feat: remove cgranges for superintervals

.github/workflows/publish_bedspec.yml

@@ -16,7 +16,6 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-          submodules: true
 
       - uses: rickstaa/action-contains-tag@v1
         id: contains_tag
@@ -102,7 +101,6 @@ jobs:
         with:
           fetch-depth: 0
           ref: ${{ github.ref_name }}
-          submodules: true
 
       - name: Generate a Changelog
         uses: orhun/git-cliff-action@v3

.github/workflows/tests.yml

@@ -19,8 +19,6 @@ jobs:
         PYTHON_VERSION: ["3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
-        with:
-          submodules: "true"
 
       - name: Set up Python ${{ matrix.PYTHON_VERSION }}
         uses: actions/setup-python@v5

.github/workflows/wheels.yml

@@ -7,55 +7,26 @@ on:
 
 jobs:
   build-wheels:
-    name: Build wheels for ${{ matrix.python }}-${{ matrix.platform.target }}_${{ matrix.platform.arch }} on ${{ matrix.platform.os }}
-    runs-on: ${{ matrix.platform.os }}
+    name: Build wheels for ${{ matrix.PYTHON_VERSION }}
+    runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: [cp312]
-        platform:
-          - os: ubuntu-latest
-            target: manylinux
-            arch: x86_64
-          - os: ubuntu-latest
-            target: musllinux
-            arch: x86_64
-          # These don't work right now - they just hang while pulling the build image from quay.
-          # If this doesn't resolve itself, we could try to configure different images:
-          # https://cibuildwheel.readthedocs.io/en/stable/options/.
-          # - os: ubuntu-latest
-          #   target: manylinux
-          #   arch: aarch64
-          # - os: ubuntu-latest
-          #   target: musllinux
-          #   arch: aarch64
-          - os: macos-latest
-            target: macosx
-            arch: x86_64
-          - os: macos-latest
-            target: macosx
-            arch: arm64
+        PYTHON_VERSION: ["3.10", "3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v4
-        with:
-          submodules: "true"
 
-      - uses: actions/setup-python@v5
+      - name: Set up Python ${{ matrix.PYTHON_VERSION }}
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.12
-
-      - name: Install cibuildwheel
-        run: python -m pip install cibuildwheel==2.17.0
+          python-version: ${{ matrix.PYTHON_VERSION }}
 
       - name: Build wheels
-        run: python -m cibuildwheel --output-dir wheelhouse
-        env:
-          CIBW_ARCHS: ${{ matrix.platform.arch }}
-          CIBW_BUILD: ${{ matrix.python }}-${{ matrix.platform.target }}_${{ matrix.platform.arch }}
-          CIBW_BUILD_VERBOSITY: 1
+        run: pip wheel --no-deps -w wheelhouse .
 
-      - uses: actions/upload-artifact@v4
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
         with:
-          name: bedspec-wheels-${{ matrix.python }}-${{ matrix.platform.target }}_${{ matrix.platform.arch }}
-          path: ./wheelhouse/*.whl
+          name: bedspec-wheels-${{ matrix.PYTHON_VERSION }}
+          path: ./wheelhouse/bedspec*.whl
           if-no-files-found: error

README.md

@@ -107,7 +107,7 @@ For example, to create a custom BED3+1 class:
 >>> 
 >>> from bedspec import SimpleBed
 >>> 
->>> @dataclass(eq=True)
+>>> @dataclass
 ... class Bed3Plus1(SimpleBed):
 ...     refname: str
 ...     start: int

bedspec/_bedspec.py

@@ -181,7 +181,7 @@ def territory(self) -> Iterator[ReferenceSpan]:
         yield self.bed2
 
 
-@dataclass(eq=True, slots=True)
+@dataclass(slots=True, unsafe_hash=True)
 class BedColor:
     """The color of a BED record in red, green, and blue color values."""
 
@@ -209,15 +209,15 @@ def __str__(self) -> str:
         return f"{self.r},{self.g},{self.b}"
 
 
-@dataclass(eq=True, slots=True)
+@dataclass(slots=True, unsafe_hash=True)
 class Bed2(PointBed):
     """A BED2 record that describes a single 0-based 1-length point."""
 
     refname: str
     start: int
 
 
-@dataclass(eq=True, slots=True)
+@dataclass(slots=True, unsafe_hash=True)
 class Bed3(SimpleBed):
     """A BED3 record that describes a contiguous linear interval."""
 
@@ -226,7 +226,7 @@ class Bed3(SimpleBed):
     end: int = field(kw_only=True)
 
 
-@dataclass(eq=True, slots=True)
+@dataclass(slots=True, unsafe_hash=True)
 class Bed4(SimpleBed):
     """A BED4 record that describes a contiguous linear interval."""
 
