junifer 0.0.5__tar.gz → 0.0.5.dev11__tar.gz

{junifer-0.0.5 → junifer-0.0.5.dev11}/.github/workflows/ci.yml

@@ -66,43 +66,36 @@ jobs:
         sudo tcsh @update.afni.binaries -package linux_ubuntu_16_64 -bindir /afni
         echo "/afni" >> $GITHUB_PATH
       if: matrix.python-version == 3.11
-      # Bypass AFNI installation failure
-      continue-on-error: true
     - name: Check AFNI
       run: |
         echo "Using AFNI : $(afni --version)"
       if: matrix.python-version == 3.11
-      # Bypass AFNI installation failure
-      continue-on-error: true
     - name: Install ANTs
       run: |
         sudo apt-get install -y -qq unzip
-        curl -fsSL -o ants.zip https://github.com/ANTsX/ANTs/releases/download/v2.5.2/ants-2.5.2-ubuntu-22.04-X64-gcc.zip
+        curl -fsSL -o ants.zip https://github.com/ANTsX/ANTs/releases/download/v2.5.1/ants-2.5.1-ubuntu-22.04-X64-gcc.zip
         unzip ants.zip -d /opt
-        mv /opt/ants-2.5.2/bin/* /opt/ants-2.5.2
+        mv /opt/ants-2.5.1/bin/* /opt/ants-2.5.1
         rm ants.zip
-        echo "/opt/ants-2.5.2" >> $GITHUB_PATH
+        echo "/opt/ants-2.5.1" >> $GITHUB_PATH
       if: matrix.python-version == 3.11
-      # Bypass ANTs installation failure
-      continue-on-error: true
     - name: Check ANTs
       run: |
         echo "Using ANTs : $(antsRegistration --version)"
       if: matrix.python-version == 3.11
-      # Bypass ANTs installation failure
-      continue-on-error: true
     - name: Install FSL
       run: |
-        curl -fsSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | python - -d /opt/fsl/
+        sudo apt-get install -y -qq python3
+        curl -fsSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | python3 - -d /opt/fsl-6.0.6.4 -V 6.0.6.4
         FSLOUTPUTTYPE="NIFTI_GZ"
         FSLMULTIFILEQUIT="TRUE"
-        FSLTCLSH="/opt/fsl/bin/fsltclsh"
-        FSLWISH="/opt/fsl/bin/fslwish"
+        FSLTCLSH="/opt/fsl-6.0.6.4/bin/fsltclsh"
+        FSLWISH="/opt/fsl-6.0.6.4/bin/fslwish"
         FSLLOCKDIR=""
         FSLMACHINELIST=""
         FSLREMOTECALL=""
         FSLGECUDAQ="cuda.q"
-        echo "/opt/fsl" >> $GITHUB_PATH
+        echo "/opt/fsl-6.0.6.4" >> $GITHUB_PATH
       if: matrix.python-version == 3.11
       # Bypass FSL installation failure
       continue-on-error: true

{junifer-0.0.5 → junifer-0.0.5.dev11}/.github/workflows/docs.yml

@@ -68,7 +68,7 @@ jobs:
         touch docs/_build/.nojekyll
         cp docs/redirect.html docs/_build/index.html
     - name: Publish docs to gh-pages
-      uses: peaceiris/actions-gh-pages@v4
+      uses: peaceiris/actions-gh-pages@v3
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: docs/_build

junifer-0.0.5.dev11/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "junifer/external/h5io"]
+	path = junifer/external/h5io
+	url = https://github.com/juaml/h5io

