revert: revert the decision to put ContextManager in parent

prymer/api/variant_lookup.py

@@ -59,13 +59,13 @@
 import logging
 from abc import ABC
 from abc import abstractmethod
-from contextlib import AbstractContextManager
 from dataclasses import dataclass
 from dataclasses import field
 from enum import auto
 from enum import unique
 from pathlib import Path
 from types import TracebackType
+from typing import ContextManager
 from typing import Optional
 from typing import final
 
@@ -76,7 +76,6 @@
 from pysam import VariantFile
 from pysam import VariantRecord
 from strenum import UppercaseStrEnum
-from typing_extensions import override
 
 from prymer.api.span import Span
 from prymer.api.span import Strand
@@ -236,7 +235,7 @@ def build(simple_variant: SimpleVariant) -> "_VariantInterval":
         )
 
 
-class VariantLookup(AbstractContextManager, ABC):
+class VariantLookup(ABC):
     """Base class to represent a variant from a given genomic range.
 
     Attributes:
@@ -322,23 +321,8 @@ def to_variants(
     def _query(self, refname: str, start: int, end: int) -> list[SimpleVariant]:
         """Subclasses must implement this method."""
 
-    def close(self) -> None:
-        """Close this variant lookup."""
-        return None
-
-    def __exit__(
-        self,
-        exc_type: Optional[type[BaseException]],
-        exc_value: Optional[BaseException],
-        traceback: Optional[TracebackType],
-    ) -> None:
-        """Exit this context manager by closing the variant lookup."""
-        super().__exit__(exc_type, exc_value, traceback)
-        self.close()
-        return None
 
-
-class FileBasedVariantLookup(VariantLookup):
+class FileBasedVariantLookup(ContextManager, VariantLookup):
     """Implementation of `VariantLookup` that queries against indexed VCF files each time a query is
     performed. Assumes the index is located adjacent to the VCF file and has the same base name with
     either a .csi or .tbi suffix.
@@ -381,12 +365,22 @@ def _query(self, refname: str, start: int, end: int) -> list[SimpleVariant]:
             simple_variants.extend(self.to_variants(variants, source_vcf=path))
         return sorted(simple_variants, key=lambda x: x.pos)
 
-    @override
     def close(self) -> None:
         """Close the underlying VCF file handles."""
         for handle in self._readers:
             handle.close()
 
+    def __exit__(
+        self,
+        exc_type: Optional[type[BaseException]],
+        exc_value: Optional[BaseException],
+        traceback: Optional[TracebackType],
+    ) -> None:
+        """Exit this context manager while closing the underlying VCF handles."""
+        super().__exit__(exc_type, exc_value, traceback)
+        self.close()
+        return None
+
 
 class VariantOverlapDetector(VariantLookup):
     """Implements `VariantLookup` by reading the entire VCF into memory and loading the resulting

tests/api/test_picking.py

@@ -383,25 +383,29 @@ def test_build_primer_pairs_fails_when_primers_on_wrong_reference(
     assert next(picks) is not None
 
     with pytest.raises(ValueError, match="Left primers exist on different reference"):
-        _picks = list(picking.build_primer_pairs(
-            left_primers=invalid_lefts,
-            right_primers=valid_rights,
-            target=target,
-            amplicon_sizes=MinOptMax(0, 100, 500),
-            amplicon_tms=MinOptMax(0, 80, 150),
-            max_heterodimer_tm=None,
-            weights=weights,
-            fasta_path=fasta,
-        ))
+        _picks = list(
+            picking.build_primer_pairs(
+                left_primers=invalid_lefts,
+                right_primers=valid_rights,
+                target=target,
+                amplicon_sizes=MinOptMax(0, 100, 500),
+                amplicon_tms=MinOptMax(0, 80, 150),
+                max_heterodimer_tm=None,
+                weights=weights,
+                fasta_path=fasta,
+            )
+        )
 
     with pytest.raises(ValueError, match="Right primers exist on different reference"):
-        _picks = list(picking.build_primer_pairs(
-            left_primers=valid_lefts,
-            right_primers=invalid_rights,
-            target=target,
-            amplicon_sizes=MinOptMax(0, 100, 500),
-            amplicon_tms=MinOptMax(0, 80, 150),
-            max_heterodimer_tm=None,
-            weights=weights,
-            fasta_path=fasta,
-        ))
+        _picks = list(
+            picking.build_primer_pairs(
+                left_primers=valid_lefts,
+                right_primers=invalid_rights,
+                target=target,
+                amplicon_sizes=MinOptMax(0, 100, 500),
+                amplicon_tms=MinOptMax(0, 80, 150),
+                max_heterodimer_tm=None,
+                weights=weights,
+                fasta_path=fasta,
+            )
+        )

tests/api/test_variant_lookup.py

@@ -538,9 +538,6 @@ def test_variant_overlap_detector_query(vcf_path: Path) -> None:
         vcf_paths=[vcf_path], min_maf=0.0, include_missing_mafs=True
     )
 
-    # test that we can close the variant overlap detector and make no side effects
-    variant_overlap_detector.close()
-
     # query for all variants
     assert VALID_SIMPLE_VARIANTS_APPROX == variant_overlap_detector_query(
         variant_overlap_detector, refname="chr2", start=8000, end=9101
@@ -566,9 +563,6 @@ def test_variant_overlap_detector_query(vcf_path: Path) -> None:
         variant_overlap_detector, refname="chr2", start=8000, end=9000
     ) == get_simple_variant_approx_by_id("complex-variant-sv-1/1", "rare-dbsnp-snp1-1/1")
 
-    # test that we can close the variant overlap detector and make no side effects
-    variant_overlap_detector.close()
-
 
 @pytest.mark.parametrize("include_missing_mafs", [False, True])
 def test_variant_overlap_query_maf_filter(vcf_path: Path, include_missing_mafs: bool) -> None: