Remove support for Python 3.8 (#29)

- Added support for 3.13

.github/workflows/build-docs.yml

@@ -6,19 +6,17 @@ on:
       - "*"
 
 jobs:
-  test:
+  build_docs:
     name: Build docs 
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
-        with:
-          submodules: true
+      - uses: actions/checkout@v4
 
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v2
+      - name: Set up python
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.12
           cache: 'pip'
 
       - name: Set up HDF5
@@ -29,7 +27,10 @@ jobs:
       - name: Install Python dependencies
         run: |
           python -m pip install --upgrade pip setuptools
-          pip install cmake pybind11 numpy tox
+          DEPENDENCIES=$(python -c 'from setuptools.config.setupcfg import read_configuration as c; a = c("setup.cfg"); print(" ".join(a["options"]["install_requires"][1:]))')
+          pip install ${DEPENDENCIES}
+          DOCDEPENDENCIES=$(python -c 'with open("docs/requirements.txt") as a: available = list(a); print(" ".join(map(lambda x : x.strip(), filter(lambda x : not x.startswith("#"), available))))')
+          pip install ${DOCDEPENDENCIES}
 
       - name: Build docs
         run: |
@@ -39,8 +40,9 @@ jobs:
           touch ./docs/_build/html/.nojekyll
 
       - name: GH Pages Deployment
-        uses: JamesIves/[email protected]
+        if: github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags/')
+        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
+          clean: true # Automatically remove deleted files from the deploy branch

.github/workflows/publish-pypi.yml

@@ -11,27 +11,28 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Build wheels
         uses: pypa/[email protected]
         env:
           CIBW_ARCHS: x86_64
-          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8"
+          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9"
           CIBW_MANYLINUX_X86_64_IMAGE: ghcr.io/artifactdb/prebuilt-hdf5/manylinux_x86_64:0.0.4
           CIBW_MUSLLINUX_X86_64_IMAGE: ghcr.io/artifactdb/prebuilt-hdf5/musllinux_x86_64:0.0.4
           CIBW_SKIP: pp*
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: cibw-wheels-ubuntu-x86_64
           path: ./wheelhouse/*.whl
 
   build_macosx_x86_64:
     name: Build wheels for macosx x86_64
     runs-on: macos-13
     steps:
       - name: Check out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Grab prebuilt dependencies
         run: |
@@ -42,22 +43,23 @@ jobs:
         uses: pypa/[email protected]
         env:
           CIBW_ARCHS: x86_64
-          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8"
+          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9"
           CIBW_ENVIRONMENT: "MORE_CMAKE_OPTIONS=\"-DCMAKE_INSTALL_PREFIX=$(pwd)/installed -DCMAKE_OSX_ARCHITECTURES=x86_64\""
           CIBW_BUILD_VERBOSITY: 3
           CIBW_SKIP: pp*
           MACOSX_DEPLOYMENT_TARGET: 11.7
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: cibw-wheels-macos-x86_64
           path: ./wheelhouse/*.whl
 
   build_macosx_arm64:
     name: Build wheels for macosx arm64
-    runs-on: macos-13
+    runs-on: macos-latest
     steps:
       - name: Check out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Grab prebuilt dependencies
         run: |
@@ -68,79 +70,77 @@ jobs:
         uses: pypa/[email protected]
         env:
           CIBW_ARCHS: arm64
-          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8"
+          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9"
           CIBW_ENVIRONMENT: "MORE_CMAKE_OPTIONS=\"-DCMAKE_INSTALL_PREFIX=$(pwd)/installed -DCMAKE_OSX_ARCHITECTURES=arm64\""
           CIBW_BUILD_VERBOSITY: 3
           MACOSX_DEPLOYMENT_TARGET: 13.0
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: cibw-wheels-maxos_arm64
           path: ./wheelhouse/*.whl
 
 #  build_windows_x86_64:
 #    name: Build wheels for windows x86_64
 #    runs-on: windows-2019
 #    steps:
 #      - name: Check out repository
-#        uses: actions/checkout@v3
-
+#        uses: actions/checkout@v4
+#
 #      - name: Grab prebuilt dependencies
 #        run: |
 #            curl -L https://github.com/ArtifactDB/prebuilt-hdf5/releases/download/0.0.4/windows_x86_64.tar.gz > bundle.tar.gz
 #            tar -xvf bundle.tar.gz
 #        shell: bash
-
+#
 #      - name: Store path
 #        run: |
 #            $wd = pwd
 #            echo "INSTALL_DIR=$wd\\installed" >> $env:GITHUB_ENV
 #        shell: powershell
-
+#
 #      - name: Build wheels
 #        uses: pypa/[email protected]
 #        env:
 #          CIBW_ARCHS: AMD64
-#          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8"
+#          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9"
 #          CIBW_ENVIRONMENT: "MORE_CMAKE_OPTIONS=\"-DCMAKE_INSTALL_PREFIX=${INSTALL_DIR}\" VERBOSE=1"
 #          CIBW_BEFORE_BUILD_WINDOWS: "pip install delvewheel"
 #          CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: "delvewheel repair -w {dest_dir} {wheel}"
 #          CIBW_TEST_EXTRAS: "testing"
 #          CIBW_TEST_COMMAND: "pytest {package}/tests"
 #          CIBW_BUILD_VERBOSITY: 3
-
-#       - uses: actions/upload-artifact@v3
-#         with:
-#           path: ./wheelhouse/*.whl
+      # - uses: actions/upload-artifact@v3
+      #   with:
+      #     path: ./wheelhouse/*.whl
 
