.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     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
+  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.1.1
+    rev: 24.4.2
     hooks:
       - id: black
         exclude: ^(docs/|examples/|tools/)
         args: [--check]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.15
+    rev: v0.4.2
     hooks:
       - id: ruff
         types_or: [python, jupyter]
@@ -38,7 +38,7 @@ repos:
     hooks:
       - id: codespell
         exclude: ^(.github/|docs/)
-        args: [--config, tox.ini]
+        args: [--toml, pyproject.toml]
   - repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.10.0
     hooks:
@@ -47,3 +47,10 @@ 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]

docs/changes/newsfragments/337.misc

@@ -0,0 +1 @@
+Update ``pre-commit`` dependency versions, add ``blacken-docs`` to ``pre-commit``, add ``__all__`` for modules, sub-packages and package, update ``ruff`` and ``pytest`` configs in ``pyproject.toml`` by `Synchon Mandal`_

docs/extending/coordinates.rst

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

docs/extending/datagrabber.rst

@@ -144,7 +144,6 @@ 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 = {
@@ -180,7 +179,6 @@ use the :func:`.register_datagrabber` decorator.
 
     @register_datagrabber
     class ExampleBIDSDataGrabber(PatternDataGrabber):
-
         def __init__(self, datadir: str | Path) -> None:
             types = ["T1w", "BOLD"]
             patterns = {
@@ -267,7 +265,6 @@ And we can create our DataGrabber:
 
     @register_datagrabber
     class ExampleBIDSDataGrabber(PatternDataladDataGrabber):
-
         def __init__(self) -> None:
             types = ["T1w", "BOLD"]
             patterns = {
@@ -448,8 +445,9 @@ So, to summarise, our DataGrabber will look like this:
 
    @register_datagrabber
    class ExampleBIDSDataGrabber(BaseDataGrabber):
-
+       def get_item(
-      def get_item(self, subject: str, session: str) -> dict[str, dict[str, str]]:
+           self, subject: str, session: str
+       ) -> dict[str, dict[str, str]]:
            out = {
                "T1w": {
                    "path": f"{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",
@@ -522,9 +520,7 @@ this:
 
 .. code-block:: python
 
-   def get_item(
+   def get_item(self, subject: str, session: str) -> dict:
-      self, subject: str, session: str
-   ) -> dict:
        out = {
            "BOLD": {
                "path": f"{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz",

docs/extending/dependencies.rst

@@ -93,6 +93,7 @@ that it shows the problem a bit better and how we solve it:
             self, using: str, reference: str, on: Union[List[str], str]
         ) -> None:
             # validation and setting up
+            ...
 
 
 Here, you see a new class attribute ``_CONDITIONAL_DEPENDENCIES`` which is a
@@ -129,6 +130,7 @@ similar. ``FSLWarper`` looks like this (only the relevant part is shown here):
             extra_input: Dict[str, Any],
         ) -> Dict[str, Any]:
             # implementation
+            ...
 
 Here you can see the familiar ``_DEPENDENCIES`` and ``_EXT_DEPENDENCIES`` class
 attributes. The validation process starts by looking up the ``using`` value of

docs/extending/marker.rst

@@ -269,7 +269,6 @@ Template for a custom Marker
 
     @register_marker
     class TemplateMarker(BaseMarker):
-
         def __init__(self, on=None, name=None):
             # TODO: add marker-specific parameters
             super().__init__(on=on, name=name)

docs/extending/parcellations.rst

@@ -83,7 +83,7 @@ look like this:
       name="my_custom_parcellation",
       parcellation_path=path_to_parcellation,
       parcels_labels=my_labels,
-      space="MNI152NLin2009cAsym"
+      space="MNI152NLin2009cAsym",
   )
 
 We can run this code and it seems to work, however, how can we actually

docs/extending/preprocessor.rst

@@ -43,9 +43,11 @@ For input we can accept ``T1w``, ``T2w`` and ``BOLD``
 
     ...
 
+
     def get_valid_inputs(self) -> list[str]:
         return ["T1w", "T2w", "BOLD"]
 
+
     ...
 
 The output definition of the Preprocessor is unused now but is kept for
@@ -55,9 +57,11 @@ completeness.
 
     ...
 
+
     def get_output_type(self, input_type: str) -> str:
         return input_type
 
+
     ...
 
 .. _extending_preprocessors_init:
@@ -90,6 +94,7 @@ you configure it. Our class will have the following arguments:
 
     ...
 
+
     def __init__(
         self,
         fwhm: int | float | ArrayLike | Literal["fast"] | None,
@@ -98,6 +103,7 @@ you configure it. Our class will have the following arguments:
         self.fwhm = fwhm
         super().__init__(on=on)
 
+
     ...
 
 .. caution::
@@ -147,6 +153,7 @@ and it has two return values:
 
     ...
 
+
     def preprocess(
         self,
         input: dict[str, Any],
@@ -155,8 +162,10 @@ and it has two return values:
         input["data"] = nimg.smooth_img(imgs=input["data"], fwhm=self.fwhm)
         return input, None
 
+
     ...
 
+
 Step 4: Finalise the Preprocessor
 ---------------------------------
 

docs/understanding/data.rst

@@ -12,7 +12,7 @@ This is the *object* that traverses the steps of the pipeline. It is indeed a
 dictionary of dictionaries. The first level of keys are the :ref:`data types <data_types>`
 and the values are the corresponding information as dictionaries.
 
-.. code-block:: python
+.. code-block::
 
    {'BOLD': {...}, 'T1w': {...}}
 
@@ -24,7 +24,7 @@ The :ref:`Data Grabber <datagrabber>` step adds the ``path`` second-level key
 which gives the path to the file containing the data. The ``meta`` key in this
 step only contains information about the DataGrabber used.
 
-.. code-block:: python
+.. code-block::
 
    {'BOLD': {'meta': {'datagrabber': {'class': 'SPMAuditoryTestingDataGrabber',
                                       'types': ['BOLD', 'T1w']},
@@ -41,7 +41,7 @@ The :ref:`Data Reader <datareader>` step adds the ``data`` second-level key
 which is the actual data loaded into memory. The ``meta`` key in this step
 adds information about the DataReader used to read the data.
 
