Merge branch 'main' into ruff

PennLINC · Jan 28, 2025 · d4fbbe2 · d4fbbe2
2 parents 0006256 + 49d9e88
commit d4fbbe2
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Showing 9 changed files with 595 additions and 847 deletions.
diff --git a/cubids/__init__.py b/cubids/__init__.py
@@ -33,16 +33,7 @@
     The credits for the CuBIDS package.
 """
 
-from cubids import (
-    cli,
-    config,
-    constants,
-    cubids,
-    metadata_merge,
-    utils,
-    validator,
-    workflows,
-)
+from cubids import cli, config, constants, cubids, metadata_merge, validator, workflows
 from cubids.__about__ import __copyright__, __credits__, __packagename__, __version__
 
 __all__ = [
@@ -55,7 +46,6 @@
     "constants",
     "cubids",
     "metadata_merge",
-    "utils",
     "validator",
     "workflows",
 ]
diff --git a/cubids/cli.py b/cubids/cli.py
@@ -151,12 +151,6 @@ def _parse_validate():
         help="Run the BIDS validator sequentially on each subject.",
         required=False,
     )
-    parser.add_argument(
-        "--container",
-        action="store",
-        help="Docker image tag or Singularity image file.",
-        default=None,
-    )
     parser.add_argument(
         "--ignore-nifti-headers",
         action="store_true",
@@ -442,11 +436,6 @@ def _parse_group():
             "then output files will go to the specified location."
         ),
     )
-    parser.add_argument(
-        "--container",
-        action="store",
-        help="Docker image tag or Singularity image file.",
-    )
     parser.add_argument(
         "--acq-group-level",
         default="subject",
@@ -595,11 +584,6 @@ def _parse_apply():
         default=False,
         help="ensure that there are no untracked changes before finding groups",
     )
-    parser.add_argument(
-        "--container",
-        action="store",
-        help="Docker image tag or Singularity image file.",
-    )
     parser.add_argument(
         "--acq-group-level",
         default="subject",
@@ -692,11 +676,6 @@ def _parse_datalad_save():
         action="store",
         help="message for this commit",
     )
-    parser.add_argument(
-        "--container",
-        action="store",
-        help="Docker image tag or Singularity image file.",
-    )
 
     return parser
 
@@ -775,11 +754,6 @@ def _parse_undo():
             "sub-X directories and dataset_description.json"
         ),
     )
-    parser.add_argument(
-        "--container",
-        action="store",
-        help="Docker image tag or Singularity image file.",
-    )
 
     return parser
 
@@ -923,11 +897,6 @@ def _parse_copy_exemplars():
     #                     help='only include an exemplar subject from these '
     #                     'listed Acquisition Groups in the exemplar dataset ',
     #                     required=False)
-    parser.add_argument(
-        "--container",
-        action="store",
-        help="Docker image tag or Singularity image file.",
-    )
     parser.add_argument(
         "--force-unlock",
         action="store_true",
@@ -1021,11 +990,6 @@ def _parse_add_nifti_info():
         default=False,
         help="unlock dataset before adding nifti info ",
     )
-    parser.add_argument(
-        "--container",
-        action="store",
-        help="Docker image tag or Singularity image file.",
-    )
     return parser
 
 
@@ -1122,11 +1086,6 @@ def _parse_purge():
         default=False,
         help="ensure that there are no untracked changes before finding groups",
     )
-    parser.add_argument(
-        "--container",
-        action="store",
-        help="Docker image tag or Singularity image file.",
-    )
     return parser
 
 
@@ -1212,11 +1171,6 @@ def _parse_remove_metadata_fields():
         default=[],
         help="space-separated list of metadata fields to remove.",
     )
-    parser.add_argument(
-        "--container",
-        action="store",
-        help="Docker image tag or Singularity image file.",
-    )
 
     return parser
 
@@ -1298,11 +1252,6 @@ def _parse_print_metadata_fields():
             "sub-X directories and dataset_description.json"
         ),
     )
-    parser.add_argument(
-        "--container",
-        action="store",
-        help="Docker image tag or Singularity image file.",
-    )
 
     return parser
 

diff --git a/cubids/config.py b/cubids/config.py
@@ -1,7 +1,8 @@
 """Functions for configuring CuBIDS."""
 
-from pathlib import Path
 import importlib.resources
+from pathlib import Path
+
 import yaml