.github/ISSUE_TEMPLATE/dataset-request.yml

@@ -10,7 +10,7 @@ body:
     attributes:
       value: |
         Fill in this form if you want that junifer includes a new dataset.
-        
+
         As a reminder, junifer supports customising the `PatternDataGrabber` and `PatternDataladDatagrabber` which should work in most cases.
 
         If it is a widely used dataset, we could alternatevely create a new _DataGrabber_ that simplifies the usage, by already configuring the underlying `PatternDataGrabber` or `PatternDataladDatagrabber`

.github/workflows/ci-docs.yml

@@ -47,4 +47,4 @@ jobs:
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true
           flags: docs
-        if: success() && matrix.python-version == 3.10
+        if: success() && matrix.python-version == 3.10

.gitignore

@@ -134,4 +134,4 @@ cython_debug/
 
 junifer/_version.py
 scratch/
-junifer_jobs/
+junifer_jobs/

.pre-commit-config.yaml

@@ -0,0 +1,48 @@
+ci:
+  autofix_prs: false
+  autoupdate_commit_msg: "chore: bump pre-commit repositories"
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-ast
+      - id: check-docstring-first
+      - id: check-executables-have-shebangs
+      - id: check-merge-conflict
+      - id: check-yaml
+      - id: check-toml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.12.2
+    hooks:
+      - id: validate-pyproject
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+      - id: black
+        exclude: ^(docs/|examples/|tools/)
+        args: [--check]
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.267
+    hooks:
+      - id: ruff
+        exclude: ^(__init__.py)
+        args: [--format, grouped, --show-fixes]
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+      - id: codespell
+        exclude: ^(.github/|docs/)
+        args: [--config, tox.ini]
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: python-no-eval
+      - id: python-no-log-warn
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal

LICENSE.md

@@ -648,4 +648,4 @@ specific requirements.
 You should also get your employer (if you work as a programmer) or school,
 if any, to sign a “copyright disclaimer” for the program, if necessary.
 For more information on this, and how to apply and follow the GNU AGPL, see
-&lt;<http://www.gnu.org/licenses/>&gt;.
+&lt;<http://www.gnu.org/licenses/>&gt;.

README.md

@@ -10,6 +10,7 @@
 ![Codecov](https://img.shields.io/codecov/c/github/juaml/junifer?style=flat-square)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg?style=flat-square)](https://github.com/psf/black)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/charliermarsh/ruff)
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
 
 ## About
 

codecov.yml

@@ -36,4 +36,4 @@ flag_management:
           threshold: 1%
         - type: patch
           target: 95%
-          threshold: 1%
+          threshold: 1%

docs/Makefile

@@ -22,7 +22,7 @@ clean:
 local: news
 	make _build_local; STATUS=$$?; make news_cleanup; exit $$STATUS
 
-news: 
+news:
 	@echo "Generating whats_new.rst"
 	cd ../ && towncrier build --keep
 

docs/_static/css/custom.css

@@ -43,4 +43,4 @@ body:not([data-theme="light"]) .mermaid svg .edgeLabel {
 body:not([data-theme="light"]) .mermaid svg .marker{
   stroke: white !important;
   fill: white !important;
-}
+}

docs/_static/js/custom.js

@@ -11,4 +11,4 @@ for (i = 0; i < coll.length; i++) {
       content.style.display = "block";
     }
   });
-}
+}

docs/_templates/versions.html

@@ -2,7 +2,7 @@
 <div class="sidebar-tree">
   <p class="version-select">
     <span class="caption-text">Other Versions</span>
-  </p> 
+  </p>
   <div id="versions">
     {% if versions.branches %}
     <span class="caption-text">{{ _('Branches') }}</span>

docs/api/index.rst

@@ -41,8 +41,8 @@ Configs
 External
 --------
 
-.. toctree:: 
+.. toctree::
    :maxdepth: 2
    :caption: Contents:
 