-.. code-block:: python
+.. code-block::
 
    {'BOLD': {'data': <nibabel.nifti1.Nifti1Image object at 0x16b5d8910>,
              'meta': {'datagrabber': {'class': 'SPMAuditoryTestingDataGrabber',
@@ -58,6 +58,7 @@ adds information about the DataReader used to read the data.
                      'element': {'subject': 'sub001'}},
             'path': PosixPath('/var/folders/dv/2lbr8f8j0q12zrx3mz3ll5m40000gp/T/tmpe49321ce/sub001_T1w.nii.gz')}}
 
+
 The :ref:`Preprocess <preprocess>` step, if used, modifies the ``data``
 second-level key's value and appends the ``meta`` key with information about
 the preprocessor.
@@ -66,7 +67,7 @@ The :ref:`Marker <marker>` step removes the ``path`` second-level key,
 replaces the ``data`` second-level key's value with the marker's computed value
 and adds further keys needed for the storage, for example, ``col_names``.
 
-.. code-block:: python
+.. code-block::
 
    {'BOLD': {'col_names': ['root_sum_of_squares_ets'],
              'data': ...,

docs/understanding/preprocess.rst

@@ -69,7 +69,7 @@ Example in python format:
     strategy = {
         "motion": "basic",
         "wm_csf": "full",
-        "global_signal": "derivatives"
+        "global_signal": "derivatives",
     }
 
 or in YAML format:
@@ -85,11 +85,7 @@ The default value is to use all the *noise components* with the ``full`` *confou
 
 .. code-block:: python
 
-    strategy = {
+    strategy = {"motion": "full", "wm_csf": "full", "global_signal": "full"}
-        "motion": "full",
-        "wm_csf": "full",
-        "global_signal": "full"
-    }
 
