docs/changes/newsfragments/226.enh

@@ -0,0 +1 @@
+Adopt ``DataGrabber`` consistently throughout codebase to match with the documentation by `Synchon Mandal`_

docs/understanding/data.rst

@@ -22,7 +22,7 @@ data type including source and previous transformation steps.
 
 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.
+step only contains information about the DataGrabber used.
 
 .. code-block:: python
 

docs/understanding/datagrabber.rst

@@ -9,29 +9,29 @@ Description
 -----------
 
 The ``DataGrabber`` is an object that can provide an interface to datasets you
-want to work with in junifer. Every concrete implementation of a datagrabber is
+want to work with in junifer. Every concrete implementation of a DataGrabber is
 aware of a particular dataset's structure and thus allows you to fetch specific
 elements of interest from the dataset. It adds the ``path`` key to each
 :ref:`data type <data_types>` in the :ref:`Data object <data_object>`.
 
-Datagrabbers are intended to be used as context managers. When used within a
+DataGrabbers are intended to be used as context managers. When used within a
-context, a datagrabber takes care of any pre and post steps for interacting with
+context, a DataGrabber takes care of any pre and post steps for interacting with
 the dataset, for example, downloading and cleaning up. As the interface
-is consistent, you always use the same procedure to interact with the datagrabber.
+is consistent, you always use the same procedure to interact with the DataGrabber.
 
 For example, a concrete implementation of :class:`.DataladDataGrabber` can
-provide junifer with data from a Datalad dataset. Of course, datagrabbers are not
+provide junifer with data from a Datalad dataset. Of course, DataGrabbers are not
 only meant to work with Datalad datasets but any dataset.
 
-If you are interested in using already provided datagrabbers, please go to
+If you are interested in using already provided DataGrabbers, please go to
-:doc:`../builtin`. And, if you want to implement your own datagrabber, you need
+:doc:`../builtin`. And, if you want to implement your own DataGrabber, you need
 to provide concrete implementations of base classes already provided.
 
 Base Classes
 ------------
 
 In this section, we showcase different abstract base classes you might want to
-use to implement your own datagrabber.
+use to implement your own DataGrabber.
 
 .. list-table::
    :widths: auto
@@ -41,16 +41,16 @@ use to implement your own datagrabber.
      - Description
    * - :class:`.BaseDataGrabber`
      - | The abstract base class providing you an interface to implement your
-       | own datagrabber. You should try to avoid using this directly and
+       | own DataGrabber. You should try to avoid using this directly and
        | instead use :class:`.PatternDataGrabber` or
        | :class:`.DataladDataGrabber`. To build your own custom *low-level*
-       | datagrabber, you need to override the ``get_elements_keys``,
+       | DataGrabber, you need to override the ``get_elements_keys``,
        | ``get_elements`` and ``get_item`` methods, and most of the time you
        | should also override other existing methods like ``__enter__`` and
        | ``__exit__``.
    * - :class:`.PatternDataGrabber`
      - | It implements functionality to help you define the pattern of the
-       | dataset you want to get. For example, you know that T1 images are
+       | dataset you want to get. For example, you know that T1w images are
        | found in a directory following the pattern:
        | ``{subject}/anat/{subject}_T1w.nii.gz`` inside of the dataset. Now you
        | can provide this to the :class:`.PatternDataGrabber` and it will be

docs/using/codeless.rst

@@ -75,10 +75,10 @@ Data Grabber
 ^^^^^^^^^^^^
 
 The ``datagrabber`` section must be configured using the ``kind`` key to specify
-the datagrabber to use. Additional keys correspond to the parameters of the
+the DataGrabber to use. Additional keys correspond to the parameters of the
-datagrabber.
+DataGrabber constructor.
 
-For example, to use the :class:`.DataladAOMICPIOP1` datagrabber, we just need to
+For example, to use the :class:`.DataladAOMICPIOP1` DataGrabber, we just need to
 specify its name as the ``kind`` key.
 
 .. code-block:: yaml
@@ -86,8 +86,9 @@ specify its name as the ``kind`` key.
   datagrabber:
     kind: DataladAOMICPIOP1
 
-However, it is also possible to pass parameters to the datagrabber. In this case,
+However, it is also possible to pass parameters to the DataGrabber constructor.
-we can restrict the datagrabber to fetch only the ``restingstate`` task.
+In this case, we can restrict the DataGrabber to fetch only the ``restingstate``
+task.
 
 .. code-block:: yaml
 

examples/run_datagrabber_bids_datalad.py

@@ -1,8 +1,8 @@
 """
-Generic BIDS datagrabber for datalad.
+Generic BIDS DataGrabber for datalad.
 =====================================
 
-This example uses a generic BIDS datagraber to get the data from a BIDS dataset
+This example uses a generic BIDS DataGraber to get the data from a BIDS dataset
 store in a datalad remote sibling.
 
 Authors: Federico Raimondo
@@ -20,9 +20,9 @@ configure_logging(level="INFO")
 
 
 ###############################################################################
-# The BIDS datagrabber requires three parameters: the types of data we want,
+# The BIDS DataGrabber requires three parameters: the types of data we want,
 # the specific pattern that matches each type, and the variables that will be
-# replaced int he patterns.
+# replaced in the patterns.
 types = ["T1w", "BOLD"]
 patterns = {
     "T1w": "{subject}/anat/{subject}_T1w.nii.gz",
@@ -30,15 +30,15 @@ patterns = {
 }
 replacements = ["subject"]
 ###############################################################################
-# Additionally, a datalad datagrabber requires the URI of the remote sibling
+# Additionally, a datalad-based DataGrabber requires the URI of the remote
-# and the location of the dataset within the remote sibling.
+# sibling and the location of the dataset within the remote sibling.
 repo_uri = "https://gin.g-node.org/juaml/datalad-example-bids"
 rootdir = "example_bids"
 
 ###############################################################################
-# Now we can use the datagrabber within a `with` context
+# Now we can use the DataGrabber within a `with` context.
-# One thing we can do with any datagrabber is iterate over the elements.
+# One thing we can do with any DataGrabber is iterate over the elements.
-# In this case, each element of the datagrabber is one session.
+# In this case, each element of the DataGrabber is one session.
 with PatternDataladDataGrabber(
     rootdir=rootdir,
     types=types,
@@ -50,9 +50,9 @@ with PatternDataladDataGrabber(
         print(elem)
 
 ###############################################################################
-# Another feature of the datagrabber is the ability to get a specific
+# Another feature of the DataGrabber is the ability to get a specific
 # element by its name. In this case, we index `sub-01` and we get the file
-# paths for the two types of data we want (T1w and bold).
+# paths for the two types of data we want (T1w and BOLD).
 with PatternDataladDataGrabber(
     rootdir=rootdir,
     types=types,

examples/run_ets_rss_marker.py

@@ -25,7 +25,7 @@ from junifer.utils import configure_logging
 configure_logging(level="INFO")
 
 ##############################################################################
-# Define the datagrabber interface
+# Define the DataGrabber interface
 datagrabber = {
     "kind": "SPMAuditoryTestingDataGrabber",
 }

junifer/api/decorators.py

@@ -11,20 +11,24 @@ from ..pipeline.registry import register
 
 
 def register_datagrabber(klass: Type) -> Type:
-    """Datagrabber registration decorator.
+    """Register DataGrabber.
 
-    Registers the datagrabber so it can be used by name.
+    Registers the DataGrabber so it can be used by name.
 
     Parameters
     ----------
     klass: class
-        The class of the datagrabber to register.
+        The class of the DataGrabber to register.
 
     Returns
     -------
     klass: class
         The unmodified input class.
 
+    Notes
+    -----
+    It should only be used as a decorator.
+
     """
     register(
         step="datagrabber",

junifer/api/functions.py

@@ -24,17 +24,17 @@ from .utils import yaml
 
 
 def _get_datagrabber(datagrabber_config: Dict) -> BaseDataGrabber:
-    """Get datagrabber.
+    """Get DataGrabber.
 
     Parameters
     ----------
     datagrabber_config : dict
-        The config to get the datagrabber using.
+        The config to get the DataGrabber using.
 
     Returns
     -------
-    dict
+    object
-        The datagrabber.
+        The DataGrabber.
 
     """
     datagrabber_params = datagrabber_config.copy()
@@ -90,8 +90,8 @@ def run(
     workdir : str or pathlib.Path
         Directory where the pipeline will be executed.
     datagrabber : dict
-        Datagrabber to use. Must have a key ``kind`` with the kind of
+        DataGrabber to use. Must have a key ``kind`` with the kind of
-        datagrabber to use. All other keys are passed to the datagrabber
+        DataGrabber to use. All other keys are passed to the DataGrabber
         init function.
     markers : list of dict
         List of markers to extract. Each marker is a dict with at least two
@@ -108,7 +108,7 @@ def run(
         preprocessor to use. All other keys are passed to the preprocessor
         init function (default None).
     elements : str or tuple or list of str or tuple, optional
-        Element(s) to process. Will be used to index the datagrabber
+        Element(s) to process. Will be used to index the DataGrabber
         (default None).
 
