fix docstrings and update validate logic

- remove mention of uncommenting lines
- rephrased "Enable by default..." to "Boilerplate starts with the
validator plugin enabled..." in the overview doc
- focused docstring of validation using pybids in `generate_inputs()`
- updated boilerplate logic for performing pybids validation based on
plugin success
- instantiate validator plugin in boilerplate
- moved docstring under `__call__`
- replaced `__init__` with attr

snakebids/core/input_generation.py

@@ -149,8 +149,8 @@ def generate_inputs(  # noqa: PLR0913
         the default behaviour
 
     validate
-        If False, skips validation of BIDS directory. Otherwise use node.js 
-        implementation of bids-validator, falling back on pybids validation.
+        If True performs validation of BIDS directory using pybids, otherwise 
+        skips validation.
 
     Returns
     -------

snakebids/plugins/validator.py

@@ -3,6 +3,8 @@
 import subprocess
 import tempfile
 
+import attr
+
 from snakebids.app import SnakeBidsApp
 from snakebids.exceptions import SnakebidsPluginError
 
@@ -13,21 +15,21 @@ class InvalidBidsError(SnakebidsPluginError):
     """Error raised if an input BIDS dataset is invalid."""
 
 
+@attr.define
 class BidsValidator:
-    """Perform BIDS validation of dataset, falling back to the pybids
-    version of validation if the node-version of bids-validator is
-    not found.
-
-    Parameters
-    ----------
-    app
-        Snakebids application to be run
-    """
-
-    def __init__(self, raise_invalid_bids: bool = True) -> None:
-        self.raise_invalid_bids = raise_invalid_bids
+    raise_invalid_bids: bool = attr.field(default=True)
 
     def __call__(self, app: SnakeBidsApp) -> None:
+        """Perform BIDS validation of dataset, falling back to the pybids
+        version of validation if the node-version of bids-validator is
+        not found. If the validation of the dataset fails, an InvalidBidsError
+        is raised.
+
+        Parameters
+        ----------
+        app
+            Snakebids application to be run
+        """
         # Skip bids validation
         if app.config["plugins.validator.skip"]:
             return

snakebids/project_template/{{cookiecutter.app_name}}/config/snakebids.yml

@@ -79,10 +79,9 @@ parse_args:
  # custom command-line parameters can then be added, these will get added to the config and also accessible to plugins
  # below are examples for plugin and custom parameters (e.g. config['smoothing_fwhm'])
   --skip_bids_validation:
-    help: 'Skip validation of BIDS dataset. BIDS validation is performed by 
-          default using the bids-validator (if installed) or with the pybids
-          validator implementation (if bids-validator is not installed). 
-          (default: %(default)s)'
+    help: 'Skip validation of BIDS dataset. BIDS validation is performed by
+          default using the bids-validator plugin (if installed/enabled) or with the pybids 
+          validator implementation (if bids-validator is not installed/enabled).'
     dest: "plugins.validator.skip"
     action: "store_true"
     default: False

snakebids/project_template/{{cookiecutter.app_name}}/workflow/Snakefile

@@ -13,9 +13,17 @@ inputs = generate_inputs(
     derivatives=config.get("derivatives", None),
     participant_label=config.get("participant_label", None),
     exclude_participant_label=config.get("exclude_participant_label", None),
-    validate=config.get("plugins.validator.success", False),
+    validate=(
+        not config.get("plugins.validator.success") and 
+        not config.get("plugins.validator.skip")
+    )
 )
 
+# If skip -> False and __ -> False
+# If validate success -> False and True -> False
+# If validate fail/None -> True and True -> True
+
+# if bids-validator not run, pybids will run (assuming not InvalidBidsError)
 
 
 #this adds constraints to the bids naming

snakebids/project_template/{{cookiecutter.app_name}}/{{cookiecutter.app_name}}/run.py

@@ -14,7 +14,7 @@ def get_parser():
 def main():
     app = SnakeBidsApp(
         Path(__file__).resolve().parent.parent,  # to get repository root
-        plugins=[BidsValidator],
+        plugins=[BidsValidator()],
     )
     app.run_snakemake()
 

snakebids/tests/mock/config.py

@@ -38,8 +38,8 @@
     },
     "--skip_bids_validation": {
         "help": "Skip validation of BIDS dataset. BIDS validation is performed by "
-        "default using the bids-validator (if installed) or with the pybids "
-        "validator implementation (if bids-validator is not installed). "
+        "default using the bids-validator plugin (if installed/enabled) or with the pybids "
+        "validator implementation (if bids-validator is not installed/enabled). "
         "(default: %(default)s)",
         "dest": "plugins.validator.skip",
         "action": "store_true",

snakebids/tests/mock/config.yaml

@@ -69,10 +69,9 @@ parse_args:
     nargs: '+'
 
   --skip_bids_validation:
-    help: 'Skip validation of BIDS dataset. BIDS validation is performed by 
-          default using the bids-validator (if installed) or with the pybids
-          validator implementation (if bids-validator is not installed). 
-          (default: %(default)s)'
+    help: 'Skip validation of BIDS dataset. BIDS validation is performed by
+          default using the bids-validator plugin (if installed/enabled) or with the pybids 
+          validator implementation (if bids-validator is not installed/enabled).'
     dest: "plugins.validator.skip"
     action: "store_true"
     default: False

snakebids/tests/test_template.py

@@ -33,7 +33,7 @@ def test_template_dry_runs_successfully(tmp_path: Path):
                 "path_bold": None,
                 "participant_label": None,
                 "exclude_participant_label": None,
-                "skip_bids_validation": True,
+                "plugins.validator.skip": True,
             },
         ),
     )