{junifer-0.0.5 → junifer-0.0.5.dev11}/.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v4.5.0
     hooks:
       - id: check-ast
       - id: check-docstring-first
@@ -20,14 +20,14 @@ repos:
     rev: v0.16
     hooks:
       - id: validate-pyproject
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.4.2
+  - repo: https://github.com/psf/black
+    rev: 24.1.1
     hooks:
       - id: black
         exclude: ^(docs/|examples/|tools/)
         args: [--check]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.2
+    rev: v0.1.15
     hooks:
       - id: ruff
         types_or: [python, jupyter]
@@ -38,7 +38,7 @@ repos:
     hooks:
       - id: codespell
         exclude: ^(.github/|docs/)
-        args: [--toml, pyproject.toml]
+        args: [--config, tox.ini]
   - repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.10.0
     hooks:
@@ -47,10 +47,3 @@ repos:
       - id: rst-backticks
       - id: rst-directive-colons
       - id: rst-inline-touching-normal
-  - repo: https://github.com/adamchainz/blacken-docs
-    rev: "1.16.0"
-    hooks:
-      - id: blacken-docs
-        additional_dependencies:
-          - black==24.4.2
-        args: [-l 79]

{junifer-0.0.5 → junifer-0.0.5.dev11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5
+Version: 0.0.5.dev11
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
@@ -29,20 +29,19 @@ Description-Content-Type: text/markdown
 License-File: LICENSE.md
 License-File: AUTHORS.rst
 Requires-Dist: click<8.2,>=8.1.3
-Requires-Dist: numpy<2.0.0,>=1.24.0
-Requires-Dist: scipy<=1.14.0,>=1.10.0
-Requires-Dist: datalad<1.2.0,>=1.0.0
-Requires-Dist: pandas<2.3.0,>=2.0.0
-Requires-Dist: nibabel<5.3.0,>=5.2.0
-Requires-Dist: nilearn<=0.10.4,>=0.10.3
-Requires-Dist: sqlalchemy<=2.1.0,>=2.0.25
+Requires-Dist: numpy<1.27,>=1.24
+Requires-Dist: scipy<=1.11.4,>=1.9.0
+Requires-Dist: datalad<0.20,>=0.15.4
+Requires-Dist: pandas<2.2,>=1.4.0
+Requires-Dist: nibabel<5.11,>=3.2.0
+Requires-Dist: nilearn<=0.10.2,>=0.9.0
+Requires-Dist: sqlalchemy<=2.1.0,>=1.4.27
 Requires-Dist: ruamel.yaml<0.18,>=0.17
 Requires-Dist: h5py>=3.10
 Requires-Dist: httpx[http2]==0.26.0
 Requires-Dist: tqdm==4.66.1
 Requires-Dist: templateflow>=23.0.0
-Requires-Dist: lapy<2.0.0,>=1.0.0
-Requires-Dist: importlib_metadata; python_version < "3.9"
+Requires-Dist: importlib_metadata; python_version < "3.10"
 Requires-Dist: looseversion==1.3.0; python_version >= "3.12"
 Provides-Extra: all
 Requires-Dist: bctpy==0.6.0; extra == "all"
@@ -57,14 +56,14 @@ Provides-Extra: dev
 Requires-Dist: tox; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
 Provides-Extra: docs
-Requires-Dist: seaborn<0.14.0,>=0.13.0; extra == "docs"
-Requires-Dist: sphinx<7.4.0,>=7.3.0; extra == "docs"
-Requires-Dist: sphinx-gallery<0.17.0,>=0.15.0; extra == "docs"
-Requires-Dist: furo<2024.6.0,>=2024.4.27; extra == "docs"
-Requires-Dist: numpydoc<1.8.0,>=1.6.0; extra == "docs"
-Requires-Dist: julearn==0.3.3; extra == "docs"
+Requires-Dist: seaborn<0.13,>=0.11.2; extra == "docs"
+Requires-Dist: sphinx<7.3,>=5.3.0; extra == "docs"
+Requires-Dist: sphinx-gallery<0.15.0,>=0.11.0; extra == "docs"
+Requires-Dist: furo<2023.10.0,>=2022.9.29; extra == "docs"
+Requires-Dist: numpydoc<1.6,>=1.5.0; extra == "docs"
+Requires-Dist: julearn<0.4,>=0.3.0; extra == "docs"
 Requires-Dist: sphinx-copybutton<0.5.3,>=0.5.1; extra == "docs"
-Requires-Dist: towncrier<23.12.0,>=23.10.0; extra == "docs"
+Requires-Dist: towncrier<23.7,>=22.12.0; extra == "docs"
 Requires-Dist: sphinxcontrib-mermaid<0.10,>=0.8.1; extra == "docs"
 