 Other Parameters
 ~~~~~~~~~~~~~~~~

junifer/__init__.py

@@ -20,3 +20,20 @@ from . import (
     onthefly,
 )
 from ._version import __version__
+
+
+__all__ = [
+    "api",
+    "configs",
+    "data",
+    "datagrabber",
+    "datareader",
+    "markers",
+    "pipeline",
+    "preprocess",
+    "stats",
+    "storage",
+    "utils",
+    "external",
+    "onthefly",
+]

junifer/api/__init__.py

@@ -7,3 +7,6 @@
 from . import decorators
 from .cli import cli
 from .functions import collect, queue, run
+
+
+__all__ = ["decorators", "cli", "collect", "queue", "run"]

junifer/api/decorators.py

@@ -10,6 +10,15 @@ from typing import Type
 from ..pipeline.registry import register
 
 
+__all__ = [
+    "register_datagrabber",
+    "register_datareader",
+    "register_preprocessor",
+    "register_marker",
+    "register_storage",
+]
+
+
 def register_datagrabber(klass: Type) -> Type:
     """Register DataGrabber.
 

junifer/api/functions.py

@@ -23,6 +23,9 @@ from .queue_context import GnuParallelLocalAdapter, HTCondorAdapter
 from .utils import yaml
 
 
+__all__ = ["run", "collect", "queue", "reset", "list_elements"]
+
+
 def _get_datagrabber(datagrabber_config: Dict) -> BaseDataGrabber:
     """Get DataGrabber.
 
@@ -92,7 +95,7 @@ def run(
     datagrabber : dict
         DataGrabber to use. Must have a key ``kind`` with the kind of
         DataGrabber to use. All other keys are passed to the DataGrabber
-        init function.
+        constructor.
     markers : list of dict
         List of markers to extract. Each marker is a dict with at least two
         keys: ``name`` and ``kind``. The ``name`` key is used to name the
@@ -102,11 +105,11 @@ def run(
     storage : dict
         Storage to use. Must have a key ``kind`` with the kind of
         storage to use. All other keys are passed to the storage
-        init function.
+        constructor.
     preprocessors : list of dict, optional
         List of preprocessors to use. Each preprocessor is a dict with at
         least a key ``kind`` specifying the preprocessor to use. All other keys
-        are passed to the preprocessor init function (default None).
+        are passed to the preprocessor constructor (default None).
     elements : str or tuple or list of str or tuple, optional
         Element(s) to process. Will be used to index the DataGrabber
         (default None).
@@ -188,7 +191,7 @@ def collect(storage: Dict) -> None:
     storage : dict
         Storage to use. Must have a key ``kind`` with the kind of
         storage to use. All other keys are passed to the storage
-        init function.
+        constructor.
 
     """
     storage_params = storage.copy()

junifer/api/parser.py

@@ -14,6 +14,9 @@ from ..utils.logging import logger, raise_error
 from .utils import yaml
 
 
+__all__ = ["parse_yaml"]
+
+
 def parse_yaml(filepath: Union[str, Path]) -> Dict:
     """Parse YAML.
 

junifer/api/queue_context/__init__.py

@@ -6,3 +6,6 @@
 from .queue_context_adapter import QueueContextAdapter
 from .htcondor_adapter import HTCondorAdapter
 from .gnu_parallel_local_adapter import GnuParallelLocalAdapter
+
+
+__all__ = ["QueueContextAdapter", "HTCondorAdapter", "GnuParallelLocalAdapter"]

junifer/api/res/afni/run_afni_docker.sh

@@ -31,7 +31,7 @@ if [ -d "${var}" ]; then
 done
 
 echo "Docker args: ${docker_args[*]}" >&2
-echo "Corrected args for afni: ${corrected_args[*]}" >&2
+echo "Corrected args for AFNI: ${corrected_args[*]}" >&2
 
 cwd=$(pwd)
 cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} afni/afni_make_build ${corrected_args[*]}"

junifer/api/res/ants/run_ants_docker.sh

@@ -31,7 +31,7 @@ if [ -d "${var}" ]; then
 done
 
 echo "Docker args: ${docker_args[*]}" >&2
-echo "Corrected args for fsl: ${corrected_args[*]}" >&2
+echo "Corrected args for ANTs: ${corrected_args[*]}" >&2
 
 cwd=$(pwd)
 cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} antsx/ants ${corrected_args[*]}"

junifer/api/res/fsl/run_fsl_docker.sh

@@ -31,7 +31,7 @@ if [ -d "${var}" ]; then
 done
 
 echo "Docker args: ${docker_args[*]}" >&2
-echo "Corrected args for fsl: ${corrected_args[*]}" >&2
+echo "Corrected args for FSL: ${corrected_args[*]}" >&2
 
 cwd=$(pwd)
 cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} brainlife/fsl ${corrected_args[*]}"

junifer/configs/juseless/__init__.py

@@ -4,3 +4,6 @@
 # License: AGPL
 
 from . import datagrabbers
+
+
+__all__ = ["datagrabbers"]

junifer/configs/juseless/datagrabbers/__init__.py

@@ -10,3 +10,12 @@ from .camcan_vbm import JuselessDataladCamCANVBM
 from .ixi_vbm import JuselessDataladIXIVBM
 from .ucla import JuselessUCLA
 from .ukb_vbm import JuselessDataladUKBVBM
+
+
+__all__ = [
+    "JuselessDataladAOMICID1000VBM",
+    "JuselessDataladCamCANVBM",
+    "JuselessDataladIXIVBM",
+    "JuselessUCLA",
+    "JuselessDataladUKBVBM",
+]

junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py

@@ -11,6 +11,9 @@ from ....api.decorators import register_datagrabber
 from ....datagrabber import PatternDataladDataGrabber
 
 
+__all__ = ["JuselessDataladAOMICID1000VBM"]
+
+
 @register_datagrabber
 class JuselessDataladAOMICID1000VBM(PatternDataladDataGrabber):
     """Concrete implementation for Juseless AOMIC ID1000 VBM data fetching.

junifer/configs/juseless/datagrabbers/camcan_vbm.py

@@ -12,6 +12,9 @@ from ....api.decorators import register_datagrabber
 from ....datagrabber import PatternDataladDataGrabber
 
 
+__all__ = ["JuselessDataladCamCANVBM"]
+
+
 @register_datagrabber
 class JuselessDataladCamCANVBM(PatternDataladDataGrabber):
     """Concrete implementation for Juseless CamCAN VBM data fetching.

junifer/configs/juseless/datagrabbers/ixi_vbm.py

@@ -13,6 +13,9 @@ from ....datagrabber import PatternDataladDataGrabber
 from ....utils import raise_error
 
 
+__all__ = ["JuselessDataladIXIVBM"]
+
+
 @register_datagrabber
 class JuselessDataladIXIVBM(PatternDataladDataGrabber):
