Migrate upstream changes from SE and GRanges (#72)

Author: jkanche

.github/workflows/publish-pypi.yml

@@ -1,6 +1,3 @@
-# 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:
@@ -19,10 +16,10 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Install dependencies
         run: |
@@ -33,6 +30,14 @@ jobs:
         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
@@ -45,11 +50,3 @@ jobs:
           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
-
-      # This uses the trusted publisher workflow so no token is required.
-      - name: Publish to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/run-tests.yml

@@ -1,32 +1,73 @@
-name: Run tests
+name: Test the library
 
 on:
   push:
-    branches: [master]
+    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:
-  build:
-    runs-on: ubuntu-latest
+  test:
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
-
-    name: Python ${{ matrix.python-version }}
+        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
 
-      - name: Setup Python
-        uses: actions/setup-python@v5
+      - uses: actions/setup-python@v5
+        id: setup-python
         with:
-          python-version: ${{ matrix.python-version }}
-          cache: "pip"
+          python-version: ${{ matrix.python }}
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install tox
+          pip install tox coverage
 
-      - name: Test with tox
-        run: |
+      - 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

@@ -1,5 +1,10 @@
 # Changelog
 
+## Version 0.6.0
+
+- Changed related to SummarizedExperiment and implementation of `CompressedGenomicRangesList` in the genomic ranges package.
+- Update versions of relevant dependency packages.
+
 ## Version 0.5.8 - 0.5.9
 
 - Rename `reduced_dims` to `reduced_dimensions`. Constructor accepts both these arguments for backwards compatibility.

setup.cfg

@@ -49,7 +49,8 @@ python_requires = >=3.9
 # For more information, check out https://semver.org/.
 install_requires =
     importlib-metadata; python_version<"3.8"
-    summarizedexperiment>=0.5.3
+    summarizedexperiment>=0.6.3
+    compressed-lists>=0.4.3
 
 [options.packages.find]
 where = src

src/singlecellexperiment/SingleCellExperiment.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from collections import OrderedDict
 from typing import Any, Dict, List, Optional, Sequence, Union
 from warnings import warn
@@ -105,15 +107,15 @@ def __init__(
         column_data: Optional[biocframe.BiocFrame] = None,
         row_names: Optional[List[str]] = None,
         column_names: Optional[List[str]] = None,
-        metadata: Optional[dict] = None,
+        metadata: Optional[Union[Dict[str, Any], ut.NamedList]] = None,
         reduced_dimensions: Optional[Dict[str, Any]] = None,
         reduced_dims: Optional[Dict[str, Any]] = None,  # deprecated name
         main_experiment_name: Optional[str] = None,
         alternative_experiments: Optional[Dict[str, Any]] = None,
         row_pairs: Optional[Any] = None,
         column_pairs: Optional[Any] = None,
         alternative_experiment_check_dim_names: bool = True,
-        validate: bool = True,
+        _validate: bool = True,
         **kwargs,
     ) -> None:
         """Initialize a single-cell experiment.
@@ -198,7 +200,7 @@ def __init__(
 
                 Defaults to None.
 
-            validate:
+            _validate:
                 Internal use only.
 
             kwargs:
@@ -213,7 +215,7 @@ def __init__(
             row_names=row_names,
             column_names=column_names,
             metadata=metadata,
-            validate=validate,
+            _validate=_validate,
             **kwargs,
         )
         self._main_experiment_name = main_experiment_name
@@ -234,7 +236,7 @@ def __init__(
         self._row_pairs = row_pairs if row_pairs is not None else {}
         self._column_pairs = column_pairs if column_pairs is not None else {}
 
-        if validate:
+        if _validate:
             _validate_reduced_dims(self._reduced_dims, self._shape)
             _validate_alternative_experiments(
                 self._alternative_experiments,
@@ -283,6 +285,7 @@ def __deepcopy__(self, memo=None, _nil=[]):
             alternative_experiments=_alt_expt_copy,
             row_pairs=_row_pair_copy,
             column_pairs=_col_pair_copy,
+            _validate=False,
         )
 
     def __copy__(self):
@@ -304,6 +307,7 @@ def __copy__(self):
             alternative_experiments=self._alternative_experiments,
             row_pairs=self._row_pairs,
             column_pairs=self._column_pairs,
+            _validate=False,
         )
 
     def copy(self):
@@ -403,7 +407,7 @@ def get_reduced_dims(self) -> Dict[str, Any]:
         """Alias for :py:meth:`~get_reduced_dimensions`, for back-compatibility."""
         return self.get_reduced_dimensions()
 
-    def set_reduced_dimensions(self, reduced_dims: Dict[str, Any], in_place: bool = False) -> "SingleCellExperiment":
+    def set_reduced_dimensions(self, reduced_dims: Dict[str, Any], in_place: bool = False) -> SingleCellExperiment:
         """Set new reduced dimensions.
 