 ![Junifer logo](docs/images/junifer_logo.png "junifer logo")

{junifer-0.0.5 → junifer-0.0.5.dev11}/docs/api/nilearn.rst

@@ -1,6 +1,8 @@
 Nilearn
 =======
 
+This package provides re-implementations of some of the functions in `nilearn`_.
+
 .. automodule:: junifer.external.nilearn
    :members:
    :imported-members:

{junifer-0.0.5 → junifer-0.0.5.dev11}/docs/api/onthefly.rst

@@ -1,6 +1,8 @@
 On-the-fly
 ==========
 
+This package provides functions for quick transform operations on stored data.
+
 .. automodule:: junifer.onthefly
    :members:
    :imported-members:

{junifer-0.0.5 → junifer-0.0.5.dev11}/docs/builtin.rst

@@ -729,6 +729,14 @@ Available
      - | Compute a brain mask for the images by guessing the value of the
        | background from the border of the image.
        | See :func:`nilearn.masking.compute_background_mask`
+   * - ``nilearn``'s ICBM152 template gray-matter mask
+     - | ``fetch_icbm152_brain_gm_mask``
+     - ``MNI152NLin2009aAsym``
+     - 0.0.2
+     - | Compute a gray-matter mask from the asymmetrical ICBM152 2009 template,
+       | release a.
+       | See :func:`nilearn.datasets.fetch_icbm152_brain_gm_mask`
+
 
 ..
    Planned

junifer-0.0.5.dev11/docs/changes/newsfragments/273.feature

@@ -0,0 +1 @@
+Add support for choosing between ``bash`` and ``zsh`` shells when queueing by `Synchon Mandal`_

{junifer-0.0.5 → junifer-0.0.5.dev11}/docs/conf.py

@@ -170,7 +170,6 @@ numpydoc_xref_ignore = {
     "Engine",
     "positive",
     "negative",
-    "estimator",
 }
 # numpydoc_validation_checks = {
 #     "all",

{junifer-0.0.5 → junifer-0.0.5.dev11}/docs/extending/coordinates.rst

@@ -70,7 +70,10 @@ with the DMN. Here, we use the DMN coordinates used in a
 .. code-block:: python
 
   dmn_coords = np.array(
-      [[0, -52, 18], [-46, -68, 32], [46, -68, 32], [1, 50, -5]]
+      [[0, -52, 18],
+      [-46, -68, 32],
+      [46, -68, 32],
+      [1, 50, -5]]
   )
   voi_names = [
       "Posterior Cingulate Cortex",
@@ -87,7 +90,10 @@ simply use this to register our coordinates:
 .. code-block:: python
 
   register_coordinates(
-      name="DMNCustom", coordinates=dmn_coords, voi_names=voi_names, space="MNI"
+      name="DMNCustom",
+      coordinates=dmn_coords,
+      voi_names=voi_names,
+      space="MNI"
   )
 
 Now, when we run this script, ``junifer`` registers these coordinates and we can

{junifer-0.0.5 → junifer-0.0.5.dev11}/docs/extending/datagrabber.rst

@@ -115,14 +115,14 @@ For example, in our BIDS example, the variables will be:
 
     types = ["T1w", "BOLD"]
     patterns = {
-        "T1w": {
-            "pattern": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
-            "space": "native",
-        },
-        "BOLD": {
-            "pattern": "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
-            "space": "MNI152NLin6Asym",
-        },
+       "T1w": {
+           "pattern": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
+           "space": "native",
+       },
+       "BOLD": {
+           "pattern": "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
+           "space": "MNI152NLin6Asym",
+       },
     }
     replacements = ["subject", "session"]
 
