style: clean some stuff #336
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| name: CI-CD | |
| # only run on pushes to main or pull requests | |
| on: | |
| push: | |
| # push to any branch * | |
| branches: [ "*"] | |
| pull_request: | |
| branches: [ main , development] | |
| jobs: | |
| Unit-Tests: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, macos-14] | |
| python-version: ["3.12", "3.11"] # "3.10", | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install poetry | |
| uses: snok/install-poetry@v1 | |
| - name: Install dependencies | |
| run: poetry install | |
| - name: Test with pytest | |
| run: | | |
| # Github action runners now have 4 cores | |
| poetry run pytest -n 4 --cov --cov-report xml:coverage-report/coverage.xml | |
| - name: Upload coverage report artifact to be used by Codecov | |
| # only upload if matrix.os is ubuntu-latest and matrix.python-version is 3.12 | |
| if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12' | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: coverage-report | |
| path: coverage-report | |
| Codecov: | |
| needs: Unit-Tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| - name: Download coverage.xml artifact | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: coverage-report | |
| path: coverage-report | |
| - name: Use Codecov to track coverage | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| files: ./coverage-report/coverage.xml | |
| fail_ci_if_error: true | |
| verbose: true | |
| name: codecov-umbrella | |
| Build-Documentation: | |
| runs-on: ubuntu-latest | |
| if: github.ref == 'refs/heads/docs' | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.10.4 | |
| - name: Install poetry | |
| uses: snok/install-poetry@v1 | |
| - name: Install dependencies | |
| run: poetry install | |
| - name: Build documentation | |
| run: | | |
| pip install -r docs/requirements.txt | |
| pip install . | |
| make html --directory=docs | |
| Continuous-Deployment: | |
| permissions: | |
| contents: write | |
| packages: write | |
| issues: write | |
| pull-requests: write | |
| needs: [Unit-Tests] | |
| # if pulling to main, deploy to PyPI | |
| if: github.ref == 'refs/heads/main' | |
| # Set up operating system | |
| runs-on: ubuntu-latest | |
| # Define job steps | |
| steps: | |
| - name: Set up Python 3.12 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.12 | |
| - name: Check-out repository | |
| uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Install poetry | |
| uses: snok/install-poetry@v1 | |
| - name: Install package | |
| run: poetry install | |
| # This action uses Python Semantic Release v8 | |
| # What this action does: | |
| # - Determines the next version number based on the commit history | |
| # - Creates a new tag with the new version number | |
| # - Pushes the new tag to GitHub | |
| # - Creates a GitHub release with the new version number | |
| - name: Python Semantic Release | |
| id: release | |
| uses: python-semantic-release/python-semantic-release@master | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Install packaging-related tool | |
| run: | |
| python3 -m pip install build twine | |
| # Build Package step: | |
| # After semantic release, we should have a new tag if the commit history | |
| # has been updated. If there isnt a new tag, then we dont need to build | |
| # a new package. If there is a new tag, then we need to build a new package | |
| # and publish it to PyPI | |
| - name: Build package | |
| if: steps.release.outputs.released == 'true' | |
| run: | | |
| poetry version $(git describe --tags --abbrev=0 | sed 's/^v//') | |
| python -m build --sdist --wheel --outdir dist/ . | |
| echo "LATEST_TAG=$(poetry version | sed 's/^nbiatoolkit //')" >> "$GITHUB_ENV" | |
| - name: Publish package distributions to PyPI | |
| if: steps.release.outputs.released == 'true' | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| verbose: true | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} | |
| - name: Print branch name | |
| run: | | |
| printf "LATEST TAG: %s\n" "${LATEST_TAG}" | |
| echo "DOCKER_IMAGE_TAG=${LATEST_TAG}" >> "$GITHUB_ENV" | |
| printf "DOCKER_IMAGE_TAG: %s\n" "${DOCKER_IMAGE_TAG}" | |
| - name: Print outputs from semantic release | |
| run: | | |
| # Semantic release gha provides the following outputs: | |
| # - released: true if a new release was created, false otherwise | |
| # - version: the new version number | |
| # - tag: The Git tag that was created | |
| echo "${{ steps.release.outputs.released }}" | |
| echo "${{ steps.release.outputs.version }}" | |
| echo "${{ steps.release.outputs.tag }}" | |
| echo "${{ steps.release.outputs.release_notes }}" | |
| - name: Set up QEMU | |
| if: steps.release.outputs.released == 'true' | |
| uses: docker/setup-qemu-action@v3 | |
| - name: Set up Docker Buildx | |
| if: steps.release.outputs.released == 'true' | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Login to Docker Hub | |
| if: steps.release.outputs.released == 'true' | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Login to the GitHub Container Registry | |
