run pre-commit magic!

Author: bpinsard

README.rst

@@ -71,7 +71,7 @@ You can run your conversion automatically (which will produce a ``.heudiconv`` d
 .. image:: figs/workflow.png
 
 
-``heudiconv`` comes with `existing heuristics <https://github.com/nipy/heudiconv/tree/master/heudiconv/heuristics>`_ which can be used as is, or as examples. 
+``heudiconv`` comes with `existing heuristics <https://github.com/nipy/heudiconv/tree/master/heudiconv/heuristics>`_ which can be used as is, or as examples.
 For instance, the Heuristic `convertall <https://github.com/nipy/heudiconv/blob/master/heudiconv/heuristics/convertall.py>`_ extracts standard metadata from all matching DICOMs.
 ``heudiconv`` creates mapping files, ``<something>.edit.text`` which lets researchers simply establish their own conversion mapping.
 

heudiconv/convert.py

@@ -223,7 +223,7 @@ def prep_conversion(
                 custom_grouping=getattr(heuristic, "grouping", None),
                 # callable which will be provided dcminfo and returned
                 # structure extend seqinfo
-                custom_seqinfo=getattr(heuristic, 'custom_seqinfo', None),
+                custom_seqinfo=getattr(heuristic, "custom_seqinfo", None),
             )
         elif seqinfo is None:
             raise ValueError("Neither 'dicoms' nor 'seqinfo' is given")

heudiconv/dicoms.py

@@ -9,7 +9,18 @@
 from pathlib import Path
 import sys
 import tarfile
-from typing import TYPE_CHECKING, Any, Dict, Hashable, List, NamedTuple, Optional, Union, Protocol, overload
+from typing import (
+    TYPE_CHECKING,
+    Any,
+    Dict,
+    Hashable,
+    List,
+    NamedTuple,
+    Optional,
+    Protocol,
+    Union,
+    overload,
+)
 from unittest.mock import patch
 import warnings
 
@@ -90,14 +101,19 @@ def create_seqinfo(
     global total_files
     total_files += len(series_files)
 
-    custom_seqinfo_data = custom_seqinfo(wrapper=mw, series_files=series_files) \
-        if custom_seqinfo else None
+    custom_seqinfo_data = (
+        custom_seqinfo(wrapper=mw, series_files=series_files)
+        if custom_seqinfo
+        else None
+    )
     try:
         hash(custom_seqinfo_data)
     except TypeError:
-        raise RuntimeError("Data returned by the heuristics custom_seqinfo is not hashable. "
-                           "See https://heudiconv.readthedocs.io/en/latest/heuristics.html#custom_seqinfo for more "
-                           "details.")
+        raise RuntimeError(
+            "Data returned by the heuristics custom_seqinfo is not hashable. "
+            "See https://heudiconv.readthedocs.io/en/latest/heuristics.html#custom_seqinfo for more "
+            "details."
+        )
 
     return SeqInfo(
         total_files_till_now=total_files,

heudiconv/heuristics/convertall.py

@@ -6,7 +6,7 @@
 from heudiconv.dicoms import dw
 from heudiconv.utils import SeqInfo
 
-lgr = logging.getLogger('heudiconv')
+lgr = logging.getLogger("heudiconv")
 
 
 def create_key(
@@ -25,6 +25,7 @@ def custom_seqinfo(wrapper: dw.Wrapper, series_files: list[str]) -> tuple[str, s
     # the sample series file as was requested
     # in https://github.com/nipy/heudiconv/pull/333
     from nibabel.nicom.dicomwrappers import WrapperError
+
     try:
         affine = wrapper.affine.tobytes()
     except WrapperError:

heudiconv/parser.py

@@ -224,7 +224,7 @@ def get_study_sessions(
             file_filter=getattr(heuristic, "filter_files", None),
             dcmfilter=getattr(heuristic, "filter_dicom", None),
             custom_grouping=getattr(heuristic, "grouping", None),
-            custom_seqinfo=getattr(heuristic, 'custom_seqinfo', None),
+            custom_seqinfo=getattr(heuristic, "custom_seqinfo", None),
         )
 
         if sids:

heudiconv/tests/test_dicoms.py

@@ -107,14 +107,12 @@ def test_custom_seqinfo() -> None:
     dcmfiles = glob(op.join(TESTS_DATA_PATH, "phantom.dcm"))
 
     seqinfos = group_dicoms_into_seqinfos(
-        dcmfiles,
-        "studyUID",
-        flatten=True,
-        custom_seqinfo=custom_seqinfo)
+        dcmfiles, "studyUID", flatten=True, custom_seqinfo=custom_seqinfo
+    )
 
     seqinfo = list(seqinfos.keys())[0]
 
-    assert hasattr(seqinfo, 'custom')
+    assert hasattr(seqinfo, "custom")
     assert isinstance(seqinfo.custom, tuple)
     assert len(seqinfo.custom) == 2
     assert seqinfo.custom[1] == dcmfiles[0]