@@ -144,24 +144,25 @@ With the variables defined above, we can create our DataGrabber and name it
 
 
     class ExampleBIDSDataGrabber(PatternDataGrabber):
+
         def __init__(self, datadir: str | Path) -> None:
             types = ["T1w", "BOLD"]
             patterns = {
-                "T1w": {
-                    "pattern": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
-                    "space": "native",
-                },
-                "BOLD": {
-                    "pattern": "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
-                    "space": "MNI152NLin6Asym",
-                },
+               "T1w": {
+                   "pattern": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
+                   "space": "native",
+               },
+               "BOLD": {
+                   "pattern": "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
+                   "space": "MNI152NLin6Asym",
+               },
             }
             replacements = ["subject", "session"]
             super().__init__(
-                datadir=datadir,
-                types=types,
-                patterns=patterns,
-                replacements=replacements,
+               datadir=datadir,
+               types=types,
+               patterns=patterns,
+               replacements=replacements,
             )
 
 Our DataGrabber is ready to be used by ``junifer``. However, it is still unknown
@@ -179,24 +180,25 @@ use the :func:`.register_datagrabber` decorator.
 
     @register_datagrabber
     class ExampleBIDSDataGrabber(PatternDataGrabber):
+
         def __init__(self, datadir: str | Path) -> None:
             types = ["T1w", "BOLD"]
             patterns = {
-                "T1w": {
-                    "pattern": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
-                    "space": "native",
-                },
-                "BOLD": {
-                    "pattern": "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
-                    "space": "MNI152NLin6Asym",
-                },
+               "T1w": {
+                   "pattern": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
+                   "space": "native",
+               },
+               "BOLD": {
+                   "pattern": "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
+                   "space": "MNI152NLin6Asym",
+               },
             }
             replacements = ["subject", "session"]
             super().__init__(
-                datadir=datadir,
-                types=types,
-                patterns=patterns,
-                replacements=replacements,
+               datadir=datadir,
+               types=types,
+               patterns=patterns,
+               replacements=replacements,
             )
 
 
@@ -265,28 +267,29 @@ And we can create our DataGrabber:
 
     @register_datagrabber
     class ExampleBIDSDataGrabber(PatternDataladDataGrabber):
+
         def __init__(self) -> None:
             types = ["T1w", "BOLD"]
             patterns = {
-                "T1w": {
-                    "pattern": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
-                    "space": "native",
-                },
-                "BOLD": {
-                    "pattern": "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
-                    "space": "MNI152NLin6Asym",
-                },
+               "T1w": {
+                   "pattern": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
+                   "space": "native",
+               },
+               "BOLD": {
+                   "pattern": "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
+                   "space": "MNI152NLin6Asym",
+               },
             }
             replacements = ["subject", "session"]
             uri = "https://gin.g-node.org/juaml/datalad-example-bids"
             rootdir = "example_bids_ses"
             super().__init__(
-                datadir=None,
-                uri=uri,
-                rootdir=rootdir,
-                types=types,
-                patterns=patterns,
-                replacements=replacements,
+               datadir=None,
+               uri=uri,
+               rootdir=rootdir,
+               types=types,
+               patterns=patterns,
+               replacements=replacements,
             )
 
 This approach can be used directly from the YAML, like so:
@@ -294,69 +297,22 @@ This approach can be used directly from the YAML, like so:
 .. code-block:: yaml
 