-   nilearn.rst
+   nilearn.rst

docs/changes/newsfragments/.gitignore

@@ -1 +1 @@
-!.gitignore
+!.gitignore

docs/changes/newsfragments/220.doc

@@ -1 +1 @@
-Improve general prose, formatting and code blocks in docs and set line length for ``.rst`` files to 80 by `Synchon Mandal`_
+Improve general prose, formatting and code blocks in docs and set line length for ``.rst`` files to 80 by `Synchon Mandal`_

docs/changes/newsfragments/222.change

@@ -1 +1 @@
-Rename ``junifer.testing.datagrabbers.SPMAuditoryTestingDatagrabber`` to :class:`.SPMAuditoryTestingDataGrabber` and ``junifer.testing.datagrabbers.OasisVBMTestingDatagrabber`` to :class:`.OasisVBMTestingDataGrabber` by `Synchon Mandal`_
+Rename ``junifer.testing.datagrabbers.SPMAuditoryTestingDatagrabber`` to :class:`.SPMAuditoryTestingDataGrabber` and ``junifer.testing.datagrabbers.OasisVBMTestingDatagrabber`` to :class:`.OasisVBMTestingDataGrabber` by `Synchon Mandal`_

docs/changes/newsfragments/222.enh

@@ -1 +1 @@
-Rename instances of "Datagrabber" to "DataGrabber" especially in ``junifer.testing`` to be consistent by `Synchon Mandal`_
+Rename instances of "Datagrabber" to "DataGrabber" especially in ``junifer.testing`` to be consistent by `Synchon Mandal`_

docs/changes/newsfragments/223.bugfix

@@ -1 +1 @@
-Enable YAML 1.2 support and allow multiline strings in YAML which would not work earlier by `Synchon Mandal`_
+Enable YAML 1.2 support and allow multiline strings in YAML which would not work earlier by `Synchon Mandal`_

docs/changes/newsfragments/223.enh

@@ -1 +1 @@
-Use ``ruamel.yaml`` instead of ``pyyaml`` as YAML I/O library by `Synchon Mandal`_
+Use ``ruamel.yaml`` instead of ``pyyaml`` as YAML I/O library by `Synchon Mandal`_

docs/changes/newsfragments/229.misc

@@ -1 +1 @@
-Adopt ``ruff`` as the only linter for the codebase by `Synchon Mandal`_
+Adopt ``ruff`` as the only linter for the codebase by `Synchon Mandal`_

docs/changes/newsfragments/232.misc

@@ -0,0 +1 @@
+Adopt ``pre-commmit`` for adding and managing git pre-commit hooks by `Synchon Mandal`_

docs/contribution.rst

@@ -38,6 +38,12 @@ Setting up the local development environment
 
    Now you can make your changes locally.
 
+#. Make sure you install git pre-commit hooks like so:
+
+   .. code-block:: bash
+
+       pre-commit install
+
 #. When making changes locally, it is helpful to ``git commit`` your work
    regularly. On one hand to save your work and on the other hand, the smaller
    the steps, the easier it is to review your work later. Please use `semantic
@@ -49,6 +55,14 @@ Setting up the local development environment
        git add .
        git commit -m "<prefix>: <summary of changes>"
 
+   In case, you want to commit some WIP (work-in-progress) code, please indicate
+   that in the commit message and use the flag ``--no-verify`` with
+   ``git commit`` like so:
+
+   .. code-block:: bash
+
+       git commit --no-verify -m "WIP: <summary of changes>"
+
 #. When you're done making changes, check that your changes pass our test suite.
    This is all included with ``tox``.
 
@@ -62,7 +76,6 @@ Setting up the local development environment
 
        tox --parallel
 
-
 #. Push your branch to GitHub.
 
