Remove container support

cubids/cli.py

@@ -67,12 +67,6 @@ 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",
@@ -171,11 +165,6 @@ 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",
@@ -267,11 +256,6 @@ 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",
@@ -325,11 +309,6 @@ 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
 
@@ -362,11 +341,6 @@ 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
 
@@ -449,11 +423,6 @@ 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.",
-    )
     return parser
 
 
@@ -501,11 +470,6 @@ 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
 
 
@@ -551,11 +515,6 @@ 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
 
 
@@ -593,12 +552,6 @@ 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
 
 
@@ -632,12 +585,6 @@ 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/tests/test_bond.py

@@ -1028,31 +1028,6 @@ def test_validator(tmp_path):
     assert isinstance(parsed, pd.DataFrame)
 
 
-def test_docker():
-    """Verify that docker is installed and the user has permission to run docker images.
-
-    Returns
-    -------
-    -1  Docker can't be found
-     0  Docker found, but user can't connect to daemon
-     1  Test run OK
-    """
-    try:
-        return_status = 1
-        ret = subprocess.run(["docker", "version"], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-    except OSError as e:
-        from errno import ENOENT
-
-        if e.errno == ENOENT:
-            print("Cannot find Docker engine!")
-            return_status = 0
-        raise e
-    if ret.stderr.startswith(b"Cannot connect to the Docker daemon."):
-        print("Cannot connect to Docker daemon!")
-        return_status = 0
-    assert return_status
-
-
 # def test_image(image='pennlinc/bond:latest'):
 #     """Check whether image is present on local system."""
 #     ret = subprocess.run(['docker', 'images', '-q', image],

cubids/validator.py

@@ -14,7 +14,6 @@
 
 def build_validator_call(path, ignore_headers=False):
     """Build a subprocess command to the bids validator."""
-    # build docker call
     # CuBIDS automatically ignores subject consistency.
     command = ["bids-validator", "--verbose", "--json", "--ignoreSubjectConsistency"]