junifer 0.0.6.dev277__tar.gz → 0.0.6.dev299__tar.gz

{junifer-0.0.6.dev277 → junifer-0.0.6.dev299}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev277
+Version: 0.0.6.dev299
 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-0.0.6.dev299/docs/changes/newsfragments/402.change

@@ -0,0 +1 @@
+Allow ``workdir`` to also be a mapping in YAML, with ``path`` and ``cleanup`` keys by `Synchon Mandal`_

junifer-0.0.6.dev299/docs/changes/newsfragments/402.enh

@@ -0,0 +1 @@
+Allow ``workdir`` mapping form in YAML for easy debugging of single element ``run`` by disabling cleanup of :class:`junifer.pipeline.WorkDirManager` by `Synchon Mandal`_

junifer-0.0.6.dev299/docs/changes/newsfragments/403.enh

@@ -0,0 +1 @@
+Use :func:`junifer.utils.ConfigManager` to skip time-consuming dataset ID and dirty checks for :class:`.DataladDataGrabber` by `Fede Raimondo`_

{junifer-0.0.6.dev277 → junifer-0.0.6.dev299}/docs/conf.py

@@ -96,6 +96,7 @@ nitpick_ignore_regex = [
     ("py:obj", "sqlalchemy.engine.Engine"),  # ignore sqlalchemy
     ("py:class", "pipeline.Pipeline"),  # nilearn
     ("py:obj", "neurokit2.*"),  # ignore neurokit2
+    ("py:obj", "datalad.*"),  # ignore datalad
 ]
 
 # -- Options for HTML output -------------------------------------------------

{junifer-0.0.6.dev277 → junifer-0.0.6.dev299}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev277'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev277')
+__version__ = version = '0.0.6.dev299'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev299')

{junifer-0.0.6.dev277 → junifer-0.0.6.dev299}/junifer/api/functions.py

@@ -21,7 +21,7 @@ from ..pipeline import (
 from ..preprocess import BasePreprocessor
 from ..storage import BaseFeatureStorage
 from ..typing import DataGrabberLike, MarkerLike, PreprocessorLike, StorageLike
-from ..utils import logger, raise_error, yaml
+from ..utils import logger, raise_error, warn_with_log, yaml
 
 
 __all__ = ["collect", "list_elements", "queue", "reset", "run"]
@@ -116,18 +116,18 @@ def _get_storage(storage_config: dict) -> StorageLike:
 
 
 def run(
-    workdir: Union[str, Path],
+    workdir: Union[str, Path, dict],
     datagrabber: dict,
     markers: list[dict],
     storage: dict,
     preprocessors: Optional[list[dict]] = None,
-    elements: Union[str, list[Union[str, tuple]], tuple, None] = None,
+    elements: Optional[list[tuple[str, ...]]] = None,
 ) -> None:
     """Run the pipeline on the selected element.
 
     Parameters
     ----------
-    workdir : str or pathlib.Path
+    workdir : str or pathlib.Path or dict
         Directory where the pipeline will be executed.
     datagrabber : dict
         DataGrabber to use. Must have a key ``kind`` with the kind of
@@ -143,23 +143,38 @@ def run(
         Storage to use. Must have a key ``kind`` with the kind of
         storage to use. All other keys are passed to the storage
         constructor.
-    preprocessors : list of dict, optional
+    preprocessors : list of dict or None, optional
         List of preprocessors to use. Each preprocessor is a dict with at
         least a key ``kind`` specifying the preprocessor to use. All other keys
         are passed to the preprocessor constructor (default None).
-    elements : str or tuple or list of str or tuple, optional
+    elements : list of tuple or None, optional
         Element(s) to process. Will be used to index the DataGrabber
         (default None).
 
