adds docstring #3179
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| # GitHub Action workflow for testing, building, and releasing the Synapse Python Client. | |
| # - all pushes, releases, and pull requests are tested against unit tests, and additionally | |
| # integration tests if account configuration secrets are available. | |
| # - releases are additionally packaged, uploaded as build and release artifacts, | |
| # and deployed to pypi servers (test.pypi.org for prereleases, and pypi.org for releases) | |
| # Release tags must conform to our semver versioning, e.g. v1.2.3 in order to be packaged | |
| # for pypi deployment. | |
| # - all pushes to the `develop` branch of the repository trigger a docker build and push to ghcr.io | |
| # with the image tag named after the sha of the commit, | |
| # e.g. `ghcr.io/sage-bionetworks/synapsepythonclient:develop-abc123` | |
| # - all non-prerelease releases trigger a docker build and push to ghcr.io with the image tag named | |
| # after the release tag, e.g. `ghcr.io/sage-bionetworks/synapsepythonclient:1.2.3` | |
| name: build | |
| on: | |
| push: | |
| # we test all pushed branches, but not tags. | |
| # we only push tags with releases, and we handle releases explicitly | |
| branches: | |
| - '**' | |
| tags-ignore: | |
| - '**' | |
| release: | |
| types: | |
| - 'published' | |
| jobs: | |
| pre-commit: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - uses: pre-commit/[email protected] | |
| # run unit (and integration tests if account secrets available) on our build matrix | |
| test: | |
| needs: [pre-commit] | |
| strategy: | |
| matrix: | |
| os: [ubuntu-20.04, macos-12, windows-2022] | |
| # if changing the below change the run-integration-tests versions and the check-deploy versions | |
| python: [3.8, '3.9', '3.10', '3.11'] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: get-dependencies-location | |
| shell: bash | |
| run: | | |
| SITE_PACKAGES_LOCATION=$(python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())") | |
| SITE_BIN_DIR=$(python3 -c "import os; import platform; import distutils.sysconfig; pre = distutils.sysconfig.get_config_var('prefix'); bindir = os.path.join(pre, 'Scripts' if platform.system() == 'Windows' else 'bin'); print(bindir)") | |
| echo "site_packages_loc=$SITE_PACKAGES_LOCATION" >> $GITHUB_OUTPUT | |
| echo "site_bin_dir=$SITE_BIN_DIR" >> $GITHUB_OUTPUT | |
| id: get-dependencies | |
| - name: Cache py-dependencies | |
| id: cache-dependencies | |
| uses: actions/cache@v4 | |
| env: | |
| cache-name: cache-py-dependencies | |
| with: | |
| path: | | |
| ${{ steps.get-dependencies.outputs.site_packages_loc }} | |
| ${{ steps.get-dependencies.outputs.site_bin_dir }} | |
| key: ${{ runner.os }}-${{ matrix.python }}-build-${{ env.cache-name }}-${{ hashFiles('setup.py') }}-v17 | |
| - name: Install py-dependencies | |
| if: steps.cache-dependencies.outputs.cache-hit != 'true' | |
| shell: bash | |
| run: | | |
| pip install -e ".[boto3,pandas,pysftp,tests]" | |
| # ensure that numpy c extensions are installed on windows | |
| # https://stackoverflow.com/a/59346525 | |
| if [ "${{startsWith(runner.os, 'Windows')}}" == "true" ]; then | |
| pip uninstall -y numpy | |
| pip uninstall -y setuptools | |
| pip install setuptools | |
| pip install numpy | |
| fi | |
| - name: run-unit-tests | |
| shell: bash | |
| run: | | |
| pytest -sv --cov-append --cov=. --cov-report xml tests/unit | |
| - name: Check for Secret availability | |
| id: secret-check | |
| if: ${{ contains(fromJSON('["3.9"]'), matrix.python) }} | |
| # perform secret check & put boolean result as an output | |
| shell: bash | |
| run: | | |
| if [ -z "${{ secrets.encrypted_d17283647768_key }}" ] || [ -z "${{ secrets.encrypted_d17283647768_iv }}" ]; then | |