     """
@@ -220,7 +220,7 @@ def queue(
     overwrite : bool, optional
         Whether to overwrite if job directory already exists (default False).
     elements : str or tuple or list of str or tuple, optional
-        Element(s) to process. Will be used to index the datagrabber
+        Element(s) to process. Will be used to index the DataGrabber
         (default None).
     **kwargs : dict
         The keyword arguments to pass to the job queue system.
@@ -339,7 +339,7 @@ def _queue_condor(
     yaml_config : pathlib.Path
         The path to the YAML config file.
     elements : list of str or tuple
-        Element(s) to process. Will be used to index the datagrabber.
+        Element(s) to process. Will be used to index the DataGrabber.
     config : dict
         The configuration to be used for queueing the job.
     env : dict, optional
@@ -559,7 +559,7 @@ def _queue_slurm(
     yaml_config : pathlib.Path
         The path to the YAML config file.
     elements : str or tuple or list[str or tuple], optional
-        Element(s) to process. Will be used to index the datagrabber
+        Element(s) to process. Will be used to index the DataGrabber
         (default None).
     config : dict
         The configuration to be used for queueing the job.

junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py

@@ -1,4 +1,4 @@
-"""Provide class for AOMIC1000 VBM juseless datalad datagrabber."""
+"""Provide concrete implementation for AOMIC ID1000 VBM DataGrabber."""
 
 # Authors: Felix Hoffstaedter <f.hoffstaedter@fz-juelich.de>
 #          Synchon Mandal <s.mandal@fz-juelich.de>
@@ -13,13 +13,13 @@ from ....datagrabber import PatternDataladDataGrabber
 
 @register_datagrabber
 class JuselessDataladAOMICID1000VBM(PatternDataladDataGrabber):
-    """Juseless AOMICID1000 VBM Data Grabber class.
+    """Concrete implementation for Juseless AOMIC ID1000 VBM data fetching.
 
-    Implements a Data Grabber to access the AOMICID1000 VBM data in Juseless.
+    Implements a DataGrabber to access the AOMIC ID1000 VBM data in Juseless.
 
     Parameters
     ----------
-    datadir : str or pathlib.Path, optional
+    datadir : str or pathlib.Path or None, optional
         The directory where the datalad dataset will be cloned. If None,
         the datalad dataset will be cloned into a temporary directory
         (default None).

junifer/configs/juseless/datagrabbers/camcan_vbm.py

@@ -1,4 +1,4 @@
-"""Provide class for CamCAN VBM juseless datalad datagrabber."""
+"""Provide concrete implementation for CamCAN VBM DataGrabber."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
@@ -14,13 +14,13 @@ from ....datagrabber import PatternDataladDataGrabber
 
 @register_datagrabber
 class JuselessDataladCamCANVBM(PatternDataladDataGrabber):
-    """Juseless CamCAN VBM Data Grabber class.
+    """Concrete implementation for Juseless CamCAN VBM data fetching.
 
-    Implements a Data Grabber to access the CamCAN VBM data in Juseless.
+    Implements a DataGrabber to access the CamCAN VBM data in Juseless.
 
     Parameters
     ----------
-    datadir : str or pathlib.Path, optional
+    datadir : str or pathlib.Path or None, optional
         The directory where the datalad dataset will be cloned. If None,
         the datalad dataset will be cloned into a temporary directory
         (default None).

junifer/configs/juseless/datagrabbers/ixi_vbm.py

@@ -1,4 +1,4 @@
-"""Provide class for IXI VBM juseless datalad datagrabber."""
+"""Provide concrete implementation for IXI VBM DataGrabber."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
@@ -15,19 +15,20 @@ from ....utils import raise_error
 
 @register_datagrabber
 class JuselessDataladIXIVBM(PatternDataladDataGrabber):
-    """Juseless IXI VBM Data Grabber class.
+    """Concrete implementation for Juseless IXI VBM data fetching.
 
-    Implements a Data Grabber to access the IXI VBM data in Juseless.
+    Implements a DataGrabber to access the IXI VBM data in Juseless.
 
     Parameters
     ----------
-    datadir : str or pathlib.Path, optional
+    datadir : str or pathlib.Path or None, optional
         The directory where the datalad dataset will be cloned. If None,
         the datalad dataset will be cloned into a temporary directory
         (default None).
-    sites : {"Guys", "HH", "IOP"} or list of the options, optional.
+    sites : {"Guys", "HH", "IOP"} or list of the options or None, optional
         Which sites to access data from. If None, all available sites are
         selected (default None).
+
     """
 
     def __init__(

junifer/configs/juseless/datagrabbers/tests/test_aomic_id1000_vbm.py

@@ -1,4 +1,4 @@
-"""Provide tests for AOMICID1000 VBM juseless datagrabber."""
+"""Provide tests for JuselessDataladAOMICID1000VBM."""
 
 # Authors: Felix Hoffstaedter <f.hoffstaedter@fz-juelich.de>
 #          Synchon Mandal <s.mandal@fz-juelich.de>
@@ -19,8 +19,8 @@ if socket.gethostname() != "juseless":
 configure_logging(level="DEBUG")
 
 
-def test_juselessdataladaomicid1000vbm_datagrabber() -> None:
+def test_JuselessDataladAOMICID1000VBM() -> None:
-    """Test datalad AOMICID1000VBM datagrabber."""
+    """Test JuselessDataladAOMICID1000VBM."""
     with JuselessDataladAOMICID1000VBM() as dg:
         all_elements = dg.get_elements()
         test_element = all_elements[0]

junifer/configs/juseless/datagrabbers/tests/test_camcan_vbm.py

@@ -1,4 +1,4 @@
-"""Provide tests for CamCAN VBM juseless datagrabber."""
+"""Provide tests for JuselessDataladCamCANVBM."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
@@ -20,8 +20,8 @@ if socket.gethostname() != "juseless":
 configure_logging(level="DEBUG")
 
 
-def test_juselessdataladcamcanvbm_datagrabber() -> None:
+def test_JuselessDataladCamCANVBM() -> None:
-    """Test datalad CamCANVBM datagrabber."""
+    """Test JuselessDataladCamCANVBM."""
     with JuselessDataladCamCANVBM() as dg:
         all_elements = dg.get_elements()
         test_element = all_elements[0]

junifer/configs/juseless/datagrabbers/tests/test_ixi_vbm.py

@@ -1,4 +1,4 @@
-"""Provide tests for IXI VBM juseless datagrabber."""
+"""Provide tests for JuselessDataladIXIVBM."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
@@ -20,8 +20,8 @@ if socket.gethostname() != "juseless":
 configure_logging(level="DEBUG")
 
 
-def test_juselessdataladixivbm_datagrabber() -> None:
+def test_JuselessDataladIXIVBM() -> None:
-    """Test datalad IXIVBM datagrabber."""
+    """Test JuselessDataladIXIVBM."""
     with JuselessDataladIXIVBM() as dg:
         all_elements = dg.get_elements()
         test_element = all_elements[0]
@@ -33,8 +33,8 @@ def test_juselessdataladixivbm_datagrabber() -> None:
         assert out["VBM_GM"]["path"].exists()
 
 
-def test_juselessdataladixivbm_datagrabber_invalid_site() -> None:
+def test_JuselessDataladIXIVBM_invalid_site() -> None:
-    """Test datalad IXIVBM datagrabber with invalid site."""
+    """Test JuselessDataladIXIVBM with invalid site."""
     with pytest.raises(ValueError, match="notavalidsite not a valid site"):
         with JuselessDataladIXIVBM(sites="notavalidsite"):
             pass

junifer/configs/juseless/datagrabbers/tests/test_ucla.py

@@ -1,4 +1,4 @@
-"""Provide tests for UCLA juseless datagrabber."""
+"""Provide tests for JuselessUCLA."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
@@ -21,8 +21,8 @@ if socket.gethostname() != "juseless":
 configure_logging(level="DEBUG")
 
 
-def test_juseless_ucla_datagrabber() -> None:
+def test_JuselessUCLA() -> None:
-    """Test juseless ucla datagrabber."""
+    """Test JuselessUCLA."""
     with JuselessUCLA() as dg:
         all_elements = dg.get_elements()
         test_element = all_elements[0]
@@ -46,8 +46,8 @@ def test_juseless_ucla_datagrabber() -> None:
     "tasks",
     [None, "rest", ["rest", "stopsignal"]],
 )
-def test_juseless_ucla_datagrabber_task_params(tasks: Optional[str]) -> None:
+def test_JuselessUCLA_task_params(tasks: Optional[str]) -> None:
-    """Test juseless ucla datagrabber with different task parameters.
+    """Test JuselessUCLA with different task parameters.
 
     Parameters
     ----------
@@ -81,8 +81,8 @@ def test_juseless_ucla_datagrabber_task_params(tasks: Optional[str]) -> None:
                 assert el[1] in ["rest", "stopsignal"]
 
 
-def test_juseless_ucla_datagrabber_invalid_tasks() -> None:
+def test_JuselessUCLA_invalid_tasks() -> None:
-    """Test juseless ucla datagrabber with invalid task parameters."""
+    """Test JuselessUCLA with invalid task parameters."""
     with pytest.raises(
         ValueError, match="invalid is not a valid task in the UCLA"
     ):

junifer/configs/juseless/datagrabbers/tests/test_ukb_vbm.py

@@ -1,4 +1,4 @@
-"""Provide tests for juseless datagrabber."""
+"""Provide tests for JuselessDataladUKBVBM."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
@@ -20,8 +20,8 @@ if socket.gethostname() != "juseless":
 configure_logging(level="DEBUG")
 
 
-def test_juselessdataladukbvbm_datagrabber() -> None:
+def test_JuselessDataladUKBVBM() -> None:
-    """Test datalad UKBVBM datagrabber."""
+    """Test JuselessDataladUKBVBM."""
     with JuselessDataladUKBVBM() as dg:
         all_elements = dg.get_elements()
         test_element = all_elements[0]

junifer/configs/juseless/datagrabbers/ucla.py

@@ -1,4 +1,4 @@
-"""Provide a concrete implementation for UCLA dataset."""
+"""Provide concrete implementation for UCLA DataGrabber."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
@@ -14,16 +14,18 @@ from ....utils import raise_error
 
 @register_datagrabber
 class JuselessUCLA(PatternDataGrabber):
-    """Concrete implementation for pattern-based data fetching of UCLA data.
+    """Concrete implementation for Juseless UCLA data fetching.
+
+    Implements a DataGrabber to access the UCLA data in Juseless.
 
