chore: remove Python 3.8 support

.github/workflows/pypi-publish.yml

@@ -13,11 +13,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: 3.11
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/pypi-test.yml

@@ -15,13 +15,13 @@ jobs:
     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
+    - uses: actions/checkout@v4
     - name: Setup Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'

.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

CHANGELOG.md

@@ -1,7 +1,10 @@
 # Changelog
 
-## Version 0.1 (development)
+## Version 0.2.0
 
-- Feature A added
-- FIX: nasty bug #1729 fixed
-- add your changes here!
+- chore: Remove Python 3.8 (EOL)
+- precommit: Replace docformatter with ruff's formatter
+
+## Version 0.1.o
+
+- Initial version of the package.

docs/conf.py

@@ -72,6 +72,7 @@
     "sphinx.ext.ifconfig",
     "sphinx.ext.mathjax",
     "sphinx.ext.napoleon",
+    "sphinx_autodoc_typehints",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -166,12 +167,23 @@
 # If this is True, todo emits a warning for each TODO entries. The default is False.
 todo_emit_warnings = True
 
+autodoc_default_options = {
+    # 'members': 'var1, var2',
+    # 'member-order': 'bysource',
+    "special-members": True,
+    "undoc-members": True,
+    "exclude-members": "__weakref__, __dict__, __str__, __module__",
+}
+
+autosummary_generate = True
+autosummary_imported_members = True
+
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = "alabaster"
+html_theme = "furo"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the

docs/requirements.txt

@@ -1,6 +1,9 @@
+furo
+myst-nb
 # Requirements file for ReadTheDocs, check .readthedocs.yml.
 # To build the module reference correctly, make sure every external package
 # under `install_requires` in `setup.cfg` is also listed here!
 # sphinx_rtd_theme
 myst-parser[linkify]
 sphinx>=3.2.1
+sphinx-autodoc-typehints

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"]
 

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

src/tiledbarray/TileDBArraySeed.py

@@ -44,9 +44,7 @@ def __init__(self, path: str, attribute_name: str) -> None:
             _all_attr.append(_schema.attr(i).name)
 
         if self._attribute_name not in _all_attr:
-            raise ValueError(
-                f"Attribute '{self._attribute_name}' not in the tiledb schema."
-            )
+            raise ValueError(f"Attribute '{self._attribute_name}' not in the tiledb schema.")
 
         _attr_schema = _schema.attr(self._attribute_name)
         self._dtype = _attr_schema.dtype
@@ -166,15 +164,11 @@ def _extract_array(x: TileDbArraySeed, subset: Tuple[Sequence[int], ...]):
                 _parsed_subset,
             )
 
-        return (len(_first_subset), len(_second_subset)), numpy.array(
-            _data[x._attribute_name]
-        )
+        return (len(_first_subset), len(_second_subset)), numpy.array(_data[x._attribute_name])
 
 
 @extract_dense_array.register
-def extract_dense_array_TileDbArraySeed(
-    x: TileDbArraySeed, subset: Tuple[Sequence[int], ...]
-) -> numpy.ndarray:
+def extract_dense_array_TileDbArraySeed(x: TileDbArraySeed, subset: Tuple[Sequence[int], ...]) -> numpy.ndarray:
     """See :py:meth:`~delayedarray.extract_dense_array.extract_dense_array`.
 
     Subset parameter is passed to tiledb's
@@ -184,9 +178,7 @@ def extract_dense_array_TileDbArraySeed(
     return _output
 
 
-def _SparseNdarray_contents_from_coordinates(
-    rows, cols, vals, shape, val_dtype, parsed_subset
-):
+def _SparseNdarray_contents_from_coordinates(rows, cols, vals, shape, val_dtype, parsed_subset):
     output = [None] * shape[-1]
     for i, val in enumerate(vals):
         _offset_col = parsed_subset[1].index(cols[i])
@@ -214,9 +206,7 @@ def _SparseNdarray_contents_from_coordinates(
 
 
 @extract_sparse_array.register
-def extract_sparse_array_TileDbArraySeed(
-    x: TileDbArraySeed, subset: Tuple[Sequence[int], ...]
-) -> SparseNdarray:
+def extract_sparse_array_TileDbArraySeed(x: TileDbArraySeed, subset: Tuple[Sequence[int], ...]) -> SparseNdarray:
     """See :py:meth:`~delayedarray.extract_sparse_array.extract_sparse_array`.
 
     Subset parameter is passed to tiledb's
@@ -233,9 +223,7 @@ def extract_sparse_array_TileDbArraySeed(
         _output[3],
     )
 
-    return SparseNdarray(
-        shape=_subset_shape, contents=_content, dtype=x._dtype, index_dtype=numpy.int32
-    )
+    return SparseNdarray(shape=_subset_shape, contents=_content, dtype=x._dtype, index_dtype=numpy.int32)
 
 
 class TileDbArray(DelayedArray):