| echo "secrets_available=false" >> $GITHUB_OUTPUT; | |
| else | |
| echo "secrets_available=true" >> $GITHUB_OUTPUT; | |
| fi | |
| if [ -z "${{ secrets.synapse_personal_access_token }}" ]; then | |
| echo "synapse_pat_available=false" >> $GITHUB_OUTPUT; | |
| else | |
| echo "synapse_pat_available=true" >> $GITHUB_OUTPUT; | |
| fi | |
| - name: OpenTelemtry pre-check | |
| id: otel-check | |
| if: ${{ steps.secret-check.outputs.secrets_available == 'true' && steps.secret-check.outputs.synapse_pat_available == 'true' }} | |
| shell: bash | |
| run: | | |
| # Leave disabled during normal integration test runs - Enable when we want to | |
| # collect the data. | |
| # echo "run_opentelemetry=true" >> $GITHUB_OUTPUT; | |
| echo "run_opentelemetry=false" >> $GITHUB_OUTPUT; | |
| # AWS CLI is pre-installed on github hosted runners - Commented out for GH runs | |
| # curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip" | |
| # unzip awscliv2.zip | |
| # sudo ./aws/install | |
| # curl "https://s3.amazonaws.com/session-manager-downloads/plugin/latest/ubuntu_64bit/session-manager-plugin.deb" -o "session-manager-plugin.deb" | |
| # sudo dpkg -i session-manager-plugin.deb | |
| # - name: Create AWS Config | |
| # if: ${{ steps.otel-check.outputs.run_opentelemetry == 'true' }} | |
| # shell: bash | |
| # run: | | |
| # touch test.awsConfig | |
| # printf "[default]\nregion = us-east-1\ncredential_process = \"tests/integration/synapse_creds.sh\" \"https://sc.sageit.org\" \"${{ secrets.synapse_personal_access_token }}\"\n" >> test.awsConfig | |
| # chmod +x tests/integration/synapse_creds.sh | |
| # If you are exporting data using `otlp` you can start a port forwading session | |
| # - name: SSM Port Forward Start | |
| # if: ${{ steps.otel-check.outputs.run_opentelemetry == 'true' }} | |
| # shell: bash | |
| # env: | |
| # AWS_CONFIG_FILE: "test.awsConfig" | |
| # run: | | |
| # # Start a port-forwarding session in a non-interactive way. AWS will clean-up | |
| # # stale sessions after 20 minutes of inactivity | |
| # aws ssm start-session --target i-0ffcdecd1edf375ee --document-name AWS-StartPortForwardingSession --parameters "portNumber"=["4318"],"localPortNumber"=["4318"] & disown | |
| # sleep 15 | |
| # run integration tests iff the decryption keys for the test configuration are available. | |
| # they will not be available in pull requests from forks. | |
| # run integration tests on the oldest and newest supported versions of python. | |
| # we don't run on the entire matrix to avoid a 3xN set of concurrent tests against | |
| # the target server where N is the number of supported python versions. | |
| - name: run-integration-tests | |
| shell: bash | |
| # keep versions consistent with the first and last from the strategy matrix | |
| if: ${{ contains(fromJSON('["3.9"]'), matrix.python) && steps.secret-check.outputs.secrets_available == 'true'}} | |
| run: | | |
| # decrypt the encrypted test synapse configuration | |
| openssl aes-256-cbc -K ${{ secrets.encrypted_d17283647768_key }} -iv ${{ secrets.encrypted_d17283647768_iv }} -in test.synapseConfig.enc -out test.synapseConfig -d | |
| mv test.synapseConfig ~/.synapseConfig | |
| if [ "${{ startsWith(matrix.os, 'ubuntu') }}" == "true" ]; then | |
| # on linux only we can build and run a docker container to serve as an SFTP host for our SFTP tests. | |
| # Docker is not available on GH Action runners on Mac and Windows. | |
| docker build -t sftp_tests - < tests/integration/synapseclient/core/upload/Dockerfile_sftp | |
| docker run -d sftp_tests:latest | |
| # get the internal IP address of the just launched container | |
| export SFTP_HOST=$(docker inspect -f '{{range .NetworkSettings.Networks}}{{.IPAddress}}{{end}}' $(docker ps -q)) | |