+    Raises
+    ------
+    ValueError
+        If ``workdir.cleanup=False`` when ``len(elements) > 1``.
+
     """
-    # Convert str to Path
-    if isinstance(workdir, str):
-        workdir = Path(workdir)
-    # Initiate working directory manager
-    WorkDirManager(workdir)
+    # Conditional to handle workdir config
+    if isinstance(workdir, (str, Path)):
+        if isinstance(workdir, str):
+            workdir = {"workdir": Path(workdir), "cleanup": True}
+        else:
+            workdir = {"workdir": workdir, "cleanup": True}
+    elif isinstance(workdir, dict):
+        workdir["workdir"] = workdir.pop("path")
 
-    if not isinstance(elements, list) and elements is not None:
-        elements = [elements]
+    # Initiate working directory manager with correct variation
+    if not workdir["cleanup"]:
+        if elements is None or len(elements) > 1:
+            raise_error(
+                "Cannot disable `workdir.cleanup` as "
+                f"{len(elements) if elements is not None else 'all'} "
+                "elements will be processed"
+            )
+    WorkDirManager(**workdir)
 
     # Get datagrabber to use
     datagrabber_object = _get_datagrabber(datagrabber.copy())
@@ -228,7 +243,7 @@ def queue(
     kind: str,
     jobname: str = "junifer_job",
     overwrite: bool = False,
-    elements: Union[str, list[Union[str, tuple]], tuple, None] = None,
+    elements: Optional[list[tuple[str, ...]]] = None,
     **kwargs: Union[str, int, bool, dict, tuple, list],
 ) -> None:
     """Queue a job to be executed later.
@@ -243,7 +258,7 @@ def queue(
         The name of the job (default "junifer_job").
     overwrite : bool, optional
         Whether to overwrite if job directory already exists (default False).
-    elements : str or tuple or list of str or tuple, optional
+    elements : list of tuple or None, optional
         Element(s) to process. Will be used to index the DataGrabber
         (default None).
     **kwargs : dict
@@ -282,6 +297,16 @@ def queue(
             shutil.rmtree(jobdir)
     jobdir.mkdir(exist_ok=True, parents=True)
 
+    # Check workdir config
+    if "workdir" in config:
+        if isinstance(config["workdir"], dict):
+            if not config["workdir"]["cleanup"]:
+                warn_with_log(
+                    "`workdir.cleanup` will be set to True when queueing"
+                )
+            # Set cleanup
+            config["workdir"]["cleanup"] = True
+
     # Load modules
     if "with" in config:
         to_load = config["with"]
@@ -381,7 +406,7 @@ def reset(config: dict) -> None:
 
 def list_elements(
     datagrabber: dict,
-    elements: Union[str, list[Union[str, tuple]], tuple, None] = None,
+    elements: Optional[list[tuple[str, ...]]] = None,
 ) -> str:
     """List elements of the datagrabber filtered using `elements`.
 
@@ -391,7 +416,7 @@ def list_elements(
         DataGrabber to index. Must have a key ``kind`` with the kind of
         DataGrabber to use. All other keys are passed to the DataGrabber
         constructor.
-    elements : str or tuple or list of str or tuple, optional
+    elements : list of tuple or None, optional
         Element(s) to filter using. Will be used to index the DataGrabber
         (default None).
 

{junifer-0.0.6.dev277 → junifer-0.0.6.dev299}/junifer/api/tests/test_functions.py

@@ -88,7 +88,7 @@ def test_run_single_element(
         datagrabber=datagrabber,
         markers=markers,
         storage=storage,
-        elements=["sub-01"],
+        elements=[("sub-01",)],
     )
     # Check files
     files = list(tmp_path.glob("*.sqlite"))
@@ -116,7 +116,7 @@ def test_run_single_element_with_preprocessing(
     storage["uri"] = str((tmp_path / "out.sqlite").resolve())
     # Run operations
     run(
-        workdir=tmp_path,
+        workdir={"path": tmp_path, "cleanup": False},
         datagrabber={
             "kind": "PartlyCloudyTestingDataGrabber",
             "reduce_confounds": False,
@@ -128,7 +128,7 @@ def test_run_single_element_with_preprocessing(
                 "kind": "fMRIPrepConfoundRemover",
             }
         ],
-        elements=["sub-01"],
+        elements=[("sub-01",)],
     )
     # Check files
     files = list(tmp_path.glob("*.sqlite"))
@@ -164,7 +164,7 @@ def test_run_multi_element_multi_output(
         datagrabber=datagrabber,
         markers=markers,
         storage=storage,
-        elements=["sub-01", "sub-03"],
+        elements=[("sub-01",), ("sub-03",)],
     )
     # Check files
     files = list(tmp_path.glob("*.sqlite"))
@@ -200,7 +200,7 @@ def test_run_multi_element_single_output(
         datagrabber=datagrabber,
         markers=markers,
         storage=storage,
-        elements=["sub-01", "sub-03"],
+        elements=[("sub-01",), ("sub-03",)],
     )
     # Check files
     files = list(tmp_path.glob("*.sqlite"))
@@ -287,7 +287,10 @@ def test_queue_correct_yaml_config(
             queue(
                 config={
                     "with": "junifer.testing.registry",
-                    "workdir": str(tmp_path.resolve()),
+                    "workdir": {
+                        "path": str(tmp_path.resolve()),
+                        "cleanup": True,
+                    },
                     "datagrabber": datagrabber,
                     "markers": markers,
                     "storage": storage,
@@ -342,7 +345,7 @@ def test_queue_invalid_job_queue(
         with monkeypatch.context() as m:
             m.chdir(tmp_path)
             queue(
-                config={"elements": ["sub-001"]},
+                config={"elements": [("sub-001",)]},
                 kind="ABC",
             )
 