    .. code-block:: bash

docs/extending/datagrabber.rst

@@ -35,9 +35,9 @@ c. the experiment included resting-stage fMRI and a task named *stroop*
 
 then the *element* should be composed of 3 items:
 
-* ``subject``: The subject IDs, e.g. `sub001`, `sub002`, ... `sub020`
+* ``subject``: The subject IDs, e.g. ``sub001``, ``sub002``, ... ``sub020``
-* ``session``: The session number, e.g. `ses1`, `ses2`
+* ``session``: The session number, e.g. ``ses1``, ``ses2``
-* ``task``: The task performed, e.g. `rest`, `stroop`
+* ``task``: The task performed, e.g. ``rest``, ``stroop``
 
 If any of these items were not part of the element, then we will have more than
 one ``T1w`` and / or ``BOLD`` image for each subject, which is not allowed.
@@ -49,9 +49,10 @@ for the element (``sub001``, ``ses1``, ``rest``) will be the same as the
 ``T1w`` image for the element (``sub001``, ``ses1``, ``stroop``).
 
 We will now continue this section using as an example, a dataset in BIDS format
-in which 9 subjects (`sub-01` to `sub-09`) were scanned each during 3
+in which 9 subjects (``sub-01`` to ``sub-09``) were scanned each during 3
-sessions (`ses-01`, `ses-02`, `ses-03`) and each session included a `T1w` and
+sessions (``ses-01``, ``ses-02``, ``ses-03``) and each session included a
-a `BOLD` image (resting-state), except for `ses-03` which was only anatomical.
+``T1w`` and a ``BOLD`` image (resting-state), except for ``ses-03`` which was
+only anatomical.
 
 Step 2: Think about the dataset's structure
 -------------------------------------------
@@ -63,7 +64,7 @@ the Data Grabber needs to be implemented.
 Junifer provides an abstract class to deal with datasets that can be thought in
 terms of *patterns*. A *pattern* is a string that contains placeholders that are
 replaced by the actual values of the element. In our BIDS example, the path
-to the T1w image of subject `sub-01` and session `ses-01`, relative to the
+to the T1w image of subject ``sub-01`` and session ``ses-01``, relative to the
 dataset location, is ``sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz``. By
 replacing ``sub-01`` with ``sub-02``, we can obtain the T1w image of the first
 session of the second subject. Indeed, the path to the T1w images can be

docs/links.inc

@@ -42,4 +42,4 @@
 
 .. _`HTCondor`: https://research.cs.wisc.edu/htcondor/
 .. _`SLURM`: https://slurm.schedmd.com
-.. _`GNU Parallel`: https://www.gnu.org/software/parallel/
+.. _`GNU Parallel`: https://www.gnu.org/software/parallel/

docs/redirect.html

@@ -6,4 +6,4 @@
     <meta http-equiv="refresh" content="0; url=./main/index.html">
     <link rel="canonical" href="https://juaml.github.io/junifer/main/index.html">
   </head>
-</html>
+</html>

examples/README.rst

@@ -1,4 +1,4 @@
 Examples
 ========
 
-The following are a set of examples.
+The following are a set of examples.

examples/yamls/ukb_gmd_mean.yaml

@@ -19,7 +19,6 @@ markers:
     kind: ParcelAggregation
     parcellation: Schaefer1000x7
     method: std
-storage: 
+storage:
   kind: SQLiteFeatureStorage
   uri: /data/project/ukb_motor/junifer_test/test.sqlite
-

junifer/api/res/afni/3dAFNItoNIFTI

@@ -1,3 +1,3 @@
 #!/bin/bash
 
-run_afni_docker.sh 3dAFNItoNIFTI "$@"
+run_afni_docker.sh 3dAFNItoNIFTI "$@"

junifer/api/res/afni/3dRSFC

@@ -1,3 +1,3 @@
 #!/bin/bash
 
-run_afni_docker.sh 3dRSFC "$@"
+run_afni_docker.sh 3dRSFC "$@"

junifer/api/res/afni/3dReHo

@@ -1,3 +1,3 @@
 #!/bin/bash
 
-run_afni_docker.sh 3dReHo "$@"
+run_afni_docker.sh 3dReHo "$@"

