Remove default arguments for populate-intended-for functions

(`get_key_info_for_fmap_assignment`, `find_compatible_fmaps_for_run`, `find_compatible_fmaps_for_session` and `populate_intended_for`)

Modify unit tests accordingly.

Author: pvelasco

heudiconv/bids.py

@@ -581,7 +581,7 @@ def find_fmap_groups(fmap_dir):
     return fmap_groups
 
 
-def get_key_info_for_fmap_assignment(json_file, matching_parameter='ImagingVolume'):
+def get_key_info_for_fmap_assignment(json_file, matching_parameter):
     """
     Gets key information needed to assign fmaps to other modalities.
 
@@ -639,7 +639,7 @@ def get_key_info_for_fmap_assignment(json_file, matching_parameter='ImagingVolum
     return key_info
 
 
-def find_compatible_fmaps_for_run(json_file, fmap_groups, matching_parameters=['ImagingVolume']):
+def find_compatible_fmaps_for_run(json_file, fmap_groups, matching_parameters):
     """
     Finds compatible fmaps for a given run, for populate_intended_for.
 
@@ -694,7 +694,7 @@ def find_compatible_fmaps_for_run(json_file, fmap_groups, matching_parameters=['
     return compatible_fmap_groups
 
 
-def find_compatible_fmaps_for_session(path_to_bids_session, matching_parameters=['ImagingVolume']):
+def find_compatible_fmaps_for_session(path_to_bids_session, matching_parameters):
     """
     Finds compatible fmaps for all non-fmap runs in a session.
 
@@ -835,7 +835,7 @@ def select_fmap_from_compatible_groups(json_file, compatible_fmap_groups, criter
     return selected_fmap_key
 
 
-def populate_intended_for(path_to_bids_session, matching_parameters='ImagingVolume', criterion='Closest'):
+def populate_intended_for(path_to_bids_session, matching_parameters, criterion):
     """
     Adds the 'IntendedFor' field to the fmap .json files in a session folder.
     It goes through the session folders and for every json file, it finds

heudiconv/tests/test_bids.py

@@ -100,7 +100,7 @@ def test_get_key_info_for_fmap_assignment(tmpdir):
 
     # 1) Call for a non-existing file should give an error:
     with pytest.raises(FileNotFoundError):
-        assert get_key_info_for_fmap_assignment('foo.json')
+        assert get_key_info_for_fmap_assignment('foo.json', 'ImagingVolume')
 
     # 2) matching_parameters = 'Shims'
     json_name = op.join(TESTS_DATA_PATH, remove_suffix(nifti_file, '.nii.gz') + '.json')

heudiconv/tests/test_main.py

@@ -325,12 +325,13 @@ def test_populate_intended_for(session, expected_folder, capfd):
     # Because the function .utils.populate_intended_for already has its own
     # tests, here we just test that "process_extra_commands", when 'command'
     # is 'populate_intended_for' does what we expect (loop through the list of
-    # subjects and calls 'populate_intended_for'). We call it using folders
+    # subjects and calls 'populate_intended_for' using the 'POPULATE_INTENDED_FOR_OPTS'
+    # defined in the heuristic file 'example.py'). We call it using folders
     # that don't exist, and check that the output is the expected.
     bids_folder = expected_folder.split('sub-')[0]
     subjects = ['1', '2']
     process_extra_commands(bids_folder, 'populate-intended-for', [], '',
-                           '', session, subjects, None)
+                           'example', session, subjects, None)
     captured_output = capfd.readouterr().err
     for s in subjects:
         expected_info = 'Adding "IntendedFor" to the fieldmaps in ' + expected_folder.format(sID=s)