@@ -366,13 +369,13 @@ def test_queue_assets_disallow_overwrite(
             m.chdir(tmp_path)
             # First generate assets
             queue(
-                config={"elements": ["sub-001"]},
+                config={"elements": [("sub-001",)]},
                 kind="HTCondor",
                 jobname="prevent_overwrite",
             )
             # Re-run to trigger error
             queue(
-                config={"elements": ["sub-001"]},
+                config={"elements": [("sub-001",)]},
                 kind="HTCondor",
                 jobname="prevent_overwrite",
             )
@@ -399,14 +402,14 @@ def test_queue_assets_allow_overwrite(
         m.chdir(tmp_path)
         # First generate assets
         queue(
-            config={"elements": ["sub-001"]},
+            config={"elements": [("sub-001",)]},
             kind="HTCondor",
             jobname="allow_overwrite",
         )
         with caplog.at_level(logging.INFO):
             # Re-run to overwrite
             queue(
-                config={"elements": ["sub-001"]},
+                config={"elements": [("sub-001",)]},
                 kind="HTCondor",
                 jobname="allow_overwrite",
                 overwrite=True,
@@ -448,10 +451,16 @@ def test_queue_with_imports(
         (tmp_path / "a.py").touch()
         with caplog.at_level(logging.DEBUG):
             queue(
-                config={"with": with_},
+                config={
+                    "with": with_,
+                    "workdir": {
+                        "path": str(tmp_path.resolve()),
+                        "cleanup": False,
+                    },
+                },
                 kind="HTCondor",
                 jobname="with_import_check",
-                elements="sub-001",
+                elements=[("sub-001",)],
             )
             assert "Copying" in caplog.text
             assert "Queue done" in caplog.text
@@ -465,10 +474,8 @@ def test_queue_with_imports(
 @pytest.mark.parametrize(
     "elements",
     [
-        "sub-001",
-        ["sub-001"],
-        ["sub-001", "sub-002"],
-        ("sub-001", "ses-001"),
+        [("sub-001",)],
+        [("sub-001",), ("sub-002",)],
         [("sub-001", "ses-001")],
         [("sub-001", "ses-001"), ("sub-001", "ses-002")],
     ],
@@ -477,7 +484,7 @@ def test_queue_with_elements(
     tmp_path: Path,
     monkeypatch: pytest.MonkeyPatch,
     caplog: pytest.LogCaptureFixture,
-    elements: Union[str, list[Union[str, tuple[str]]], tuple[str]],
+    elements: list[tuple[str, ...]],
 ) -> None:
     """Test queue with elements.
 
@@ -489,7 +496,7 @@ def test_queue_with_elements(
         The pytest.MonkeyPatch object.
     caplog : pytest.LogCaptureFixture
         The pytest.LogCaptureFixture object.
-    elements : str of list of str
+    elements : list of tuple
         The parametrized elements for the queue.
 
     """
@@ -562,7 +569,7 @@ def test_reset_run(
         datagrabber=datagrabber,
         markers=markers,
         storage=storage,
-        elements=["sub-01"],
+        elements=[("sub-01",)],
     )
     # Reset operation
     reset(config={"storage": storage})
@@ -642,13 +649,13 @@ def test_reset_queue(
 @pytest.mark.parametrize(
     "elements",
     [
-        ["sub-01"],
+        [("sub-01",)],
         None,
     ],
 )
 def test_list_elements(
     datagrabber: dict[str, str],
-    elements: Optional[list[str]],
+    elements: Optional[list[tuple[str, ...]]],
 ) -> None:
     """Test elements listing.
 

