junifer/api/cli.py

@@ -4,10 +4,10 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+import pathlib
 from typing import Dict, List, Union
 
 import click
-import pathlib
 
 from ..utils.logging import configure_logging, logger, warn_with_log
 from .functions import collect as api_collect
@@ -59,8 +59,10 @@ def cli() -> None:  # pragma: no cover
 
 @cli.command()
 @click.argument(
-    "filepath", type=click.Path(
+    "filepath",
-        exists=True, readable=True, dir_okay=False, path_type=pathlib.Path)
+    type=click.Path(
+        exists=True, readable=True, dir_okay=False, path_type=pathlib.Path
+    ),
 )
 @click.option("--element", type=str, multiple=True)
 @click.option(
@@ -102,8 +104,11 @@ def run(filepath: click.Path, element: str, verbose: click.Choice) -> None:
 
 @cli.command()
 @click.argument(
-    "filepath", type=click.Path(
+    "filepath",
-        exists=True, readable=True, dir_okay=False, path_type=pathlib.Path))
+    type=click.Path(
+        exists=True, readable=True, dir_okay=False, path_type=pathlib.Path
+    ),
+)
 @click.option(
     "-v",
     "--verbose",
@@ -131,8 +136,10 @@ def collect(filepath: click.Path, verbose: click.Choice) -> None:
 
 @cli.command()
 @click.argument(
-    "filepath", type=click.Path(
+    "filepath",
-        exists=True, readable=True, dir_okay=False, path_type=pathlib.Path)
+    type=click.Path(
+        exists=True, readable=True, dir_okay=False, path_type=pathlib.Path
+    ),
 )
 @click.option("--element", type=str, multiple=True)
 @click.option("--overwrite", is_flag=True)
@@ -180,3 +187,9 @@ def queue(
         submit=submit,
         **queue_config,
     )
+
+
+@cli.command()
+def selftest() -> None:
+    """Selftest command for CLI."""
+    pass

junifer/api/functions.py

@@ -7,9 +7,9 @@
 
 import shutil
 import subprocess
-from pathlib import Path
-from typing import Dict, List, Optional, Union, Tuple
 import typing
+from pathlib import Path
+from typing import Dict, List, Optional, Tuple, Union
 
 import yaml
 

junifer/api/registry.py

@@ -8,9 +8,11 @@
 from typing import TYPE_CHECKING, Dict, List, Optional, Union
 
 from ..utils.logging import logger, raise_error
+
+
 if TYPE_CHECKING:
     from ..datagrabber.base import BaseDataGrabber
-    from ..markers.base import PipelineStepMixin
+    from ..pipeline import PipelineStepMixin
     from ..storage.base import BaseFeatureStorage
 
 # Define valid steps for operation

junifer/api/tests/test_registry.py

@@ -4,10 +4,9 @@
 #          Leonard Sasse <l.sasse@fz-juelich.de>
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
-from typing import Type
-
 import logging
 from abc import ABC
+from typing import Type
 
 import pytest
 

junifer/data/atlases.py

@@ -10,7 +10,7 @@ import shutil
 import tempfile
 import zipfile
 from pathlib import Path
-from typing import TYPE_CHECKING, List, Optional, Tuple, Union, Any, Dict
+from typing import TYPE_CHECKING, Any, Dict, List, Optional, Tuple, Union
 
 import nibabel as nib
 import numpy as np
@@ -536,7 +536,8 @@ def _retrieve_tian(
         if space != "MNI6thgeneration":
             raise_error(
                 f"The parameter `space` ({space}) for 7T needs to be "
-                f"MNI6thgeneration")
+                f"MNI6thgeneration"
+            )
     else:
         raise_error(
             f"The parameter `magneticfield` ({magneticfield}) needs to be "
@@ -592,7 +593,7 @@ def _retrieve_tian(
             "A simple numbering scheme for distinction was therefore used."
         )
     else:  # pragma: no cover
-        raise_error('This should not happen. Please report this error.')
+        raise_error("This should not happen. Please report this error.")
 