| printf "[sftp://$SFTP_HOST]\nusername: test\npassword: test\n" >> ~/.synapseConfig | |
| # add to known_hosts so the ssh connections can be made without any prompting/errors | |
| mkdir -p ~/.ssh | |
| ssh-keyscan -H $SFTP_HOST >> ~/.ssh/known_hosts | |
| fi | |
| # set env vars used in external bucket tests from secrets | |
| export EXTERNAL_S3_BUCKET_NAME="${{secrets.EXTERNAL_S3_BUCKET_NAME}}" | |
| export EXTERNAL_S3_BUCKET_AWS_ACCESS_KEY_ID="${{secrets.EXTERNAL_S3_BUCKET_AWS_ACCESS_KEY_ID}}" | |
| export EXTERNAL_S3_BUCKET_AWS_SECRET_ACCESS_KEY="${{secrets.EXTERNAL_S3_BUCKET_AWS_SECRET_ACCESS_KEY}}" | |
| if [ ${{ steps.otel-check.outputs.run_opentelemetry }} == "true" ]; then | |
| # Set to 'file' to enable OpenTelemetry export to file | |
| export SYNAPSE_OTEL_INTEGRATION_TEST_EXPORTER="file" | |
| fi | |
| # use loadscope to avoid issues running tests concurrently that share scoped fixtures | |
| pytest -sv --reruns 3 --cov-append --cov=. --cov-report xml tests/integration -n auto --ignore=tests/integration/synapseclient/test_command_line_client.py --dist loadscope | |
| # Execute the CLI tests in a non-dist way because they were causing some test instability when being run concurrently | |
| pytest -sv --reruns 3 --cov-append --cov=. --cov-report xml tests/integration/synapseclient/test_command_line_client.py | |
| - name: Upload otel spans | |
| uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: otel_spans_integration_testing_${{ matrix.os }} | |
| path: tests/integration/otel_spans_integration_testing_*.ndjson | |
| if-no-files-found: ignore | |
| - name: Upload coverage report | |
| id: upload_coverage_report | |
| uses: actions/upload-artifact@v4 | |
| if: ${{ contains(fromJSON('["3.9"]'), matrix.python) && contains(fromJSON('["ubuntu-20.04"]'), matrix.os)}} | |
| with: | |
| name: coverage-report | |
| path: coverage.xml | |
| sonarcloud: | |
| needs: [test] | |
| if: ${{ always() && !cancelled()}} | |
| name: SonarCloud | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis | |
| - name: Check coverage-report artifact existence | |
| id: check_coverage_report | |
| uses: LIT-Protocol/artifact-exists-action@v0 | |
| with: | |
| name: "coverage-report" | |
| - name: Download coverage report | |
| uses: actions/download-artifact@v4 | |
| if: steps.check_coverage_report.outputs.exists == 'true' | |
| with: | |
| name: coverage-report | |
| - name: Check coverage.xml file existence | |
| id: check_coverage_xml | |
| uses: andstor/file-existence-action@v3 | |
| with: | |
| files: "coverage.xml" | |
| # This is a workaround described in https://community.sonarsource.com/t/sonar-on-github-actions-with-python-coverage-source-issue/36057 | |
| - name: Override Coverage Source Path for Sonar | |
| if: steps.check_coverage_xml.outputs.files_exists == 'true' | |
| run: sed -i "s/<source>\/home\/runner\/work\/synapsePythonClient<\/source>/<source>\/github\/workspace<\/source>/g" coverage.xml | |
| - name: SonarCloud Scan | |
| uses: SonarSource/sonarcloud-github-action@master | |
| if: ${{ always() }} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} | |
| # on a GitHub release, build the pip package and upload it as a GitHub release asset | |
| package: | |
| needs: [test,pre-commit] | |
| runs-on: ubuntu-20.04 | |
| if: github.event_name == 'release' | |
| outputs: | |
| sdist-package-name: ${{ steps.build-package.outputs.sdist-package-name }} | |
| bdist-package-name: ${{ steps.build-package.outputs.bdist-package-name }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.8 | |
| - name: set-release-env | |
| shell: bash | |
| run: | | |
| RELEASE_TAG="${{ github.event.release.tag_name }}" | |
| if [[ $RELEASE_TAG =~ ^v?([[:digit:]\.]+)(-rc)? ]]; then | |