junifer/api/res/afni/afni

@@ -1,3 +1,3 @@
 #!/bin/bash
 
-run_afni_docker.sh afni "$@"
+run_afni_docker.sh afni "$@"

junifer/api/res/afni/run_afni_docker.sh

@@ -4,7 +4,7 @@ corrected_args=()
 docker_args=()
 mounts=0
 for var in "$@"
-do 
+do
 if [ -d "${var}" ]; then
         echo "$var is a directory"
         var=$(realpath "${var}")
@@ -36,4 +36,4 @@ echo "Corrected args for afni: ${corrected_args[*]}"
 cwd=$(pwd)
 cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} afni/afni_make_build ${corrected_args[*]}"
 echo "Running command: ${cmd}"
-${cmd}
+${cmd}

junifer/api/res/run_conda.sh

@@ -20,4 +20,4 @@ if [ -f "pre_run.sh" ]; then
 fi
 
 echo "Running ${*} in virtual environment"
-"$@"
+"$@"

junifer/data/VOIs/meta/CogAC_VOIs.txt

@@ -16,4 +16,4 @@
 48.0	19.0	6.0	rIFG
 8.0	29.0	30.0	aMCC
 -45.0	27.0	30.0	lIFG
-11.0	7.0	7.0	rNcaud
+11.0	7.0	7.0	rNcaud

junifer/data/VOIs/meta/CogAR_VOIs.txt

@@ -6,4 +6,3 @@
 -36	-46	46	Parietal_Inf_L
 38	-46	44	Parietal_Inf_R
 -26	0	54	Frontal_Mid_L
-

junifer/data/VOIs/meta/DMNBuckner_VOIs.txt

@@ -4,4 +4,3 @@
 46	-62	32	rAG
 -24	-22	-20	lHF
 24	-22	-20	rHF
-

junifer/data/VOIs/meta/Dosenbach2010_MNI_VOIs.txt

@@ -157,4 +157,4 @@
 -29	-88	8	post occipital
 13	-91	2	post occipital
 27	-91	2	post occipital
--4	-94	12	post occipital
+-4	-94	12	post occipital

junifer/data/VOIs/meta/MultiTask_VOIs.txt

@@ -7,4 +7,3 @@
 -34	-52	56	Parietal_Inf_L
 32	-52	50	Parietal_Inf_R
 32	6	58	Frontal_Mid_R
-

junifer/data/VOIs/meta/Power2011_MNI_VOIs.txt

@@ -261,4 +261,4 @@
 -32	-1	54	261
 -42	-60	-9	262
 -17	-59	64	263
-29	-5	54	264
+29	-5	54	264

junifer/data/VOIs/meta/ToM_VOIs.txt

@@ -12,4 +12,4 @@
 -58.0	-44.0	4.0	lpSTS
 54.0	28.0	6.0	rIFG
 -48.0	30.0	-12.0	lIFG
-48.0	-72.0	8.0	rV5
+48.0	-72.0	8.0	rV5

junifer/data/VOIs/meta/VigAtt_VOIs.txt

@@ -1,5 +1,5 @@
--2.0	8.0	50.0	aParacentralL 
+-2.0	8.0	50.0	aParacentralL
-8.0	32.0	46.0	rmpSFG 
+8.0	32.0	46.0	rmpSFG
 0.0	26.0	34.0	dMCC
 50.0	8.0	32.0	rIFJ
 40.0	22.0	-4.0	raI