     """Concrete implementation for Juseless IXI VBM data fetching.

junifer/configs/juseless/datagrabbers/ucla.py

@@ -12,6 +12,9 @@ from ....datagrabber import PatternDataGrabber
 from ....utils import raise_error
 
 
+__all__ = ["JuselessUCLA"]
+
+
 @register_datagrabber
 class JuselessUCLA(PatternDataGrabber):
     """Concrete implementation for Juseless UCLA data fetching.

junifer/configs/juseless/datagrabbers/ukb_vbm.py

@@ -12,6 +12,9 @@ from ....api.decorators import register_datagrabber
 from ....datagrabber import PatternDataladDataGrabber
 
 
+__all__ = ["JuselessDataladUKBVBM"]
+
+
 @register_datagrabber
 class JuselessDataladUKBVBM(PatternDataladDataGrabber):
     """Concrete implementation for Juseless UKB VBM data fetching.

junifer/data/__init__.py

@@ -28,3 +28,23 @@ from .masks import (
 from .template_spaces import get_template, get_xfm
 
 from . import utils
+
+
+__all__ = [
+    "list_coordinates",
+    "load_coordinates",
+    "register_coordinates",
+    "get_coordinates",
+    "list_parcellations",
+    "load_parcellation",
+    "register_parcellation",
+    "merge_parcellations",
+    "get_parcellation",
+    "list_masks",
+    "load_mask",
+    "register_mask",
+    "get_mask",
+    "get_template",
+    "get_xfm",
+    "utils",
+]

junifer/data/coordinates.py

@@ -16,6 +16,14 @@ from ..pipeline import WorkDirManager
 from ..utils import logger, raise_error, run_ext_cmd
 
 
+__all__ = [
+    "register_coordinates",
+    "list_coordinates",
+    "get_coordinates",
+    "load_coordinates",
+]
+
+
 # Path to the VOIs
 _vois_path = Path(__file__).parent / "VOIs"
 

junifer/data/masks.py

@@ -35,6 +35,16 @@ from .utils import closest_resolution
 if TYPE_CHECKING:
     from nibabel import Nifti1Image
 
+
+__all__ = [
+    "compute_brain_mask",
+    "register_mask",
+    "list_masks",
+    "get_mask",
+    "load_mask",
+]
+
+
 # Path to the masks
 _masks_path = Path(__file__).parent / "masks"
 

junifer/data/parcellations.py

@@ -30,6 +30,15 @@ if TYPE_CHECKING:
     from nibabel import Nifti1Image
 
 
+__all__ = [
+    "register_parcellation",
+    "list_parcellations",
+    "get_parcellation",
+    "load_parcellation",
+    "merge_parcellations",
+]
+
+
 # A dictionary containing all supported parcellations and their respective
 # valid parameters.
 

junifer/data/template_spaces.py

@@ -15,6 +15,9 @@ from ..utils import logger, raise_error
 from .utils import closest_resolution
 
 
+__all__ = ["get_xfm", "get_template"]
+
+
 def get_xfm(
     src: str, dst: str, xfms_dir: Union[str, Path, None] = None
 ) -> Path:  # pragma: no cover

junifer/data/utils.py

@@ -7,6 +7,9 @@ import numpy as np
 from ..utils.logging import logger
 
 
+__all__ = ["closest_resolution"]
+
+
 def closest_resolution(
     resolution: Optional[Union[float, int]],
     valid_resolution: Union[List[float], List[int], np.ndarray],

junifer/datagrabber/__init__.py

@@ -16,3 +16,18 @@ from .aomic import DataladAOMICID1000, DataladAOMICPIOP1, DataladAOMICPIOP2
 from .hcp1200 import HCP1200, DataladHCP1200
 from .multiple import MultipleDataGrabber
 from .dmcc13_benchmark import DMCC13Benchmark
+
+
+__all__ = [
+    "BaseDataGrabber",
+    "DataladDataGrabber",
+    "PatternDataGrabber",
+    "PatternDataladDataGrabber",
+    "DataladAOMICID1000",
+    "DataladAOMICPIOP1",
+    "DataladAOMICPIOP2",
+    "HCP1200",
+    "DataladHCP1200",
+    "MultipleDataGrabber",
+    "DMCC13Benchmark",
+]

junifer/datagrabber/aomic/__init__.py

@@ -7,3 +7,6 @@
 from .id1000 import DataladAOMICID1000
 from .piop1 import DataladAOMICPIOP1
 from .piop2 import DataladAOMICPIOP2
+
+
+__all__ = ["DataladAOMICID1000", "DataladAOMICPIOP1", "DataladAOMICPIOP2"]

junifer/datagrabber/aomic/id1000.py

@@ -14,6 +14,9 @@ from ...api.decorators import register_datagrabber
 from ..pattern_datalad import PatternDataladDataGrabber
 
 
+__all__ = ["DataladAOMICID1000"]
+
+
 @register_datagrabber
 class DataladAOMICID1000(PatternDataladDataGrabber):
     """Concrete implementation for datalad-based data fetching of AOMIC ID1000.

junifer/datagrabber/aomic/piop1.py

@@ -16,6 +16,9 @@ from ...utils import raise_error
 from ..pattern_datalad import PatternDataladDataGrabber
 
 
+__all__ = ["DataladAOMICPIOP1"]
+
+
 @register_datagrabber
 class DataladAOMICPIOP1(PatternDataladDataGrabber):
     """Concrete implementation for pattern-based data fetching of AOMIC PIOP1.

junifer/datagrabber/aomic/piop2.py

@@ -16,6 +16,9 @@ from ...utils import raise_error
 from ..pattern_datalad import PatternDataladDataGrabber
 
 
+__all__ = ["DataladAOMICPIOP2"]
+
+
 @register_datagrabber
 class DataladAOMICPIOP2(PatternDataladDataGrabber):
     """Concrete implementation for pattern-based data fetching of AOMIC PIOP2.

junifer/datagrabber/base.py

@@ -14,6 +14,9 @@ from ..utils import logger, raise_error
 from .utils import validate_types
 
 
+__all__ = ["BaseDataGrabber"]
+
+
 class BaseDataGrabber(ABC, UpdateMetaMixin):
     """Abstract base class for DataGrabber.
 

junifer/datagrabber/datalad_base.py

@@ -21,6 +21,9 @@ from ..utils import logger, raise_error, warn_with_log
 from .base import BaseDataGrabber
 
 
+__all__ = ["DataladDataGrabber"]
+
+
 class DataladDataGrabber(BaseDataGrabber):
     """Abstract base class for datalad-based data fetching.
 

junifer/datagrabber/hcp1200/__init__.py

@@ -5,3 +5,6 @@
 
 from .hcp1200 import HCP1200
 from .datalad_hcp1200 import DataladHCP1200
+
+
+__all__ = ["HCP1200", "DataladHCP1200"]

junifer/datagrabber/hcp1200/datalad_hcp1200.py

@@ -14,6 +14,9 @@ from ...api.decorators import register_datagrabber
 from .hcp1200 import HCP1200
 
 
+__all__ = ["DataladHCP1200"]
+
+
 @register_datagrabber
 class DataladHCP1200(DataladDataGrabber, HCP1200):
     """Concrete implementation for datalad-based data fetching of HCP1200.

junifer/datagrabber/hcp1200/hcp1200.py

@@ -14,6 +14,9 @@ from ..pattern import PatternDataGrabber