     # check existence of atlas
     if not (atlas_fname.exists() and atlas_lname.exists()):
@@ -625,9 +626,7 @@ def _retrieve_tian(
 
 
 def _retrieve_suit(
-    atlas_dir: Path,
+    atlas_dir: Path, resolution: Optional[float], space: str = "MNI"
-    resolution: Optional[float],
-    space: str = "MNI"
 ) -> Tuple[Path, List[str]]:
     """Retrieve SUIT atlas.
 

junifer/data/tests/test_atlases.py

@@ -443,7 +443,8 @@ def test_tian_7T_6thgeneration(
     assert fname.name == fname1
     assert len(lbl) == n_label
     assert_array_almost_equal(
-        img.header["pixdim"][1:4], [1.6, 1.6, 1.6])  # type: ignore
+        img.header["pixdim"][1:4], [1.6, 1.6, 1.6]
+    )  # type: ignore
 
 
 def test_retrieve_tian_incorrect_space(tmp_path: Path) -> None:

junifer/datagrabber/datalad_base.py

@@ -120,7 +120,8 @@ class DataladDataGrabber(BaseDataGrabber):
         """Install the datalad dataset into the datadir."""
         logger.debug(f"Installing dataset {self.uri} to {self._datadir}")
         self._dataset = dl.install(  # type: ignore because of datalad
-            self._datadir, source=self.uri)
+            self._datadir, source=self.uri
+        )
         logger.debug("Dataset installed")
 
     def remove(self):

junifer/datareader/default.py

@@ -10,7 +10,7 @@ from typing import Dict, List
 import nibabel as nib
 import pandas as pd
 
-from ..markers.base import PipelineStepMixin
+from ..pipeline.pipeline_mixin import PipelineStepMixin
 from ..utils.logging import logger, warn_with_log
 
 

junifer/markers/__init__.py

@@ -7,4 +7,3 @@
 from .base import BaseMarker
 from .collection import MarkerCollection
 from .parcel import ParcelAggregation
-from .pipeline_mixin import PipelineStepMixin

junifer/markers/base.py

@@ -6,8 +6,8 @@
 
 from typing import Dict, List, Optional, Union
 
+from ..pipeline.pipeline_mixin import PipelineStepMixin
 from ..utils import logger, raise_error
-from .pipeline_mixin import PipelineStepMixin
 
 
 class BaseMarker(PipelineStepMixin):
@@ -23,9 +23,7 @@ class BaseMarker(PipelineStepMixin):
     """
 
     def __init__(
-        self,
+        self, on: Union[List[str], str], name: Optional[str] = None
-        on: Union[List[str], str],
-        name: Optional[str] = None
     ) -> None:
         """Initialize the class."""
         if not isinstance(on, list):

junifer/markers/collection.py

@@ -5,14 +5,13 @@
 # License: AGPL
 
 from collections import Counter
-from typing import Dict, Optional, List
+from typing import Dict, List, Optional
 
-from junifer.markers.pipeline_mixin import PipelineStepMixin
+from ..datareader.default import DefaultDataReader
-
+from ..markers.base import BaseMarker
-from ..datareader import DefaultDataReader
+from ..pipeline import PipelineStepMixin
-from ..utils import logger
-from .base import BaseMarker
 from ..storage.base import BaseFeatureStorage
+from ..utils import logger
 
 
 class MarkerCollection:
@@ -32,7 +31,7 @@ class MarkerCollection:
         markers: List[BaseMarker],
         datareader: Optional[PipelineStepMixin] = None,
         preprocessing: Optional[PipelineStepMixin] = None,
-        storage: Optional[BaseFeatureStorage] = None
+        storage: Optional[BaseFeatureStorage] = None,
     ):
         """Initialize the class."""
         # Check that the markers have different names

junifer/markers/parcel.py

@@ -116,7 +116,8 @@ class ParcelAggregation(BaseMarker):
         )
         logger.debug("Masking")
         masker = NiftiMasker(
-            atlas_bin, target_affine=t_input.affine)  # type: ignore
+            atlas_bin, target_affine=t_input.affine
+        )  # type: ignore
 
         # Mask the input data and the atlas
         data = masker.fit_transform(t_input)

junifer/markers/tests/test_collection.py

@@ -9,7 +9,7 @@ from numpy.testing import assert_array_equal
 
 from junifer.datareader.default import DefaultDataReader
 from junifer.markers import MarkerCollection, ParcelAggregation
-from junifer.markers.base import PipelineStepMixin
+from junifer.pipeline import PipelineStepMixin
 from junifer.storage import SQLiteFeatureStorage
 from junifer.testing.datagrabbers import OasisVBMTestingDatagrabber
 
