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()`
- associte pybids validate logic to plugins.validator.skip
(--skip-bids-validation), which will make it simpler for downstream devs
  - left plugins.validator.success in as it can still be used for more
complex logic if desired
- instantiate validator plugin in boilerplate
- moved docstring under `__call__`
- replaced `__init__` with attr
- remove logic comments in Snakefile
- replace individual #noqa: PLR0913 calls to ignore under ruff
configuration

pyproject.toml

@@ -125,3 +125,4 @@ reportImportCycles = false
 
 [tool.ruff]
 select = ["E", "F", "PL", "RUF"]
+ignore = ["PLR0913"]

snakebids/core/construct_bids.py

@@ -6,7 +6,7 @@
 from typing import Optional
 
 
-def bids(  # noqa: PLR0913
+def bids(
     root: Optional[str | Path] = None,
     datatype: Optional[str] = None,
     prefix: Optional[str] = None,

snakebids/core/input_generation.py

@@ -31,7 +31,7 @@
 
 
 @overload
-def generate_inputs(  # noqa: PLR0913
+def generate_inputs(
     bids_dir: Path | str,
     pybids_inputs: InputsConfig,
     pybidsdb_dir: Path | str | None = ...,
@@ -50,7 +50,7 @@ def generate_inputs(  # noqa: PLR0913
 
 
 @overload
-def generate_inputs(  # noqa: PLR0913
+def generate_inputs(
     bids_dir: Path | str,
     pybids_inputs: InputsConfig,
     pybidsdb_dir: Path | str | None = ...,
@@ -68,7 +68,7 @@ def generate_inputs(  # noqa: PLR0913
     ...
 
 
-def generate_inputs(  # noqa: PLR0913
+def generate_inputs(
     bids_dir: Path | str,
     pybids_inputs: InputsConfig,
     pybidsdb_dir: Path | str | None = None,
@@ -150,8 +150,8 @@ 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/exceptions.py

@@ -45,6 +45,6 @@ def __init__(self, misspecified_filter: str):
             "{entity}={filter} or {entity}:{REQUIRED|OPTIONAL|NONE} (case-insensitive)."
         )
 
-        
+
 class SnakebidsPluginError(Exception):
     """Exception raised when a Snakebids plugin encounters a problem"""

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

@@ -13,11 +13,9 @@ 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.skip", False)
 )
 
-
-
 #this adds constraints to the bids naming
 wildcard_constraints:  **get_wildcard_constraints(config['pybids_inputs'])
 

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/strategies.py

@@ -78,7 +78,7 @@ def _filter_invalid_entity_lists(entities: Container[BidsEntity | str]):
 
 
 @st.composite
-def bids_path(  # noqa: PLR0913
+def bids_path(
     draw: st.DrawFn,
     *,
     root: PathLike[str] | str | None = None,
@@ -177,7 +177,7 @@ def inputs_configs() -> st.SearchStrategy[InputsConfig]:
 
 
 @st.composite
-def zip_lists(  # noqa: PLR0913
+def zip_lists(
     draw: st.DrawFn,
     *,
     min_entities: int = 1,
@@ -232,7 +232,7 @@ def zip_lists(  # noqa: PLR0913
 
 
 @st.composite
-def bids_component_row(  # noqa: PLR0913
+def bids_component_row(
     draw: st.DrawFn,
     *,
     min_values: int = 1,
@@ -267,7 +267,7 @@ def bids_component_row(  # noqa: PLR0913
 
 
 @st.composite
-def bids_partial_components(  # noqa: PLR0913
+def bids_partial_components(
     draw: st.DrawFn,
     *,
     min_entities: int = 1,
@@ -331,7 +331,7 @@ def bids_partial_components(  # noqa: PLR0913
 
 
 @st.composite
-def bids_components(  # noqa: PLR0913
+def bids_components(
     draw: st.DrawFn,
     *,
     min_entities: int = 1,
@@ -382,7 +382,7 @@ def bids_components(  # noqa: PLR0913
 
 
 @st.composite
-def expandables(  # noqa: PLR0913
+def expandables(
     draw: st.DrawFn,
     *,
     max_entities: int = 5,
@@ -481,7 +481,7 @@ def datasets(
 
 
 @st.composite
-def datasets_one_comp(  # noqa: PLR0913
+def datasets_one_comp(
     draw: st.DrawFn,
     *,
     root: Optional[Path] = None,

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,
             },
         ),
     )