 from ..utils import raise_error
 
 
+__all__ = ["HCP1200"]
+
+
 @register_datagrabber
 class HCP1200(PatternDataGrabber):
     """Concrete implementation for pattern-based data fetching of HCP1200.

junifer/datagrabber/multiple.py

@@ -11,6 +11,9 @@ from ..utils import raise_error
 from .base import BaseDataGrabber
 
 
+__all__ = ["MultipleDataGrabber"]
+
+
 class MultipleDataGrabber(BaseDataGrabber):
     """Concrete implementation for multi sourced data fetching.
 

junifer/datagrabber/pattern.py

@@ -18,6 +18,9 @@ from .base import BaseDataGrabber
 from .utils import validate_patterns, validate_replacements
 
 
+__all__ = ["PatternDataGrabber"]
+
+
 # Accepted formats for confounds specification
 _CONFOUNDS_FORMATS = ("fmriprep", "adhoc")
 

junifer/datagrabber/pattern_datalad.py

@@ -12,6 +12,9 @@ from .datalad_base import DataladDataGrabber
 from .pattern import PatternDataGrabber
 
 
+__all__ = ["PatternDataladDataGrabber"]
+
+
 @register_datagrabber
 class PatternDataladDataGrabber(DataladDataGrabber, PatternDataGrabber):
     """Concrete implementation for pattern and datalad based data fetching.

junifer/datagrabber/utils.py

@@ -9,6 +9,9 @@ from typing import Dict, List
 from ..utils import logger, raise_error
 
 
+__all__ = ["validate_types", "validate_replacements", "validate_patterns"]
+
+
 # Define schema for pattern-based datagrabber's patterns
 PATTERNS_SCHEMA = {
     "T1w": {

junifer/datareader/__init__.py

@@ -6,3 +6,6 @@
 # License: AGPL
 
 from .default import DefaultDataReader
+
+
+__all__ = ["DefaultDataReader"]

junifer/datareader/default.py

@@ -15,6 +15,9 @@ from ..pipeline import PipelineStepMixin, UpdateMetaMixin
 from ..utils.logging import logger, warn_with_log
 
 
+__all__ = ["DefaultDataReader"]
+
+
 # Map each file extension to a type
 _extensions = {
     ".nii": "NIFTI",

junifer/markers/__init__.py

@@ -24,3 +24,24 @@ from .temporal_snr import (
     TemporalSNRSpheres,
 )
 from .brainprint import BrainPrint
+
+
+__all__ = [
+    "BaseMarker",
+    "MarkerCollection",
+    "RSSETSMarker",
+    "ParcelAggregation",
+    "SphereAggregation",
+    "FunctionalConnectivityParcels",
+    "FunctionalConnectivitySpheres",
+    "CrossParcellationFC",
+    "EdgeCentricFCParcels",
+    "EdgeCentricFCSpheres",
+    "ReHoParcels",
+    "ReHoSpheres",
+    "ALFFParcels",
+    "ALFFSpheres",
+    "TemporalSNRParcels",
+    "TemporalSNRSpheres",
+    "BrainPrint",
+]

junifer/markers/base.py

@@ -15,16 +15,22 @@ if TYPE_CHECKING:
     from junifer.storage import BaseFeatureStorage
 
 
+__all__ = ["BaseMarker"]
+
+
 class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
     """Abstract base class for all markers.
 
+    For every interface that is required, one needs to provide a concrete
+    implementation of this abstract class.
+
     Parameters
     ----------
-    on : str or list of str
+    on : str or list of str or None, optional
-        The kind of data to apply the marker to. By default, will work on all
+        The data type to apply the marker on. If None,
-        available data.
+        will work on all available data types (default None).
     name : str, optional
-        The name of the marker. By default, it will use the class name as the
+        The name of the marker. If None, will use the class name as the
         name of the marker (default None).
 
     Raises
@@ -192,17 +198,25 @@ class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
         for type_ in self._on:
             if type_ in input.keys():
                 logger.info(f"Computing {type_}")
+                # Get data dict for data type
                 t_input = input[type_]
+                # Pass the other data types as extra input, removing
+                # the current type
                 extra_input = input.copy()
                 extra_input.pop(type_)
+                logger.debug(
+                    f"Extra data type for feature extraction: "
+                    f"{extra_input.keys()}"
+                )
+                # Copy metadata
                 t_meta = t_input["meta"].copy()
                 t_meta["type"] = type_
-
+                # Compute marker
                 t_out = self.compute(input=t_input, extra_input=extra_input)
                 t_out["meta"] = t_meta
-
+                # Update metadata for step
                 self.update_meta(t_out, "marker")
-
+                # Check storage
                 if storage is not None:
                     logger.info(f"Storing in {storage}")
                     self.store(type_=type_, out=t_out, storage=storage)

junifer/markers/brainprint.py

@@ -43,6 +43,9 @@ if TYPE_CHECKING:
     from junifer.storage import BaseFeatureStorage
 
 
+__all__ = ["BrainPrint"]
+
+
 @register_marker
 class BrainPrint(BaseMarker):
     """Class for BrainPrint.

junifer/markers/collection.py

@@ -19,6 +19,9 @@ if TYPE_CHECKING:
     from junifer.datagrabber import BaseDataGrabber
 
 
+__all__ = ["MarkerCollection"]
+
+
 class MarkerCollection:
     """Class for marker collection.
 

junifer/markers/complexity/__init__.py

@@ -25,3 +25,13 @@ else:
     from .weighted_perm_entropy import WeightedPermEntropy
     from .sample_entropy import SampleEntropy
     from .multiscale_entropy_auc import MultiscaleEntropyAUC
+
+    __all__ = [
+        "HurstExponent",
+        "RangeEntropy",
+        "RangeEntropyAUC",
+        "PermEntropy",
+        "WeightedPermEntropy",
+        "SampleEntropy",
+        "MultiscaleEntropyAUC",
+    ]

junifer/markers/complexity/complexity_base.py

@@ -24,6 +24,9 @@ if TYPE_CHECKING:
     import numpy as np
 
 
+__all__ = ["ComplexityBase"]
+
+
 class ComplexityBase(BaseMarker):
     """Base class for complexity computation.
 

junifer/markers/complexity/hurst_exponent.py

@@ -14,6 +14,9 @@ from ...utils import logger, warn_with_log
