SingleCellExperiment 0.4.7__tar.gz → 0.5.0__tar.gz

singlecellexperiment-0.5.0/.github/workflows/pypi-publish.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/gh-action-pypi-publish@v1.12.2
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

singlecellexperiment-0.5.0/.github/workflows/pypi-test.yml

@@ -0,0 +1,33 @@
+name: Run tests
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+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

{singlecellexperiment-0.4.7 → singlecellexperiment-0.5.0}/.pre-commit-config.yaml

@@ -17,26 +17,27 @@ repos:
   - id: mixed-line-ending
     args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
 
-- repo: https://github.com/PyCQA/docformatter
-  rev: v1.7.5
-  hooks:
-    - id: docformatter
-      additional_dependencies: [tomli]
-      args: [--in-place, --wrap-descriptions=120, --wrap-summaries=120]
-      # --config, ./pyproject.toml
+# - repo: https://github.com/PyCQA/docformatter
+#   rev: master
+#   hooks:
+#     - id: docformatter
+#       additional_dependencies: [tomli]
+#       args: [--in-place, --wrap-descriptions=120, --wrap-summaries=120]
+#       # --config, ./pyproject.toml
 
-- repo: https://github.com/psf/black
-  rev: 24.4.2
-  hooks:
-  - id: black
-    language_version: python3
+# - repo: https://github.com/psf/black
+#   rev: 24.8.0
+#   hooks:
+#   - id: black
+#     language_version: python3
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.5.0
+  rev: v0.6.8
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]
+    - id: ruff-format
 
 ## If like to embrace black styles even in the docs:
 # - repo: https://github.com/asottile/blacken-docs

{singlecellexperiment-0.4.7 → singlecellexperiment-0.5.0}/CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## Version 0.5.0
+
+- chore: Remove Python 3.8 (EOL)
+- precommit: Replace docformatter with ruff's formatter
+
 ## Version 0.4.7
 
 - Fix package version issues to support Python<=3.9. Mostly related to how anndata dependencies are versioned in the MuData package discussed [here](https://github.com/scverse/mudata/issues/82).

{singlecellexperiment-0.4.7 → singlecellexperiment-0.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SingleCellExperiment
-Version: 0.4.7
+Version: 0.5.0
 Summary: Container class for single-cell experiments
 Home-page: https://github.com/BiocPy/SingleCellExperiment
 Author: jkanche
@@ -10,7 +10,7 @@ Project-URL: Documentation, https://github.com/BiocPy/SingleCellExperiment
 Platform: any
 Classifier: Development Status :: 4 - Beta
 Classifier: Programming Language :: Python
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
 License-File: LICENSE.txt
 Requires-Dist: importlib-metadata; python_version < "3.8"

{singlecellexperiment-0.4.7 → singlecellexperiment-0.5.0}/docs/changelog.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## Version 0.5.0
+
+- chore: Remove Python 3.8 (EOL)
+- precommit: Replace docformatter with ruff's formatter
+
 ## Version 0.4.7
 
 - Fix package version issues to support Python<=3.9. Mostly related to how anndata dependencies are versioned in the MuData package discussed [here](https://github.com/scverse/mudata/issues/82).

{singlecellexperiment-0.4.7 → singlecellexperiment-0.5.0}/pyproject.toml

@@ -16,6 +16,10 @@ extend-ignore = ["F821"]
 [tool.ruff.pydocstyle]
 convention = "google"
 
+[tool.ruff.format]
+docstring-code-format = true
+docstring-code-line-length = 20
+
 [tool.ruff.per-file-ignores]
 "__init__.py" = ["E402", "F401"]
 

{singlecellexperiment-0.4.7 → singlecellexperiment-0.5.0}/setup.cfg

@@ -21,7 +21,7 @@ packages = find_namespace:
 include_package_data = True
 package_dir = 
 	=src
-python_requires = >=3.8
+python_requires = >=3.9
 install_requires = 
 	importlib-metadata; python_version<"3.8"
 	summarizedexperiment>=0.4.5

