python workflow

.github/workflows/C.yml

@@ -12,7 +12,6 @@ on:
       - '.github/workflows/C.yml'
       - 'src/**'
 
-
 jobs:
   build:
     if: "! contains(github.event.head_commit.message, '[skip ci]')"
@@ -40,6 +39,11 @@ jobs:
           echo "GSL_LIBS=-L$(RUNNER_TEMP)/gsl-2.7/lib/x64" >> $GITHUB_ENV
         shell: bash
 
+      - name: Add Msys64 to PATH (https://github.com/actions/runner-images/issues/1613)
+        if: runner.os == 'Windows'
+        run: echo "::add-path::/c/msys64/mingw64/bin:/c/msys64/usr/bin"
+        shell: bash
+
       - run: cd src && ./configure
       - run: make -C src all DEBUG=1 WARN_FLAGS='-Werror'
       - run: make -C src all DEBUG=0 WARN_FLAGS='-Werror'

.github/workflows/R.yml

@@ -30,7 +30,8 @@ jobs:
     runs-on: ${{ matrix.config.os }}
     name: Check ${{ matrix.config.os }} (${{ matrix.config.r }})
     strategy:
-      fail-fast: false
+      # When set to true, GitHub cancels all in-progress jobs if any matrix job fails.
+      fail-fast: true
       matrix:
         config:
           - {os: windows-latest, r: 'release'}
@@ -43,6 +44,10 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
+      - name: Disable autocrlf
+        if: runner.os == 'Windows'
+        run: git config --global core.autocrlf false
+
       - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
@@ -210,6 +215,6 @@ jobs:
           git config --local user.email "[email protected]"
           git config --local user.name "GitHub Actions"
           setwd("R/")
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE, run_dont_run = TRUE)'
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE, run_dont_run = TRUE, subdir = "r")'
         shell: bash {0}
 

.github/workflows/python.yml

@@ -0,0 +1,207 @@
+name: Python
+
+on:
+  push:
+    branches-ignore: [gh-pages]
+    paths:
+      - ".github/workflows/python.yml"
+      - "src/**"
+      - "python/**"
+  pull_request:
+    branches-ignore: [gh-pages]
+    paths:
+      - ".github/workflows/python.yml"
+      - "src/**"
+      - "python/**"
+
+concurrency:
+  group: ${{ github.event.pull_request.number || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  lint-black:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: psf/black@stable
+        src: "./python"
+
+  run-tests:
+    timeout-minutes: 15
+    needs: lint-black
+    if: "! contains(github.event.head_commit.message, '[skip ci]')"
+    name: Test ${{ matrix.c.os }} (${{ matrix.c.python-version }})
+    runs-on: ${{ matrix.c.os }}
+    strategy:
+      # When set to true, GitHub cancels all in-progress jobs if any matrix job fails.
+      fail-fast: true
+      # The maximum number of jobs that can run simultaneously
+      max-parallel: 1
+      matrix:
+        c:
+          - {os: ubuntu-latest,  python-version: '3.9'}
+          - {os: ubuntu-latest,  python-version: '3.10'}
+          - {os: ubuntu-latest,  python-version: '3.11'}
+          - {os: windows-latest, python-version: '3.11'}
+          - {os: macos-latest,   python-version: '3.11'}
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.c.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.c.python-version }}
+          cache: 'pip'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install tox tox-gh-actions
+
+      - name: Run tox
+        run: cd python && tox
+
+  build-package:
+    timeout-minutes: 10
+    needs: run-tests
+    if: "! contains(github.event.head_commit.message, '[skip ci]')"
+    runs-on:  ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.10"]
+        os: [ubuntu-latest, windows-latest, macos-latest]
+    steps:
+      - name: Checkout sources
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          python3 -m pip install --upgrade build
+
+      - name: Build the packages
+        run: |
+          cd python
+          python3 -m build
+
+      - name: Publish artifacts
+        uses: actions/upload-artifact@v2
+        with:
+          name: distributions
+          path: python/dist/
+
+  build-doc:
+    timeout-minutes: 10
+    needs: build-package
+    if: "! contains(github.event.head_commit.message, '[skip ci]')"
+    runs-on:  ubuntu-latest
+    steps:
+      - name: Checkout sources
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Ensure Pip and Build
+        run: 
+          pip install --upgrade pip
+          pip install --upgrade build
+
+      - name: build the package
+        run: |
+          cd python
+          python3 -m build
+          
+      - name: install the package
+        run: |
+          cd python
+          pip install .
+          
+      - name: install the doc build requirements
+        run: |
+          cd python
+          pip install -r requirements_dev.txt
+          
+      - name: Build the docs
+        run: |
+          cd python
+          make -C doc clean
+          tox -e docs
+          make -C doc html
+          
+      - name: Upload docs as github pages artifact
+        uses: actions/upload-pages-artifact@main
+        with:
+          path: python/doc/_build/html/
+
+  deploy-doc:
+    needs: build-doc
+    if: "! contains(github.event.head_commit.message, '[skip ci]')"
+    permissions:
+      pages: write      # to deploy to Pages
+      id-token: write   # to verify the deployment originates from an appropriate source
+
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    runs-on: ubuntu-latest
+    steps:
+      - name: Get the built docs
+        uses: actions/download-artifact@v3
+        with:
+          name: github-pages
+
+      - name: Deploy 🚀
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: . # The folder the action should deploy.
+          target-folder: python
+
+  coverage:
+    timeout-minutes: 15
+    needs: build-doc
+    if: "! contains(github.event.head_commit.message, '[skip ci]')"
+    name: Coverage ${{ matrix.c.os }} (${{ matrix.c.python-version }})
+    runs-on: ${{ matrix.c.os }}
+    strategy:
+      # When set to true, GitHub cancels all in-progress jobs if any matrix job fails.
+      fail-fast: true
+      # The maximum number of jobs that can run simultaneously
+      max-parallel: 1
+      matrix:
+        c:
+          - {os: ubuntu-latest,  python-version: '3.11'}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.c.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.c.python-version }}
+          cache: 'pip'
+
+      - name: Install dependencies
+        run: |
+          cd python
+          python -m pip install --upgrade pip
+          python -m pip install tox tox-gh-actions
+
+      - name: Run coverage using tox
+        run: |
+          cd python
+          tox -e coverage
+        
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true
+          verbose: true
+