 from .complexity_base import ComplexityBase
 
 
+__all__ = ["HurstExponent"]
+
+
 @register_marker
 class HurstExponent(ComplexityBase):
     """Class for Hurst exponent of a time series.

junifer/markers/complexity/multiscale_entropy_auc.py

@@ -14,6 +14,9 @@ from ...utils import logger, warn_with_log
 from .complexity_base import ComplexityBase
 
 
+__all__ = ["MultiscaleEntropyAUC"]
+
+
 @register_marker
 class MultiscaleEntropyAUC(ComplexityBase):
     """Class for AUC of multiscale entropy of a time series.

junifer/markers/complexity/perm_entropy.py

@@ -14,6 +14,9 @@ from ...utils import logger, warn_with_log
 from .complexity_base import ComplexityBase
 
 
+__all__ = ["PermEntropy"]
+
+
 @register_marker
 class PermEntropy(ComplexityBase):
     """Class for permutation entropy of a time series.

junifer/markers/complexity/range_entropy.py

@@ -14,6 +14,9 @@ from ...utils import logger, warn_with_log
 from .complexity_base import ComplexityBase
 
 
+__all__ = ["RangeEntropy"]
+
+
 @register_marker
 class RangeEntropy(ComplexityBase):
     """Class for range entropy of a time series.

junifer/markers/complexity/range_entropy_auc.py

@@ -14,6 +14,9 @@ from ...utils import logger, warn_with_log
 from .complexity_base import ComplexityBase
 
 
+__all__ = ["RangeEntropyAUC"]
+
+
 @register_marker
 class RangeEntropyAUC(ComplexityBase):
     """Class for AUC of range entropy values of a time series over r = 0 to 1.

junifer/markers/complexity/sample_entropy.py

@@ -14,6 +14,9 @@ from ...utils import logger, warn_with_log
 from .complexity_base import ComplexityBase
 
 
+__all__ = ["SampleEntropy"]
+
+
 @register_marker
 class SampleEntropy(ComplexityBase):
     """Class for sample entropy of a time series.

junifer/markers/complexity/tests/test_hurst_exponent.py

@@ -14,6 +14,7 @@ pytest.importorskip("neurokit2")
 
 from junifer.datareader import DefaultDataReader  # noqa: E402
 from junifer.markers.complexity import HurstExponent  # noqa: E402
+from junifer.pipeline.utils import _check_ants  # noqa: E402
 from junifer.storage import SQLiteFeatureStorage  # noqa: E402
 from junifer.testing.datagrabbers import (  # noqa: E402
     SPMAuditoryTestingDataGrabber,
@@ -24,6 +25,9 @@ from junifer.testing.datagrabbers import (  # noqa: E402
 PARCELLATION = "Schaefer100x17"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_compute() -> None:
     """Test HurstExponent compute()."""
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -45,6 +49,9 @@ def test_get_output_type() -> None:
     assert marker.get_output_type("BOLD") == "vector"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test HurstExponent store().
 

junifer/markers/complexity/tests/test_multiscale_entropy_auc.py

@@ -13,6 +13,7 @@ pytest.importorskip("neurokit2")
 
 from junifer.datareader import DefaultDataReader  # noqa: E402
 from junifer.markers.complexity import MultiscaleEntropyAUC  # noqa: E402
+from junifer.pipeline.utils import _check_ants  # noqa: E402
 from junifer.storage import SQLiteFeatureStorage  # noqa: E402
 from junifer.testing.datagrabbers import (  # noqa: E402
     SPMAuditoryTestingDataGrabber,
@@ -23,6 +24,9 @@ from junifer.testing.datagrabbers import (  # noqa: E402
 PARCELLATION = "Schaefer100x17"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_compute() -> None:
     """Test MultiscaleEntropyAUC compute()."""
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -44,6 +48,9 @@ def test_get_output_type() -> None:
     assert marker.get_output_type("BOLD") == "vector"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test MultiscaleEntropyAUC store().
 

junifer/markers/complexity/tests/test_perm_entropy.py

@@ -13,6 +13,7 @@ pytest.importorskip("neurokit2")
 
 from junifer.datareader import DefaultDataReader  # noqa: E402
 from junifer.markers.complexity import PermEntropy  # noqa: E402
+from junifer.pipeline.utils import _check_ants  # noqa: E402
 from junifer.storage import SQLiteFeatureStorage  # noqa: E402
 from junifer.testing.datagrabbers import (  # noqa: E402
     SPMAuditoryTestingDataGrabber,
@@ -23,6 +24,9 @@ from junifer.testing.datagrabbers import (  # noqa: E402
 PARCELLATION = "Schaefer100x17"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_compute() -> None:
     """Test PermEntropy compute()."""
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -44,6 +48,9 @@ def test_get_output_type() -> None:
     assert marker.get_output_type("BOLD") == "vector"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test PermEntropy store().
 

junifer/markers/complexity/tests/test_range_entropy.py

@@ -14,6 +14,7 @@ pytest.importorskip("neurokit2")
 
 from junifer.datareader import DefaultDataReader  # noqa: E402
 from junifer.markers.complexity import RangeEntropy  # noqa: E402
+from junifer.pipeline.utils import _check_ants  # noqa: E402
 from junifer.storage import SQLiteFeatureStorage  # noqa: E402
 from junifer.testing.datagrabbers import (  # noqa: E402
     SPMAuditoryTestingDataGrabber,
@@ -24,6 +25,9 @@ from junifer.testing.datagrabbers import (  # noqa: E402
 PARCELLATION = "Schaefer100x17"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_compute() -> None:
     """Test RangeEntropy compute()."""
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -45,6 +49,9 @@ def test_get_output_type() -> None:
     assert marker.get_output_type("BOLD") == "vector"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test RangeEntropy store().
 

junifer/markers/complexity/tests/test_range_entropy_auc.py

@@ -14,6 +14,7 @@ pytest.importorskip("neurokit2")
 
 from junifer.datareader import DefaultDataReader  # noqa: E402
 from junifer.markers.complexity import RangeEntropyAUC  # noqa: E402
+from junifer.pipeline.utils import _check_ants  # noqa: E402
 from junifer.storage import SQLiteFeatureStorage  # noqa: E402
 from junifer.testing.datagrabbers import (  # noqa: E402
     SPMAuditoryTestingDataGrabber,