{junifer-0.0.6.dev277 → junifer-0.0.6.dev299}/junifer/cli/cli.py

@@ -117,15 +117,16 @@ def run(
     filepath : click.Path
         The filepath to the configuration file.
     element : tuple of str
-        The element to operate on.
+        The element(s) to operate on.
     verbose : click.Choice
         The verbosity level: warning, info or debug (default "info").
 
     """
+    # Setup logging
     configure_logging(level=verbose)
     # TODO(synchon): add validation
     # Parse YAML
-    config = parse_yaml(filepath)  # type: ignore
+    config = parse_yaml(filepath)
     # Retrieve working directory
     workdir = config["workdir"]
     # Fetch datagrabber
@@ -179,9 +180,12 @@ def collect(filepath: click.Path, verbose: Union[str, int]) -> None:
         The verbosity level: warning, info or debug (default "info").
 
     """
+    # Setup logging
     configure_logging(level=verbose)
     # TODO: add validation
-    config = parse_yaml(filepath)  # type: ignore
+    # Parse YAML
+    config = parse_yaml(filepath)
+    # Fetch storage
     storage = config["storage"]
     # Perform operation
     cli_func.collect(storage=storage)
@@ -206,7 +210,7 @@ def collect(filepath: click.Path, verbose: Union[str, int]) -> None:
 )
 def queue(
     filepath: click.Path,
-    element: str,
+    element: tuple[str],
     overwrite: bool,
     submit: bool,
     verbose: Union[str, int],
@@ -219,8 +223,8 @@ def queue(
     ----------
     filepath : click.Path
         The filepath to the configuration file.
-    element : str
-        The element to operate using.
+    element : tuple of str
+        The element(s) to operate on.
     overwrite : bool
         Whether to overwrite existing directory.
     submit : bool
@@ -228,15 +232,26 @@ def queue(
     verbose : click.Choice
         The verbosity level: warning, info or debug (default "info").
 
+    Raises
+    ------
+    ValueError
+        If no ``queue`` section is found in the YAML.
+
     """
+    # Setup logging
     configure_logging(level=verbose)
     # TODO: add validation
+    # Parse YAML
     config = parse_yaml(filepath)  # type: ignore
-    elements = parse_elements(element, config)
+    # Check queue section
     if "queue" not in config:
         raise_error(f"No queue configuration found in {filepath}.")
+    # Parse elements
+    elements = parse_elements(element, config)
+    # Separate out queue section
     queue_config = config.pop("queue")
     kind = queue_config.pop("kind")
+    # Perform operation
     cli_func.queue(
         config=config,
         kind=kind,
@@ -366,6 +381,7 @@ def reset(
         The verbosity level: warning, info or debug (default "info").
 
     """
+    # Setup logging
     configure_logging(level=verbose)
     # Parse YAML
     config = parse_yaml(filepath)
@@ -408,7 +424,7 @@ def list_elements(
     filepath : click.Path
         The filepath to the configuration file.
     element : tuple of str
-        The element to operate on.
+        The element(s) to operate on.
     output_file : click.Path or None
         The path to write the output to. If not None, writing to
         stdout is not performed.
@@ -416,9 +432,10 @@ def list_elements(
         The verbosity level: warning, info or debug (default "info").
 
     """
+    # Setup logging
     configure_logging(level=verbose)
     # Parse YAML
-    config = parse_yaml(filepath)  # type: ignore
+    config = parse_yaml(filepath)
     # Fetch datagrabber
     datagrabber = config["datagrabber"]
     # Parse elements

{junifer-0.0.6.dev277 → junifer-0.0.6.dev299}/junifer/cli/parser.py

@@ -140,7 +140,9 @@ def parse_yaml(filepath: Union[str, Path]) -> dict:  # noqa: C901
     return contents
 
 
-def parse_elements(element: tuple[str], config: dict) -> Union[list, None]:
+def parse_elements(
+    element: tuple[str, ...], config: dict
+) -> Union[list[tuple[str, ...]], None]:
     """Parse elements from cli.
 
