Merge branch 'main' into schema

.gitignore

@@ -136,4 +136,5 @@ data/*
 .DS_Store
 notebooks/testdata
 .vscode/settings.json
-notebooks/test1
+notebooks/test1
+docs/generated

cubids/cli.py

@@ -118,6 +118,7 @@ def _parse_validate():
     parser = argparse.ArgumentParser(
         description="cubids validate: Wrapper around the official BIDS Validator",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
 
@@ -245,6 +246,7 @@ def _parse_bids_version():
     parser = argparse.ArgumentParser(
         description="cubids bids-version: Get BIDS Validator and Schema version",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
 
@@ -328,6 +330,7 @@ def _parse_bids_sidecar_merge():
     parser = argparse.ArgumentParser(
         description=("bids-sidecar-merge: merge critical keys from one sidecar to another"),
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     IsFile = partial(_is_file, parser=parser)
 
@@ -412,6 +415,7 @@ def _parse_group():
     parser = argparse.ArgumentParser(
         description="cubids group: find key and parameter groups in BIDS",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
 
@@ -534,6 +538,7 @@ def _parse_apply():
     parser = argparse.ArgumentParser(
         description=("cubids apply: apply the changes specified in a tsv to a BIDS directory"),
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
     IsFile = partial(_is_file, parser=parser)
@@ -549,7 +554,7 @@ def _parse_apply():
     )
     parser.add_argument(
         "edited_summary_tsv",
-        type=IsFile,
+        type=Path,
         action="store",
         help=(
             "path to the _summary.tsv that has been edited "
@@ -561,7 +566,7 @@ def _parse_apply():
     )
     parser.add_argument(
         "files_tsv",
-        type=IsFile,
+        type=Path,
         action="store",
         help=(
             "path to the _files.tsv that has been edited "
@@ -669,6 +674,7 @@ def _parse_datalad_save():
     parser = argparse.ArgumentParser(
         description=("cubids datalad-save: perform a DataLad save on a BIDS directory"),
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
 
@@ -756,6 +762,7 @@ def _parse_undo():
     parser = argparse.ArgumentParser(
         description="cubids undo: revert most recent commit",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
 
@@ -852,9 +859,10 @@ def _parse_copy_exemplars():
             "one subject from each Acquisition Group in the BIDS dataset"
         ),
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
-    IsFile = partial(_is_file, parser=parser)
+    # IsFile = partial(_is_file, parser=parser)
 
     parser.add_argument(
         "bids_dir",
@@ -868,7 +876,7 @@ def _parse_copy_exemplars():
     )
     parser.add_argument(
         "exemplars_dir",
-        type=PathExists,
+        type=Path,
         action="store",
         help=(
             "name of the directory to create where to store exemplar dataset. "
@@ -879,7 +887,7 @@ def _parse_copy_exemplars():
     )
     parser.add_argument(
         "exemplars_tsv",
-        type=IsFile,
+        type=Path,
         action="store",
         help=(
             "path to the .tsv that lists one "
@@ -987,6 +995,7 @@ def _parse_add_nifti_info():
             "files to the sidecars of each dataset"
         ),
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
 
@@ -1081,6 +1090,7 @@ def _parse_purge():
     parser = argparse.ArgumentParser(
         description="cubids purge: purge associations from the dataset",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
     IsFile = partial(_is_file, parser=parser)
@@ -1182,6 +1192,7 @@ def _parse_remove_metadata_fields():
     parser = argparse.ArgumentParser(
         description="cubids remove-metadata-fields: delete fields from metadata",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
 
@@ -1274,6 +1285,7 @@ def _parse_print_metadata_fields():
     parser = argparse.ArgumentParser(
         description="cubids print-metadata-fields: print all unique metadata fields",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
 
@@ -1359,7 +1371,7 @@ def _get_parser():
     """
     from cubids import __version__
 
-    parser = argparse.ArgumentParser(prog="cubids")
+    parser = argparse.ArgumentParser(prog="cubids", allow_abbrev=False)
     parser.add_argument("-v", "--version", action="version", version=__version__)
     subparsers = parser.add_subparsers(help="CuBIDS commands")
 
@@ -1371,6 +1383,7 @@ def _get_parser():
             parents=[subparser],
             help=subparser.description,
             add_help=False,
+            allow_abbrev=False,
         )
 
     return parser