@@ -24,6 +25,9 @@ from junifer.testing.datagrabbers import (  # noqa: E402
 PARCELLATION = "Schaefer100x17"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_compute() -> None:
     """Test RangeEntropyAUC compute()."""
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -45,6 +49,9 @@ def test_get_output_type() -> None:
     assert marker.get_output_type("BOLD") == "vector"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test RangeEntropyAUC store().
 

junifer/markers/complexity/tests/test_sample_entropy.py

@@ -13,6 +13,7 @@ pytest.importorskip("neurokit2")
 
 from junifer.datareader import DefaultDataReader  # noqa: E402
 from junifer.markers.complexity import SampleEntropy  # noqa: E402
+from junifer.pipeline.utils import _check_ants  # noqa: E402
 from junifer.storage import SQLiteFeatureStorage  # noqa: E402
 from junifer.testing.datagrabbers import (  # noqa: E402
     SPMAuditoryTestingDataGrabber,
@@ -23,6 +24,9 @@ from junifer.testing.datagrabbers import (  # noqa: E402
 PARCELLATION = "Schaefer100x17"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_compute() -> None:
     """Test SampleEntropy compute()."""
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -44,6 +48,9 @@ def test_get_output_type() -> None:
     assert marker.get_output_type("BOLD") == "vector"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test SampleEntropy store().
 

junifer/markers/complexity/tests/test_weighted_perm_entropy.py

@@ -13,6 +13,7 @@ pytest.importorskip("neurokit2")
 
 from junifer.datareader import DefaultDataReader  # noqa: E402
 from junifer.markers.complexity import WeightedPermEntropy  # noqa: E402
+from junifer.pipeline.utils import _check_ants  # noqa: E402
 from junifer.storage import SQLiteFeatureStorage  # noqa: E402
 from junifer.testing.datagrabbers import (  # noqa: E402
     SPMAuditoryTestingDataGrabber,
@@ -23,6 +24,9 @@ from junifer.testing.datagrabbers import (  # noqa: E402
 PARCELLATION = "Schaefer100x17"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_compute() -> None:
     """Test WeightedPermEntropy compute()."""
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -44,6 +48,9 @@ def test_get_output_type() -> None:
     assert marker.get_output_type("BOLD") == "vector"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test WeightedPermEntropy store().
 

junifer/markers/complexity/weighted_perm_entropy.py

@@ -14,6 +14,9 @@ from ...utils import logger, warn_with_log
 from .complexity_base import ComplexityBase
 
 
+__all__ = ["WeightedPermEntropy"]
+
+
 @register_marker
 class WeightedPermEntropy(ComplexityBase):
     """Class for weighted permutation entropy of a time series.

junifer/markers/ets_rss.py

@@ -17,6 +17,9 @@ from .parcel_aggregation import ParcelAggregation
 from .utils import _ets
 
 
+__all__ = ["RSSETSMarker"]
+
+
 @register_marker
 class RSSETSMarker(BaseMarker):
     """Class for root sum of squares of edgewise timeseries.

junifer/markers/falff/__init__.py

@@ -5,3 +5,6 @@
 
 from .falff_parcels import ALFFParcels
 from .falff_spheres import ALFFSpheres
+
+
+__all__ = ["ALFFParcels", "ALFFSpheres"]

junifer/markers/falff/_afni_falff.py

@@ -26,6 +26,9 @@ if TYPE_CHECKING:
     from nibabel import Nifti1Image
 
 
+__all__ = ["AFNIALFF"]
+
+
 @singleton
 class AFNIALFF:
     """Class for computing ALFF using AFNI.

junifer/markers/falff/_junifer_falff.py

@@ -27,6 +27,9 @@ if TYPE_CHECKING:
     from nibabel import Nifti1Image
 
 
+__all__ = ["JuniferALFF"]
+
+
 @singleton
 class JuniferALFF:
     """Class for computing ALFF using junifer.

junifer/markers/falff/falff_base.py

@@ -29,6 +29,9 @@ if TYPE_CHECKING:
     from nibabel import Nifti1Image
 
 
+__all__ = ["ALFFBase"]
+
+
 class ALFFBase(BaseMarker):
     """Base class for (fractional) Amplitude Low Frequency Fluctuation.
 

junifer/markers/falff/falff_parcels.py

@@ -14,6 +14,9 @@ from ..parcel_aggregation import ParcelAggregation
 from .falff_base import ALFFBase
 
 
+__all__ = ["ALFFParcels"]
+
+
 @register_marker
 class ALFFParcels(ALFFBase):
     """Class for ALFF / fALFF on parcels.

junifer/markers/falff/falff_spheres.py

@@ -14,6 +14,9 @@ from ..sphere_aggregation import SphereAggregation
 from .falff_base import ALFFBase
 
 
+__all__ = ["ALFFSpheres"]
+
+
 @register_marker
 class ALFFSpheres(ALFFBase):
     """Class for computing ALFF / fALFF on spheres.

junifer/markers/functional_connectivity/__init__.py

@@ -8,3 +8,12 @@ from .functional_connectivity_spheres import FunctionalConnectivitySpheres
 from .crossparcellation_functional_connectivity import CrossParcellationFC
 from .edge_functional_connectivity_parcels import EdgeCentricFCParcels
 from .edge_functional_connectivity_spheres import EdgeCentricFCSpheres
+
+
+__all__ = [
+    "FunctionalConnectivityParcels",
+    "FunctionalConnectivitySpheres",
+    "CrossParcellationFC",
+    "EdgeCentricFCParcels",
+    "EdgeCentricFCSpheres",
+]

junifer/markers/functional_connectivity/crossparcellation_functional_connectivity.py

@@ -15,6 +15,9 @@ from ..parcel_aggregation import ParcelAggregation
 from ..utils import _correlate_dataframes
 
 
+__all__ = ["CrossParcellationFC"]
+
+
 @register_marker
 class CrossParcellationFC(BaseMarker):
     """Class for calculating parcel-wise correlations with 2 parcellations.

junifer/markers/functional_connectivity/edge_functional_connectivity_parcels.py

@@ -12,6 +12,9 @@ from ..utils import _ets
 from .functional_connectivity_base import FunctionalConnectivityBase
 
 
+__all__ = ["EdgeCentricFCParcels"]
+
+
 @register_marker
 class EdgeCentricFCParcels(FunctionalConnectivityBase):
     """Class for edge-centric FC using parcellations.

junifer/markers/functional_connectivity/edge_functional_connectivity_spheres.py

@@ -12,6 +12,9 @@ from ..utils import _ets, raise_error
 from .functional_connectivity_base import FunctionalConnectivityBase
 
 
+__all__ = ["EdgeCentricFCSpheres"]
