update github actions to use cibuildwheel

Author: jkanche

.github/workflows/build-docs.yml

@@ -0,0 +1,40 @@
+name: Build documentation
+
+on:
+  push:
+    tags:
+      - "*"
+
+jobs:
+  test:
+    name: Build docs
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+          cache: 'pip'
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          pip install cmake pybind11 numpy tox
+
+      - name: Build docs
+        run: |
+          python setup.py build_ext --inplace
+          cp build/lib*/biostrings/lib_biostrings* src/biostrings/
+          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/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

.github/workflows/publish-pypi.yml

@@ -2,51 +2,64 @@ name: Publish to PyPI
 
 on:
   push:
-    tags: "*"
+    tags:
+      - "*"
 
 jobs:
-  build:
-    runs-on: ubuntu-latest
-    permissions:
-      id-token: write
-      repository-projects: write
-      contents: write
-      pages: write
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        # macos-13 is an intel runner, higher macos's are apple silicon
+        # At some point, maybe get this to work on windows-latest
+        os: [ubuntu-latest, macos-13, macos-latest]
 
     steps:
-      - uses: actions/checkout@v4
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+          CIBW_ARCHS_LINUX: x86_64
+          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9"
+          CIBW_SKIP: pp*
 
-      - name: Set up Python 3.12
-        uses: actions/setup-python@v5
+      - uses: actions/upload-artifact@v4
         with:
-          python-version: 3.12
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
 
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install tox
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
 
-      - name: Test with tox
-        run: |
-          tox
+      - name: Build sdist
+        run: pipx run build --sdist
 
-      - name: Build Project and Publish
-        run: |
-          python -m tox -e clean,build
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
 
       # This uses the trusted publisher workflow so no token is required.
       - name: Publish to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
-
-      - 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

.github/workflows/run-tests.yml

@@ -48,6 +48,9 @@ jobs:
           python -m pip install --upgrade pip
           pip install tox coverage
 
+      - name: Get latest CMake
+        uses: lukka/get-cmake@latest
+
       - name: Run tests
         run: >-
           pipx run --python '${{ steps.setup-python.outputs.python-path }}'