     Parameters
     ----------
-    datadir : str or Path, optional
+    datadir : str or pathlib.Path, optional
         The directory where the dataset is stored
-        (default '/data/project/psychosis_thalamus/data/fmriprep').
+        (default "/data/project/psychosis_thalamus/data/fmriprep").
     tasks : {"rest", "bart", "bht", "pamenc", "pamret", \
             "scap", "taskswitch", "stopsignal"} or \
-            list of the options, optional
+            list of the options or None, optional
         UCLA task sessions. If None, all available task sessions are
         selected (default None).
 
@@ -118,5 +120,6 @@ class JuselessUCLA(PatternDataGrabber):
         elements : list
             The list of elements that can be grabbed in the dataset after
             imposing constraints based on specified tasks.
+
         """
         return [x for x in super().get_elements() if x[1] in self.tasks]

junifer/configs/juseless/datagrabbers/ukb_vbm.py

@@ -1,4 +1,4 @@
-"""Provide class for juseless datalad datagrabber."""
+"""Provide concrete implementation for UKB VBM DataGrabber."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
@@ -14,13 +14,13 @@ from ....datagrabber import PatternDataladDataGrabber
 
 @register_datagrabber
 class JuselessDataladUKBVBM(PatternDataladDataGrabber):
-    """Juseless UKB VBM Data Grabber class.
+    """Concrete implementation for Juseless UKB VBM data fetching.
 
-    Implements a Data Grabber to access the UKB VBM data in Juseless.
+    Implements a DataGrabber to access the UKB VBM data in Juseless.
 
     Parameters
     ----------
-    datadir : str or pathlib.Path, optional
+    datadir : str or pathlib.Path or None, optional
         The directory where the datalad dataset will be cloned. If None,
         the datalad dataset will be cloned into a temporary directory
         (default None).

junifer/configs/tests/test_juseless.py

@@ -1,32 +0,0 @@
-"""Provide tests for juseless datagrabber."""
-
-# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
-#          Leonard Sasse <l.sasse@fz-juelich.de>
-#          Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
-
-import socket
-
-import pytest
-
-from junifer.datagrabber.hcp import DataladHCP1200
-from junifer.utils.logging import configure_logging
-
-
-# Check if the test is running on juseless
-if socket.gethostname() != "juseless":
-    pytest.skip("These tests are only for juseless", allow_module_level=True)
-
-configure_logging(level="DEBUG")
-
-
-def test_juselessdataladhcp_datagrabber() -> None:
-    """Test datalad HCP datagrabber."""
-    with DataladHCP1200() as dg:
-        all_elements = dg.get_elements()
-        test_element = all_elements[0]
-
-        out = dg[test_element]
-
-        assert out["BOLD"]["path"].exists()
-        assert out["BOLD"]["path"].isfile()

junifer/datagrabber/__init__.py

@@ -2,6 +2,7 @@
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
 
@@ -12,5 +13,5 @@ from .pattern import PatternDataGrabber
 from .pattern_datalad import PatternDataladDataGrabber
 
 from .aomic import DataladAOMICID1000, DataladAOMICPIOP1, DataladAOMICPIOP2
-from .hcp import HCP1200, DataladHCP1200
+from .hcp1200 import HCP1200, DataladHCP1200
 from .multiple import MultipleDataGrabber

junifer/datagrabber/aomic/__init__.py

@@ -1,4 +1,4 @@
-"""Provide imports for datagrabber 'aomic' sub-package."""
+"""Provide imports for aomic sub-package."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>

junifer/datagrabber/aomic/id1000.py

@@ -1,4 +1,4 @@
-"""Provide concrete implementations for AOMIC1000 data access."""
+"""Provide concrete implementation for AOMIC ID1000 DataGrabber."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Vera Komeyer <v.komeyer@fz-juelich.de>
@@ -9,21 +9,21 @@
 from pathlib import Path
 from typing import Dict, Union
 
-from junifer.datagrabber import PatternDataladDataGrabber
-
 from ...api.decorators import register_datagrabber
+from ..pattern_datalad import PatternDataladDataGrabber
 
 
 @register_datagrabber
 class DataladAOMICID1000(PatternDataladDataGrabber):
-    """Concrete implementation for pattern-based data fetching of AOMICID1000.
+    """Concrete implementation for datalad-based data fetching of AOMIC ID1000.
 
     Parameters
     ----------
-    datadir : str or Path, optional
+    datadir : str or Path or None, optional
         The directory where the datalad dataset will be cloned. If None,
         the datalad dataset will be cloned into a temporary directory
         (default None).
+
     """
 
     def __init__(
@@ -115,6 +115,7 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
         out : dict
             Dictionary of paths for each type of data required for the
             specified element.
+
         """
         out = super().get_item(subject=subject)
         out["BOLD"]["mask_item"] = "BOLD_mask"

junifer/datagrabber/aomic/piop1.py

@@ -1,4 +1,4 @@
-"""Provide concrete implementations for AOMICPIOP1 data access."""
+"""Provide concrete implementation for AOMIC PIOP1 DataGrabber."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Vera Komeyer <v.komeyer@fz-juelich.de>
@@ -10,19 +10,18 @@ from itertools import product
 from pathlib import Path
 from typing import Dict, List, Union
 
-from junifer.datagrabber import PatternDataladDataGrabber
-
 from ...api.decorators import register_datagrabber
 from ...utils import raise_error
+from ..pattern_datalad import PatternDataladDataGrabber
 
 
 @register_datagrabber
 class DataladAOMICPIOP1(PatternDataladDataGrabber):
-    """Concrete implementation for pattern-based data fetching of AOMICPIOP1.
+    """Concrete implementation for pattern-based data fetching of AOMIC PIOP1.
 
     Parameters
     ----------
-    datadir : str or Path, optional
+    datadir : str or Path or None, optional
         The directory where the datalad dataset will be cloned. If None,
         the datalad dataset will be cloned into a temporary directory
         (default None).
@@ -30,6 +29,7 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
             "gstroop", "workingmemory"} or list of the options, optional
         AOMIC PIOP1 task sessions. If None, all available task sessions are
         selected (default None).
+
     """
 
     def __init__(
@@ -147,6 +147,7 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
         out : dict
             Dictionary of paths for each type of data required for the
             specified element.
+
         """
 
         task_acqs = {

junifer/datagrabber/aomic/piop2.py

@@ -1,4 +1,4 @@
-"""Provide concrete implementations for AOMICPIOP2 data access."""
+"""Provide concrete implementation for AOMIC PIOP2 DataGrabber."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Vera Komeyer <v.komeyer@fz-juelich.de>
@@ -9,19 +9,18 @@
 from pathlib import Path
 from typing import Dict, List, Union
 
-from junifer.datagrabber import PatternDataladDataGrabber
-
 from ...api.decorators import register_datagrabber
 from ...utils import raise_error
+from ..pattern_datalad import PatternDataladDataGrabber
 
 
 @register_datagrabber
 class DataladAOMICPIOP2(PatternDataladDataGrabber):
-    """Concrete implementation for pattern-based data fetching of AOMICPIOP2.
+    """Concrete implementation for pattern-based data fetching of AOMIC PIOP2.
 
     Parameters
     ----------
-    datadir : str or Path, optional
+    datadir : str or Path or None, optional
         The directory where the datalad dataset will be cloned. If None,
         the datalad dataset will be cloned into a temporary directory
         (default None).
@@ -29,6 +28,7 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
             or list of the options, optional
         AOMIC PIOP2 task sessions. If None, all available task sessions are
         selected (default None).
+
     """
 
     def __init__(
@@ -136,6 +136,7 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
         list
             The list of elements that can be grabbed in the dataset after
             imposing constraints based on specified tasks.
+
         """
         all_elements = super().get_elements()
         return [x for x in all_elements if x[1] in self.tasks]
@@ -156,6 +157,7 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
         out : dict
             Dictionary of paths for each type of data required for the
             specified element.
+
         """
         out = super().get_item(subject=subject, task=task)
         out["BOLD"]["mask_item"] = "BOLD_mask"

junifer/datagrabber/aomic/tests/test_id1000.py

@@ -1,4 +1,4 @@
-"""Provide tests for aomicid1000."""
+"""Provide tests for DataladAOMICID1000 DataGrabber."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Vera Komeyer <v.komeyer@fz-juelich.de>
@@ -6,12 +6,12 @@
 #          Leonard Sasse <l.sasse@fz-juelich.de>
 # License: AGPL
 
-from junifer.datagrabber.aomic.id1000 import DataladAOMICID1000
+from junifer.datagrabber import DataladAOMICID1000
 from junifer.utils import configure_logging
 
 
-def test_aomic1000_datagrabber() -> None:
+def test_DataladAOMICID1000() -> None:
-    """Test datalad AOMIC1000 datagrabber."""
+    """Test DataladAOMICID1000 DataGrabber."""
 
     uri_ID1000 = "https://gin.g-node.org/juaml/datalad-example-aomic1000"
     configure_logging(level="DEBUG")

junifer/datagrabber/aomic/tests/test_piop1.py

@@ -1,4 +1,4 @@
-"""Provide tests for aomic piop1."""
+"""Provide tests for DataladAOMICPIOP1 DataGrabber."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Vera Komeyer <v.komeyer@fz-juelich.de>
@@ -8,12 +8,12 @@
 
 import pytest
 
-from junifer.datagrabber.aomic.piop1 import DataladAOMICPIOP1
+from junifer.datagrabber import DataladAOMICPIOP1
 from junifer.utils import configure_logging
 
