junifer 0.0.8.dev349__tar.gz → 0.0.9.dev6__tar.gz

{junifer-0.0.8.dev349/junifer.egg-info → junifer-0.0.9.dev6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.8.dev349
+Version: 0.0.9.dev6
 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-0.0.9.dev6/docs/changes/newsfragments/536.misc

@@ -0,0 +1 @@
+Update ``pillow`` to 13.0.0, ``virtualenv`` to 21.14.13, ``filelock`` to 4.2.4, ``setuptools`` to 84.2.1 and ``certifi`` to 2026.10.23 in ``uv.lock``, fixing their security alerts by `Fede Raimondo`_

junifer-0.0.9.dev6/docs/changes/newsfragments/538.enh

@@ -0,0 +1 @@
+Use the ``datareader`` section of the YAML configuration in ``junifer run``, passing it to :func:`.run` as the new ``datareader`` parameter, so a registered DataReader can be used instead of :class:`.DefaultDataReader` by `Fede Raimondo`_

{junifer-0.0.8.dev349 → junifer-0.0.9.dev6}/junifer/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '0.0.8.dev349'
-__version_tuple__ = version_tuple = (0, 0, 8, 'dev349')
+__version__ = version = '0.0.9.dev6'
+__version_tuple__ = version_tuple = (0, 0, 9, 'dev6')
 
-__commit_id__ = commit_id = 'g2b4aae01d'
+__commit_id__ = commit_id = 'g945cebd37'

{junifer-0.0.8.dev349 → junifer-0.0.9.dev6}/junifer/api/functions.py

@@ -21,6 +21,7 @@ from ..markers import BaseMarker
 from ..pipeline import (
     MarkerCollection,
     PipelineComponentRegistry,
+    PipelineStepMixin,
     WorkDirManager,
 )
 from ..preprocess import BasePreprocessor
@@ -70,6 +71,28 @@ def _get_datagrabber(datagrabber_config: dict) -> DataGrabberLike:
     )
 
 
+def _get_datareader(datareader_config: dict) -> PipelineStepMixin:
+    """Get DataReader.
+
+    Parameters
+    ----------
+    datareader_config : dict
+        The config to get the DataReader using.
+
+    Returns
+    -------
+    object
+        The DataReader.
+
+    """
+    return PipelineComponentRegistry().build_component_instance(
+        step="datareader",
+        name=datareader_config.pop("kind"),
+        baseclass=PipelineStepMixin,
+        init_params=datareader_config,
+    )
+
+
 def _get_preprocessor(preprocessing_config: dict) -> PreprocessorLike:
     """Get Preprocessor.
 
@@ -182,6 +205,7 @@ def run(
     storage: dict,
     preprocessors: list[dict] | None = None,
     elements: Elements | None = None,
+    datareader: dict | None = None,
 ) -> None:
     """Run the pipeline on the selected element.
 
@@ -210,6 +234,11 @@ def run(
     elements : list or None, optional
         Element(s) to process. Will be used to index the DataGrabber
         (default None).
+    datareader : dict or None, optional
+        DataReader to use. Must have a key ``kind`` with the kind of
+        DataReader to use. All other keys are passed to the DataReader
+        constructor. If None, will use :class:`.DefaultDataReader`
+        (default None).
 
     Raises
     ------
@@ -249,9 +278,16 @@ def run(
     else:
         built_preprocessors = None
 
+    # Get datareader to use (if provided)
+    if datareader is not None:
+        datareader_object = _get_datareader(datareader.copy())
+    else:
+        datareader_object = None
+
     # Create new marker collection
     mc = MarkerCollection(
         markers=built_markers,
+        datareader=datareader_object,
         preprocessors=built_preprocessors,
         storage=storage_object,
     )