+
+
 @register_marker
 class EdgeCentricFCSpheres(FunctionalConnectivityBase):
     """Class for edge-centric FC using coordinates (spheres).

junifer/markers/functional_connectivity/functional_connectivity_base.py

@@ -14,6 +14,9 @@ from ...utils import raise_error
 from ..base import BaseMarker
 
 
+__all__ = ["FunctionalConnectivityBase"]
+
+
 class FunctionalConnectivityBase(BaseMarker):
     """Abstract base class for functional connectivity markers.
 

junifer/markers/functional_connectivity/functional_connectivity_parcels.py

@@ -12,6 +12,9 @@ from ..parcel_aggregation import ParcelAggregation
 from .functional_connectivity_base import FunctionalConnectivityBase
 
 
+__all__ = ["FunctionalConnectivityParcels"]
+
+
 @register_marker
 class FunctionalConnectivityParcels(FunctionalConnectivityBase):
     """Class for functional connectivity using parcellations.

junifer/markers/functional_connectivity/functional_connectivity_spheres.py

@@ -13,6 +13,9 @@ from ..utils import raise_error
 from .functional_connectivity_base import FunctionalConnectivityBase
 
 
+__all__ = ["FunctionalConnectivitySpheres"]
+
+
 @register_marker
 class FunctionalConnectivitySpheres(FunctionalConnectivityBase):
     """Class for functional connectivity using coordinates (spheres).

junifer/markers/parcel_aggregation.py

@@ -17,6 +17,9 @@ from ..utils import logger, raise_error, warn_with_log
 from .base import BaseMarker
 
 
+__all__ = ["ParcelAggregation"]
+
+
 @register_marker
 class ParcelAggregation(BaseMarker):
     """Class for parcel aggregation.

junifer/markers/reho/__init__.py

@@ -5,3 +5,6 @@
 
 from .reho_parcels import ReHoParcels
 from .reho_spheres import ReHoSpheres
+
+
+__all__ = ["ReHoParcels", "ReHoSpheres"]

junifer/markers/reho/_afni_reho.py

@@ -26,6 +26,9 @@ if TYPE_CHECKING:
     from nibabel import Nifti1Image
 
 
+__all__ = ["AFNIReHo"]
+
+
 @singleton
 class AFNIReHo:
     """Class for computing ReHo using AFNI.

junifer/markers/reho/_junifer_reho.py

@@ -28,6 +28,9 @@ if TYPE_CHECKING:
     from nibabel import Nifti1Image
 
 
+__all__ = ["JuniferReHo"]
+
+
 @singleton
 class JuniferReHo:
     """Class for computing ReHo using junifer.

junifer/markers/reho/reho_base.py

@@ -26,6 +26,8 @@ from ._junifer_reho import JuniferReHo
 if TYPE_CHECKING:
     from nibabel import Nifti1Image
 
+__all__ = ["ReHoBase"]
+
 
 class ReHoBase(BaseMarker):
     """Base class for regional homogeneity computation.

junifer/markers/reho/reho_parcels.py

@@ -14,6 +14,9 @@ from ..parcel_aggregation import ParcelAggregation
 from .reho_base import ReHoBase
 
 
+__all__ = ["ReHoParcels"]
+
+
 @register_marker
 class ReHoParcels(ReHoBase):
     """Class for regional homogeneity on parcels.

junifer/markers/reho/reho_spheres.py

@@ -14,6 +14,9 @@ from ..sphere_aggregation import SphereAggregation
 from .reho_base import ReHoBase
 
 
+__all__ = ["ReHoSpheres"]
+
+
 @register_marker
 class ReHoSpheres(ReHoBase):
     """Class for regional homogeneity on spheres.

junifer/markers/sphere_aggregation.py

@@ -14,6 +14,9 @@ from ..utils import logger, raise_error, warn_with_log
 from .base import BaseMarker
 
 
+__all__ = ["SphereAggregation"]
+
+
 @register_marker
 class SphereAggregation(BaseMarker):
     """Class for sphere aggregation.

junifer/markers/temporal_snr/__init__.py

@@ -5,3 +5,6 @@
 
 from .temporal_snr_parcels import TemporalSNRParcels
 from .temporal_snr_spheres import TemporalSNRSpheres
+
+
+__all__ = ["TemporalSNRParcels", "TemporalSNRSpheres"]

junifer/markers/temporal_snr/temporal_snr_base.py

@@ -13,6 +13,9 @@ from ...utils import raise_error
 from ..base import BaseMarker
 
 
+__all__ = ["TemporalSNRBase"]
+
+
 class TemporalSNRBase(BaseMarker):
     """Abstract base class for temporal SNR markers.
 

junifer/markers/temporal_snr/temporal_snr_parcels.py

@@ -10,6 +10,9 @@ from ..parcel_aggregation import ParcelAggregation
 from .temporal_snr_base import TemporalSNRBase
 
 
+__all__ = ["TemporalSNRParcels"]
+
+
 @register_marker
 class TemporalSNRParcels(TemporalSNRBase):
     """Class for temporal signal-to-noise ratio using parcellations.

junifer/markers/temporal_snr/temporal_snr_spheres.py

@@ -11,6 +11,9 @@ from ..utils import raise_error
 from .temporal_snr_base import TemporalSNRBase
 
 
+__all__ = ["TemporalSNRSpheres"]
+
+
 @register_marker
 class TemporalSNRSpheres(TemporalSNRBase):
     """Class for temporal signal-to-noise ratio using coordinates (spheres).

junifer/onthefly/__init__.py

@@ -4,3 +4,6 @@
 # License: AGPL
 
 from .read_transform import read_transform
+
+
+__all__ = ["read_transform"]

junifer/onthefly/read_transform.py

@@ -15,6 +15,9 @@ if TYPE_CHECKING:
     from junifer.storage import BaseFeatureStorage
 
 
+__all__ = ["read_transform"]
+
+
 def read_transform(
     storage: Type["BaseFeatureStorage"],
     transform: str,

junifer/pipeline/__init__.py

@@ -7,3 +7,11 @@ from . import registry
 from .pipeline_step_mixin import PipelineStepMixin
 from .update_meta_mixin import UpdateMetaMixin
 from .workdir_manager import WorkDirManager
+
+
+__all__ = [
+    "registry",
+    "PipelineStepMixin",
+    "UpdateMetaMixin",
+    "WorkDirManager",
+]

junifer/pipeline/pipeline_step_mixin.py

@@ -17,6 +17,9 @@ from ..utils import raise_error
 from .utils import check_ext_dependencies
 
 
+__all__ = ["PipelineStepMixin"]
+
+
 class PipelineStepMixin:
     """Mixin class for a pipeline step."""
 

junifer/pipeline/registry.py

@@ -16,6 +16,9 @@ if TYPE_CHECKING:
     from .pipeline_step_mixin import PipelineStepMixin
 
 
+__all__ = ["register", "get_step_names", "get_class", "build"]
+
+
 # Define valid steps for operation
 _VALID_STEPS: List[str] = [
     "datagrabber",

junifer/pipeline/singleton.py

@@ -6,6 +6,9 @@
 from typing import Any, Dict, Type
 
 
+__all__ = ["singleton"]
+
+
 def singleton(cls: Type) -> Type:
     """Make a class singleton.