add test + description.json for passing validation

- also includes quality fixes"

snakebids/cli.py

@@ -150,7 +150,7 @@ def create_parser(include_snakemake=False):
         "--skip-bids-validation",
         "--skip_bids-validation",
         action="store_true",
-        help=("Skip bids validation of input dataset")
+        help=("Skip bids validation of input dataset"),
     )
 
     standard_group.add_argument(

snakebids/core/input_generation.py

@@ -270,7 +270,7 @@ def generate_inputs(
 
     # Attempt to validate with node bids-validator, if needed
     validated = _validate_input_dir if not skip_bids_validation else None
-    
+
     # Generates a BIDSLayout
     # If not skipping validation, set validate indicator to opposite of output
     # from _validate_input_dir, otherwise do not validate
@@ -351,7 +351,7 @@ def _gen_bids_layout(
         derivatives subdirectory of the input dataset.
 
     validate : bool
-        A boolean that indicates whether validation should be performed on 
+        A boolean that indicates whether validation should be performed on
         input dataset
 
     pybids_database_dir : str
@@ -394,9 +394,9 @@ def _validate_input_dir(
     bids_dir: Union[Path, str],
 ) -> bool:
     """Perform validation of dataset. Initial attempt at validation performed
-    with node-version of bids-validator. If not found, will fall back to 
+    with node-version of bids-validator. If not found, will fall back to
     validation integrated into pybids.
-    
+
     Parameters
     ----------
     bids_dir : str
@@ -408,16 +408,14 @@ def _validate_input_dir(
         Indication of whether validation was successfully performed using
         the node-version of bids-validator
     """
-    try: 
-        validator_config_dict = {
-            "ignoredFiles": ['/participants.tsv']
-        }
+    try:
+        validator_config_dict = {"ignoredFiles": ["/participants.tsv"]}
 
         with tempfile.NamedTemporaryFile(mode="w+", suffix=".json") as temp:
             temp.write(json.dumps(validator_config_dict))
             temp.flush()
 
-        subprocess.check_call(['bids-validator', str(bids_dir), '-c', temp.name])
+        subprocess.check_call(["bids-validator", str(bids_dir), "-c", temp.name])
 
         return True
     except FileNotFoundError:

snakebids/tests/data/dataset_description.json

@@ -0,0 +1,4 @@
+{
+    "Name": "Snakebids - test dataset",
+    "BIDSVersion": "1.8.0"
+}

snakebids/tests/test_app.py

@@ -100,7 +100,7 @@ def test_runs_in_correct_mode(
                 "pybids_db_reset": True,
                 "snakefile": Path("Snakefile"),
                 "output_dir": outputdir.resolve(),
-                "skip_bids_validation": False
+                "skip_bids_validation": False,
             }
         )
         if root == "app" and tail == "":

snakebids/tests/test_generate_inputs.py

@@ -98,10 +98,7 @@ def test_ambiguous_paths_with_extra_entities_leads_to_error(
 
         with pytest.raises(ConfigError):
             generate_inputs(
-                root, 
-                pybids_inputs, 
-                skip_bids_validation=True, 
-                use_bids_inputs=True
+                root, pybids_inputs, skip_bids_validation=True, use_bids_inputs=True
             )
 
     @settings(
@@ -129,10 +126,7 @@ def test_ambiguous_paths_with_missing_entity_leads_to_error(
 
         with pytest.raises(ConfigError):
             generate_inputs(
-                root, 
-                pybids_inputs, 
-                skip_bids_validation=True, 
-                use_bids_inputs=True
+                root, pybids_inputs, skip_bids_validation=True, use_bids_inputs=True
             )
 
     @settings(
@@ -169,10 +163,7 @@ def test_entity_excluded_when_filter_false(
         )
 
         data = generate_inputs(
-            root, 
-            pybids_inputs, 
-            skip_bids_validation=True, 
-            use_bids_inputs=True
+            root, pybids_inputs, skip_bids_validation=True, use_bids_inputs=True
         )
         assert data == expected
 
@@ -252,10 +243,7 @@ def test_entity_excluded_when_filter_true(self, tmpdir: Path, dataset: BidsDatas
         )
 
         data = generate_inputs(
-            root, 
-            pybids_inputs, 
-            skip_bids_validation=True, 
-            use_bids_inputs=True
+            root, pybids_inputs, skip_bids_validation=True, use_bids_inputs=True
         )
         assert data == expected
 
@@ -1007,24 +995,36 @@ def start(self, tmpdir):
 
         # Copy test data
         shutil.copytree(self.bids_dir, f"{self.tmp_dir}/data")
+        assert filecmp.dircmp("snakebids/tests/data/bids_t1w", f"{self.tmp_dir}/data")
 
+        # Copy dataset description
+        shutil.copy(
+            "snakebids/tests/data/dataset_description.json", f"{self.tmp_dir}/data"
+        )
 
     def test_check_validator(self):
-        """Test validator defaults to pybids"""
-        assert _validate_input_dir(self.bids_dir) == False 
-
+        """Test validator defaults to pybids (i.e. False)"""
+        assert _validate_input_dir(self.bids_dir) == False
 
-    # Test for validation failure
     def test_pybids_validation_fail(self):
         with pytest.raises(BIDSValidationError):
             _gen_bids_layout(
-                bids_dir=f"{self.tmp_dir}/data",
+                bids_dir=self.bids_dir,
                 derivatives=False,
                 pybids_database_dir=None,
                 pybids_reset_database=False,
                 validate=True,
             )
 
+    def test_pybids_validation_pass(self):
+        assert _gen_bids_layout(
+            bids_dir=f"{self.tmp_dir}/data",
+            derivatives=False,
+            pybids_database_dir=None,
+            pybids_reset_database=False,
+            validate=True,
+        )
+
 
 class TestDB:
     @pytest.fixture(autouse=True)