@@ -90,8 +90,7 @@ def test_marker_collection():
         for t_marker in markers:
             t_name = t_marker.name
             assert_array_equal(
-                out[t_name]["VBM_GM"]["data"],
+                out[t_name]["VBM_GM"]["data"], out2[t_name]["VBM_GM"]["data"]
-                out2[t_name]["VBM_GM"]["data"]
             )
 
 

junifer/pipeline/__init__.py

@@ -0,0 +1,6 @@
+"""Provide imports for pipeline sub-package."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from .pipeline_mixin import PipelineStepMixin

junifer/pipeline/tests/test_pipeline_mixin.py

@@ -6,7 +6,7 @@
 
 import pytest
 
-from junifer.markers.pipeline_mixin import PipelineStepMixin
+from junifer.pipeline.pipeline_mixin import PipelineStepMixin
 
 
 def test_PipelineStepMixin() -> None:

junifer/preprocess/confounds.py

@@ -13,12 +13,12 @@ from nilearn._utils.niimg_conversions import check_niimg_4d
 from nilearn.image import clean_img
 from nilearn.masking import compute_brain_mask
 
-from ..markers import PipelineStepMixin
+from ..pipeline import PipelineStepMixin
 from ..utils import logger, raise_error
 
 
 if TYPE_CHECKING:
-    from nibabel import Nifti1Image, Nifti2Image, MGHImage
+    from nibabel import MGHImage, Nifti1Image, Nifti2Image
 
 
 class BaseConfoundRemover(PipelineStepMixin):

junifer/stats.py

@@ -5,7 +5,7 @@
 # License: AGPL
 
 from functools import partial
-from typing import Callable, Dict, Any, Optional
+from typing import Any, Callable, Dict, Optional
 
 import numpy as np
 from scipy.stats import trim_mean
@@ -15,8 +15,8 @@ from .utils import logger, raise_error
 
 
 def get_aggfunc_by_name(
-        name: str,
+    name: str, func_params: Optional[Dict[str, Any]]
-        func_params: Optional[Dict[str, Any]]) -> Callable:
+) -> Callable:
     """Get an aggregation function by its name.
 
     Parameters

junifer/storage/sqlite.py

@@ -108,8 +108,9 @@ class SQLiteFeatureStorage(PandasBaseFeatureStorage):
                 )
             prefix = element_to_prefix(element)
         # Format URI for engine creation
-        uri = "sqlite:///" \
+        uri = (
-            f"{self.uri.parent}/{prefix}{self.uri.name}"  # type: ignore
+            "sqlite:///" f"{self.uri.parent}/{prefix}{self.uri.name}"
+        )  # type: ignore
         return create_engine(uri, echo=False)
 
     def _save_upsert(
@@ -231,7 +232,8 @@ class SQLiteFeatureStorage(PandasBaseFeatureStorage):
         )
         # Prepare new dataframe
         data_df = pd.DataFrame(
-            data, columns=columns, index=idx)  # type: ignore
+            data, columns=columns, index=idx
+        )  # type: ignore
         # Store dataframe
         self.store_df(df=data_df, meta=meta)
 
@@ -525,8 +527,9 @@ class SQLiteFeatureStorage(PandasBaseFeatureStorage):
         """
         if self.single_output is True:
             raise_error(msg="collect() is not implemented for single output.")
-        logger.info("Collecting data from "
+        logger.info(
-                    f"{self.uri.parent}/*{self.uri.name}")  # type: ignore
+            "Collecting data from " f"{self.uri.parent}/*{self.uri.name}"
+        )  # type: ignore
         # Create new instance
         out_storage = SQLiteFeatureStorage(
             uri=self.uri, single_output=True, upsert="ignore"

junifer/storage/tests/test_sqlite.py

@@ -4,9 +4,8 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Union, List
-
 from pathlib import Path
+from typing import List, Union
 
 import numpy as np
 import pandas as pd
@@ -59,8 +58,9 @@ df_ignore = pd.DataFrame(
 ).set_index(["element", "pk2"])
 
 
-def _read_sql(table_name: str, uri: str,
+def _read_sql(
-              index_col: Union[str, List[str]]) -> pd.DataFrame:
+    table_name: str, uri: str, index_col: Union[str, List[str]]
+) -> pd.DataFrame:
     """Read database table into a pandas DataFrame.
 