   build_sdist:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
 
       - name: Build sdist
         run: pipx run build --sdist
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: cibw-sdist
           path: dist/*.tar.gz
 
   upload_pypi:
     needs: [build_linux_x86_64, build_macosx_x86_64, build_macosx_arm64, build_sdist]
     runs-on: ubuntu-latest
-    # upload to PyPI on every tag starting with 'v'
-    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
-          # unpacks default artifact into dist/
-          # if `name: artifact` is omitted, the action will create extra parent dir
-          name: artifact
+          pattern: cibw-*
           path: dist
+          merge-multiple: true
 
-      - uses: pypa/gh-action-pypi-publish@v1.8.3
+      - uses: pypa/gh-action-pypi-publish@v1.12.2
         with:
           user: __token__
           password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/run-tests.yml

@@ -1,56 +1,37 @@
-name: Run unit tests
+name: Test the library
 
 on:
   push:
-    branches: [ master ]
+    branches:
+      - master
   pull_request:
-    branches: [ master ]
 
 jobs:
   test:
-
     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@v3
-        with:
-          submodules: true
+      - uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - name: Setup Python
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
+          cache: "pip"
 
       - name: Set up HDF5
         run: |
           sudo apt-get update
           sudo apt-get install libhdf5-dev
 
-      - name: Install Python dependencies
-        run: |
-          python -m pip install --upgrade pip setuptools
-          DEPENDENCIES=$(python -c 'from setuptools.config.setupcfg import read_configuration as c; a = c("setup.cfg"); print(" ".join(a["options"]["install_requires"][1:] + a["options"]["extras_require"]["testing"][1:]))')
-          pip install ${DEPENDENCIES} pybind11
+      - name: Get latest CMake
+        uses: lukka/get-cmake@latest
 
-      # We do proper tests if we're on the master branch, or if we're creating a new release.
       - name: Test with tox
-        if: github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags/')
         run: |
           pip install tox
           tox
-
-      # Otherwise we do some cached builds and tests for faster merging of PRs.
-      - name: Set up ccache
-        if: github.ref != 'refs/heads/master' && !startsWith(github.ref, 'refs/tags')
-        uses: hendrikmuhs/[email protected]
-
-      - name: Quickly build and test
-        if: github.ref != 'refs/heads/master' && !startsWith(github.ref, 'refs/tags')
-        run: |
-          CC="ccache gcc" python setup.py install
-          pytest

.pre-commit-config.yaml

@@ -0,0 +1,32 @@
+exclude: '^docs/conf.py'
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+  - id: trailing-whitespace
+  - id: check-added-large-files
+  - id: check-ast
+  - id: check-json
+  - id: check-merge-conflict
+  - id: check-xml
+  - id: check-yaml
+  - id: debug-statements
+  - id: end-of-file-fixer
+  - id: requirements-txt-fixer
+  - 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/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.8.2
+  hooks:
+    - id: ruff
+      args: [--fix, --exit-non-zero-on-fix]
+    - id: ruff-format
+
+## Check for misspells in documentation files:
+# - repo: https://github.com/codespell-project/codespell
+#   rev: v2.2.5
+#   hooks:
+#   - id: codespell

CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## Version 0.4.0
+
+- chore: Remove Python 3.8 (EOL).
+- precommit: Replace docformatter with ruff's formatter.
+
 ## Version 0.3.0
 
 - Fixes to support NumPy 2.0 release.

docs/requirements.txt

@@ -1,4 +1,5 @@
 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!

pyproject.toml

@@ -7,3 +7,19 @@ build-backend = "setuptools.build_meta"
 # For smarter version schemes and other configuration options,
 # check out https://github.com/pypa/setuptools_scm
 version_scheme = "no-guess-dev"
+
+[tool.ruff]
+line-length = 120
+src = ["src"]
+exclude = ["tests"]
+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