     Parameters
@@ -170,7 +172,7 @@ def parse_elements(element: tuple[str], config: dict) -> Union[list, None]:
     """
     logger.debug(f"Parsing elements: {element}")
     # Early return None to continue with all elements
-    if len(element) == 0:
+    if not element:
         return None
     # Check if the element is a file for single element;
     # if yes, then parse elements from it

{junifer-0.0.6.dev277 → junifer-0.0.6.dev299}/junifer/datagrabber/datalad_base.py

@@ -17,7 +17,7 @@ from datalad.support.exceptions import IncompleteResultsError
 from datalad.support.gitrepo import GitRepo
 
 from ..pipeline import WorkDirManager
-from ..utils import logger, raise_error, warn_with_log
+from ..utils import config, logger, raise_error, warn_with_log
 from .base import BaseDataGrabber
 
 
@@ -143,27 +143,49 @@ class DataladDataGrabber(BaseDataGrabber):
         """
         return super().datadir / self._rootdir
 
-    def _get_dataset_id_remote(self) -> str:
+    def _get_dataset_id_remote(self) -> tuple[str, bool]:
         """Get the dataset ID from the remote.
 
         Returns
         -------
         str
             The dataset ID.
+        bool
+            Whether the dataset is dirty.
+
+        Raises
+        ------
+        ValueError
+            If the dataset ID cannot be obtained from the remote.
 
         """
         remote_id = None
+        is_dirty = False
         with tempfile.TemporaryDirectory() as tmpdir:
-            logger.debug(f"Querying {self.uri} for dataset ID")
-            repo = GitRepo.clone(
-                self.uri, path=tmpdir, clone_options=["-n", "--depth=1"]
+            if not config.get("datagrabber.skipidcheck", False):
+                logger.debug(f"Querying {self.uri} for dataset ID")
+                repo = GitRepo.clone(
+                    self.uri, path=tmpdir, clone_options=["-n", "--depth=1"]
+                )
+                repo.checkout(name=".datalad/config", options=["HEAD"])
+                remote_id = repo.config.get("datalad.dataset.id", None)
+                logger.debug(f"Got remote dataset ID = {remote_id}")
+
+                if not config.get("datagrabber.skipdirtycheck", False):
+                    is_dirty = repo.dirty
+                else:
+                    logger.debug("Skipping dirty check")
+                    is_dirty = False
+            else:
+                logger.debug("Skipping dataset ID check")
+                remote_id = self._dataset.id
+                is_dirty = False
+            logger.debug(
+                f"Remote dataset is {'' if is_dirty else 'not'} dirty"
             )
-            repo.checkout(name=".datalad/config", options=["HEAD"])
-            remote_id = repo.config.get("datalad.dataset.id", None)
-            logger.debug(f"Got remote dataset ID = {remote_id}")
         if remote_id is None:
             raise_error("Could not get dataset ID from remote")
-        return remote_id
+        return remote_id, is_dirty
 
     def _dataset_get(self, out: dict) -> dict:
         """Get the dataset found from the path in ``out``.
@@ -178,6 +200,11 @@ class DataladDataGrabber(BaseDataGrabber):
         dict
             The unmodified input dictionary.
 
+        Raises
+        ------
+        datalad.support.exceptions.IncompleteResultsError
+            If there is a datalad-related problem while fetching data.
+
         """
         to_get = []
         for type_val in out.values():
@@ -230,6 +257,8 @@ class DataladDataGrabber(BaseDataGrabber):
         ------
         ValueError
             If the dataset is already installed but with a different ID.
+        datalad.support.exceptions.IncompleteResultsError
+            If there is a datalad-related problem while cloning dataset.
 
         """
         isinstalled = dl.Dataset(self._datadir).is_installed()
@@ -238,23 +267,23 @@ class DataladDataGrabber(BaseDataGrabber):
             self._got_files = []
             self._dataset: dl.Dataset = dl.Dataset(self._datadir)
 
-            remote_id = self._get_dataset_id_remote()
+            # Check if dataset is already installed with a different ID
+            remote_id, is_dirty = self._get_dataset_id_remote()
             if remote_id != self._dataset.id:
                 raise_error(
                     "Dataset already installed but with a different "
                     f"ID: {self._dataset.id} (local) != {remote_id} (remote)"
                 )
 
