fix: remove unncessary add_all in OverlapDetector

bedspec/_bedspec.py

@@ -102,8 +102,7 @@ def __init_subclass__(cls) -> None:
         return super().__init_subclass__()
 
     @final
-    @property
-    def length(self) -> int:
+    def __len__(self) -> int:
         """The length of this record."""
         return 1
 
@@ -132,8 +131,7 @@ def __post_init__(self) -> None:
             raise ValueError("start must be greater than 0 and less than end!")
 
     @final
-    @property
-    def length(self) -> int:
+    def __len__(self) -> int:
         """The length of this record."""
         return self.end - self.start
 

bedspec/overlap/_overlap.py

@@ -36,26 +36,22 @@ def __init__(self, features: Iterable[ReferenceSpanType] | None = None) -> None:
         self._refname_to_tree: dict[Refname, cr.cgranges] = defaultdict(cr.cgranges)  # type: ignore[attr-defined,name-defined]  # pyright: ignore[reportUnknownArgumentType, reportUnknownMemberType]
         self._refname_to_is_indexed: dict[Refname, bool] = defaultdict(lambda: False)
         if features is not None:
-            self.add_all(features)
+            self.add(*features)
 
     @override
     def __iter__(self) -> Iterator[ReferenceSpanType]:
         """Iterate over the features in the overlap detector."""
         return chain(*self._refname_to_features.values())
 
-    def add(self, feature: ReferenceSpanType) -> None:
+    def add(self, *features: ReferenceSpanType) -> None:
         """Add a feature to this overlap detector."""
-        refname: Refname = feature.refname
-        feature_idx: int = len(self._refname_to_features[refname])
-
-        self._refname_to_features[refname].append(feature)
-        self._refname_to_tree[refname].add(refname, feature.start, feature.end, feature_idx)  # pyright: ignore[reportUnknownMemberType]
-        self._refname_to_is_indexed[refname] = False  # mark that this tree needs re-indexing
-
-    def add_all(self, features: Iterable[ReferenceSpanType]) -> None:
-        """Adds one or more features to this overlap detector."""
         for feature in features:
-            self.add(feature)
+            refname: Refname = feature.refname
+            feature_idx: int = len(self._refname_to_features[refname])
+
+            self._refname_to_features[refname].append(feature)
+            self._refname_to_tree[refname].add(refname, feature.start, feature.end, feature_idx)  # pyright: ignore[reportUnknownMemberType]
+            self._refname_to_is_indexed[refname] = False  # mark that this tree needs re-indexing
 
     def overlapping(self, feature: ReferenceSpan) -> Iterator[ReferenceSpanType]:
         """Yields all the overlapping features for a given query feature."""

tests/test_bedspec.py

@@ -152,7 +152,7 @@ def test_point_bed_types_have_a_territory() -> None:
 
 def test_point_bed_types_are_length_1() -> None:
     """Test that a point BED has a length of 1."""
-    assert Bed2(refname="chr1", start=1).length == 1
+    assert len(Bed2(refname="chr1", start=1)) == 1
 
 
 def test_simple_bed_types_have_a_territory() -> None:
@@ -169,9 +169,9 @@ def test_simple_bed_types_have_a_territory() -> None:
 
 def test_simple_bed_types_have_length() -> None:
     """Test that a simple BED has the right length."""
-    assert Bed3(refname="chr1", start=1, end=2).length == 1
-    assert Bed3(refname="chr1", start=1, end=3).length == 2
-    assert Bed3(refname="chr1", start=1, end=4).length == 3
+    assert len(Bed3(refname="chr1", start=1, end=2)) == 1
+    assert len(Bed3(refname="chr1", start=1, end=3)) == 2
+    assert len(Bed3(refname="chr1", start=1, end=4)) == 3
 
 
 def test_simple_bed_validates_start_and_end() -> None:

tests/test_overlap.py

@@ -34,7 +34,8 @@ def test_we_can_add_all_features_to_the_overlap_detector() -> None:
     bed1 = Bed3(refname="chr1", start=1, end=2)
     bed2 = Bed4(refname="chr2", start=4, end=5, name="Clint Valentine")
     detector: OverlapDetector[Bed3 | Bed4] = OverlapDetector()
-    detector.add_all([bed1, bed2])
+    beds: list[Bed3 | Bed4] = [bed1, bed2]
+    detector.add(*beds)
     assert list(detector) == [bed1, bed2]