@@ -236,7 +236,7 @@ class Bed4(SimpleBed):
     name: str | None = field(kw_only=True)
 
 
-@dataclass(eq=True, slots=True)
+@dataclass(slots=True, unsafe_hash=True)
 class Bed5(SimpleBed, Named):
     """A BED5 record that describes a contiguous linear interval."""
 
@@ -247,7 +247,7 @@ class Bed5(SimpleBed, Named):
     score: int | None = field(kw_only=True)
 
 
-@dataclass(eq=True, slots=True)
+@dataclass(slots=True, unsafe_hash=True)
 class Bed6(SimpleBed, Named, Stranded):
     """A BED6 record that describes a contiguous linear interval."""
 
@@ -259,7 +259,7 @@ class Bed6(SimpleBed, Named, Stranded):
     strand: BedStrand | None = field(kw_only=True)
 
 
-@dataclass(eq=True, slots=True)
+@dataclass(slots=True, unsafe_hash=True)
 class Bed12(SimpleBed, Named, Stranded):
     """A BED12 record that describes a contiguous linear interval."""
 
@@ -301,7 +301,7 @@ def __post_init__(self) -> None:
                 raise ValueError("The last defined block's end must be equal to the BED end!")
 
 
-@dataclass(eq=True, slots=True)
+@dataclass(slots=True, unsafe_hash=True)
 class BedGraph(SimpleBed):
     """A bedGraph feature for continuous-valued data."""
 
@@ -311,7 +311,7 @@ class BedGraph(SimpleBed):
     value: float = field(kw_only=True)
 
 
-@dataclass(eq=True, slots=True)
+@dataclass(slots=True, unsafe_hash=True)
 class BedPE(PairBed, Named):
     """A BED record that describes a pair of BED records as per the bedtools spec."""
 

bedspec/overlap/_overlap.py

@@ -6,9 +6,11 @@
 from typing import TypeAlias
 from typing import TypeVar
 
+from superintervals import (  # type: ignore[import-untyped]  # pyright: ignore[reportMissingTypeStubs]
+    IntervalSet,  # pyright: ignore[reportUnknownVariableType]
+)
 from typing_extensions import override
 
-import cgranges as cr
 from bedspec._bedspec import ReferenceSpan
 
 ReferenceSpanType = TypeVar("ReferenceSpanType", bound=ReferenceSpan)
@@ -33,7 +35,7 @@ class OverlapDetector(Iterable[ReferenceSpanType], Generic[ReferenceSpanType]):
 
     def __init__(self, features: Iterable[ReferenceSpanType] | None = None) -> None:
         self._refname_to_features: dict[Refname, list[ReferenceSpanType]] = defaultdict(list)
-        self._refname_to_tree: dict[Refname, cr.cgranges] = defaultdict(cr.cgranges)  # type: ignore[attr-defined,name-defined]  # pyright: ignore[reportUnknownArgumentType, reportUnknownMemberType]
+        self._refname_to_tree: dict[Refname, IntervalSet] = defaultdict(IntervalSet)  # pyright: ignore[reportUnknownArgumentType]
         self._refname_to_is_indexed: dict[Refname, bool] = defaultdict(lambda: False)
         if features is not None:
             self.add(*features)
@@ -47,10 +49,10 @@ def add(self, *features: ReferenceSpanType) -> None:
         """Add a feature to this overlap detector."""
         for feature in features:
             refname: Refname = feature.refname
-            feature_idx: int = len(self._refname_to_features[refname])
+            feature_index: 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_tree[refname].add(feature.start, feature.end - 1, feature_index)  # pyright: ignore[reportUnknownMemberType]
             self._refname_to_is_indexed[refname] = False  # mark that this tree needs re-indexing
 
     def overlapping(self, feature: ReferenceSpan) -> Iterator[ReferenceSpanType]:
@@ -60,9 +62,9 @@ def overlapping(self, feature: ReferenceSpan) -> Iterator[ReferenceSpanType]:
         if refname in self._refname_to_tree.keys() and not self._refname_to_is_indexed[refname]:  # pyright: ignore[reportUnknownMemberType]
             self._refname_to_tree[refname].index()  # pyright: ignore[reportUnknownMemberType]
 
-        idx: int
-        for *_, idx in self._refname_to_tree[refname].overlap(refname, feature.start, feature.end):  # pyright: ignore[reportUnknownMemberType, reportUnknownVariableType]
-            yield self._refname_to_features[refname][idx]
+        index: int
+        for index in self._refname_to_tree[refname].find_overlaps(feature.start, feature.end - 1):  # pyright: ignore[reportUnknownMemberType, reportUnknownVariableType]
+            yield self._refname_to_features[refname][index]
 
     def overlaps(self, feature: ReferenceSpan) -> bool:
         """Determine if a query feature overlaps any other features."""