chore: remove Python 3.8 support

.github/workflows/build-docs.yml

@@ -2,45 +2,38 @@ name: Build documentation
 
 on:
   push:
-    branches:
-      - master
+    tags:
+      - "*"
 
 jobs:
   test:
     name: Build docs
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
 
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v2
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.11
           cache: 'pip'
 
-      - name: Set up ccache
-        uses: hendrikmuhs/[email protected]
-
       - 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:]))')
-          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}
+          pip install cmake pybind11 numpy tox assorthead mattress>=0.1.4
 
-      # Note that doc building requires the inplace shared library.
       - name: Build docs
         run: |
-          CC="ccache gcc" python setup.py build_ext --inplace
-          sphinx-build --color -b html -d docs/doctrees docs docs/_build/html
+          python setup.py build_ext --inplace
+          cp build/lib*/rds2py/lib_rds_parser* src/rds2py/
+          tox -e docs
           touch ./docs/_build/html/.nojekyll
 
       - name: GH Pages Deployment
-        if: github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags/')
         uses: JamesIves/[email protected]
         with:
           branch: gh-pages # The branch the action should deploy to.

.github/workflows/pypi-publish.yml

@@ -0,0 +1,146 @@
+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - "*"
+
+jobs:
+  build_linux_x86_64:
+    name: Build wheels for linux x86_64
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+          CIBW_ARCHS: x86_64
+          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
+        with:
+          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@v4
+
+      - name: Grab prebuilt dependencies
+        run: |
+            curl -L https://github.com/ArtifactDB/prebuilt-hdf5/releases/download/0.0.4/macosx_x86_64.tar.gz > bundle.tar.gz
+            tar -xvf bundle.tar.gz
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+          CIBW_ARCHS: x86_64
+          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9"
+          CIBW_ENVIRONMENT: "MORE_CMAKE_OPTIONS=\"-DCMAKE_INSTALL_PREFIX=$(pwd)/installed -DCMAKE_OSX_ARCHITECTURES=x86_64\""
+          CIBW_BUILD_VERBOSITY: 3
+          CIBW_SKIP: pp*
+          MACOSX_DEPLOYMENT_TARGET: 11.7
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./wheelhouse/*.whl
+
+  build_macosx_arm64:
+    name: Build wheels for macosx arm64
+    runs-on: macos-13
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Grab prebuilt dependencies
+        run: |
+            curl -L https://github.com/ArtifactDB/prebuilt-hdf5/releases/download/0.0.4-manual/macosx_arm64.tar.gz > bundle.tar.gz
+            tar -xvf bundle.tar.gz
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+          CIBW_ARCHS: arm64
+          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9"
+          CIBW_ENVIRONMENT: "MORE_CMAKE_OPTIONS=\"-DCMAKE_INSTALL_PREFIX=$(pwd)/installed -DCMAKE_OSX_ARCHITECTURES=arm64\""
+          CIBW_BUILD_VERBOSITY: 3
+          MACOSX_DEPLOYMENT_TARGET: 13.0
+
+      - uses: actions/upload-artifact@v3
+        with:
+          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
+#
+#      - 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" >> $env:GITHUB_ENV
+#        shell: powershell
+#
+#      - name: Build wheels
+#        uses: pypa/[email protected]
+#        env:
+#          CIBW_ARCHS: AMD64
+#          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8"
+#          CIBW_ENVIRONMENT: "MORE_CMAKE_OPTIONS=\"-DCMAKE_INSTALL_PREFIX=${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
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v3
+        with:
+          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
+        with:
+          # unpacks default artifact into dist/
+          # if `name: artifact` is omitted, the action will create extra parent dir
+          name: artifact
+          path: dist
+
+      - uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/pypi-test.yml

@@ -1,48 +1,45 @@
-# 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 unit tests
 
 on:
   push:
-    branches:
-      - master
-    tags:
-      - "*"
+    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
+      - uses: actions/checkout@v4
         with:
           submodules: true
 
-      - name: Setup Python
-        uses: actions/setup-python@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
 
-      - name: Install python dependencies
+      - 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}
+          pip install ${DEPENDENCIES} pybind11
 
+      # 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
 
-      # In a PR, we don't need the full clean test.
+      # 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]
@@ -52,62 +49,3 @@ jobs:
         run: |
           CC="ccache gcc" python setup.py install
           pytest
-
-  build_wheels:
-    name: Build wheels on ${{ matrix.os }}
-    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ubuntu-20.04, macos-11] # at some point get this to work on windows-2019
-
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          submodules: true
-
-      - name: Build wheels
-        uses: pypa/[email protected]
-        env:
-          CIBW_ARCHS_MACOS: x86_64 arm64
-          CIBW_ARCHS_LINUX: x86_64 # remove this later so we build for all linux archs
-          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8"
-          CIBW_SKIP: pp*
-      - uses: actions/upload-artifact@v3
-        with:
-          path: ./wheelhouse/*.whl
-
-  build_sdist:
-    name: Build source distribution
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          submodules: true
-
-      - name: Build sdist
-        run: pipx run build --sdist
-
-      - uses: actions/upload-artifact@v3
-        with:
-          path: dist/*.tar.gz
-
-  upload_pypi:
-    needs: [test, build_wheels, 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/')
-    # alternatively, to publish when a GitHub Release is created, use the following rule:
-    # if: github.event_name == 'release' && github.event.action == 'published'
-    steps:
-      - uses: actions/download-artifact@v3
-        with:
-          # unpacks default artifact into dist/
-          # if `name: artifact` is omitted, the action will create extra parent dir
-          name: artifact
-          path: dist
-
-      - uses: pypa/[email protected]
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_PASSWORD }}

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ exclude: '^docs/conf.py'
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.6.0
   hooks:
   - id: trailing-whitespace
   - id: check-added-large-files
@@ -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: 23.9.1
-  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: v0.0.287
+  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

@@ -1,5 +1,10 @@
 # Changelog
 
-## Version 0.1.0 (development)
+## Version 0.2.0
+
+- chore: Remove Python 3.8 (EOL).
+- precommit: Replace docformatter with ruff's formatter.
+
+## Version 0.1.0
 
 - Added overlord functions for basic, multi-modal and multi-sample analyses from matrices, SummarizedExperiments and SingleCellExperiments.

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