{singlecellexperiment-0.4.7 → singlecellexperiment-0.5.0}/src/SingleCellExperiment.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SingleCellExperiment
-Version: 0.4.7
+Version: 0.5.0
 Summary: Container class for single-cell experiments
 Home-page: https://github.com/BiocPy/SingleCellExperiment
 Author: jkanche
@@ -10,7 +10,7 @@ Project-URL: Documentation, https://github.com/BiocPy/SingleCellExperiment
 Platform: any
 Classifier: Development Status :: 4 - Beta
 Classifier: Programming Language :: Python
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
 License-File: LICENSE.txt
 Requires-Dist: importlib-metadata; python_version < "3.8"

{singlecellexperiment-0.4.7 → singlecellexperiment-0.5.0}/src/singlecellexperiment/SingleCellExperiment.py

@@ -30,9 +30,7 @@ __license__ = "MIT"
 
 def _validate_reduced_dims(reduced_dims, shape):
     if reduced_dims is None:
-        raise ValueError(
-            "'reduced_dims' cannot be `None`, must be assigned to an empty dictionary."
-        )
+        raise ValueError("'reduced_dims' cannot be `None`, must be assigned to an empty dictionary.")
 
     if not isinstance(reduced_dims, dict):
         raise TypeError("'reduced_dims' is not a dictionary.")
@@ -40,21 +38,16 @@ def _validate_reduced_dims(reduced_dims, shape):
     for rdname, mat in reduced_dims.items():
         if not hasattr(mat, "shape"):
             raise TypeError(
-                f"Reduced dimension: '{rdname}' must be a matrix-like object."
-                "Does not contain a `shape` property."
+                f"Reduced dimension: '{rdname}' must be a matrix-like object." "Does not contain a `shape` property."
             )
 
         if shape[1] != mat.shape[0]:
-            raise ValueError(
-                f"Reduced dimension: '{rdname}' does not contain embeddings for all cells."
-            )
+            raise ValueError(f"Reduced dimension: '{rdname}' does not contain embeddings for all cells.")
 
 
 def _validate_alternative_experiments(alternative_experiments, shape):
     if alternative_experiments is None:
-        raise ValueError(
-            "'alternative_experiments' cannot be `None`, must be assigned to an empty dictionary."
-        )
+        raise ValueError("'alternative_experiments' cannot be `None`, must be assigned to an empty dictionary.")
 
     if not isinstance(alternative_experiments, dict):
         raise TypeError("'alternative_experiments' is not a dictionary.")
@@ -67,10 +60,7 @@ def _validate_alternative_experiments(alternative_experiments, shape):
             )
 
         if shape[1] != alternative_experiment.shape[1]:
-            raise ValueError(
-                f"Alternative experiment: '{alt_name}' does not contain same number of"
-                " cells."
-            )
+            raise ValueError(f"Alternative experiment: '{alt_name}' does not contain same number of" " cells.")
 
 
 def _validate_pairs(pairs):
@@ -204,18 +194,14 @@ class SingleCellExperiment(RangedSummarizedExperiment):
 
         self._reduced_dims = reduced_dims if reduced_dims is not None else {}
 
-        self._alternative_experiments = (
-            alternative_experiments if alternative_experiments is not None else {}
-        )
+        self._alternative_experiments = alternative_experiments if alternative_experiments is not None else {}
 
         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:
             _validate_reduced_dims(self._reduced_dims, self._shape)
-            _validate_alternative_experiments(
-                self._alternative_experiments, self._shape
-            )
+            _validate_alternative_experiments(self._alternative_experiments, self._shape)
             _validate_pairs(self._row_pairs)
             _validate_pairs(self._column_pairs)
 
