Merge pull request #67 from Clinical-Genomics/add_workflows

Fix #48 - add GitHub Actions workflows

.github/workflows/build_and_publish.yml

@@ -0,0 +1,55 @@
+name: Publish to PyPI, Docker Hub and GitHub IO
+
+on:
+ release:
+  types:
+   - created
+
+jobs:
+ build-n-publish:
+  name: Build and publish Python distribution to PyPI
+  runs-on: ubuntu-latest
+  permissions:
+    id-token: write
+  steps:
+   - name: Check out git repository
+     uses: actions/checkout@v4
+
+   - name: Set up Python 3.11
+     uses: actions/setup-python@v5
+     with:
+      python-version: 3.11
+
+   - name: Install build tools
+     run: >-
+        python -m
+        pip install
+        wheel
+        twine
+        --user
+
+   - name: Build a binary wheel and a source tarball
+     run: >-
+        python
+        setup.py
+        sdist
+        bdist_wheel
+
+   - name: Publish distribution 📦 to PyPI
+     uses: pypa/gh-action-pypi-publish@release/v1
+
+ docker-image-CI:
+   name: Docker Image CI
+   runs-on: ubuntu-latest
+   steps:
+
+    - name: Check out git repository
+      uses: actions/checkout@v3
+
+    - name: Publish main image (Dockerfile) to Registry
+      uses: elgohr/Publish-Docker-Github-Action@v5
+      with:
+        name: clinicalgenomics/stranger
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+        tags: "latest,${{ github.event.release.tag_name }}"

.github/workflows/keep_a_changelog.yml

@@ -0,0 +1,15 @@
+name: "Changelog Reminder"
+on:
+  pull_request:
+      types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled]
+
+jobs:
+  # Enforces the update of a changelog file on every pull request
+  changelog:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: dangoslen/changelog-enforcer@v3
+      with:
+        changeLogPath: 'CHANGELOG.md'
+        skipLabels: 'Skip-Changelog'

.github/workflows/linting_and_fixing.yml

@@ -0,0 +1,42 @@
+name: Lint files and fix lint errors
+
+# This will only correct linting in local PRs
+on: ["push"]
+
+jobs:
+  build:
+
+    name: Lint-and-fix
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.12]
+
+    steps:
+
+    # Check out code
+    - name: Check out git repository
+      uses: actions/checkout@v4
+
+    # Set up python
+    - name: Set up Python ${{ matrix.python-version}}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version}}
+
+    - name: Install Python Dependencies
+      run: |
+        pip install black flake8
+
+    - name: Run linters
+      uses: wearerequired/lint-action@v2
+      # Let linters fix problems if they can
+      with:
+        github_token: ${{ secrets.github_token }}
+        auto_fix: true
+        # Enable linters
+        black: true
+        black_args: "-l 100"
+        # stop the build if there are Python syntax errors or undefined names
+        flake8: true
+        flake8_args: "stranger/ --count --select=E9,F63,F7,F82 --show-source --statistics"

.github/workflows/linting_only.yml

@@ -0,0 +1,47 @@
+name: Lint files - no fixing
+
+# This will check linting in local PRs
+on: ["push", "pull_request"]
+
+jobs:
+  build:
+
+    name: Lint-only
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.12]
+
+    steps:
+
+    # Check out code
+    - name: Check out git repository
+      uses: actions/checkout@v4
+
+    # Set up python
+    - name: Set up Python ${{ matrix.python-version}}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version}}
+
+    - name: Install Python Dependencies
+      run: |
+        pip install black flake8 isort
+
+    - name: Run linters
+      uses: wearerequired/lint-action@v2
+      # Let linters fix problems if they can
+      with:
+        github_token: ${{ secrets.github_token }}
+        auto_fix: false
+        # Enable linters
+        black: true
+        black_args: "--check -l 100"
+        # stop the build if there are Python syntax errors or undefined names
+        flake8: true
+        flake8_args: "stranger/ --count --select=E9,F63,F7,F82 --show-source --statistics"
+
+    - name: Run isort
+      uses: jamescurtin/isort-action@master
+      with:
+          configuration: "--check-only --diff -m 3 --tc --fgw 0 --up -n -l 100"

