chore: remove Python 3.8 support (#15)

BiocPy · Dec 20, 2024 · 4ce41f3 · 4ce41f3
1 parent c2c04da
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diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml
@@ -9,43 +9,44 @@ on:
 
 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 }}
+      - 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 }}
diff --git a/.github/workflows/pypi-test.yml b/.github/workflows/pypi-test.yml
@@ -1,40 +1,33 @@
-# 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
+name: Run tests
 
 on:
   push:
-    branches: [ master ]
+    branches: [master]
   pull_request:
-    branches: [ master ]
+    branches: [master]
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.8', '3.9', '3.10', '3.11', '3.12' ]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     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
+      - 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
diff --git a/.pre-commit-config.yaml b/.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: 24.8.0
-  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: v0.6.8
   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

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,10 @@
 # Changelog
 
+## Version 0.3.0
+
+- chore: Remove Python 3.8 (EOL)
+- precommit: Replace docformatter with ruff's formatter
+
 ## Version 0.2.0
 
 - Compatibility with NumPy 2.0

diff --git a/docs/conf.py b/docs/conf.py
@@ -170,6 +170,15 @@ def setup(app):
 # If this is True, todo emits a warning for each TODO entries. The default is False.
 todo_emit_warnings = True
 
+autodoc_default_options = {
+    'special-members': True,
+    'undoc-members': False,
+    'exclude-members': '__weakref__, __dict__, __str__, __module__, __init__'
+}
+
+autosummary_generate = True
+autosummary_imported_members = True
+
 
 # -- Options for HTML output -------------------------------------------------
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -17,6 +17,10 @@ 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"]
 

diff --git a/setup.cfg b/setup.cfg
@@ -41,7 +41,7 @@ package_dir =
     =src
 
 # Require a min/specific Python version (comma-separated conditions)
-python_requires = >=3.8
+python_requires = >=3.9
 
 # Add here dependencies of your project (line-separated), e.g. requests>=2.2,<3.0.
 # Version specifiers like >=2.2,<3.0 avoid problems due to API changes in

diff --git a/src/hdf5array/Hdf5CompressedSparseMatrixSeed.py b/src/hdf5array/Hdf5CompressedSparseMatrixSeed.py
@@ -98,22 +98,14 @@ def __init__(
 
         with File(self._path, "r") as handle:
             self._indptr = handle[self._indptr_name][:]
-            if len(self._indptr.shape) != 1 or not issubdtype(
-                self._indptr.dtype, integer
-            ):
-                raise ValueError(
-                    "'indptr' dataset should be 1-dimensional and contain integers"
-                )
+            if len(self._indptr.shape) != 1 or not issubdtype(self._indptr.dtype, integer):
+                raise ValueError("'indptr' dataset should be 1-dimensional and contain integers")
             if by_column:
                 if len(self._indptr) != shape[1] + 1:
-                    raise ValueError(
-                        "'indptr' dataset should have length equal to the number of columns + 1"
-                    )
+                    raise ValueError("'indptr' dataset should have length equal to the number of columns + 1")
             else:
                 if len(self._indptr) != shape[0] + 1:
-                    raise ValueError(
-                        "'indptr' dataset should have length equal to the number of columns + 1"
-                    )
+                    raise ValueError("'indptr' dataset should have length equal to the number of columns + 1")
             if self._indptr[0] != 0:
                 raise ValueError("first entry of 'indptr' dataset should be zero")
             for i in range(1, len(self._indptr)):
@@ -122,9 +114,7 @@ def __init__(
 
