Improvements to package workflow and documentation

.github/workflows/publish-pypi.yml

@@ -0,0 +1,52 @@
+name: Publish to PyPI
+
+on:
+  push:
+    tags: "*"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      repository-projects: write
+      contents: write
+      pages: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox
+
+      - name: Test with tox
+        run: |
+          tox
+
+      - name: Build Project and Publish
+        run: |
+          python -m tox -e clean,build
+
+      # This uses the trusted publisher workflow so no token is required.
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+      - 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

.github/workflows/run-tests.yml

@@ -0,0 +1,73 @@
+name: Test the library
+
+on:
+  push:
+    branches:
+      - master # for legacy repos
+      - main
+  pull_request:
+    branches:
+      - master # for legacy repos
+      - main
+  workflow_dispatch: # Allow manually triggering the workflow
+  schedule:
+    # Run roughly every 15 days at 00:00 UTC
+    # (useful to check if updates on dependencies break the package)
+    - cron: "0 0 1,16 * *"
+
+permissions:
+  contents: read
+
+concurrency:
+  group: >-
+    ${{ github.workflow }}-${{ github.ref_type }}-
+    ${{ github.event.pull_request.number || github.sha }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        python: ["3.10", "3.11", "3.12", "3.13", "3.14"]
+        platform:
+          - ubuntu-latest
+          - macos-latest
+          - windows-latest
+    runs-on: ${{ matrix.platform }}
+    name: Python ${{ matrix.python }}, ${{ matrix.platform }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        id: setup-python
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox coverage
+
+      - name: Run tests
+        run: >-
+          pipx run --python '${{ steps.setup-python.outputs.python-path }}'
+          tox
+          -- -rFEx --durations 10 --color yes --cov --cov-branch --cov-report=xml  # pytest args
+
+      - name: Check for codecov token availability
+        id: codecov-check
+        shell: bash
+        run: |
+          if [ ${{ secrets.CODECOV_TOKEN }} != '' ]; then
+            echo "codecov=true" >> $GITHUB_OUTPUT;
+          else
+            echo "codecov=false" >> $GITHUB_OUTPUT;
+          fi
+
+      - name: Upload coverage reports to Codecov with GitHub Action
+        uses: codecov/codecov-action@v5
+        if: ${{ steps.codecov-check.outputs.codecov == 'true' }}
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          slug: ${{ github.repository }}
+          flags: ${{ matrix.platform }} - py${{ matrix.python }}

CHANGELOG.md

@@ -1,8 +1,16 @@
 # Changelog
 
-## Version 0.3.0
+## Version 0.3.0 - 0.3.1
 
 - Provide a base `BiocObject` class similar to the `Annotated` class in Bioconductor. The class provides `metadata` slot, accessors and validation functions.
+- Renaming code files to follow pep guidelines
+- Update Github actions and workflow to the new biocsetup versions
+- Changes to improve `NamedList`, `Names` classes
+  - get name at index
+  - delete method for namedlist/names
+  - add is_unique
+  - add lint errors
+- linting documentation, typehints etc
 
 ## Version 0.2.3
 

setup.py

@@ -4,6 +4,7 @@
 PyScaffold helps you to put up the scaffold of your new Python project.
 Learn more under: https://pyscaffold.org/
 """
+
 from setuptools import setup
 
 if __name__ == "__main__":

src/biocutils/__init__.py

@@ -15,13 +15,13 @@
 finally:
     del version, PackageNotFoundError
 
-from .Factor import Factor
-from .StringList import StringList
-from .IntegerList import IntegerList
-from .FloatList import FloatList
-from .BooleanList import BooleanList
-from .Names import Names
-from .NamedList import NamedList
+from .factor import Factor
+from .string_list import StringList
+from .integer_list import IntegerList
+from .float_list import FloatList
+from .boolean_list import BooleanList
+from .names import Names
+from .named_list import NamedList
 
 from .factorize import factorize
 from .intersect import intersect
@@ -60,3 +60,5 @@
 
 from .get_height import get_height
 from .is_high_dimensional import is_high_dimensional
+
+from .bioc_object import BiocObject

src/biocutils/_utils_combine.py

@@ -26,6 +26,8 @@ def _check_array_dimensions(x, active: int) -> bool:
                     + ")"
                 )
 
+    return True
+
 
 def _coerce_sparse_matrix(first, combined, module):
     if isinstance(first, module.csr_matrix):

src/biocutils/assign.py

@@ -14,7 +14,8 @@ def assign(x: Any, indices: Sequence[int], replacement: Any) -> Any:
     :py:func:`~biocutils.assign_sequence.assign_sequence` instead.
 