    datagrabber:
-     kind: PatternDataladDataGrabber
-     types:
-       - BOLD
-       - T1w
-     patterns:
-       BOLD:
-         pattern: "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz"
-         space: MNI152NLin6Asym
-       T1w:
-         pattern: "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz"
-         space: native
-     replacements:
-       - subject
-       - session
-     uri: "https://gin.g-node.org/juaml/datalad-example-bids"
-     rootdir: example_bids_ses
-
-Advanced: Using Unix-like path expansion directives
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-It is also possible to use some advanced Unix-like path expansion tricks to
-define our patterns.
-
-A very common thing would be to use ``*`` to match any number of
-characters but we cannot use it right after a replacement like:
-
-.. code-block:: python
-
-    "derivatives/freesurfer/{subject}*"
-
-or if there are multiple files or no files which can be globbed.
-
-We can also use ``[]`` and ``[!]`` to glob certain tricky files like with the
-case of FreeSurfer derivatives. The file structure seen in a typical
-FreeSurfer derivative of a dataset (like ``AOMIC`` ones) is like so:
-
-.. code-block::
-
-      .
-      └── derivatives
-          └── freesurfer
-             ├── fsaverage
-             │   ├── mri
-             │   |   ├── T1.mgz
-             │   |   └── ...
-             │   └── ...
-             ├── sub-01
-             │   ├── mri
-             │   |   ├── T1.mgz
-             │   |   └── ...
-             │   |   └── ...
-             │   └── ...
-             ...
-
-With a structure like this, it would be cumbersome to write custom methods
-for the class and thus we could use a pattern like this:
-
-.. code-block:: python
-
-    "derivatives/freesurfer/[!f]{subject}/mri/T1.mg[z]"
-
-This would ignore the ``fsaverage`` directory as a subject and let ``T1.mgz`` be
-fetched as there can be many files with the same prefix.
+     - kind: PatternDataladDataGrabber
+       types:
+         - BOLD
+         - T1w
+       patterns:
+         BOLD:
+           pattern: "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz"
+           space: MNI152NLin6Asym
+         T1w:
+           pattern: "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz"
+           space: native
+       replacements:
+         - subject
+         - session
+       uri: "https://gin.g-node.org/juaml/datalad-example-bids"
+       rootdir: example_bids_ses
 
 .. _extending_datagrabbers_base:
 
@@ -388,17 +344,17 @@ and ``session``, we will use them as parameters of ``get_item``:
 .. code-block:: python
 
    def get_item(self, subject: str, session: str) -> dict[str, dict[str, str]]:
-       out = {
-           "T1w": {
-               "path": f"{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
-               "space": "native",
-           },
-           "BOLD": {
-               "path": f"{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
-               "space": "MNI152NLin6Asym",
-           },
-       }
-       return out
+      out = {
+         "T1w": {
+             "path": f"{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
+             "space": "native",
+         },
+         "BOLD": {
+             "path": f"{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
+             "space": "MNI152NLin6Asym",
+         },
+      }
+      return out
 
 
 The second method, ``get_elements``, needs to return a list of all the elements
@@ -412,16 +368,16 @@ need to remember that for session *ses-03* there is no BOLD data.
 
 
    def get_elements(self) -> list[str]:
-       subjects = ["sub-01", "sub-02", "sub-03"]
-       sessions = ["ses-01", "ses-02"]
+      subjects = ["sub-01", "sub-02", "sub-03"]
+      sessions = ["ses-01", "ses-02"]
 
-       # If we are not working on BOLD data, we can add "ses-03"
-       if "BOLD" not in self.types:
-           sessions.append("ses-03")
-       elements = []
-       for subject, element in product(subjects, sessions):
-           elements.append({"subject": subject, "session": session})
-       return elements
+      # If we are not working on BOLD data, we can add "ses-03"
+      if "BOLD" not in self.types:
+         sessions.append("ses-03")
+      elements = []
+      for subject, element in product(subjects, sessions):
+         elements.append({"subject": subject, "session": session})
+      return elements
 
 
 And finally, we can implement the ``get_element_keys`` method. This method needs
@@ -432,7 +388,7 @@ method, in the same order.
 .. code-block:: python
 
    def get_element_keys(self) -> list[str]:
-       return ["subject", "session"]
+      return ["subject", "session"]
 
 
 So, to summarise, our DataGrabber will look like this:
@@ -445,36 +401,35 @@ So, to summarise, our DataGrabber will look like this:
 