junifer/data/VOIs/meta/WM_VOIs.txt

@@ -1,5 +1,5 @@
--32.0	22.0	-2.0	aIns_l 
+-32.0	22.0	-2.0	aIns_l
--48.0	10.0	26.0	IFG_l 
+-48.0	10.0	26.0	IFG_l
 -46.0	26.0	24.0	lPFCc_l
 -38.0	50.0	10.0	lPFCr_l
 36.0	22.0	-6.0	aIns_r
@@ -18,6 +18,6 @@
 -12.0	-12.0	12.0	Thal_l
 -16.0	2.0	14.0	Ncaud_l
 -16.0	0.0	2.0	GP_l
-12.0	-10.0	10.0	Thal_r 
+12.0	-10.0	10.0	Thal_r
 -34.0	-66.0	-20.0	Cb_FG_l
-32.0	-64.0	-18.0	Cb_FG_r
+32.0	-64.0	-18.0	Cb_FG_r

junifer/data/VOIs/meta/eMDN_VOIs.txt

@@ -14,4 +14,4 @@
 10.0	-12.0	8.0	Thal_r
 -46.0	-60.0	-10.0	ITG_l
 22.0	6.0	4.0	Put_r
--10.0	-16.0	6.0	Thal_l
+-10.0	-16.0	6.0	Thal_l

junifer/data/coordinates.py

@@ -20,14 +20,12 @@ _vois_path = Path(__file__).parent / "VOIs"
 # Path to the metadata of the VOIs
 _vois_meta_path = _vois_path / "meta"
 
-"""
+# A dictionary containing all supported coordinates and their respective file
-A dictionary containing all supported coordinates and their respective file or
+# or data.
-data.
 
-The built-in coordinates are files that are shipped with the package in the
+# The built-in coordinates are files that are shipped with the package in the
-data/VOIs directory. The user can also register their own coordinates, which
+# data/VOIs directory. The user can also register their own coordinates, which
-will be stored as numpy arrays in the dictionary.
+# will be stored as numpy arrays in the dictionary.
-"""
 _available_coordinates: Dict[
     str, Union[Path, Dict[str, Union[ArrayLike, List[str]]]]
 ] = {

junifer/data/masks.py

@@ -63,16 +63,14 @@ def _fetch_icbm152_brain_gm_mask(
     return mask
 
 
-"""
+# A dictionary containing all supported masks and their respective file or
-A dictionary containing all supported masks and their respective file or
+# data.
-data.
 
-The built-in masks are files that are shipped with the package in the
+# The built-in masks are files that are shipped with the package in the
-data/masks directory. The user can also register their own masks.
+# data/masks directory. The user can also register their own masks.
 
-Callable masks should be functions that take at least one parameter:
+# Callable masks should be functions that take at least one parameter:
-* `target_img`: the image to which the mask will be applied.
+# * `target_img`: the image to which the mask will be applied.
-"""
 _available_masks: Dict[str, Dict[str, Any]] = {
     "GM_prob0.2": {"family": "Vickery-Patil"},
     "GM_prob0.2_cortex": {"family": "Vickery-Patil"},

junifer/data/parcellations.py

@@ -26,18 +26,16 @@ if TYPE_CHECKING:
     from nibabel import Nifti1Image
 
 
-"""
+# A dictionary containing all supported parcellations and their respective
-A dictionary containing all supported parcellations and their respective valid
+# valid parameters.
-parameters.
 
-Each entry is a dictionary that must contain at least the following keys:
+# Each entry is a dictionary that must contain at least the following keys:
-* 'family': the parcellation's family name (e.g. 'Schaefer', 'SUIT')
+# * 'family': the parcellation's family name (e.g. 'Schaefer', 'SUIT')
 
-Optional keys:
+# Optional keys:
-* 'valid_resolutions': a list of valid resolutions for the parcellation
+# * 'valid_resolutions': a list of valid resolutions for the parcellation
-(e.g. [1, 2])
+# (e.g. [1, 2])
 
-"""
 # TODO: have separate dictionary for built-in
 _available_parcellations: Dict[str, Dict[Any, Any]] = {
     "SUITxSUIT": {"family": "SUIT", "space": "SUIT"},

junifer/external/nilearn/junifer_nifti_spheres_masker.py

@@ -29,39 +29,37 @@ if TYPE_CHECKING:
     from pandas import DataFrame
 
 
-"""
+# New BSD License
-New BSD License
 
-Copyright (c) 2007 - 2022 The nilearn developers.
+# Copyright (c) 2007 - 2022 The nilearn developers.
-All rights reserved.
+# All rights reserved.
 
