workflows

Author: telatin

.github/workflows/publish-pypi.yml

@@ -0,0 +1,52 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:  # Allow manual trigger
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+
+      - name: Build package
+        run: python -m build
+
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish-to-pypi:
+    name: Publish to PyPI
+    needs: [build]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/votuderep
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/test.yml

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+name: Test
+
+on:
+  push:
+    branches: [ main, master, develop ]
+  pull_request:
+    branches: [ main, master, develop ]
+  workflow_dispatch:
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+          cache: 'pip'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install black ruff
+
+      - name: Check formatting with black
+        run: black --check src/ tests/
+
+      - name: Lint with ruff
+        run: ruff check src/ tests/
+
+  test:
+    name: Test Python ${{ matrix.python-version }} on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+
+      - name: Install BLAST+ (Ubuntu)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y ncbi-blast+
+          blastn -version
+
+      - name: Install BLAST+ (macOS)
+        if: runner.os == 'macOS'
+        run: |
+          brew install blast
+          blastn -version
+
+      - name: Install package and dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev]"
+
+      - name: Run tests with coverage
+        run: |
+          pytest --cov=votuderep --cov-report=xml --cov-report=term
+
+      - name: Upload coverage to Codecov
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
+        uses: codecov/codecov-action@v4
+        with:
+          file: ./coverage.xml
+          fail_ci_if_error: false
+          verbose: true
+
+  test-install:
+    name: Test installation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Test installation
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+          votuderep --version
+          votuderep --help