 
-def test_aomic_piop1_datagrabber() -> None:
+def test_DataladAOMICPIOP1() -> None:
-    """Test datalad AOMICPIOP1 datagrabber."""
+    """Test DataladAOMICPIOP1 DataGrabber."""
     configure_logging(level="DEBUG")
 
     uri_PIOP1 = "https://gin.g-node.org/juaml/datalad-example-aomicpiop1"
@@ -138,7 +138,7 @@ def test_aomic_piop1_datagrabber() -> None:
             assert sub == meta["element"]["subject"]
 
 
-def test_piop1_invalid_tasks():
+def test_DataladAOMICPIOP1_invalid_tasks():
     """Test whether invalid task fails."""
     with pytest.raises(
         ValueError,

junifer/datagrabber/aomic/tests/test_piop2.py

@@ -1,4 +1,4 @@
-"""Provide tests for aomic piop2."""
+"""Provide tests DataladAOMICPIOP2 DataGrabber."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Vera Komeyer <v.komeyer@fz-juelich.de>
@@ -8,12 +8,12 @@
 
 import pytest
 
-from junifer.datagrabber.aomic import DataladAOMICPIOP2
+from junifer.datagrabber import DataladAOMICPIOP2
 from junifer.utils import configure_logging
 
 
-def test_aomic_piop2_datagrabber() -> None:
+def test_DataladAOMICPIOP2() -> None:
-    """Test datalad AOMICPIOP2 datagrabber."""
+    """Test DataladAOMICPIOP2 DataGrabber."""
     configure_logging(level="DEBUG")
 
     uri_PIOP2 = "https://gin.g-node.org/juaml/datalad-example-aomicpiop2"
@@ -132,7 +132,7 @@ def test_aomic_piop2_datagrabber() -> None:
             assert sub == meta["element"]["subject"]
 
 
-def test_piop2_invalid_tasks():
+def test_DataladAOMICPIOP2_invalid_tasks():
     """Test whether invalid task fails."""
     with pytest.raises(
         ValueError,

junifer/datagrabber/base.py

@@ -1,4 +1,4 @@
-"""Provide abstract base class for datagrabber."""
+"""Provide abstract base class for DataGrabber."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
@@ -15,7 +15,7 @@ from .utils import validate_types
 
 
 class BaseDataGrabber(ABC, UpdateMetaMixin):
-    """Abstract base class for datagrabber.
+    """Abstract base class for DataGrabber.
 
     For every interface that is required, one needs to provide a concrete
     implementation of this abstract class.
@@ -31,6 +31,7 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
     ----------
     datadir : pathlib.Path
         The directory where the data is / will be stored.
+
     """
 
     def __init__(self, types: List[str], datadir: Union[str, Path]) -> None:
@@ -52,7 +53,7 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
         Yields
         ------
         object
-            An element that can be indexed by the datagrabber.
+            An element that can be indexed by the DataGrabber.
 
         """
         for elem in self.get_elements():
@@ -126,7 +127,7 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
 
         Returns
         -------
-        str
+        list of str
             The element keys.
 
         """
@@ -144,7 +145,7 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
         list
             List of elements that can be grabbed. The elements can be strings,
             tuples or any object that will be then used as a key to index the
-            datagrabber.
+            DataGrabber.
 
         """
         raise_error(

junifer/datagrabber/datalad_base.py

@@ -1,4 +1,4 @@
-"""Provide abstract base class for datalad datagrabber."""
+"""Provide abstract base class for datalad-based DataGrabber."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
@@ -24,20 +24,20 @@ from .base import BaseDataGrabber
 
 @register_datagrabber
 class DataladDataGrabber(BaseDataGrabber):
-    """Abstract base class for data fetching via Datalad.
+    """Abstract base class for datalad-based data fetching.
 
-    Defines a Data Grabber that gets data from a datalad sibling.
+    Defines a DataGrabber that gets data from a datalad sibling.
 
     Parameters
     ----------
-    rootdir : str or Path, optional
+    rootdir : str or pathlib.Path, optional
         The path within the datalad dataset to the root directory
         (default ".").
-    datadir : str or Path, optional
+    datadir : str or pathlib.Path or None, optional
         That directory where the datalad dataset will be cloned. If None,
         the datalad dataset will be cloned into a temporary directory
         (default None).
-    uri : str, optional
+    uri : str or None, optional
         URI of the datalad sibling (default None).
     **kwargs
         Keyword arguments passed to superclass.
@@ -45,23 +45,26 @@ class DataladDataGrabber(BaseDataGrabber):
     Methods
     -------
     install:
-        Installs (clones) the datalad dataset into the `datadir`. This method
+        Installs (clones) the datalad dataset into the ``datadir``. This method
         is called automatically when the datagrabber is used within a context.
     remove:
-        Removes the datalad dataset from the `datadir`. This method is called
+        Removes the datalad dataset from the ``datadir``. This method is called
         automatically when the datagrabber is used within a context.
 
     See Also
     --------
-    BaseDataGrabber
+    BaseDataGrabber:
-        For the abstract base class of any datagrabber.
+        Abstract base class for DataGrabber.
+    PatternDataGrabber:
+        Concrete implementation for pattern-based data fetching.
+    PatternDataladDataGrabber:
+        Concrete implementation for pattern and datalad based data fetching.
 
     Notes
     -----
-    By itself, this class is still abstract as the `__getitem__` method relies
+    This class is intended to be used as a superclass of a subclass
-    on the parent class `BaseDataGrabber.__getitem__` which is not yet
-    implemented. This class is intended to be used as a superclass of a class
     with multiple inheritance.
+
     """
 
     def __init__(
@@ -129,16 +132,23 @@ class DataladDataGrabber(BaseDataGrabber):
 
     @property
     def datadir(self) -> Path:
-        """Get data directory path."""
+        """Get data directory path.
+
+        Returns
+        -------
+        pathlib.Path
+            Path to the data directory.
+
+        """
         return super().datadir / self._rootdir
 
     def _get_dataset_id_remote(self) -> str:
-        """Get the dataset id from the remote.
+        """Get the dataset ID from the remote.
 
         Returns
         -------
         str
-            The dataset id.
+            The dataset ID.
 
         """
         remote_id = None
@@ -155,7 +165,7 @@ class DataladDataGrabber(BaseDataGrabber):
         return remote_id
 
     def _dataset_get(self, out: Dict) -> Dict:
-        """Get the dataset found from the path in `out`.
+        """Get the dataset found from the path in ``out``.
 
         Parameters
         ----------
@@ -165,7 +175,7 @@ class DataladDataGrabber(BaseDataGrabber):
         Returns
         -------
         dict
-            The modified dictionary with meta updated.
+            The unmodified input dictionary.
 
         """
         to_get = [v["path"] for v in out.values() if "path" in v]
@@ -197,12 +207,13 @@ class DataladDataGrabber(BaseDataGrabber):
         return out
 
     def install(self) -> None:
-        """Install the datalad dataset into the datadir.
+        """Install the datalad dataset into the ``datadir``.
 
         Raises
         ------
         ValueError
             If the dataset is already installed but with a different ID.
+
         """
         isinstalled = dl.Dataset(self._datadir).is_installed()
         if isinstalled:
@@ -256,9 +267,7 @@ class DataladDataGrabber(BaseDataGrabber):
         """Implement single element indexing in the Datalad database.
 
         It will first obtain the paths from the parent class and then
-        `datalad get` each of the files.
+        ``datalad get`` each of the files.
-
-        This method only works with multiple inheritance.
 
         Parameters
         ----------
@@ -279,12 +288,12 @@ class DataladDataGrabber(BaseDataGrabber):
         out = self._dataset_get(out)
         return out
 
-    def __enter__(self):
+    def __enter__(self) -> "DataladDataGrabber":
         """Implement context entry."""
         self.install()
         return self
 
-    def __exit__(self, exc_type, exc_value, exc_traceback):
+    def __exit__(self, exc_type, exc_value, exc_traceback) -> None:
         """Implement context exit."""
         logger.debug("Cleaning up dataset")
         self.cleanup()

junifer/datagrabber/hcp1200/__init__.py

@@ -0,0 +1,7 @@
+"""Provide imports for hcp1200 sub-package."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from .hcp1200 import HCP1200
+from .datalad_hcp1200 import DataladHCP1200

junifer/datagrabber/hcp1200/datalad_hcp1200.py

@@ -0,0 +1,68 @@
+"""Provide concrete implementation for datalad-based HCP1200 DataGrabber."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Leonard Sasse <l.sasse@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from pathlib import Path
+from typing import List, Union
+
+from junifer.datagrabber.datalad_base import DataladDataGrabber
+
+from ...api.decorators import register_datagrabber
+from .hcp1200 import HCP1200
+
+
+@register_datagrabber
+class DataladHCP1200(DataladDataGrabber, HCP1200):
+    """Concrete implementation for datalad-based data fetching of HCP1200.
+
+    Parameters
+    ----------
+    datadir : str or Path or None, optional
+        The directory where the datalad dataset will be cloned. If None,
+        the datalad dataset will be cloned into a temporary directory
+        (default None).
+    tasks : {"REST1", "REST2", "SOCIAL", "WM", "RELATIONAL", "EMOTION", \
+            "LANGUAGE", "GAMBLING", "MOTOR"} or list of the options or None \
+            , optional
+        HCP task sessions. If None, all available task sessions are selected
+        (default None).
+    phase_encodings : {"LR", "RL"} or list of the options or None, optional
+        HCP phase encoding directions. If None, both will be used
+        (default None).
+    ica_fix : bool, optional
+        Whether to retrieve data that was processed with ICA+FIX.
+        Only "REST1" and "REST2" tasks are available with ICA+FIX (default
+        False).
+
+    """
+
+    def __init__(
+        self,
+        datadir: Union[str, Path, None] = None,
+        tasks: Union[str, List[str], None] = None,
+        phase_encodings: Union[str, List[str], None] = None,
+        ica_fix: bool = False,
+    ) -> None:
+        uri = (
+            "https://github.com/datalad-datasets/"
+            "human-connectome-project-openaccess.git"
+        )
+        rootdir = "HCP1200"
+        super().__init__(
+            datadir=datadir,
+            tasks=tasks,
+            phase_encodings=phase_encodings,
+            uri=uri,
+            rootdir=rootdir,
+            ica_fix=ica_fix,
+        )
+
+    # Needed here as HCP1200's subjects are sub-datasets, so will not be
+    # found when elements are checked.
+    @property
+    def skip_file_check(self) -> bool:
+        """Skip file check existence."""
+        return True

junifer/datagrabber/hcp1200/hcp1200.py

@@ -1,14 +1,17 @@
-"""Provide concrete implementations for HCP data access."""
+"""Provide concrete implementation for pattern-based HCP1200 DataGrabber."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Leonard Sasse <l.sasse@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
 
 from itertools import product
 from pathlib import Path
 from typing import Dict, List, Union
 
