/nifti_labels_masker.py

@@ -645,7 +645,7 @@ def inverse_transform(self, signals):
 
         Any mask given at initialization is taken into account.
 
-        .. versionchanged:: 0.9.2dev
+        .. versionchanged:: 0.9.2
 
             This method now supports 1D arrays, which will produce 3D images.
 

nilearn/mass_univariate/permuted_least_squares.py

@@ -445,7 +445,7 @@ def permuted_ols(
             Additionally, if ``tfce`` is True or ``threshold`` is not None,
             ``output_type`` will automatically be set to 'dict'.
 
-        .. deprecated:: 0.9.2.dev
+        .. deprecated:: 0.9.2
 
             The default value for this parameter will change from 'legacy' to
             'dict' in 0.13, and the parameter will be removed completely in
@@ -464,7 +464,7 @@ def permuted_ols(
 
             This is returned if ``output_type`` == 'legacy'.
 
-        .. deprecated:: 0.9.2.dev
+        .. deprecated:: 0.9.2
 
             The 'legacy' option for ``output_type`` is deprecated.
             The default value will change to 'dict' in 0.13,
@@ -480,7 +480,7 @@ def permuted_ols(
 
             This is returned if ``output_type`` == 'legacy'.
 
-        .. deprecated:: 0.9.2.dev
+        .. deprecated:: 0.9.2
 
             The 'legacy' option for ``output_type`` is deprecated.
             The default value will change to 'dict' in 0.13,
@@ -494,7 +494,7 @@ def permuted_ols(
 
             This is returned if ``output_type`` == 'legacy'.
 
-        .. deprecated:: 0.9.2.dev
+        .. deprecated:: 0.9.2
 
             The 'legacy' option for ``output_type`` is deprecated.
             The default value will change to 'dict' in 0.13,

nilearn/regions/signal_extraction.py

@@ -142,7 +142,7 @@ def signals_to_img_labels(signals, labels_img, mask_img=None,
 
     labels_img, mask_img must have the same shapes and affines.
 
-    .. versionchanged:: 0.9.2dev
+    .. versionchanged:: 0.9.2
         Support 1D signals.
 
     Parameters

nilearn/reporting/_get_clusters_table.py

@@ -222,7 +222,7 @@ def get_clusters_table(stat_img, stat_threshold, cluster_threshold=None,
 
         This center of mass may, in some cases, appear outside of the cluster.
 
-        .. versionchanged:: 0.9.2dev
+        .. versionchanged:: 0.9.2
             In this case, the cluster voxel nearest to the center of mass is
             reported.
 

nilearn/reporting/glm_reporter.py

@@ -527,7 +527,7 @@ def _make_stat_maps(model, contrasts, output_type='z_score'):
         The type of statistical map to retain from the contrast.
         Default is 'z_score'.
 
-        .. versionadded:: 0.9.2dev
+        .. versionadded:: 0.9.2
 
     Returns
     -------

nilearn/version.py

@@ -20,7 +20,7 @@
 # Dev branch marker is: 'X.Y.dev' or 'X.Y.devN' where N is an integer.
 # 'X.Y.dev0' is the canonical version of 'X.Y.dev'
 #
-__version__ = '0.9.3.dev'
+__version__ = '0.10.0'
 
 _NILEARN_INSTALL_MSG = 'See %s for installation information.' % (
     'https://nilearn.github.io/stable/introduction.html#installation')
@@ -31,35 +31,35 @@
 #   in some meaningful order (more => less 'core').
 REQUIRED_MODULE_METADATA = (
     ('numpy', {
-        'min_version': '1.16',
+        'min_version': '1.19',
         'required_at_installation': True,
         'install_info': _NILEARN_INSTALL_MSG}),
     ('scipy', {
-        'min_version': '1.2',
+        'min_version': '1.6',
         'required_at_installation': True,
         'install_info': _NILEARN_INSTALL_MSG}),
     ('sklearn', {
-        'min_version': '0.21',
+        'min_version': '1.0.0',
         'required_at_installation': True,
         'install_info': _NILEARN_INSTALL_MSG}),
     ('joblib', {
-        'min_version': '0.12',
+        'min_version': '1.0.0',
         'required_at_installation': True,
         'install_info': _NILEARN_INSTALL_MSG}),
     ('nibabel', {
-        'min_version': '2.5',
+        'min_version': '3.2',
         'required_at_installation': False}),
     ('pandas', {
-        'min_version': '0.24.0',
+        'min_version': '1.1.5',
         'required_at_installation': True,
         'install_info': _NILEARN_INSTALL_MSG}),
     ("requests", {
-        "min_version": "2",
+        "min_version": "2.25",
         "required_at_installation": False
     })
 )
 
-OPTIONAL_MATPLOTLIB_MIN_VERSION = '2.0'
+OPTIONAL_MATPLOTLIB_MIN_VERSION = '3.3.0'
 
 
 def _import_module_with_version_check(