formatting

cellxgene_schema_cli/cellxgene_schema/utils.py

@@ -16,7 +16,7 @@
 
 logger = logging.getLogger(__name__)
 
-SPARSE_MATRIX_TYPES = {"csr","csc","coo"}
+SPARSE_MATRIX_TYPES = {"csr", "csc", "coo"}
 SUPPORTED_SPARSE_MATRIX_TYPES = {"csr"}
 
 
@@ -93,7 +93,7 @@ def get_matrix_format(matrix: DaskArray) -> str:
         matrix_format = matrix_slice.format
     elif isinstance(matrix_slice, np.ndarray):
         matrix_format = "dense"
-    assert matrix_format in SPARSE_MATRIX_TYPES.union({"unknown","dense"})
+    assert matrix_format in SPARSE_MATRIX_TYPES.union({"unknown", "dense"})
     return matrix_format
 
 

cellxgene_schema_cli/cellxgene_schema/validate.py

@@ -17,7 +17,14 @@
 from scipy import sparse
 
 from . import gencode, schema
-from .utils import SPARSE_MATRIX_TYPES, SUPPORTED_SPARSE_MATRIX_TYPES, get_matrix_format, getattr_anndata, is_ontological_descendant_of, read_h5ad
+from .utils import (
+    SPARSE_MATRIX_TYPES,
+    SUPPORTED_SPARSE_MATRIX_TYPES,
+    get_matrix_format,
+    getattr_anndata,
+    is_ontological_descendant_of,
+    read_h5ad,
+)
 
 logger = logging.getLogger(__name__)
 
@@ -52,6 +59,7 @@
 
 ERROR_SUFFIX_SPARSE_FORMAT = f"Please ensure it is either a dense array or one of the supported sparse matrix encodings ({','.join(SUPPORTED_SPARSE_MATRIX_TYPES)})"
 
+
 class Validator:
     """Handles validation of AnnData"""
 
@@ -1018,7 +1026,9 @@ def _validate_sparsity(self):
             if matrix_format in SUPPORTED_SPARSE_MATRIX_TYPES:
                 continue
             elif matrix_format in SPARSE_MATRIX_TYPES and matrix_format not in SUPPORTED_SPARSE_MATRIX_TYPES:
-                self.errors.append(f"Invalid sparse encoding for {x_name} with encoding {matrix_format}. Onle {','.join(SUPPORTED_SPARSE_MATRIX_TYPES)} sparse encodings are supported.")
+                self.errors.append(
+                    f"Invalid sparse encoding for {x_name} with encoding {matrix_format}. Onle {','.join(SUPPORTED_SPARSE_MATRIX_TYPES)} sparse encodings are supported."
+                )
                 continue
             elif matrix_format == "unknown":
                 self.errors.append(f"Unknown encoding for matrix {x_name}. {ERROR_SUFFIX_SPARSE_FORMAT}")
@@ -1224,7 +1234,7 @@ def _has_valid_raw(self, force: bool = False) -> bool:
                 self.errors.append(f"Unknown encoding for matrix {xloc}. {ERROR_SUFFIX_SPARSE_FORMAT}")
                 self._raw_layer_exists = False
                 return self._raw_layer_exists
-            
+
             self._raw_layer_exists = True
             is_sparse_matrix = matrix_format in SPARSE_MATRIX_TYPES
 

cellxgene_schema_cli/tests/test_schema_compliance.py

@@ -10,7 +10,7 @@
 import numpy
 import pandas as pd
 import pytest
-import scipy.sparse 
+import scipy.sparse
 from cellxgene_schema.schema import get_schema_definition
 from cellxgene_schema.utils import getattr_anndata, read_h5ad
 from cellxgene_schema.validate import (
@@ -28,7 +28,6 @@
 )
 from cellxgene_schema.write_labels import AnnDataLabelAppender
 from dask.array import from_array
-
 from fixtures.examples_validate import visium_library_id
 
 schema_def = get_schema_definition()
@@ -278,7 +277,7 @@ def test_raw_values__contains_all_zero_rows_in_tissue_0(self, validator_with_vis
 
         # make sure it's encoded as a sparse matrix to isolate the validation to the contents of the matrix.
         validator.adata.X = validator.adata.X.map_blocks(scipy.sparse.csr_matrix)
-        
+
         validator.adata.raw = validator.adata.copy()
         validator.adata.raw.var.drop("feature_is_filtered", axis=1, inplace=True)
         validator.reset(None, 2)

cellxgene_schema_cli/tests/test_validate.py

@@ -12,13 +12,13 @@
 from cellxgene_ontology_guide.entities import Ontology
 from cellxgene_schema.schema import get_schema_definition
 from cellxgene_schema.validate import (
+    ERROR_SUFFIX_SPARSE_FORMAT,
     ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE,
     ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE_FORBIDDEN,
     ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE_IN_TISSUE_0,
     ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE_REQUIRED,
     SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE,
     SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE_VISIUM_11MM,
-    ERROR_SUFFIX_SPARSE_FORMAT,
     Validator,
     validate,
 )
@@ -386,16 +386,16 @@ def test__validate_from_file(self):
         assert not validator.errors
 
     def test__validate_spatial_visium_dense_matrix_ok(self):
-        '''
+        """
         Test visium specific requirements on a dense X matrix
-        '''
+        """
         validator: Validator = Validator()
         validator._set_schema_def()
         validator.adata = adata_visium.copy()
         validator._visium_and_is_single_true_matrix_size = 2
         _Xdense = validator.adata.X.compute()
-        _Xdense[_Xdense==0] = 1 # ensure the matrix doesn't trigger sparsity error
-        validator.adata.X = from_array(_Xdense.toarray()) # daskify
+        _Xdense[_Xdense == 0] = 1  # ensure the matrix doesn't trigger sparsity error
+        validator.adata.X = from_array(_Xdense.toarray())  # daskify
         validator.adata.raw = validator.adata.copy()
         validator.adata.raw.var.drop("feature_is_filtered", axis=1, inplace=True)
         # Confirm spatial is valid.
@@ -1281,6 +1281,4 @@ def test_has_valid_raw_with_unknown_format(self, mock_get_matrix_format):
         data = np.array([[1, 2, 3], [4, 5, 6]], dtype=np.float32)
         validator = self.create_validator(data, "unknown")
         assert validator._has_valid_raw() is False
-        assert validator.errors == [
-            f'Unknown encoding for matrix X. {ERROR_SUFFIX_SPARSE_FORMAT}'
-        ]
+        assert validator.errors == [f"Unknown encoding for matrix X. {ERROR_SUFFIX_SPARSE_FORMAT}"]