             ddset = handle[self._data_name]
             if len(ddset.shape) != 1 or ddset.shape[0] != self._indptr[-1]:
-                raise ValueError(
-                    "'data' dataset should have length equal to the number of non-zero elements"
-                )
+                raise ValueError("'data' dataset should have length equal to the number of non-zero elements")
             self._modify_dtype = dtype is not None and dtype != ddset.dtype
             if not self._modify_dtype:
                 dtype = ddset.dtype
@@ -133,14 +123,10 @@ def __init__(
             # Not going to check for consistency of the indices themselves.
             idset = handle[self._indices_name]
             if len(idset.shape) != 1 or idset.shape[0] != self._indptr[-1]:
-                raise ValueError(
-                    "'indices' dataset should have length equal to the number of non-zero elements"
-                )
+                raise ValueError("'indices' dataset should have length equal to the number of non-zero elements")
             if not issubdtype(idset.dtype, integer):
                 raise ValueError("'indices' dataset should contain integers")
-            self._modify_index_dtype = (
-                index_dtype is not None and index_dtype != idset.dtype
-            )
+            self._modify_index_dtype = index_dtype is not None and index_dtype != idset.dtype
             if not self._modify_index_dtype:
                 index_dtype = idset.dtype
             self._index_dtype = index_dtype
@@ -269,9 +255,7 @@ def _extract_array(
                 start_idx = bisect_left(curindices, secondary_start)
             end_idx = len(curindices)
             if search_end:
-                end_idx = bisect_left(
-                    curindices, secondary_end, lo=start_idx, hi=end_idx
-                )
+                end_idx = bisect_left(curindices, secondary_end, lo=start_idx, hi=end_idx)
 
             if is_consecutive:
                 mod_indices = curindices[start_idx:end_idx]
@@ -406,14 +390,7 @@ def _consecutive(r, cols, values):
 class Hdf5CompressedSparseMatrix(DelayedArray):
     """Compressed sparse matrix in a HDF5 file as a ``DelayedArray``."""
 
-    def __init__(
-        self,
-        path: str,
-        group_name: Optional[str],
-        shape: Tuple[int, int],
-        by_column: bool,
-        **kwargs
-    ):
+    def __init__(self, path: str, group_name: Optional[str], shape: Tuple[int, int], by_column: bool, **kwargs):
         """To construct a ``Hdf5CompressedSparseMatrix`` from an existing :py:class:`~Hdf5CompressedSparseMatrixSeed`,
         use :py:meth:`~delayedarray.wrap.wrap` instead.
 
@@ -439,9 +416,7 @@ def __init__(
         if isinstance(path, Hdf5CompressedSparseMatrixSeed):
             seed = path
         else:
-            seed = Hdf5CompressedSparseMatrixSeed(
-                path, group_name, shape, by_column, **kwargs
-            )
+            seed = Hdf5CompressedSparseMatrixSeed(path, group_name, shape, by_column, **kwargs)
         super(Hdf5CompressedSparseMatrix, self).__init__(seed)
 
     @property
@@ -530,13 +505,9 @@ def to_scipy_sparse_matrix_from_Hdf5CompressedSparseMatrix(
             _indptr = handle[x.indptr_name][:]
 
             if x.by_column:
-                _matrix = scipy.sparse.csc_matrix(
-                    (_data, _indices, _indptr), shape=x.shape, dtype=x.dtype
-                )
+                _matrix = scipy.sparse.csc_matrix((_data, _indices, _indptr), shape=x.shape, dtype=x.dtype)
             else:
-                _matrix = scipy.sparse.csr_matrix(
-                    (_data, _indices, _indptr), shape=x.shape, dtype=x.dtype
-                )
+                _matrix = scipy.sparse.csr_matrix((_data, _indices, _indptr), shape=x.shape, dtype=x.dtype)
 
         if format == "csc":
             return _matrix.tocsc()

diff --git a/src/hdf5array/Hdf5DenseArraySeed.py b/src/hdf5array/Hdf5DenseArraySeed.py
@@ -122,9 +122,7 @@ def chunk_grid_Hdf5DenseArraySeed(x: Hdf5DenseArraySeed):
 
 
 @extract_dense_array.register
-def extract_dense_array_Hdf5DenseArraySeed(
-    x: Hdf5DenseArraySeed, subset: Tuple[Sequence[int], ...]
-) -> numpy.ndarray:
+def extract_dense_array_Hdf5DenseArraySeed(x: Hdf5DenseArraySeed, subset: Tuple[Sequence[int], ...]) -> numpy.ndarray:
     """See :py:meth:`~delayedarray.extract_dense_array.extract_dense_array`."""
     converted = []
     num_lists = 0