| if: steps.release.outputs.released == 'true' | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Extract metadata (tags, labels) for Docker | |
| id: meta | |
| uses: docker/metadata-action@v3 | |
| with: | |
| images: | | |
| ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ env.DOCKER_IMAGE_TAG }} | |
| ghcr.io/${{ github.repository }}/nbiatoolkit:${{ env.DOCKER_IMAGE_TAG }} | |
| - name: Build | |
| if: steps.release.outputs.released == 'true' | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . | |
| platforms: linux/amd64,linux/arm64 | |
| file: ./Dockerfile | |
| push: true | |
| tags: | | |
| ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ env.DOCKER_IMAGE_TAG }} | |
| ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:latest | |
| ghcr.io/${{ github.repository }}/nbiatoolkit:${{ env.DOCKER_IMAGE_TAG }} | |
| ghcr.io/${{ github.repository }}/nbiatoolkit:latest | |
| labels: ${{ steps.meta.outputs.labels }} | |
| test_install_withPyPi: | |
| needs: Continuous-Deployment | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, macos-14] | |
| python-version: ["3.12", "3.11"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install using PyPi | |
| run: | | |
| pip install nbiatoolkit; | |
| NBIAToolkit | |
| test_image_with_new_tag: | |
| needs: Continuous-Deployment | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| - name: Test Image With new Tag | |
| run: | | |
| # get latest tag | |
| LATEST_TAG=$(curl -s \ | |
| "https://api.github.com/repos/${{ github.repository }}/releases/latest" \ | |
| | jq -r .tag_name | sed 's/^v//') | |
| echo "LATEST_TAG=${LATEST_TAG}" | |
| # test image with latest tag | |
| docker run --rm \ | |
| ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${LATEST_TAG} \ | |
| NBIAToolkit | |
| test_image_with_latest_tag: | |
| needs: Continuous-Deployment | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v2 | |
| - name: Test Image with "latest" Tag | |
| run: | | |
| docker run --rm \ | |
| ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:latest \ | |
| NBIAToolkit | |
| Update-README: | |
| needs: Continuous-Deployment | |
| runs-on: ubuntu-latest | |
| # if: github.ref == 'refs/heads/development' | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| - name: Get Current branch | |
| run: | | |
| echo "Current branch is: ${{ github.ref }}" | |
| echo "Current branch is: ${{ github.head_ref }}" | |
| echo "Current branch is: ${{ github.base_ref }}" | |
| echo "Current branch is: ${{ github.event_name }}" | |
| # if main, then git pull main | |
| if [ "${{ github.ref }}" == "refs/heads/main" ]; then | |
| git pull origin main | |
| fi | |
| # fix diverged branch | |
| git fetch origin ${{ github.head_ref }} | |
| git checkout ${{ github.head_ref }} | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install using PyPi | |
| run: | | |
| # update pip | |
| pip install . | |
| NBIAToolkit | |
| - name: Update README code block | |
| run: | | |
| awk '/``` bash NBIAToolkit-Output/ { | |
| print "``` bash NBIAToolkit-Output"; | |
| print "> NBIAToolkit --version"; | |
| system("NBIAToolkit --version"); | |
| f=1; | |
| next | |
| } f && /```/ { | |
| print "```"; | |
| f=0; | |
| next | |
| } !f' README.md > temp && mv temp README.md | |
| - name: Commit and push changes | |
| run: | | |
| LATEST_TAG=$(curl -s \ | |
| "https://api.github.com/repos/${{ github.repository }}/releases/latest" \ | |
| | jq -r .tag_name | sed 's/^v//') | |
| echo "LATEST_TAG=${LATEST_TAG}" | |
| # Check for changes | |
| if [[ $(git status --porcelain) ]]; then | |
| # Changes are present | |
| echo "Changes found. Committing and pushing..." | |
| git config --global user.name 'jjjermiah' | |
| git config --global user.email 'jjjermiah@users.noreply.github.com' | |
| # Add all changes | |
| git add . | |
| # Commit with a timestamp | |
| git commit -m "chore: Update README: $LATEST_TAG" | |
| # Push changes to the remote repository | |
| # if github.head_ref is not null | |
| # then push to the branch | |
| # else push to the base branch | |
| if [ -n "${{ github.head_ref }}" ]; then | |
| git push origin HEAD:${{ github.head_ref }} | |
| else | |
| git push origin HEAD:${{ github.ref }} | |
| fi | |
| echo "Changes committed and pushed successfully." | |
| else | |
| # No changes | |
| echo "No changes found. Nothing to commit or push." | |
| fi | |
| # # git add README.md | |
| # # git commit -m "Update README with latest version" | |
| # # git push | |
| # #!/bin/bash | |
| # # Check for changes | |
| # if [[ $(git status --porcelain) ]]; then | |
| # # Changes are present | |
| # echo "Changes found. Committing and pushing..." | |
| # # Add all changes | |
| # git add . | |
| # # Commit with a timestamp | |
| # git commit -m "Auto commit: $(date)" | |
| # # Push changes to the remote repository | |
| # git push origin <your-branch-name> | |
| # echo "Changes committed and pushed successfully." | |
| # else | |
| # # No changes | |
| # echo "No changes found. Nothing to commit or push." | |
| # fi |