@@ -309,14 +295,10 @@ class SingleCellExperiment(RangedSummarizedExperiment):
             output += ", row_ranges=" + self._row_ranges.__repr__()
 
         if self._alternative_experiments is not None:
-            output += ", alternative_experiments=" + ut.print_truncated_list(
-                self.alternative_experiment_names
-            )
+            output += ", alternative_experiments=" + ut.print_truncated_list(self.alternative_experiment_names)
 
         if self._reduced_dims is not None:
-            output += ", reduced_dims=" + ut.print_truncated_list(
-                self.reduced_dim_names
-            )
+            output += ", reduced_dims=" + ut.print_truncated_list(self.reduced_dim_names)
 
         if self._main_experiment_name is not None:
             output += ", main_experiment_name=" + self._main_experiment_name
@@ -344,10 +326,14 @@ class SingleCellExperiment(RangedSummarizedExperiment):
 
         output += f"assays({len(self.assay_names)}): {ut.print_truncated_list(self.assay_names)}\n"
 
-        output += f"row_data columns({len(self._rows.column_names)}): {ut.print_truncated_list(self._rows.column_names)}\n"
+        output += (
+            f"row_data columns({len(self._rows.column_names)}): {ut.print_truncated_list(self._rows.column_names)}\n"
+        )
         output += f"row_names({0 if self._row_names is None else len(self._row_names)}): {' ' if self._row_names is None else ut.print_truncated_list(self._row_names)}\n"
 
-        output += f"column_data columns({len(self._cols.column_names)}): {ut.print_truncated_list(self._cols.column_names)}\n"
+        output += (
+            f"column_data columns({len(self._cols.column_names)}): {ut.print_truncated_list(self._cols.column_names)}\n"
+        )
         output += f"column_names({0 if self._column_names is None else len(self._column_names)}): {' ' if self._column_names is None else ut.print_truncated_list(self._column_names)}\n"
 
         output += f"main_experiment_name: {' ' if self._main_experiment_name is None else self._main_experiment_name}\n"
@@ -373,9 +359,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         """
         return self._reduced_dims
 
-    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":
         """Set new reduced dimensions.
 
         Args:
@@ -421,9 +405,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         """
         return list(self._reduced_dims.keys())
 
-    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":
         """Replace :py:attr:`~.reduced_dims`'s names.
 
         Args:
@@ -439,9 +421,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         """
         current_names = self.get_reduced_dim_names()
         if len(names) != len(current_names):
-            raise ValueError(
-                "Length of 'names' does not match the number of `reduced_dims`."
-            )
+            raise ValueError("Length of 'names' does not match the number of `reduced_dims`.")
 
         new_reduced_dims = OrderedDict()
         for idx in range(len(names)):
@@ -499,9 +479,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
 
             return self._reduced_dims[dimension]
 
-        raise TypeError(
-            f"'dimension' must be a string or integer, provided '{type(dimension)}'."
-        )
+        raise TypeError(f"'dimension' must be a string or integer, provided '{type(dimension)}'.")
 
     ################################
     ######>> main_expt_name <<######
@@ -515,9 +493,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         """
         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:
@@ -609,9 +585,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         """
         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:
@@ -627,15 +601,11 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         """
         current_names = self.get_alternative_experiment_names()
         if len(names) != len(current_names):
-            raise ValueError(
-                "Length of 'names' does not match the number of `alternative_experiments`."
-            )
+            raise ValueError("Length of 'names' does not match the number of `alternative_experiments`.")
 
         new_alt_expts = OrderedDict()
         for idx in range(len(names)):
-            new_alt_expts[names[idx]] = self._alternative_experiments.pop(
-                current_names[idx]
-            )
+            new_alt_expts[names[idx]] = self._alternative_experiments.pop(current_names[idx])
 
         output = self._define_output(in_place)
         output._alternative_experiments = new_alt_expts
@@ -680,13 +650,9 @@ class SingleCellExperiment(RangedSummarizedExperiment):
                 raise IndexError("Index cannot be negative.")
 
             if name > len(self.alternative_experiment_names):
-                raise IndexError(
-                    "Index greater than the number of alternative experiments."
-                )
+                raise IndexError("Index greater than the number of alternative experiments.")
 
