docs: coderabbit suggestions, mkdocs error

fulcrumgenomics · Nov 27, 2024 · 86db19f · 86db19f
1 parent e2d71aa
commit 86db19f
Show file tree

Hide file tree

Showing 2 changed files with 6 additions and 9 deletions.
diff --git a/prymer/api/variant_lookup.py b/prymer/api/variant_lookup.py
@@ -1,10 +1,9 @@
 """
 # Variant Lookup Class and Methods
 
-This module contains the abstract class
-[`VariantLookup`][prymer.api.variant_lookup.VariantLookup] to facilitate retrieval of
-variants that overlap a given genomic coordinate range.  Concrete implementations must implement the
-[`query()`][prymer.api.variant_lookup.VariantLookup.query] method for retrieving variants
+This module contains the class [`VariantLookup`][prymer.api.variant_lookup.VariantLookup] to
+facilitate retrieval of variants that overlap a given genomic coordinate range.
+The [`query()`][`prymer.api.variant_lookup.VariantLookup.query`] method is used to retrieve variants
 that overlap the given range.
 
 [`VariantLookup`][prymer.api.variant_lookup.VariantLookup] needs a list of VCF files to be queried,
@@ -345,7 +344,6 @@ def query(
         maf: Optional[float] = None,
         include_missing_mafs: bool = None,
     ) -> list[SimpleVariant]:
-
         maf = maf if maf is not None else self.min_maf
         include_missing_mafs = (
             include_missing_mafs if include_missing_mafs is not None else self.include_missing_mafs

diff --git a/tests/api/test_variant_lookup.py b/tests/api/test_variant_lookup.py
@@ -19,7 +19,6 @@
 from prymer.api.variant_lookup import VariantType
 from prymer.api.variant_lookup import _DiskBasedLookup
 from prymer.api.variant_lookup import _InMemoryLookup
-from prymer.api.variant_lookup import _VariantLookup
 from prymer.api.variant_lookup import calc_maf_from_filter
 
 
@@ -380,7 +379,7 @@ def get_simple_variant_approx_by_id(*variant_id: str) -> list[SimpleVariant]:
 
 
 def variant_overlap_detector_query(
-    detector: VariantLookup | _VariantLookup,
+    detector: VariantLookup,
     refname: str,
     start: int,
     end: int,
@@ -537,8 +536,8 @@ def test_calc_maf_from_gt_only() -> None:
 
 def test_variant_overlap_detector_query(vcf_path: Path) -> None:
     """Test `VariantOverlapDetector.query()` positional filtering."""
-    variant_overlap_detector = _InMemoryLookup(
-        vcf_paths=[vcf_path], min_maf=0.0, include_missing_mafs=True
+    variant_overlap_detector = VariantLookup(
+        vcf_paths=[vcf_path], min_maf=0.0, include_missing_mafs=True, cached=True
     )
 
     # query for all variants