| VERSION="${BASH_REMATCH[1]}" | |
| if [[ "${{ github.event.release.prerelease}}" == "true" ]]; then | |
| if [[ -z "${BASH_REMATCH[2]}" ]]; then | |
| echo "A test release tag should end with \"-rc\"" | |
| exit 1 | |
| fi | |
| # for staging builds we append the build number so we have | |
| # distinct version numbers between prod and test pypi. | |
| VERSION="$VERSION.$GITHUB_RUN_NUMBER" | |
| fi | |
| else | |
| echo "Unable to parse deployment version from $RELEASE_TAG" | |
| exit 1 | |
| fi | |
| echo "VERSION=$VERSION" >> $GITHUB_ENV | |
| # ensure that the version file in the package will have the correct version | |
| # matching the name of the tag | |
| - name: update-version | |
| shell: bash | |
| run: | | |
| if [[ -n "$VERSION" ]]; then | |
| sed "s|\"latestVersion\":.*$|\"latestVersion\":\"$VERSION\",|g" synapseclient/synapsePythonClient > temp | |
| rm synapseclient/synapsePythonClient | |
| mv temp synapseclient/synapsePythonClient | |
| fi | |
| - id: build-package | |
| shell: bash | |
| run: | | |
| python3 -m pip install --upgrade pip | |
| python3 -m pip install setuptools | |
| python3 -m pip install wheel | |
| python3 -m pip install build | |
| # install synapseclient | |
| python3 -m pip install . | |
| # create distribution | |
| python3 -m build | |
| SDIST_PACKAGE_NAME="synapseclient-${{env.VERSION}}.tar.gz" | |
| BDIST_PACKAGE_NAME="synapseclient-${{env.VERSION}}-py3-none-any.whl" | |
| RELEASE_URL_PREFIX="https://uploads.github.com/repos/${{ github.event.repository.full_name }}/releases/${{ github.event.release.id }}/assets?name=" | |
| echo "sdist-package-name=$SDIST_PACKAGE_NAME" >> $GITHUB_OUTPUT | |
| echo "bdist-package-name=$BDIST_PACKAGE_NAME" >> $GITHUB_OUTPUT | |
| echo "sdist-release-url=${RELEASE_URL_PREFIX}${SDIST_PACKAGE_NAME}" >> $GITHUB_OUTPUT | |
| echo "bdist-release-url=${RELEASE_URL_PREFIX}${BDIST_PACKAGE_NAME}" >> $GITHUB_OUTPUT | |
| # upload the packages as build artifacts of the GitHub Action | |
| - name: upload-build-sdist | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ steps.build-package.outputs.sdist-package-name }} | |
| path: dist/${{ steps.build-package.outputs.sdist-package-name }} | |
| - name: upload-build-bdist | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ steps.build-package.outputs.bdist-package-name }} | |
| path: dist/${{ steps.build-package.outputs.bdist-package-name }} | |
| # upload the packages as artifacts of the GitHub release | |
| # - name: upload-release-sdist | |
| # uses: actions/upload-release-asset@v1 | |
| # env: | |
| # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # with: | |
| # upload_url: ${{ steps.build-package.outputs.sdist-release-url }} | |
| # asset_name: ${{ steps.build-package.outputs.sdist-package-name }} | |
| # asset_path: dist/${{ steps.build-package.outputs.sdist-package-name }} | |
| # asset_content_type: application/gzip | |
| # - name: upload-release-bdist | |
| # uses: actions/upload-release-asset@v1 | |
| # env: | |
| # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # with: | |
| # upload_url: ${{ steps.build-package.outputs.bdist-release-url }} | |
| # asset_name: ${{ steps.build-package.outputs.bdist-package-name }} | |
| # asset_path: dist/${{ steps.build-package.outputs.bdist-package-name }} | |
| # asset_content_type: application/zip | |
| # re-download the built package to the appropriate pypi server. | |
| # we upload prereleases to test.pypi.org and releases to pypi.org. | |
| deploy: | |
| needs: package | |
| runs-on: ubuntu-latest | |
| environment: | |
| url: ${{ github.event.release.prerelease == 'true' && 'https://test.pypi.org/p/synapseclient' || 'https://pypi.org/p/synapseclient' }} | |
| name: pypi | |