         Args:
@@ -423,7 +427,7 @@ def set_reduced_dimensions(self, reduced_dims: Dict[str, Any], in_place: bool =
         output._reduced_dims = reduced_dims
         return output
 
-    def set_reduced_dims(self, reduced_dims: Dict[str, Any], in_place: bool = False) -> "SingleCellExperiment":
+    def set_reduced_dims(self, reduced_dims: Dict[str, Any], in_place: bool = False) -> SingleCellExperiment:
         """Alias for :py:meth:`~set_reduced_dimensions`, for back-compatibility."""
         return self.set_reduced_dimensions(reduced_dims=reduced_dims, in_place=in_place)
 
@@ -471,7 +475,7 @@ def get_reduced_dim_names(self) -> Dict[str, Any]:
         """Alias for :py:meth:`~get_reduced_dimension_names`, for back-compatibility."""
         return self.get_reduced_dimension_names()
 
-    def set_reduced_dimension_names(self, names: List[str], in_place: bool = False) -> "SingleCellExperiment":
+    def set_reduced_dimension_names(self, names: List[str], in_place: bool = False) -> SingleCellExperiment:
         """Replace :py:attr:`~.reduced_dims`'s names.
 
         Args:
@@ -497,7 +501,7 @@ def set_reduced_dimension_names(self, names: List[str], in_place: bool = False)
         output._reduced_dims = new_reduced_dims
         return output
 
-    def set_reduced_dim_names(self, names: List[str], in_place: bool = False) -> "SingleCellExperiment":
+    def set_reduced_dim_names(self, names: List[str], in_place: bool = False) -> SingleCellExperiment:
         """Alias for :py:meth:`~set_reduced_dimension_names`, for back-compatibility."""
         return self.set_reduced_dimension_names(names=names, in_place=in_place)
 
@@ -573,7 +577,7 @@ def reduced_dimension(self, name: Union[str, int]) -> Any:
         """Alias for :py:meth:`~get_reduced_dimension`, for back-compatibility."""
         return self.get_reduced_dimension(name=name)
 
-    def set_reduced_dimension(self, name: str, embedding: Any, in_place: bool = False) -> "SingleCellExperiment":
+    def set_reduced_dimension(self, name: str, embedding: Any, in_place: bool = False) -> SingleCellExperiment:
         """Add or replace :py:attr:`~singlecellexperiment.SingleCellExperiment.reduced_dimension`'s.
 
         Args:
@@ -613,7 +617,7 @@ def get_main_experiment_name(self) -> Optional[str]:
         """
         return self._main_experiment_name
 
-    def set_main_experiment_name(self, name: Optional[str], in_place: bool = False) -> "SingleCellExperiment":
+    def set_main_experiment_name(self, name: Optional[str], in_place: bool = False) -> SingleCellExperiment:
         """Set new experiment data (assays).
 
         Args:
@@ -671,7 +675,7 @@ def get_alternative_experiments(self, with_dim_names: bool = True) -> Dict[str,
 
     def set_alternative_experiments(
         self, alternative_experiments: Dict[str, Any], with_dim_names: bool = True, in_place: bool = False
-    ) -> "SingleCellExperiment":
+    ) -> SingleCellExperiment:
         """Set new alternative experiments.
 
         Args:
@@ -725,7 +729,7 @@ def get_alternative_experiment_names(self) -> List[str]:
         """
         return list(self._alternative_experiments.keys())
 
-    def set_alternative_experiment_names(self, names: List[str], in_place: bool = False) -> "SingleCellExperiment":
+    def set_alternative_experiment_names(self, names: List[str], in_place: bool = False) -> SingleCellExperiment:
         """Replace :py:attr:`~.alternative_experiment`'s names.
 