     Parameters
@@ -160,8 +160,7 @@ def test_upsert_replace(tmp_path: Path) -> None:
     table_name = storage.store_metadata(meta)
     # Read stored table
     c_df1 = _read_sql(
-        table_name=table_name, uri=uri.as_posix(),
+        table_name=table_name, uri=uri.as_posix(), index_col=["element", "pk2"]
-        index_col=["element", "pk2"]
     )
     # Check if dataframes are equal
     assert_frame_equal(df1, c_df1)
@@ -169,8 +168,7 @@ def test_upsert_replace(tmp_path: Path) -> None:
     storage._save_upsert(df=df2, name=table_name, if_exists="replace")
     # Read stored table
     c_df2 = _read_sql(
-        table_name=table_name, uri=uri.as_posix(),
+        table_name=table_name, uri=uri.as_posix(), index_col=["element", "pk2"]
-        index_col=["element", "pk2"]
     )
     # Check if dataframes are equal
     assert_frame_equal(df2, c_df2)
@@ -198,9 +196,7 @@ def test_upsert_ignore(tmp_path: Path) -> None:
     table_name = storage.store_metadata(meta=meta)
     # Read stored table
     c_df1 = _read_sql(
-        table_name=table_name,
+        table_name=table_name, uri=uri.as_posix(), index_col=["element", "pk2"]
-        uri=uri.as_posix(),
-        index_col=["element", "pk2"]
     )
     # Check if dataframes are equal
     assert_frame_equal(df1, c_df1)
@@ -209,7 +205,8 @@ def test_upsert_ignore(tmp_path: Path) -> None:
         storage.store_df(df2, meta)
     # Read stored table
     c_dfignore = _read_sql(
-        table_name, uri=uri.as_posix(), index_col=["element", "pk2"])
+        table_name, uri=uri.as_posix(), index_col=["element", "pk2"]
+    )
     # Check if dataframes are equal
     assert_frame_equal(c_dfignore, df_ignore)
     # Check for error
@@ -236,8 +233,7 @@ def test_upsert_update(tmp_path: Path) -> None:
     table_name = storage.store_metadata(meta)
     # Read stored table
     c_df1 = _read_sql(
-        table_name=table_name, uri=uri.as_posix(),
+        table_name=table_name, uri=uri.as_posix(), index_col=["element", "pk2"]
-        index_col=["element", "pk2"]
     )
     # Check if dataframes are equal
     assert_frame_equal(df1, c_df1)
@@ -245,8 +241,8 @@ def test_upsert_update(tmp_path: Path) -> None:
     storage.store_df(df2, meta)
     # Read stored table
     c_dfupdate = _read_sql(
-        table_name, uri=uri.as_posix(),
+        table_name, uri=uri.as_posix(), index_col=["element", "pk2"]
-        index_col=["element", "pk2"])
+    )
     # Check if dataframes are equal
     assert_frame_equal(c_dfupdate, df_update)
 
@@ -381,8 +377,9 @@ def test_store_table(tmp_path: Path) -> None:
     table_name = storage.store_metadata(meta)
     # Read stored table
     c_df = _read_sql(
-        table_name=table_name, uri=uri.as_posix(),
+        table_name=table_name,
-        index_col=["element", "scan"]
+        uri=uri.as_posix(),
+        index_col=["element", "scan"],
     )
     # Check if dataframes are equal
     assert_frame_equal(df, c_df)
@@ -400,8 +397,9 @@ def test_store_table(tmp_path: Path) -> None:
         )
     # Read stored table
     c_df_new = _read_sql(
-        table_name=table_name, uri=uri.as_posix(),
+        table_name=table_name,
-        index_col=["element", "scan"]
+        uri=uri.as_posix(),
+        index_col=["element", "scan"],
     )
     # Check if dataframes are equal
     assert_frame_equal(df_new, c_df_new)

junifer/storage/utils.py

@@ -4,11 +4,9 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any
-
 import hashlib
 import json
-from typing import Dict, Optional, Tuple, Union
+from typing import Any, Dict, Optional, Tuple, Union
 
 import numpy as np
 import pandas as pd

junifer/utils/logging.py

@@ -273,8 +273,8 @@ def raise_error(msg: str, klass: Type[Exception] = ValueError) -> NoReturn:
 
 
 def warn_with_log(
-        msg: str,
+    msg: str, category: Optional[Type[Warning]] = RuntimeWarning
-        category: Optional[Type[Warning]] = RuntimeWarning) -> None:
+) -> None:
     """Warn, but first log it.
 
     Parameters