-            # Check for dirty datasets:
-            status = self._dataset.status()
-            if any(x["state"] != "clean" for x in status):
-                self.datalad_dirty = True
+            # Conditional reporting on dataset dirtiness
+            self.datalad_dirty = is_dirty
+            if self.datalad_dirty:
                 warn_with_log(
-                    "At least one file is not clean, Junifer will "
-                    "consider this dataset as dirty."
+                    "At least one file is not clean, "
+                    f"marking dataset (id: {self._dataset.id}) as dirty."
                 )
             else:
-                logger.debug("Dataset is clean")
+                logger.debug(f"Dataset (id: {self._dataset.id}) is clean")
 
         else:
             logger.debug(f"Installing dataset {self.uri} to {self._datadir}")

{junifer-0.0.6.dev277 → junifer-0.0.6.dev299}/junifer/datagrabber/tests/test_datalad_base.py

@@ -3,12 +3,14 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+import warnings
 from pathlib import Path
 
 import datalad.api as dl
 import pytest
 
 from junifer.datagrabber import DataladDataGrabber
+from junifer.utils import config
 
 
 _testing_dataset = {
@@ -94,6 +96,12 @@ def test_DataladDataGrabber_install_errors(
     with pytest.raises(ValueError, match=r"different ID"):
         with dg:
             pass
+    # Set config to skip id check and test
+    config.set(key="datagrabber.skipidcheck", val=True)
+    with dg:
+        pass
+    # Reset config
+    config.delete("datagrabber.skipidcheck")
 
     elem1_t1w = datadir / "example_bids/sub-01/anat/sub-01_T1w.nii.gz"
     elem1_t1w.unlink()
@@ -104,6 +112,14 @@ def test_DataladDataGrabber_install_errors(
     with pytest.warns(RuntimeWarning, match=r"one file is not clean"):
         with dg:
             pass
+    # Set config to skip dirty check and test
+    with warnings.catch_warnings():
+        warnings.simplefilter("error")
+        config.set(key="datagrabber.skipdirtycheck", val=True)
+        with dg:
+            pass
+        # Reset config
+        config.delete("datagrabber.skipdirtycheck")
 
 
 def test_DataladDataGrabber_clone_cleanup(
@@ -246,7 +262,7 @@ def test_DataladDataGrabber_previously_cloned(
         meta = elem1["BOLD"]["meta"]
         assert "datagrabber" in meta
         assert "datalad_dirty" in meta["datagrabber"]
-        assert meta["datagrabber"]["datalad_dirty"] is False
+        assert meta["datagrabber"]["datalad_dirty"] is True
         assert "datalad_commit_id" in meta["datagrabber"]
         assert meta["datagrabber"]["datalad_commit_id"] == commit
         assert "datalad_id" in meta["datagrabber"]
@@ -326,7 +342,7 @@ def test_DataladDataGrabber_previously_cloned_and_get(
         meta = elem1["BOLD"]["meta"]
         assert "datagrabber" in meta
         assert "datalad_dirty" in meta["datagrabber"]
-        assert meta["datagrabber"]["datalad_dirty"] is False
+        assert meta["datagrabber"]["datalad_dirty"] is True
         assert "datalad_commit_id" in meta["datagrabber"]
         assert meta["datagrabber"]["datalad_commit_id"] == commit
         assert "datalad_id" in meta["datagrabber"]

{junifer-0.0.6.dev277 → junifer-0.0.6.dev299}/junifer/pipeline/workdir_manager.py

@@ -30,6 +30,9 @@ class WorkDirManager(metaclass=Singleton):
     workdir : str or pathlib.Path, optional
         The path to the super-directory. If None, "TMPDIR/junifer" is used
         where TMPDIR is the platform-dependent temporary directory.
+    cleanup : bool, optional
+        If False, the directories are not cleaned up after the object is
+        destroyed. This is useful for debugging purposes (default True).
 
     Attributes
     ----------
@@ -39,14 +42,11 @@ class WorkDirManager(metaclass=Singleton):
         The path to the element directory.
     root_tempdir : pathlib.Path or None
         The path to the root temporary directory.
-    cleanup : bool, optional
-        If False, the directories are not cleaned up after the object is
-        destroyed. This is useful for debugging purposes (default True).
 
     """
 
     def __init__(
-        self, workdir: Optional[Union[str, Path]] = None, cleanup=True
+        self, workdir: Optional[Union[str, Path]] = None, cleanup: bool = True
     ) -> None:
         """Initialize the class."""
         self._workdir = Path(workdir) if isinstance(workdir, str) else workdir