Fix an issue with numpy vectors as slice arguments (#137)

.github/workflows/publish-pypi.yml

@@ -0,0 +1,52 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Publish to PyPI
+
+on:
+  push:
+    tags: "*"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox
+
+      - name: Test with tox
+        run: |
+          tox
+
+      - name: Build docs
+        run: |
+          tox -e docs
+
+      - run: touch ./docs/_build/html/.nojekyll
+
+      - name: GH Pages Deployment
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          branch: gh-pages # The branch the action should deploy to.
+          folder: ./docs/_build/html
+          clean: true # Automatically remove deleted files from the deploy branch
+
+      - name: Build Project and Publish
+        run: |
+          python -m tox -e clean,build
+
+      - name: Publish package
+        uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/run-tests.yml

@@ -0,0 +1,32 @@
+name: Run tests
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+
+    name: Python ${{ matrix.python-version }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox
+
+      - name: Test with tox
+        run: |
+          tox

CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## Version 0.5.1
+
+- Fixed an issue with numpy arrays as slice arguments. Code now uses Biocutils's subset functions to perform these operations.
+- Rename GitHub actions for consistency with the rest of the packages.
+
 ## Version 0.5.0
 
 - chore: Remove Python 3.8 (EOL)

README.md

@@ -1,6 +1,6 @@
 [![Project generated with PyScaffold](https://img.shields.io/badge/-PyScaffold-005CA0?logo=pyscaffold)](https://pyscaffold.org/)
 [![PyPI-Server](https://img.shields.io/pypi/v/GenomicRanges.svg)](https://pypi.org/project/GenomicRanges/)
-![Unit tests](https://github.com/BiocPy/GenomicRanges/actions/workflows/pypi-test.yml/badge.svg)
+![Unit tests](https://github.com/BiocPy/GenomicRanges/actions/workflows/run-tests.yml/badge.svg)
 
 # GenomicRanges
 

src/genomicranges/GenomicRanges.py

@@ -953,11 +953,11 @@ def get_subset(self, subset: Union[str, int, bool, Sequence]) -> "GenomicRanges"
 
         current_class_const = type(self)
         return current_class_const(
-            seqnames=self._seqnames[idx],
-            ranges=self._ranges[idx],
-            strand=self._strand[idx],
-            names=self._names[idx] if self._names is not None else None,
-            mcols=self._mcols[idx, :],
+            seqnames=ut.subset_sequence(self._seqnames, idx),
+            ranges=ut.subset_sequence(self._ranges, idx),
+            strand=ut.subset_sequence(self._strand, idx),
+            names=ut.subset_sequence(self._names, idx) if self._names is not None else None,
+            mcols=ut.subset(self._mcols, idx),
             seqinfo=self._seqinfo,
             metadata=self._metadata,
         )

src/genomicranges/GenomicRangesList.py

@@ -847,38 +847,24 @@ def __getitem__(self, args: Union[str, int, tuple, list, slice]) -> Union[Genomi
         else:
             idx, _ = ut.normalize_subscript(args, len(self), self._names)
 
-            if isinstance(idx, list):
-                if ut.is_list_of_type(idx, bool):
-                    if len(idx) != len(self):
-                        raise ValueError("`indices` is a boolean vector, length should match the size of the data.")
-
-                    idx = [i for i in range(len(idx)) if idx[i] is True]
-
-                new_ranges = [self.ranges[i] for i in idx]
-                new_range_lengths = [self._range_lengths[i] for i in idx]
-
-                new_names = None
-                if self.names is not None:
-                    new_names = [self.names[i] for i in idx]
-
-                new_mcols = None
-                if self.mcols is not None:
-                    new_mcols = self.mcols[idx, :]
-
-                return GenomicRangesList(new_ranges, new_range_lengths, new_names, new_mcols, self._metadata)
-            elif isinstance(idx, (slice, range)):
-                if isinstance(idx, range):
-                    idx = slice(idx.start, idx.stop, idx.step)
-
-                return GenomicRangesList(
-                    self._ranges[idx],
-                    self._range_lengths[idx],
-                    self._names[idx] if self._names is not None else self._names,
-                    self._mcols[idx, :],
-                    self._metadata,
-                )
+            if ut.is_list_of_type(idx, bool):
+                if len(idx) != len(self):
+                    raise ValueError("`indices` is a boolean vector, length should match the size of the data.")
+
+                idx = [i for i in range(len(idx)) if idx[i] is True]
+
+            new_ranges = ut.subset_sequence(self._ranges, idx)
+            new_range_lengths = ut.subset_sequence(self._range_lengths, idx)
+
+            new_names = None
+            if self.names is not None:
+                new_names = ut.subset_sequence(self.names, idx)
+
+            new_mcols = None
+            if self.mcols is not None:
+                new_mcols = ut.subset(self.mcols, idx)
 
-            raise TypeError("Arguments to subset `GenomicRangesList` is not supported.")
+            return GenomicRangesList(new_ranges, new_range_lengths, new_names, new_mcols, self._metadata)
 
     #######################################
     ######>> class initializers <<#########