-from junifer.datagrabber.datalad_base import DataladDataGrabber
+from ...api.decorators import register_datagrabber
-
+from ..pattern import PatternDataGrabber
-from ..api.decorators import register_datagrabber
 from ..utils import raise_error
-from .pattern import PatternDataGrabber
 
 
 @register_datagrabber
@@ -18,20 +21,22 @@ class HCP1200(PatternDataGrabber):
     Parameters
     ----------
     datadir : str or Path, optional
-        The directory where the datalad dataset will be cloned.
+        The directory where the data is / will be stored.
     tasks : {"REST1", "REST2", "SOCIAL", "WM", "RELATIONAL", "EMOTION", \
-            "LANGUAGE", "GAMBLING", "MOTOR"} or list of the options, optional
+            "LANGUAGE", "GAMBLING", "MOTOR"} or list of the options or None \
+            , optional
         HCP task sessions. If None, all available task sessions are selected
         (default None).
-    phase_encodings : {"LR", "RL"} or list of the options, optional
+    phase_encodings : {"LR", "RL"} or list of the options or None, optional
         HCP phase encoding directions. If None, both will be used
         (default None).
     ica_fix : bool, optional
         Whether to retrieve data that was processed with ICA+FIX.
-        Only 'REST1' and 'REST2' tasks are available with ICA+FIX (default
+        Only "REST1" and "REST2" tasks are available with ICA+FIX (default
         False).
     **kwargs
         Keyword arguments passed to superclass.
+
     """
 
     def __init__(
@@ -114,7 +119,7 @@ class HCP1200(PatternDataGrabber):
         self.phase_encodings = phase_encodings
 
     def get_item(self, subject: str, task: str, phase_encoding: str) -> Dict:
-        """Index one element in the dataset.
+        """Implement single element indexing in the database.
 
         Parameters
         ----------
@@ -128,8 +133,8 @@ class HCP1200(PatternDataGrabber):
 
         Returns
         -------
-        out : dict
+        dict
-            Dictionary of paths for each type of data required for the
+            Dictionary of dictionaries for each type of data required for the
             specified element.
 
         """
@@ -150,7 +155,7 @@ class HCP1200(PatternDataGrabber):
         Returns
         -------
         list
-            The list of elements in the dataset.
+            The list of elements that can be grabbed in the dataset.
 
         """
         subjects = [
@@ -165,53 +170,3 @@ class HCP1200(PatternDataGrabber):
             elems.append((subject, task, phase_encoding))
 
         return elems
-
-
-@register_datagrabber
-class DataladHCP1200(DataladDataGrabber, HCP1200):
-    """Concrete implementation for datalad-based data fetching of HCP1200.
-
-    Parameters
-    ----------
-    datadir : str or Path, optional
-        The directory where the datalad dataset will be cloned. If None,
-        the datalad dataset will be cloned into a temporary directory
-        (default None).
-    tasks : {"REST1", "REST2", "SOCIAL", "WM", "RELATIONAL", "EMOTION", \
-            "LANGUAGE", "GAMBLING", "MOTOR"} or list of the options, optional
-        HCP task sessions. If None, all available task sessions are selected
-        (default None).
-    phase_encodings : {"LR", "RL"} or list of the options, optional
-        HCP phase encoding directions. If None, both will be used
-        (default None).
-    ica_fix : bool, optional
-        Whether to retrieve data that was processed with ICA+FIX.
-        Only 'REST1' and 'REST2' tasks are available with ICA+FIX (default
-        False).
-    """
-
-    def __init__(
-        self,
-        datadir: Union[str, Path, None] = None,
-        tasks: Union[str, List[str], None] = None,
-        phase_encodings: Union[str, List[str], None] = None,
-        ica_fix: bool = False,
-    ) -> None:
-        uri = (
-            "https://github.com/datalad-datasets/"
-            "human-connectome-project-openaccess.git"
-        )
-        rootdir = "HCP1200"
-        super().__init__(
-            datadir=datadir,
-            tasks=tasks,
-            phase_encodings=phase_encodings,
-            uri=uri,
-            rootdir=rootdir,
-            ica_fix=ica_fix,
-        )
-
-    @property
-    def skip_file_check(self) -> bool:
-        """Skip file check existence."""
-        return True

junifer/datagrabber/hcp1200/tests/test_hcp1200.py

@@ -7,7 +7,7 @@ from typing import Iterable, Optional
 
 import pytest
 
-from junifer.datagrabber.hcp import HCP1200, DataladHCP1200
+from junifer.datagrabber import HCP1200, DataladHCP1200
 from junifer.utils import configure_logging
 
 
@@ -16,7 +16,7 @@ URI = "https://gin.g-node.org/juaml/datalad-example-hcp1200"
 
 @pytest.fixture(scope="module")
 def hcpdg() -> Iterable[DataladHCP1200]:
-    """Return a HCP1200 datagrabber."""
+    """Return a HCP1200 DataGrabber."""
     dg = DataladHCP1200()
     # Set URI to Gin
     dg.uri = URI
@@ -56,19 +56,19 @@ def hcpdg() -> Iterable[DataladHCP1200]:
         ("REST2", "RL", True, "rfMRI_REST2_RL_hp2000_clean.nii.gz"),
     ],
 )
-def test_hcp1200_datagrabber(
+def test_HCP1200(
     hcpdg: DataladHCP1200,
     tasks: Optional[str],
     phase_encodings: Optional[str],
     ica_fix: bool,
     expected_path_name: str,
 ) -> None:
-    """Test HCP1200 datagrabber.
+    """Test HCP1200 DataGrabber.
 
     Parameters
     ----------
     hcpdg : DataladHCP1200
-        The Datalad version of the datagrabber with the first subject
+        The Datalad version of the DataGrabber with the first subject
         already cloned.
     tasks : str
         The parametrized tasks.
@@ -132,17 +132,17 @@ def test_hcp1200_datagrabber(
         ("MOTOR", "RL"),
     ],
 )
-def test_hcp1200_datagrabber_single_access(
+def test_HCP1200_single_access(
     hcpdg: DataladHCP1200,
     tasks: Optional[str],
     phase_encodings: Optional[str],
 ) -> None:
-    """Test HCP1200 datagrabber single access.
+    """Test HCP1200 DataGrabber single access.
 
     Parameters
     ----------
     hcpdg : DataladHCP1200
-        The Datalad version of the datagrabber with the first subject
+        The Datalad version of the DataGrabber with the first subject
         already cloned.
     tasks : str
         The parametrized tasks.
@@ -172,17 +172,17 @@ def test_hcp1200_datagrabber_single_access(
         (["REST1", "REST2"], None),
     ],
 )
-def test_hcp1200_datagrabber_multi_access(
+def test_HCP1200_multi_access(
     hcpdg: DataladHCP1200,
     tasks: Optional[str],
     phase_encodings: Optional[str],
 ) -> None:
-    """Test HCP1200 datagrabber multiple access.
+    """Test HCP1200 DataGrabber multiple access.
 
     Parameters
     ----------
     hcpdg : DataladHCP1200
-        The Datalad version of the datagrabber with the first subject
+        The Datalad version of the DataGrabber with the first subject
         already cloned.
     tasks : str
         The parametrized tasks.
@@ -205,16 +205,17 @@ def test_hcp1200_datagrabber_multi_access(
             assert element[2] in ["LR", "RL"]
 
 
-def test_hcp1200_datagrabber_multi_access_task_simple(
+def test_HCP1200_multi_access_task_simple(
     hcpdg: DataladHCP1200,
 ) -> None:
-    """Test HCP1200 datagrabber simple multiple access for task.
+    """Test HCP1200 DataGrabber simple multiple access for task.
 
     Parameters
     ----------
     hcpdg : DataladHCP1200
-        The Datalad version of the datagrabber with the first subject
+        The Datalad version of the DataGrabber with the first subject
         already cloned.
+
     """
     configure_logging(level="DEBUG")
     dg = HCP1200(
@@ -231,16 +232,17 @@ def test_hcp1200_datagrabber_multi_access_task_simple(
             assert element[2] in ["LR", "RL"]
 
 
-def test_hcp1200_datagrabber_multi_access_phase_simple(
+def test_HCP1200_multi_access_phase_simple(
     hcpdg: DataladHCP1200,
 ) -> None:
-    """Test HCP1200 datagrabber simple multiple access for phase.
+    """Test HCP1200 DataGrabber simple multiple access for phase.
 