-            return self._alternative_experiments[
-                self.alternative_experiment_names[name]
-            ]
+            return self._alternative_experiments[self.alternative_experiment_names[name]]
         elif isinstance(name, str):
             if name not in self._alternative_experiments:
                 raise AttributeError(f"Alternative experiment: {name} does not exist.")
@@ -707,9 +673,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         """
         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:
@@ -755,9 +719,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         """
         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:
@@ -773,9 +735,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         """
         current_names = self.get_row_pair_names()
         if len(names) != len(current_names):
-            raise ValueError(
-                "Length of 'names' does not match the number of `row_pairs`."
-            )
+            raise ValueError("Length of 'names' does not match the number of `row_pairs`.")
 
         new_row_pairs = OrderedDict()
         for idx in range(len(names)):
@@ -811,9 +771,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         """
         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:
@@ -859,9 +817,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         """
         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:
@@ -877,9 +833,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         """
         current_names = self.get_column_pair_names()
         if len(names) != len(current_names):
-            raise ValueError(
-                "Length of 'names' does not match the number of `column_pairs`."
-            )
+            raise ValueError("Length of 'names' does not match the number of `column_pairs`.")
 
         new_column_pairs = OrderedDict()
         for idx in range(len(names)):
@@ -1252,9 +1206,7 @@ def relaxed_combine_columns(
 
     _new_rdim = None
     try:
-        _new_rdim = relaxed_merge_numpy_generic(
-            x, by="row", attr="reduced_dims", names_attr="reduced_dim_names"
-        )
+        _new_rdim = relaxed_merge_numpy_generic(x, by="row", attr="reduced_dims", names_attr="reduced_dim_names")
     except Exception as e:
         warn(
             f"Cannot combine 'reduced_dimensions' across experiments, {str(e)}",
@@ -1263,9 +1215,7 @@ def relaxed_combine_columns(
 
     _new_alt_expt = None
     try:
-        _new_alt_expt = relaxed_merge_generic(
-            x, by="column", attr="alternative_experiments"
-        )
+        _new_alt_expt = relaxed_merge_generic(x, by="column", attr="alternative_experiments")
     except Exception as e:
         warn(
             f"Cannot combine 'alternative_experiments' across experiments, {str(e)}",

{singlecellexperiment-0.4.7 → singlecellexperiment-0.5.0}/src/singlecellexperiment/io/tenx.py

@@ -75,9 +75,7 @@ def read_tenx_h5(path: str, realize_assays: bool = False) -> SingleCellExperimen
     # read the matrix
     shape = tuple(h5["matrix"]["shape"][:])
 
-    counts = Hdf5CompressedSparseMatrix(
-        path=path, group_name="matrix", by_column=True, shape=shape
-    )
+    counts = Hdf5CompressedSparseMatrix(path=path, group_name="matrix", by_column=True, shape=shape)
 
     if realize_assays is True:
         counts = da.to_scipy_sparse_matrix(counts, "csr")
@@ -111,6 +109,4 @@ def read_tenx_h5(path: str, realize_assays: bool = False) -> SingleCellExperimen
 
     h5.close()
 
-    return SingleCellExperiment(
-        assays={"counts": counts}, row_data=features, column_data=barcodes
-    )
+    return SingleCellExperiment(assays={"counts": counts}, row_data=features, column_data=barcodes)

singlecellexperiment-0.4.7/.github/workflows/pypi-publish.yml

@@ -1,51 +0,0 @@
-# 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@v2
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.9
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest tox
-    # - name: Lint with flake8
-    #   run: |
-    #     # stop the build if there are Python syntax errors or undefined names
-    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-    #     # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - 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@4.1.3
-      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/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_PASSWORD }}

singlecellexperiment-0.4.7/.github/workflows/pypi-test.yml

@@ -1,40 +0,0 @@
-# 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: Test the library
-
-on:
-  push:
-    branches: [ master ]
-  pull_request:
-    branches: [ master ]
-
-jobs:
-  build:
-
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [ '3.8', '3.9', '3.10', '3.11', '3.12' ]
-
-    name: Python ${{ matrix.python-version }}
-    steps:
-    - uses: actions/checkout@v2
-    - name: Setup Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-        cache: 'pip'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest tox
-    # - name: Lint with flake8
-    #   run: |
-    #     # stop the build if there are Python syntax errors or undefined names
-    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-    #     # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with tox
-      run: |
-        tox