Drop skip_bids_validation.

qsirecon/cli/parser.py

@@ -462,23 +462,6 @@ def parse_args(args=None, namespace=None):
             "Please modify the output path."
         )
 
-    # Validate inputs
-    if not opts.skip_bids_validation:
-        if opts.recon_input is not None:
-            build_log.info("Skipping BIDS validation because inputs are BIDS derivatives")
-        else:
-            from ..utils.bids import validate_input_dir
-
-            build_log.info(
-                "Making sure the input data is BIDS compliant (warnings can be ignored in most "
-                "cases)."
-            )
-            validate_input_dir(
-                config.environment.exec_env,
-                opts.bids_dir,
-                opts.participant_label,
-            )
-
     # Setup directories
     config.execution.log_dir = config.execution.output_dir / "logs"
     # Check and create output and working directories

tests/opts_tests.py

@@ -65,16 +65,3 @@ def test_set_freesurfer_license(tmpdir):
     opts = get_parser().parse_args(fsarg.split(' '))
     set_freesurfer_license(opts)
     assert os.getenv('FS_LICENSE') == f'{lic3}'
-
-
-@pytest.mark.parametrize("will_validate,opts_str", (
-  (True, base_args),                                           # run if base args
-  (False, base_args + " --skip_bids_validation"),              # not if skipped
-  (False, base_args + " --recon-only"),                        # or recon all
-  (False, base_args + " --skip_bids_validation --recon-only")  # or both
-))
-def test_validate_bids(monkeypatch, opts_str, will_validate):
-    # from ..utils.bids import validate_input_dir
-    monkeypatch.setattr("qsirecon.utils.bids.validate_input_dir", lambda *kargs: True)
-    opts = get_parser().parse_args(opts_str.split(' '))
-    assert will_validate == validate_bids(opts)