     Parameters
     ----------
     hcpdg : DataladHCP1200
-        The Datalad version of the datagrabber with the first subject
+        The Datalad version of the DataGrabber with the first subject
         already cloned.
+
     """
     configure_logging(level="DEBUG")
     dg = HCP1200(
@@ -266,11 +268,11 @@ def test_hcp1200_datagrabber_multi_access_phase_simple(
         (["FOO", "BAR"], "LR"),
     ],
 )
-def test_hcp1200_datagrabber_incorrect_access_task(
+def test_HCP1200_incorrect_access_task(
     tasks: Optional[str],
     phase_encodings: Optional[str],
 ) -> None:
-    """Test HCP1200 datagrabber incorrect access for task.
+    """Test HCP1200 DataGrabber incorrect access for task.
 
     Parameters
     ----------
@@ -298,11 +300,11 @@ def test_hcp1200_datagrabber_incorrect_access_task(
         (["REST1", "REST2"], "BAR"),
     ],
 )
-def test_hcp1200_datagrabber_incorrect_access_phase(
+def test_HCP1200_incorrect_access_phase(
     tasks: Optional[str],
     phase_encodings: Optional[str],
 ) -> None:
-    """Test HCP1200 datagrabber incorrect access for phase.
+    """Test HCP1200 DataGrabber incorrect access for phase.
 
     Parameters
     ----------
@@ -321,16 +323,17 @@ def test_hcp1200_datagrabber_incorrect_access_phase(
         )
 
 
-def test_hcp1200_datagrabber_elements(
+def test_HCP1200_elements(
     hcpdg: DataladHCP1200,
 ) -> None:
-    """Test HCP1200 datagrabber elements.
+    """Test HCP1200 DataGrabber elements.
 
     Parameters
     ----------
     hcpdg : DataladHCP1200
-        The Datalad version of the datagrabber with the first subject
+        The Datalad version of the DataGrabber with the first subject
         already cloned.
+
     """
     configure_logging(level="DEBUG")
     dg = HCP1200(
@@ -364,10 +367,10 @@ def test_hcp1200_datagrabber_elements(
         ("MOTOR", True),
     ],
 )
-def test_hcp1200_datagrabber_incorrect_access_icafix(
+def test_HCP1200_incorrect_access_icafix(
     tasks: Optional[str], ica_fix: bool
 ) -> None:
-    """Test HCP1200 datagrabber incorrect access for icafix.
+    """Test HCP1200 DataGrabber incorrect access for icafix.
 
     Parameters
     ----------

junifer/datagrabber/multiple.py

@@ -1,4 +1,4 @@
-"""Provide abstract base class for multiple source datagrabber."""
+"""Provide concrete implementation for multi sourced DataGrabber."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
@@ -7,21 +7,23 @@
 
 from typing import Dict, List, Tuple, Union
 
+from ..utils import raise_error
 from .base import BaseDataGrabber
 
 
 class MultipleDataGrabber(BaseDataGrabber):
-    """Data Grabber class for data fetching from multiple sources.
+    """Concrete implementation for multi sourced data fetching.
 
-    Defines a Data Grabber which can be used to fetch data from multiple
+    Implements a DataGrabber which can be used to fetch data from multiple
-    datagrabbers.
+    DataGrabbers.
 
     Parameters
     ----------
-    datagrabbers : list of datagrabber-like objects
+    datagrabbers : list of DataGrabber-like objects
-        The datagrabbers to use to fetch data using.
+        The DataGrabbers to use for fetching data.
     **kwargs
         Keyword arguments passed to superclass.
+
     """
 
     def __init__(self, datagrabbers: List[BaseDataGrabber], **kwargs) -> None:
@@ -30,11 +32,11 @@ class MultipleDataGrabber(BaseDataGrabber):
         first_keys = datagrabbers[0].get_element_keys()
         for dg in datagrabbers[1:]:
             if dg.get_element_keys() != first_keys:
-                raise ValueError("Datagrabbers have different element keys.")
+                raise_error("DataGrabbers have different element keys.")
         # 2) no overlapping types
         types = [x for dg in datagrabbers for x in dg.get_types()]
         if len(types) != len(set(types)):
-            raise ValueError("Datagrabbers have overlapping types.")
+            raise_error("DataGrabbers have overlapping types.")
         self._datagrabbers = datagrabbers
 
     def __getitem__(self, element: Union[str, Tuple]) -> Dict:
@@ -73,8 +75,64 @@ class MultipleDataGrabber(BaseDataGrabber):
             out[kind]["meta"]["datagrabber"]["datagrabbers"] = metas
         return out
 
-    def get_item(self, **element: Dict) -> Dict[str, Dict]:
+    def __enter__(self) -> "MultipleDataGrabber":
-        """Get item.
+        """Implement context entry."""
+        for dg in self._datagrabbers:
+            dg.__enter__()
+        return self
+
+    def __exit__(self, exc_type, exc_value, exc_traceback) -> None:
+        """Implement context exit."""
+        for dg in self._datagrabbers:
+            dg.__exit__(exc_type, exc_value, exc_traceback)
+
+    # TODO: return type should be List[List[str]], but base type is List[str]
+    def get_types(self) -> List[str]:
+        """Get types.
+
+        Returns
+        -------
+        list of list of str
+            The types of data to be grabbed.
+
+        """
+        types = [x for dg in self._datagrabbers for x in dg.get_types()]
+        return types
+
+    def get_element_keys(self) -> List[str]:
+        """Get element keys.
+
+        For each item in the ``element`` tuple passed to ``__getitem__()``,
+        this method returns the corresponding key(s).
+
+        Returns
+        -------
+        list of str
+            The element keys.
+
+        """
+        return self._datagrabbers[0].get_element_keys()
+
+    def get_elements(self) -> List:
+        """Get elements.
+
+        Returns
+        -------
+        list
+            List of elements that can be grabbed. The elements can be strings,
+            tuples or any object that will be then used as a key to index the
+            the DataGrabber. The element should be present in all of the
+            related DataGrabbers.
+
+        """
+        all_elements = [dg.get_elements() for dg in self._datagrabbers]
+        elements = set(all_elements[0])
+        for s in all_elements[1:]:
+            elements.intersection_update(s)
+        return list(elements)
+
+    def get_item(self, **_: Dict) -> Dict[str, Dict]:
+        """Get the specified item from the dataset.
 
         Parameters
         ----------
@@ -90,59 +148,12 @@ class MultipleDataGrabber(BaseDataGrabber):
         Notes
         -----
             This function is not implemented for this class as it is useless.
+
         """
-        raise NotImplementedError(
+        raise_error(
-            "get_item() is not useful for this class, hence not implemented."
+            msg=(
+                "get_item() is not useful for this class, hence not "
+                "implemented."
+            ),
+            klass=NotImplementedError,
         )
-
-    def __enter__(self) -> "BaseDataGrabber":
-        """Implement context entry."""
-        for dg in self._datagrabbers:
-            dg.__enter__()
-        return self
-
-    def __exit__(self, exc_type, exc_value, exc_traceback) -> None:
-        """Implement context exit."""
-        for dg in self._datagrabbers:
-            dg.__exit__(exc_type, exc_value, exc_traceback)
-
-    def get_elements(self) -> List:
-        """Get elements.
-
-        Returns
-        -------
-        list
-            The list of elements that can be grabbed in the dataset. It
-            corresponds to the elements that are present in all the
-            related datagrabbers.
-        """
-        all_elements = [dg.get_elements() for dg in self._datagrabbers]
-        elements = set(all_elements[0])
-        for s in all_elements[1:]:
-            elements.intersection_update(s)
-        return list(elements)
-
-    def get_element_keys(self) -> List[str]:
-        """Get element keys.
-
-        For each item in the ``element`` tuple passed to ``__getitem__()``,
-        this method returns the corresponding key(s).
-
-        Returns
-        -------
-        list of str
-            The element keys.
-        """
-        return self._datagrabbers[0].get_element_keys()
-
-    def get_types(self) -> List[str]:
-        """Get types.
-
-        Returns
-        -------
-        list of list of str
-            The types of data to be grabbed.
-
-        """
-        types = [x for dg in self._datagrabbers for x in dg.get_types()]
-        return types

junifer/datagrabber/pattern.py

@@ -1,4 +1,4 @@
-"""Provide concrete implementation for pattern-based datagrabber."""
+"""Provide concrete implementation for pattern-based DataGrabber."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
@@ -23,9 +23,9 @@ _CONFOUNDS_FORMATS = ("fmriprep", "adhoc")
 
 @register_datagrabber
 class PatternDataGrabber(BaseDataGrabber):
-    """Concrete implementation for data grabbing using patterns.
+    """Concrete implementation for pattern-based data fetching.
 
-    Implements a Data Grabber that understands patterns to grab data.
+    Implements a DataGrabber that understands patterns to grab data.
 
     Parameters
     ----------
@@ -34,12 +34,12 @@ class PatternDataGrabber(BaseDataGrabber):
     patterns : dict
         Patterns for each type of data as a dictionary. The keys are the types
         and the values are the patterns. Each occurrence of the string
-        `{subject}` in the pattern will be replaced by the indexed element.
+        ``{subject}`` in the pattern will be replaced by the indexed element.
-    replacements : list of str
+    replacements : str or list of str
         Replacements in the patterns for each item in the "element" tuple.
     datadir : str or pathlib.Path
         The directory where the data is / will be stored.
-    confounds_format : {"fmriprep", "adhoc"}, optional
+    confounds_format : {"fmriprep", "adhoc"} or None, optional
         The format of the confounds for the dataset (default None).
 
     """
@@ -83,7 +83,7 @@ class PatternDataGrabber(BaseDataGrabber):
     def _replace_patterns_regex(
         self, pattern: str
     ) -> Tuple[str, str, List[str]]:
-        """Replace the patterns in `pattern` with the named groups.
+        """Replace the patterns in ``pattern`` with the named groups.
 
         It allows elements to be obtained from the filesystem.
 
@@ -122,7 +122,7 @@ class PatternDataGrabber(BaseDataGrabber):
         return re_pattern, glob_pattern, t_replacements
 
     def _replace_patterns_glob(self, element: Dict, pattern: str) -> str:
-        """Replace patterns with the element so it can be globbed.
+        """Replace ``pattern`` with the ``element`` so it can be globbed.
 
         Parameters
         ----------
@@ -209,7 +209,7 @@ class PatternDataGrabber(BaseDataGrabber):
                     raise_error(
                         "`confounds_format` needs to be one of "
                         f"{_CONFOUNDS_FORMATS}, None provided. "
-                        "As the datagrabber used specifies "
+                        "As the DataGrabber used specifies "
                         "'BOLD_confounds', None is invalid."
                     )
                 # Set the format
@@ -228,6 +228,7 @@ class PatternDataGrabber(BaseDataGrabber):
         -------
         list
             The list of elements that can be grabbed in the dataset.
+
         """
         elements = None
 

junifer/datagrabber/pattern_datalad.py

@@ -1,4 +1,4 @@
-"""Provide base class for pattern-based datalad datagrabber."""
+"""Provide concrete implementation for pattern + datalad based DataGrabber."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
@@ -15,29 +15,29 @@ from .utils import validate_patterns
 
 @register_datagrabber
 class PatternDataladDataGrabber(DataladDataGrabber, PatternDataGrabber):
-    """Base class for pattern-based data fetching via Datalad.
+    """Concrete implementation for pattern and datalad based data fetching.
 
-    Defines a DataGrabber that gets data from a datalad sibling,
+    Implements a DataGrabber that gets data from a datalad sibling,
     interpreting patterns.
 
     Parameters
     ----------
     types : list of str
         The types of data to be grabbed.
-    patterns : dict, optional
+    patterns : dict
         Patterns for each type of data as a dictionary. The keys are the types
         and the values are the patterns. Each occurrence of the string
-        `{subject}` in the pattern will be replaced by the indexed element
+        ``{subject}`` in the pattern will be replaced by the indexed element.
-        (default None).
     **kwargs
         Keyword arguments passed to superclass.
 
     See Also
     --------
     DataladDataGrabber:
-        Base class for data fetching via Datalad.
+        Abstract base class for datalad-based data fetching.
     PatternDataGrabber:
-        Base class for pattern-based data fetching.
+        Concrete implementation for pattern-based data fetching.
+
     """
 
     def __init__(

junifer/datagrabber/tests/test_base.py

@@ -1,4 +1,4 @@
-"""Provide tests for base."""
+"""Provide tests for BaseDataGrabber."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
@@ -9,7 +9,7 @@ from pathlib import Path
 
 import pytest
 
-from junifer.datagrabber.base import BaseDataGrabber
+from junifer.datagrabber import BaseDataGrabber
 
 
 def test_BaseDataGrabber_abstractness() -> None:

junifer/datagrabber/tests/test_datalad_base.py

@@ -1,4 +1,4 @@
-"""Provide tests for datalad_base."""
+"""Provide tests for DataladDataGrabber."""
 
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
@@ -9,7 +9,7 @@ from typing import Type
 import datalad.api as dl
 import pytest
 
-from junifer.datagrabber.datalad_base import DataladDataGrabber
+from junifer.datagrabber import DataladDataGrabber
 
 
 _testing_dataset = {
@@ -26,20 +26,20 @@ _testing_dataset = {
 }
 
 
-def test_datalad_base_abstractness() -> None:
+def test_DataladDataGrabber_abstractness() -> None:
-    """Test datalad base is abstract."""
+    """Test DataladDataGrabber is abstract base class."""
     with pytest.raises(TypeError, match=r"abstract"):
         DataladDataGrabber()  # type: ignore
 
 
 @pytest.fixture
 def concrete_datagrabber() -> Type[DataladDataGrabber]:
-    """Return a concrete datagrabber class.
+    """Return a concrete datalad-based DataGrabber.
 
     Returns
     -------
     DataladDataGrabber
-        A concrete datagrabber class.
+        A concrete datalad-based DataGrabber.
 
     """
 
@@ -74,17 +74,18 @@ def concrete_datagrabber() -> Type[DataladDataGrabber]:
     return MyDataGrabber
 
 
-def test_datalad_install_errors(
+def test_DataladDataGrabber_install_errors(
     tmp_path: Path, concrete_datagrabber: Type
 ) -> None:
-    """Test datalad base install errors / warnings.
+    """Test DataladDataGrabber install errors / warnings.
 
     Parameters
     ----------
     tmp_path : pathlib.Path
         The path to the test directory.
     concrete_datagrabber : DataladDataGrabber
-        A concrete datagrabber class to use.
+        A concrete datalad-based DataGrabber class to use.
+
     """
 
     # Dataset cloned outside of datagrabber
@@ -112,17 +113,18 @@ def test_datalad_install_errors(
             pass
 
 
-def test_datalad_clone_cleanup(
+def test_DataladDataGrabber_clone_cleanup(
     tmp_path: Path, concrete_datagrabber: Type
 ) -> None:
-    """Test datalad base clone and remove.
+    """Test DataladDataGrabber clone and remove.
 
     Parameters
     ----------
     tmp_path : pathlib.Path
         The path to the test directory.
     concrete_datagrabber : DataladDataGrabber
-        A concrete datagrabber class to use.
+        A concrete datalad-based DataGrabber class to use.
+
     """
 
     # Clone whole dataset
@@ -160,13 +162,16 @@ def test_datalad_clone_cleanup(
     assert len(list(datadir.glob("*"))) == 0
 
 
-def test_datalad_clone_create_cleanup(concrete_datagrabber: Type) -> None:
+def test_DataladDataGrabber_clone_create_cleanup(
-    """Test datalad base tempdir clone and remove.
+    concrete_datagrabber: Type,
+) -> None:
+    """Test DataladDataGrabber tempdir clone and remove.
 
     Parameters
     ----------
     concrete_datagrabber : DataladDataGrabber
-        A concrete datagrabber class to use.
+        A concrete datalad-based DataGrabber class to use.
+
     """
 
     # Clone whole dataset
@@ -203,17 +208,18 @@ def test_datalad_clone_create_cleanup(concrete_datagrabber: Type) -> None:
     assert len(list(datadir.glob("*"))) == 0
 
 
-def test_datalad_previously_cloned(
+def test_DataladDataGrabber_previously_cloned(
     tmp_path: Path, concrete_datagrabber: Type
 ) -> None:
-    """Test datalad base on cloned dataset.
+    """Test DataladDataGrabber on cloned dataset.
 
     Parameters
     ----------
     tmp_path : pathlib.Path
         The path to the test directory.
     concrete_datagrabber : DataladDataGrabber
-        A concrete datagrabber class to use.
+        A concrete datalad-based DataGrabber class to use.
+
     """
 
     # Dataset cloned outside of datagrabber
@@ -271,17 +277,18 @@ def test_datalad_previously_cloned(
     assert len(list(datadir.glob("*"))) > 0
 
 
-def test_datalad_previously_cloned_and_get(
+def test_DataladDataGrabber_previously_cloned_and_get(
     tmp_path: Path, concrete_datagrabber: Type
 ) -> None:
-    """Test datalad base on cloned dataset with files present.
+    """Test DataladDataGrabber on cloned dataset with files present.
 
     Parameters
     ----------
     tmp_path : pathlib.Path
         The path to the test directory.
     concrete_datagrabber : DataladDataGrabber
-        A concrete datagrabber class to use.
+        A concrete datalad-based DataGrabber class to use.
+
     """
 
     # Dataset cloned outside of datagrabber with some files present
@@ -353,17 +360,18 @@ def test_datalad_previously_cloned_and_get(
     assert elem1_t1w.is_file() is True
 
 
-def test_datalad_previously_cloned_and_get_dirty(
+def test_DataladDataGrabber_previously_cloned_and_get_dirty(
     tmp_path: Path, concrete_datagrabber: Type
 ) -> None:
-    """Test datalad base on a dirty cloned dataset.
+    """Test DataladDataGrabber on a dirty cloned dataset.
 