    @register_datagrabber
    class ExampleBIDSDataGrabber(BaseDataGrabber):
-       def get_item(
-           self, subject: str, session: str
-       ) -> dict[str, dict[str, str]]:
-           out = {
-               "T1w": {
-                   "path": f"{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
-                   "space": "native",
-               },
-               "BOLD": {
-                   "path": f"{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
-                   "space": "MNI152NLin6Asym",
-               },
-           }
-           return out
-
-       def get_elements(self) -> list[str]:
-           subjects = ["sub-01", "sub-02", "sub-03"]
-           sessions = ["ses-01", "ses-02"]
 
-           # If we are not working on BOLD data, we can add "ses-03"
-           if "BOLD" not in self.types:
-               sessions.append("ses-03")
-           elements = []
-           for subject in subjects:
-               for session in sessions:
-                   elements.append({"subject": subject, "session": session})
-           return elements
-
-       def get_element_keys(self) -> list[str]:
-           return ["subject", "session"]
+      def get_item(self, subject: str, session: str) -> dict[str, dict[str, str]]:
+         out = {
+            "T1w": {
+                "path": f"{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
+                "space": "native",
+            },
+            "BOLD": {
+                "path": f"{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
+                "space": "MNI152NLin6Asym",
+            },
+         }
+         return out
+
+      def get_elements(self) -> list[str]:
+         subjects = ["sub-01", "sub-02", "sub-03"]
+         sessions = ["ses-01", "ses-02"]
+
+         # If we are not working on BOLD data, we can add "ses-03"
+         if "BOLD" not in self.types:
+            sessions.append("ses-03")
+         elements = []
+         for subject in subjects:
+            for session in sessions:
+               elements.append({"subject": subject, "session": session})
+         return elements
+
+      def get_element_keys(self) -> list[str]:
+         return ["subject", "session"]
 
 Optional: Using datalad
 ~~~~~~~~~~~~~~~~~~~~~~~
@@ -487,11 +442,11 @@ Step 4: Optional: Adding *BOLD confounds*
 -----------------------------------------
 
 For some analyses, it is useful to have the confounds associated with the BOLD
-data. This corresponds to the ``BOLD.confounds`` item in the
+data. This corresponds to the ``BOLD_confounds`` item in the
 :ref:`Data Object <data_object>` (see :ref:`data_types`). However, the
-``BOLD.confounds`` element does not only consists of a ``path``, but it requires
+``BOLD_confounds`` element does not only consists of a ``path``, but it requires
 more information about the format of the confounds file. Thus, the
-``BOLD.confounds`` element is a dictionary with the following keys:
+``BOLD_confounds`` element is a dictionary with the following keys:
 
 - ``path``: the path to the confounds file.
 - ``format``: the format of the confounds file. Currently, this can be either
@@ -520,24 +475,26 @@ this:
 
 .. code-block:: python
 
-   def get_item(self, subject: str, session: str) -> dict:
-       out = {
-           "BOLD": {
-               "path": f"{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
-               "space": "MNI152NLin6Asym",
-               "confounds": {
-                   "path": f"{subject}/{session}/func/{subject}_{session}_confounds.tsv",
-                   "format": "adhoc",
-                   "mappings": {
-                       "fmriprep": {
-                           "variable1": "rot_x",
-                           "variable2": "rot_z",
-                           "variable3": "rot_y",
-                       },
-                   },
-               },
-           },
-       }
+   def get_item(
+      self, subject: str, session: str
+   ) -> dict:
+      out = {
+         "BOLD": {
+             "path": f"{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",
+             "space": "MNI152NLin6Asym",
+         },
+         "BOLD_confounds": {
+             "path": f"{subject}/{session}/func/{subject}_{session}_confounds.tsv",
+             "format": "adhoc",
+             "mappings": {
+                 "fmriprep": {
+                    "variable1": "rot_x",
+                    "variable2": "rot_z",
+                    "variable3": "rot_y",
+                 },
+             },
+         },
+      }
 
 .. note::