         Args:
@@ -821,7 +825,7 @@ def alternative_experiment(self, name: Union[str, int]) -> Any:
 
     def set_alternative_experiment(
         self, name: str, alternative_experiment: Any, with_dim_names: bool = True, in_place: bool = False
-    ) -> "SingleCellExperiment":
+    ) -> SingleCellExperiment:
         """Add or replace :py:attr:`~singlecellexperiment.SingleCellExperiment.alternative_experiment`'s.
 
         Args:
@@ -872,7 +876,7 @@ def get_row_pairs(self) -> Dict[str, Any]:
         """
         return self._row_pairs
 
-    def set_row_pairs(self, pairs: Dict[str, Any], in_place: bool = False) -> "SingleCellExperiment":
+    def set_row_pairs(self, pairs: Dict[str, Any], in_place: bool = False) -> SingleCellExperiment:
         """Replace :py:attr:`~.row_pairs`'s names.
 
         Args:
@@ -918,7 +922,7 @@ def get_row_pair_names(self) -> List[str]:
         """
         return list(self._row_pairs.keys())
 
-    def set_row_pair_names(self, names: List[str], in_place: bool = False) -> "SingleCellExperiment":
+    def set_row_pair_names(self, names: List[str], in_place: bool = False) -> SingleCellExperiment:
         """Replace :py:attr:`~.row_pair`'s names.
 
         Args:
@@ -970,7 +974,7 @@ def get_column_pairs(self) -> Dict[str, Any]:
         """
         return self._column_pairs
 
-    def set_column_pairs(self, pairs: Dict[str, Any], in_place: bool = False) -> "SingleCellExperiment":
+    def set_column_pairs(self, pairs: Dict[str, Any], in_place: bool = False) -> SingleCellExperiment:
         """Replace :py:attr:`~.column_pairs`'s names.
 
         Args:
@@ -1016,7 +1020,7 @@ def get_column_pair_names(self) -> List[str]:
         """
         return list(self._column_pairs.keys())
 
-    def set_column_pair_names(self, names: List[str], in_place: bool = False) -> "SingleCellExperiment":
+    def set_column_pair_names(self, names: List[str], in_place: bool = False) -> SingleCellExperiment:
         """Replace :py:attr:`~.column_pair`'s names.
 
         Args:
@@ -1066,7 +1070,7 @@ def get_slice(
         self,
         rows: Optional[Union[str, int, bool, Sequence]],
         columns: Optional[Union[str, int, bool, Sequence]],
-    ) -> "SingleCellExperiment":
+    ) -> SingleCellExperiment:
         """Alias for :py:attr:`~__getitem__`."""
 
         slicer = self._generic_slice(rows=rows, columns=columns)
@@ -1183,7 +1187,7 @@ def to_anndata(self, include_alternative_experiments: bool = False):
         return obj, adatas
 
     @classmethod
-    def from_anndata(cls, input: "anndata.AnnData") -> "SingleCellExperiment":
+    def from_anndata(cls, input: "anndata.AnnData") -> SingleCellExperiment:
         """Create a ``SingleCellExperiment`` from :py:class:`~anndata.AnnData`.
 
          Args:
@@ -1253,19 +1257,19 @@ def to_mudata(self):
     ######>> combine ops <<#####
     ############################
 
-    def relaxed_combine_rows(self, *other) -> "SingleCellExperiment":
+    def relaxed_combine_rows(self, *other) -> SingleCellExperiment:
         """Wrapper around :py:func:`~relaxed_combine_rows`."""
         return relaxed_combine_rows(self, *other)
 
-    def relaxed_combine_columns(self, *other) -> "SingleCellExperiment":
+    def relaxed_combine_columns(self, *other) -> SingleCellExperiment:
         """Wrapper around :py:func:`~relaxed_combine_columns`."""
         return relaxed_combine_columns(self, *other)
 
-    def combine_rows(self, *other) -> "SingleCellExperiment":
+    def combine_rows(self, *other) -> SingleCellExperiment:
         """Wrapper around :py:func:`~combine_rows`."""
         return combine_rows(self, *other)
 
-    def combine_columns(self, *other) -> "SingleCellExperiment":
+    def combine_columns(self, *other) -> SingleCellExperiment:
         """Wrapper around :py:func:`~combine_columns`."""
         return combine_columns(self, *other)