     Parameters
     ----------
     tmp_path : pathlib.Path
         The path to the test directory.
     concrete_datagrabber : DataladDataGrabber
-        A concrete datagrabber class to use.
+        A concrete datalad-based DataGrabber class to use.
+
     """
 
     # Dataset cloned outside of datagrabber with some files present and dirty

junifer/datagrabber/tests/test_multiple.py

@@ -1,4 +1,4 @@
-"""Provide tests for multiple."""
+"""Provide tests for MultipleDataGrabber."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 # License: AGPL
@@ -20,8 +20,8 @@ _testing_dataset = {
 }
 
 
-def test_multiple() -> None:
+def test_MultipleDataGrabber() -> None:
-    """Test a multiple datagrabber."""
+    """Test MultipleDataGrabber."""
     repo_uri = _testing_dataset["example_bids_ses"]["uri"]
     rootdir = "example_bids_ses"
     replacements = ["subject", "session"]
@@ -77,8 +77,8 @@ def test_multiple() -> None:
         assert meta["datagrabbers"][1]["class"] == "PatternDataladDataGrabber"
 
 
-def test_multiple_no_intersection() -> None:
+def test_MultipleDataGrabber_no_intersection() -> None:
-    """Test a multiple datagrabber without intersection (0 elements)."""
+    """Test MultipleDataGrabber without intersection (0 elements)."""
     repo_uri1 = _testing_dataset["example_bids"]["uri"]
     repo_uri2 = _testing_dataset["example_bids_ses"]["uri"]
     rootdir = "example_bids_ses"
@@ -113,8 +113,8 @@ def test_multiple_no_intersection() -> None:
         assert set(subs) == set(expected_subs)
 
 
-def test_multiple_get_item() -> None:
+def test_MultipleDataGrabber_get_item() -> None:
-    """Test a multiple datagrabber get_item error."""
+    """Test MultipleDataGrabber get_item() error."""
     repo_uri1 = _testing_dataset["example_bids"]["uri"]
     rootdir = "example_bids_ses"
     replacements = ["subject", "session"]
@@ -134,8 +134,8 @@ def test_multiple_get_item() -> None:
         dg.get_item(subject="sub-01")  # type: ignore
 
 
-def test_multiple_validation() -> None:
+def test_MultipleDataGrabber_validation() -> None:
-    """Test a multiple datagrabber init validation."""
+    """Test MultipleDataGrabber init validation."""
     repo_uri1 = _testing_dataset["example_bids"]["uri"]
     repo_uri2 = _testing_dataset["example_bids_ses"]["uri"]
     rootdir = "example_bids_ses"

junifer/datagrabber/tests/test_pattern.py

@@ -1,4 +1,4 @@
-"""Provide tests for pattern."""
+"""Provide tests for PatternDataGrabber."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
@@ -9,7 +9,7 @@ from pathlib import Path
 
 import pytest
 
-from junifer.datagrabber.pattern import PatternDataGrabber
+from junifer.datagrabber import PatternDataGrabber
 
 
 def test_PatternDataGrabber_errors(tmp_path: Path) -> None:
@@ -261,7 +261,7 @@ def test_PatternDataGrabber(tmp_path: Path) -> None:
     assert out1["vbm"]["path"] != out2["vbm"]["path"]
 
 
-def test_pattern_data_grabber_confounds_format_error_on_init() -> None:
+def test_PatternDataGrabber_confounds_format_error_on_init() -> None:
     """Test PatterDataGrabber confounds format error on initialisation."""
     with pytest.raises(
         ValueError, match="Invalid value for `confounds_format`"
@@ -275,7 +275,7 @@ def test_pattern_data_grabber_confounds_format_error_on_init() -> None:
         )
 
 
-def test_pattern_data_grabber_confounds_format_error_on_fetch(
+def test_PatternDataGrabber_confounds_format_error_on_fetch(
     tmp_path: Path,
 ) -> None:
     """Test PatterDataGrabber confounds format error on fetching.
@@ -301,6 +301,6 @@ def test_pattern_data_grabber_confounds_format_error_on_fetch(
     )
     # Check error on fetch
     with pytest.raises(
-        ValueError, match="As the datagrabber used specifies 'BOLD_confounds'"
+        ValueError, match="As the DataGrabber used specifies 'BOLD_confounds'"
     ):
         datagrabber.get_item(subject="sub-001")

junifer/datagrabber/tests/test_pattern_datalad.py

@@ -1,4 +1,4 @@
-"""Provide tests for pattern_datalad."""
+"""Provide tests for PatternDataladDataGrabber."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
@@ -9,7 +9,7 @@ from pathlib import Path
 
 import pytest
 
-from junifer.datagrabber.pattern_datalad import PatternDataladDataGrabber
+from junifer.datagrabber import PatternDataladDataGrabber
 
 
 _testing_dataset = {
@@ -26,8 +26,8 @@ _testing_dataset = {
 }
 
 
-def test_bids_pattern_datalad_datagrabber_missing_uri() -> None:
+def test_bids_PatternDataladDataGrabber_missing_uri() -> None:
-    """Test check of missing URI in pattern datalad datagrabber."""
+    """Test check of missing URI in PatternDataladDataGrabber."""
     with pytest.raises(ValueError, match=r"`uri` must be provided"):
         PatternDataladDataGrabber(
             datadir=None,
@@ -37,15 +37,8 @@ def test_bids_pattern_datalad_datagrabber_missing_uri() -> None:
         )
 
 
-def test_bids_PatternDataladDataGrabber(tmp_path: Path) -> None:
+def test_bids_PatternDataladDataGrabber() -> None:
-    """Test a subject-based BIDS datalad datagrabber.
+    """Test subject-based BIDS PatternDataladDataGrabber."""
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
     # Define types
     types = ["T1w", "BOLD"]
     # Define patterns
@@ -97,15 +90,8 @@ def test_bids_PatternDataladDataGrabber(tmp_path: Path) -> None:
                 assert f.readlines()[0].startswith("placeholder")
 
 
-def test_bids_PatternDataladDataGrabber_datadir(tmp_path: Path) -> None:
+def test_bids_PatternDataladDataGrabber_datadir() -> None:
-    """Test a datalad datagrabber with a datadir set to a relative path.
+    """Test PatternDataladDataGrabber with a datadir set to a relative path."""
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
     # Define types
     types = ["T1w", "BOLD"]
     # Define patterns
@@ -144,7 +130,7 @@ def test_bids_PatternDataladDataGrabber_datadir(tmp_path: Path) -> None:
 
 
 def test_bids_PatternDataladDataGrabber_session():
-    """Test a subject and session-based BIDS datalad datagrabber."""
+    """Test a subject and session-based BIDS PatternDataladDataGrabber."""
     types = ["T1w", "BOLD"]
     patterns = {
         "T1w": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz",

junifer/markers/collection.py

@@ -104,8 +104,8 @@ class MarkerCollection:
 
         Parameters
         ----------
-        datagrabber : datagrabber-like
+        datagrabber : DataGrabber-like
-            The datagrabber to validate.
+            The DataGrabber to validate.
 
         """
         logger.info("Validating Marker Collection")

junifer/testing/datagrabbers.py

@@ -1,4 +1,4 @@
-"""Provide testing datagrabbers."""
+"""Provide testing DataGrabbers."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Synchon Mandal <s.mandal@fz-juelich.de>
@@ -15,9 +15,9 @@ from ..datagrabber.base import BaseDataGrabber
 
 
 class OasisVBMTestingDataGrabber(BaseDataGrabber):
-    """Data Grabber for Oasis VBM testing data.
+    """DataGrabber for Oasis VBM testing data.
 
-    Wrapper for :func:`nilearn.datasets.fetch_oasis_vbm`
+    Wrapper for :func:`nilearn.datasets.fetch_oasis_vbm`.
 
     """
 
@@ -83,7 +83,7 @@ class OasisVBMTestingDataGrabber(BaseDataGrabber):
 
 
 class SPMAuditoryTestingDataGrabber(BaseDataGrabber):
-    """Data Grabber for SPM Auditory dataset.
+    """DataGrabber for SPM Auditory dataset.
 
     Wrapper for :func:`nilearn.datasets.fetch_spm_auditory`.
 
@@ -147,9 +147,9 @@ class SPMAuditoryTestingDataGrabber(BaseDataGrabber):
 
 
 class PartlyCloudyTestingDataGrabber(BaseDataGrabber):
-    """Data Grabber for Partly Cloudy dataset.
+    """DataGrabber for Partly Cloudy dataset.
 
-    Wrapper for :func:`nilearn.datasets.fetch_development_fmri`
+    Wrapper for :func:`nilearn.datasets.fetch_development_fmri`.
 
     Parameters
     ----------

junifer/testing/registry.py

@@ -12,7 +12,7 @@ from .datagrabbers import (
 )
 
 
-# Register testing datagrabber
+# Register testing DataGrabbers
 register(
     step="datagrabber",
     name="OasisVBMTestingDataGrabber",

junifer/testing/tests/test_oasisvmbtesting_datagrabber.py

@@ -1,4 +1,4 @@
-"""Provide tests for Oasis VBM Testing datagrabber."""
+"""Provide tests for OasisVBMTestingDataGrabber."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 # License: AGPL
@@ -7,7 +7,7 @@ from junifer.testing.datagrabbers import OasisVBMTestingDataGrabber
 
 
 def test_OasisVBMTestingDataGrabber() -> None:
-    """Test Oasis VBM Testing datagrabber."""
+    """Test OasisVBMTestingDataGrabber."""
     expected_elements = [
         "sub-01",
         "sub-02",

junifer/testing/tests/test_partlycloudytesting_datagrabber.py

@@ -1,4 +1,4 @@
-"""Provide tests for PartlyCloudy datagrabber."""
+"""Provide tests for PartlyCloudyTestingDataGrabber."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 # License: AGPL
@@ -7,7 +7,7 @@ from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
 def test_PartlyCloudyTestingDataGrabber() -> None:
-    """Test PartlyCloudy datagrabber."""
+    """Test PartlyCloudyTestingDataGrabber."""
     expected_elements = [
         "sub-01",
         "sub-02",

junifer/testing/tests/test_spmauditory_datagrabber.py

@@ -1,4 +1,4 @@
-"""Provide tests for SPM Auditory datagrabber."""
+"""Provide tests for SPMAuditoryTestingDataGrabber."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 # License: AGPL
@@ -7,7 +7,7 @@ from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber
 
 
 def test_SPMAuditoryTestingDataGrabber() -> None:
-    """Test SPM Auditory datagrabber."""
+    """Test SPMAuditoryTestingDataGrabber."""
     expected_elements = [
         "sub001",
         "sub002",

tools/create_aomic1000_example_dataset.py

@@ -1,4 +1,4 @@
-"""Create a testing dataset for the DataladAOMICID1000 pattern datagrabber."""
+"""Create a testing dataset for DataladAOMICID1000."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Vera Komeyer <v.komeyer@fz-juelich.de>