     Args:
-        x: Object to be assignted.
+        x:
+            Object to be assignted.
 
     Returns:
         The object after assignment, typically the same type as ``x``.

src/biocutils/assign_rows.py

@@ -31,15 +31,15 @@ def assign_rows(x: Any, indices: Sequence[int], replacement: Any) -> Any:
     tmp = [slice(None)] * len(x.shape)
     tmp[0] = indices
     output[(*tmp,)] = replacement
+
     return output
 
 
 @assign_rows.register
-def _assign_rows_numpy(
-    x: numpy.ndarray, indices: Sequence[int], replacement: Any
-) -> numpy.ndarray:
+def _assign_rows_numpy(x: numpy.ndarray, indices: Sequence[int], replacement: Any) -> numpy.ndarray:
     tmp = [slice(None)] * len(x.shape)
     tmp[0] = indices
     output = numpy.copy(x)
     output[(*tmp,)] = replacement
+
     return output

src/biocutils/assign_sequence.py

@@ -41,18 +41,14 @@ def _assign_sequence_list(x: list, indices: Sequence[int], replacement: Any) ->
 
 
 @assign_sequence.register
-def _assign_sequence_numpy(
-    x: numpy.ndarray, indices: Sequence[int], replacement: Any
-) -> numpy.ndarray:
+def _assign_sequence_numpy(x: numpy.ndarray, indices: Sequence[int], replacement: Any) -> numpy.ndarray:
     output = numpy.copy(x)
     output[indices] = replacement
     return output
 
 
 @assign_sequence.register
-def _assign_sequence_range(
-    x: range, indices: Sequence[int], replacement: Any
-) -> Union[range, list]:
+def _assign_sequence_range(x: range, indices: Sequence[int], replacement: Any) -> Union[range, list]:
     if (
         isinstance(replacement, range)
         and isinstance(indices, range)

src/biocutils/bioc_object.py

@@ -4,12 +4,7 @@
 from typing import Any, Dict, Optional, Union
 from warnings import warn
 
-try:
-    from typing import Self
-except ImportError:
-    Self = "BiocObject"
-
-from .NamedList import NamedList
+from .named_list import NamedList
 
 __author__ = "Jayaram Kancherla"
 __copyright__ = "jkanche"
@@ -40,22 +35,22 @@ class BiocObject:
     Provides a standardized `metadata` slot and copy-on-write semantics.
     """
 
-    def __init__(self, metadata: Optional[Union[Dict[str, Any], NamedList]] = None, validate: bool = True) -> None:
+    def __init__(self, metadata: Optional[Union[Dict[str, Any], NamedList]] = None, _validate: bool = True) -> None:
         """Initialize the BiocObject.
 
         Args:
             metadata:
                 Additional metadata. Defaults to an empty NamedList.
 
-            validate:
+            _validate:
                 Whether to validate the input. Defaults to True.
         """
-        if validate and metadata is not None:
+        if _validate and metadata is not None:
             _validate_metadata(metadata)
 
         self._metadata = sanitize_metadata(metadata)
 
-    def _define_output(self, in_place: bool = False) -> Self:
+    def _define_output(self, in_place: bool = False) -> BiocObject:
         """Internal utility to handle in-place vs copy-on-modify."""
         if in_place:
             return self
@@ -93,7 +88,7 @@ def get_metadata(self) -> NamedList:
         """Alias for :py:attr:`~metadata` getter."""
         return self.metadata
 
-    def set_metadata(self, metadata: Optional[Union[Dict[str, Any], NamedList]], in_place: bool = False) -> Self:
+    def set_metadata(self, metadata: Optional[Union[Dict[str, Any], NamedList]], in_place: bool = False) -> BiocObject:
         """Set new metadata.
 
         Args: