update docs, rename validation fn

- update docs to include information about skipping bids validation
- renamed function from validate_input_dir -> validate_bids_dir
- added exception to skipping bids-validation with node if all paths
  provided are custom
- quality fixes

docs/bids_app/workflow.rst

@@ -14,10 +14,10 @@ To get access to these additions, the base Snakefile for a snakebids workflow sh
     inputs = snakebids.generate_inputs(
         bids_dir=config["bids_dir"],
         pybids_inputs=config["pybids_inputs"],
+        skip_bids_validation=config["skip_bids_validation"],
         derivatives=config.get("derivatives", None),
         participant_label=config.get("participant_label", None),
         exclude_participant_label=config.get("exclude_participant_label", None)
-
     )
 
     #this adds constraints to the bids naming

docs/running_snakebids/overview.md

@@ -19,6 +19,8 @@ Indexing of large datasets can be a time-consuming process. Snakebids, through `
 1. Uncomment the lines in `snakebids.yml` containing `pybids_db_dir` and `pybids_db_reset`.
 1. The variables can be updated directly in this file or through the CLI by using `-pybidsdb-dir {dir}` to specify the database path and `--reset-db` to indicate that the database should be updated. _Note: CLI arguments take precendence if both CLI and config variables are set._
 
+Input BIDS datasets are also validated via the bids-validator. By default, this feature uses the command-line (node.js) version of the [validator](https://www.npmjs.com/package/bids-validator). If this is not found to be installed on the system, the `pybids` version of validation will be performed instead. To opt-out validation, one can invoke `--skip-bids-validation`. 
+
 Workflow mode
 =============
 

snakebids/core/input_generation.py

@@ -135,10 +135,10 @@ def generate_inputs(
         be specified if participant_label is specified
 
     skip_bids_validation : bool, optional
-        If True, will not perform validation of the input dataset. Otherwise, 
+        If True, will not perform validation of the input dataset. Otherwise,
         validation is first attempted by performing a system call to `bids-validator`
-        (e.g. node version), which is has more comprehensive coverage, before falling 
-        back on the python version of the validator. 
+        (e.g. node version), which is has more comprehensive coverage, before falling
+        back on the python version of the validator.
 
     use_bids_inputs : bool, optional
         If True, opts in to the new :class:`BidsDataset` output, otherwise returns the
@@ -268,12 +268,15 @@ def generate_inputs(
         participant_label, exclude_participant_label
     )
 
-    # Attempt to validate with node bids-validator, if needed
-    validated = _validate_input_dir if not skip_bids_validation else None
+    # Attempt to validate with node bids-validator
+    validated = (
+        _validate_bids_dir
+        if not skip_bids_validation and not _all_custom_paths(pybids_inputs)
+        else None
+    )
 
-    # Generates a BIDSLayout
     # If not skipping validation, set validate indicator to opposite of output
-    # from _validate_input_dir, otherwise do not validate
+    # from _validate_bids_dir, otherwise do not validate
     layout = (
         _gen_bids_layout(
             bids_dir=bids_dir,
@@ -390,7 +393,7 @@ def _gen_bids_layout(
     )
 
 
-def _validate_input_dir(
+def _validate_bids_dir(
     bids_dir: Union[Path, str],
 ) -> bool:
     """Perform validation of dataset. Initial attempt at validation performed

snakebids/tests/test_generate_inputs.py

@@ -29,7 +29,7 @@
     _generate_filters,
     _get_lists_from_bids,
     _parse_custom_path,
-    _validate_input_dir,
+    _validate_bids_dir,
     generate_inputs,
 )
 from snakebids.exceptions import ConfigError, PybidsError
@@ -1004,7 +1004,7 @@ def start(self, tmpdir):
 
     def test_check_validator(self):
         """Test validator defaults to pybids (i.e. False)"""
-        assert _validate_input_dir(self.bids_dir) == False
+        assert _validate_bids_dir(self.bids_dir) == False
 
     def test_pybids_validation_fail(self):
         with pytest.raises(BIDSValidationError):