{junifer-0.0.8.dev349 → junifer-0.0.9.dev6}/junifer/api/tests/test_functions.py

@@ -21,9 +21,10 @@ from ruamel.yaml import YAML
 
 import junifer.testing.registry  # noqa: F401
 from junifer.api import collect, list_elements, parse_yaml, queue, reset, run
-from junifer.api.decorators import register_marker
+from junifer.api.decorators import register_datareader, register_marker
 from junifer.datagrabber import DataType, PatternDataGrabber
 from junifer.datagrabber.base import BaseDataGrabber
+from junifer.datareader import DefaultDataReader
 from junifer.markers import BaseMarker
 from junifer.pipeline import (
     MarkerCollection,
@@ -224,6 +225,52 @@ def test_run_single_element_with_preprocessing(
     assert len(files) == 1
 
 
+def test_run_single_element_with_datareader(
+    tmp_path: Path,
+    markers: list[dict[str, str]],
+    storage: dict[str, str],
+) -> None:
+    """Test run function with single element and a DataReader.
+
+    Parameters
+    ----------
+    tmp_path : pathlib.Path
+        The path to the test directory.
+    markers : list of dict
+        Testing markers as list of dictionary.
+    storage : dict
+        Testing storage as dictionary.
+
+    """
+
+    @register_datareader
+    class CountingDataReader(DefaultDataReader):
+        """DataReader counting the elements it reads."""
+
+        n_read: ClassVar[int] = 0
+
+        def _fit_transform(self, input, params=None):
+            CountingDataReader.n_read += 1
+            return super()._fit_transform(input, params)
+
+    # Set storage
+    storage["uri"] = str((tmp_path / "out.hdf5").resolve())
+    # Run operations
+    run(
+        workdir=tmp_path,
+        datagrabber=_datagrabber.copy(),
+        markers=markers,
+        storage=storage,
+        elements=["sub-01"],
+        datareader={"kind": "CountingDataReader"},
+    )
+    # Check the DataReader was used
+    assert CountingDataReader.n_read == 1
+    # Check files
+    files = list(tmp_path.glob("*.hdf5"))
+    assert len(files) == 1
+
+
 @pytest.mark.parametrize(
     "element, expect",
     [

{junifer-0.0.8.dev349 → junifer-0.0.9.dev6}/junifer/cli/cli.py

@@ -193,6 +193,8 @@ def run(
     markers = config["markers"]
     # Fetch storage
     storage = config["storage"]
+    # Fetch datareader
+    datareader = config.get("datareader")
     # Fetch preprocessors
     preprocessors = config.get("preprocess")
     # Convert to list if single preprocessor
@@ -208,6 +210,7 @@ def run(
         storage=storage,
         preprocessors=preprocessors,
         elements=elements,
+        datareader=datareader,
     )
 
 

{junifer-0.0.8.dev349 → junifer-0.0.9.dev6/junifer.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.8.dev349
+Version: 0.0.9.dev6
 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-0.0.8.dev349 → junifer-0.0.9.dev6}/junifer.egg-info/SOURCES.txt

@@ -67,6 +67,8 @@ docs/api/testing.rst
 docs/api/utils.rst
 docs/changes/contributors.inc
 docs/changes/newsfragments/.gitignore
+docs/changes/newsfragments/536.misc
+docs/changes/newsfragments/538.enh
 docs/extending/confounds_format.rst
 docs/extending/coordinates.rst
 docs/extending/data_dump_asset.rst

{junifer-0.0.8.dev349 → junifer-0.0.9.dev6}/junifer.egg-info/scm_file_list.json

@@ -51,6 +51,8 @@
     "docs/builtin.rst",
     "docs/changes/contributors.inc",
     "docs/changes/newsfragments/.gitignore",
+    "docs/changes/newsfragments/536.misc",
+    "docs/changes/newsfragments/538.enh",
     "docs/conf.py",
     "docs/contribution.rst",
     "docs/extending/confounds_format.rst",

junifer-0.0.9.dev6/junifer.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "0.0.8",
+  "distance": 6,
+  "node": "g945cebd37cb37268449f4d5fa91aff735abefee4",
+  "dirty": false,
+  "branch": "main",
+  "node_date": "2026-10-31"
+}