.github/workflows/server_stage_docker_push.yml

@@ -0,0 +1,37 @@
+name: Publish to Docker stage
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  docker-stage-push:
+    name: Create staging docker image
+    runs-on: ubuntu-latest
+    steps:
+     - name: Check out git repository
+       uses: actions/checkout@v4
+
+     - name: Get branch name
+       id: branch-name
+       uses: tj-actions/branch-names@v7
+
+     - name: Login to Docker Hub
+       uses: docker/login-action@v3
+       with:
+         username: ${{ secrets.DOCKER_USERNAME }}
+         password: ${{ secrets.DOCKER_PASSWORD }}
+
+     - name: Set up Docker Buildx
+       id: buildx
+       uses: docker/setup-buildx-action@v3
+
+     - name: Build and push
+       if: steps.branch-name.outputs.is_default == 'false'
+       uses: docker/build-push-action@v5
+       with:
+         context: ./
+         file: ./Dockerfile
+         push: true
+         tags: "clinicalgenomics/stranger-stage:${{steps.branch-name.outputs.current_branch}}, clinicalgenomics/stranger-stage:latest"

.github/workflows/tests_and_cov.yml

@@ -0,0 +1,85 @@
+name: Run tests and push coverage to Codecov
+
+on:
+  push:
+    branches:
+    - main
+  pull_request:
+    branches:
+    - main
+
+jobs:
+  setup:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+        # Cache package installation step to speed up the following step
+      - uses: actions/cache@v4
+        with:
+          path: ${{ env.pythonLocation }}
+          key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }} }}
+
+      - name: Install deps
+        run: |
+          pip install --upgrade --upgrade-strategy eager -e .
+          pip check
+
+  test:
+    needs: setup
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+        # Cache package installation step to speed up the following step
+      - uses: actions/cache@v4
+        with:
+          path: ${{ env.pythonLocation }}
+          key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}
+
+      - name: Install pytest
+        run: pip install pytest pytest-cov
+
+      - name: Run pytest
+        run: pytest --cov --rootdir=/home/runner/work/stranger
+
+      - name: Upload coverage
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage${{ matrix.group }}
+          path: .coverage
+
+  coverage:
+    needs: test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+      - name: Install deps
+        run: |
+          python -m pip install --upgrade pip
+          pip install coverage
+      - name: Download all artifacts
+        # Download and combine coverage1, coverage2, etc.
+        uses: actions/download-artifact@v4
+      - name: Run coverage
+        run: |
+          coverage combine coverage*/.coverage*
+          coverage report
+          coverage xml
+      - uses: codecov/codecov-action@v4
+        env:
+            CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/vulture.yml

@@ -0,0 +1,23 @@
+name: "Vulture - Find unused code"
+on:
+  - pull_request
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    name: vulture
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Find changed Python files
+        id: files
+        uses: Ana06/get-changed-files@v2.2.0
+        with:
+          filter: "*.py"
+
+      - name: Scavenge
+        uses: anaynayak/python-vulture-action@v1.0
+        id: vulture
+        with:
+          vulture-args: --min-confidence 80 --ignore-names cls,args,kwargs,real_variant_database ${{steps.files.outputs.all}}
+        continue-on-error: true

.github/workflows/woke.yml

@@ -0,0 +1,15 @@
+name: woke
+on:
+  - pull_request
+jobs:
+  woke:
+    name: Non-inclusive language check with woke
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: woke
+        uses: get-woke/woke-action@v0
+        with:
+          fail-on-error: false

CHANGELOG.md

@@ -3,10 +3,13 @@ All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
 ## [unreleased]
+### Added
+- Added github action test and release workflows
 ### Fixed
 - Docs for TRGT annotation
 - Fallback setting allele size to 0 if MC is only set to "." and TRGT annotation requested
 
+
 ## [0.9.0]
 - Add Docker image
 - Parse TRGT VCFs - in particular, decompose and parse FORMAT.MC