 
-Redistribution and use in source and binary forms, with or without
+# Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
+# modification, are permitted provided that the following conditions are met:
 
-  a. Redistributions of source code must retain the above copyright notice,
+#   a. Redistributions of source code must retain the above copyright notice,
-     this list of conditions and the following disclaimer.
+#      this list of conditions and the following disclaimer.
-  b. Redistributions in binary form must reproduce the above copyright
+#   b. Redistributions in binary form must reproduce the above copyright
-     notice, this list of conditions and the following disclaimer in the
+#      notice, this list of conditions and the following disclaimer in the
-     documentation and/or other materials provided with the distribution.
+#      documentation and/or other materials provided with the distribution.
-  c. Neither the name of the nilearn developers nor the names of
+#   c. Neither the name of the nilearn developers nor the names of
-     its contributors may be used to endorse or promote products
+#      its contributors may be used to endorse or promote products
-     derived from this software without specific prior written
+#      derived from this software without specific prior written
-     permission.
+#      permission.
 
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR
+# ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR
-ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+# OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-DAMAGE.
+# DAMAGE.
-"""
 
 
 def _apply_mask_and_get_affinity(

junifer/external/nilearn/tests/test_junifer_nifti_spheres_masker.py

@@ -15,39 +15,37 @@ from numpy.testing import assert_array_equal
 from junifer.external.nilearn import JuniferNiftiSpheresMasker
 
 
-"""
+# New BSD License
-New BSD License
 
-Copyright (c) 2007 - 2022 The nilearn developers.
+# Copyright (c) 2007 - 2022 The nilearn developers.
-All rights reserved.
+# All rights reserved.
 
 
-Redistribution and use in source and binary forms, with or without
+# Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
+# modification, are permitted provided that the following conditions are met:
 
-  a. Redistributions of source code must retain the above copyright notice,
+#   a. Redistributions of source code must retain the above copyright notice,
-     this list of conditions and the following disclaimer.
+#      this list of conditions and the following disclaimer.
-  b. Redistributions in binary form must reproduce the above copyright
+#   b. Redistributions in binary form must reproduce the above copyright
-     notice, this list of conditions and the following disclaimer in the
+#      notice, this list of conditions and the following disclaimer in the
-     documentation and/or other materials provided with the distribution.
+#      documentation and/or other materials provided with the distribution.
-  c. Neither the name of the nilearn developers nor the names of
+#   c. Neither the name of the nilearn developers nor the names of
-     its contributors may be used to endorse or promote products
+#      its contributors may be used to endorse or promote products
-     derived from this software without specific prior written
+#      derived from this software without specific prior written
-     permission.
+#      permission.
 
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR
+# ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR
-ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+# OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-DAMAGE.
+# DAMAGE.
-"""
 
 
 def test_seed_extraction() -> None:

pyproject.toml

@@ -61,7 +61,7 @@ repository = "https://github.com/juaml/junifer"
 junifer = "junifer.api.cli:cli"
 
 [project.optional-dependencies]
-dev = ["tox"]
+dev = ["tox", "pre-commit"]
 docs = [
     "seaborn>=0.11.2,<0.12",
     "Sphinx>=5.3.0,<5.4",

tools/create_aomicpiop1_example_dataset.py

@@ -40,7 +40,7 @@ with TemporaryDirectory() as tmpdir_name:
                     ),
                     (
                         f"anat/{t_sub}_space-MNI152NLin2009cAsym_"
-                        "desc-brain_mask.nii.gz"  
+                        "desc-brain_mask.nii.gz"
                     ),
                     (
                         f"anat/{t_sub}_space-MNI152NLin2009cAsym_label-"