junifer 0.0.5.dev131__tar.gz → 0.0.5.dev145__tar.gz

{junifer-0.0.5.dev131 → junifer-0.0.5.dev145}/.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
-    rev: 24.1.1
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    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]

{junifer-0.0.5.dev131 → junifer-0.0.5.dev145}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev131
+Version: 0.0.5.dev145
 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>

junifer-0.0.5.dev145/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`_

{junifer-0.0.5.dev131 → junifer-0.0.5.dev145}/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],
-      [-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",
@@ -90,10 +87,7 @@ 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.dev131 → junifer-0.0.5.dev145}/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"]
 
@@ -144,25 +144,24 @@ 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
@@ -180,25 +179,24 @@ 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,
             )
 
 
@@ -267,29 +265,28 @@ 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:
@@ -391,17 +388,17 @@ 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
@@ -415,16 +412,16 @@ 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
@@ -435,7 +432,7 @@ 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:
@@ -448,35 +445,36 @@ 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_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_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
 ~~~~~~~~~~~~~~~~~~~~~~~
@@ -522,26 +520,24 @@ 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",
+               "confounds": {
+                   "path": f"{subject}/{session}/func/{subject}_{session}_confounds.tsv",
+                   "format": "adhoc",
+                   "mappings": {
+                       "fmriprep": {
+                           "variable1": "rot_x",
+                           "variable2": "rot_z",
+                           "variable3": "rot_y",
+                       },
+                   },
+               },
+           },
+       }
 
 .. note::
 

{junifer-0.0.5.dev131 → junifer-0.0.5.dev145}/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

{junifer-0.0.5.dev131 → junifer-0.0.5.dev145}/docs/extending/marker.rst

@@ -82,10 +82,10 @@ parcellation to use. Thus, we can define the ``__init__`` method as follows:
 .. code-block:: python
 
     def __init__(
-       self,
-       parcellation: str,
-       on: str | list[str] | None = None,
-       name: str | None = None,
+        self,
+        parcellation: str,
+        on: str | list[str] | None = None,
+        name: str | None = None,
     ) -> None:
         self.parcellation = parcellation
         super().__init__(on=on, name=name)
@@ -137,9 +137,9 @@ the ``store`` method.
 
 
     def compute(
-       self,
-       input: dict[str, Any],
-       extra_input: dict[str, Any] | None = None,
+        self,
+        input: dict[str, Any],
+        extra_input: dict[str, Any] | None = None,
     ) -> dict[str, Any]:
         # Get the data
         data = input["data"]
@@ -207,10 +207,10 @@ Finally, we need to register the Marker using the ``@register_marker`` decorator
         _DEPENDENCIES = {"nilearn", "numpy"}
 
         def __init__(
-           self,
-           parcellation: str,
-           on: str | list[str] | None = None,
-           name: str | None = None,
+            self,
+            parcellation: str,
+            on: str | list[str] | None = None,
+            name: str | None = None,
         ) -> None:
             self.parcellation = parcellation
             super().__init__(on=on, name=name)
@@ -225,9 +225,9 @@ Finally, we need to register the Marker using the ``@register_marker`` decorator
                 return "vector"
 
         def compute(
-           self,
-           input: dict[str, Any],
-           extra_input: dict[str, Any] | None = None,
+            self,
+            input: dict[str, Any],
+            extra_input: dict[str, Any] | None = None,
         ) -> dict[str, Any]:
             # Get the data
             data = input["data"]
@@ -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)

{junifer-0.0.5.dev131 → junifer-0.0.5.dev145}/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

{junifer-0.0.5.dev131 → junifer-0.0.5.dev145}/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::
@@ -147,15 +153,18 @@ and it has two return values:
 
     ...
 
+
     def preprocess(
         self,
         input: dict[str, Any],
         extra_input: dict[str, Any] | None = None,
     ) -> tuple[dict[str, Any], dict[str, Any] | None]:
-         input["data"] = nimg.smooth_img(imgs=input["data"], fwhm=self.fwhm)
-         return input, None
+        input["data"] = nimg.smooth_img(imgs=input["data"], fwhm=self.fwhm)
+        return input, None
+
+
+    ...
 
-     ...
 
 Step 4: Finalise the Preprocessor
 ---------------------------------

{junifer-0.0.5.dev131 → junifer-0.0.5.dev145}/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': ...,

{junifer-0.0.5.dev131 → junifer-0.0.5.dev145}/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 = {
-        "motion": "full",
-        "wm_csf": "full",
-        "global_signal": "full"
-    }
+    strategy = {"motion": "full", "wm_csf": "full", "global_signal": "full"}
 
 Other Parameters
 ~~~~~~~~~~~~~~~~

{junifer-0.0.5.dev131 → junifer-0.0.5.dev145}/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-0.0.5.dev131 → junifer-0.0.5.dev145}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.5.dev131'
-__version_tuple__ = version_tuple = (0, 0, 5, 'dev131')
+__version__ = version = '0.0.5.dev145'
+__version_tuple__ = version_tuple = (0, 0, 5, 'dev145')

{junifer-0.0.5.dev131 → junifer-0.0.5.dev145}/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"]