Remove --container argument from CLIs (#394)

* Remove --container arg from CLIs.

* Remove container steps from workflows.

* Finish removing stuff.

* Reformat with black.

* Remove utils module.

* Run isort.

* Delete utils.py

* Update cubids/workflows.py

Co-authored-by: Matt Cieslak <[email protected]>

---------

Co-authored-by: Matt Cieslak <[email protected]>

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",
 ]

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
 

cubids/config.py

@@ -1,7 +1,8 @@
 """Functions for configuring CuBIDS."""
 
-from pathlib import Path
 import importlib.resources
+from pathlib import Path
+
 import yaml
 
 

cubids/tests/test_apply.py

@@ -340,7 +340,6 @@ def test_cubids_apply_intendedfor(
             edited_summary_tsv=summary_tsv,
             files_tsv=files_tsv,
             new_tsv_prefix=None,
-            container=None,
         )
 
         with open(fmap_json) as f:
@@ -357,5 +356,4 @@ def test_cubids_apply_intendedfor(
                 edited_summary_tsv=summary_tsv,
                 files_tsv=files_tsv,
                 new_tsv_prefix=None,
-                container=None,
             )

cubids/tests/test_bond.py

@@ -24,13 +24,13 @@
     get_data,
 )
 from cubids.validator import (
+    bids_validator_version,
     build_validator_call,
+    extract_summary_info,
+    get_bids_validator_version,
     parse_validator_output,
     run_validator,
-    get_bids_validator_version,
-    extract_summary_info,
     update_dataset_description,
-    bids_validator_version,
 )
 
 COMPLETE_KEY_GROUPS = [

cubids/tests/utils.py

@@ -1,6 +1,7 @@
 """Utility functions for CuBIDS' tests."""
 
 import hashlib
+import importlib.resources
 import json
 import os
 import shutil
@@ -10,7 +11,6 @@
 import nibabel as nb
 import numpy as np
 import pandas as pd
-import importlib.resources
 
 TEST_DATA = importlib.resources.files("cubids") / "tests/data"