| permissions: | |
| id-token: write | |
| steps: | |
| - name: download-sdist | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: ${{ needs.package.outputs.sdist-package-name }} | |
| path: dist | |
| - name: download-bdist | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: ${{ needs.package.outputs.bdist-package-name }} | |
| path: dist | |
| - name: deploy-to-test-pypi | |
| if: 'github.event.release.prerelease' | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| repository-url: https://test.pypi.org/legacy/ | |
| - name: deploy-to-prod-pypi | |
| if: '!github.event.release.prerelease' | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| # on each of our matrix platforms, download the newly uploaded package from pypi and confirm its version | |
| check-deploy: | |
| needs: deploy | |
| strategy: | |
| matrix: | |
| os: [ubuntu-20.04, macos-12, windows-2022] | |
| # python versions should be consistent with the strategy matrix and the runs-integration-tests versions | |
| python: [3.8, '3.9', '3.10', '3.11'] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: check-pypi | |
| shell: bash | |
| run: | | |
| if [[ "${{ github.event.release.prerelease}}" == "false" ]]; then | |
| PYPI_INDEX_URL="https://pypi.org/simple/" | |
| else | |
| PYPI_INDEX_URL="https://test.pypi.org/simple/" | |
| fi | |
| RELEASE_TAG="${{ github.event.release.tag_name }}" | |
| if [[ $RELEASE_TAG =~ ^v?([[:digit:]\.]+)(-rc)? ]]; then | |
| VERSION="${BASH_REMATCH[1]}" | |
| if [[ "${{ github.event.release.prerelease}}" == "true" ]]; then | |
| VERSION="$VERSION.$GITHUB_RUN_NUMBER" | |
| fi | |
| else | |
| echo "Unrecognized release tag" | |
| exit 1 | |
| fi | |
| # it can take some time for the packages to become available in pypi after uploading | |
| for i in 5 10 20 40; do | |
| if pip3 install --index-url $PYPI_INDEX_URL --extra-index-url https://pypi.org/simple "synapseclient==$VERSION"; then | |
| ACTUAL_VERSION=$(synapse --version) | |
| if [ -n "$(echo "$ACTUAL_VERSION" | grep -oF "$VERSION")" ]; then | |
| echo "Successfully installed version $VERSION" | |
| exit 0 | |
| else | |
| echo "Expected version $VERSION, found $ACTUAL_VERSION instead" | |
| exit 1 | |
| fi | |
| fi | |
| sleep $i | |
| done | |
| echo "Failed to install expected version $VERSION" | |
| exit 1 | |
| # containerize the package and upload to the GHCR upon new release (whether pre-release or not) | |
| ghcr-build-and-push-on-release: | |
| needs: deploy | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| packages: write | |
| steps: | |
| - name: Check out the repo | |
| uses: actions/checkout@v4 | |
| - name: Extract Release Version | |
| run: echo "RELEASE_VERSION=${GITHUB_REF#refs/tags/}" >> $GITHUB_ENV | |
| shell: bash | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| - name: Log in to GitHub Container Registry | |
| uses: docker/login-action@v2 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Build and push Docker image (official release) | |
| id: docker_build | |
| if: '!github.event.release.prerelease' | |
| uses: docker/build-push-action@v3 | |
| with: | |
| push: true | |
| provenance: false | |
| tags: ghcr.io/sage-bionetworks/synapsepythonclient:latest,ghcr.io/sage-bionetworks/synapsepythonclient:${{ env.RELEASE_VERSION }} | |
| file: ./Dockerfile | |
| platforms: linux/amd64 | |
| cache-from: type=registry,ref=ghcr.io/sage-bionetworks/synapsepythonclient:build-cache | |
| cache-to: type=registry,mode=max,ref=ghcr.io/sage-bionetworks/synapsepythonclient:build-cache | |
| - name: Build and push Docker image (pre-release) | |
| id: docker_build_prerelease | |
| if: 'github.event.release.prerelease' | |
| uses: docker/build-push-action@v3 | |
| with: | |
| push: true | |
| provenance: false | |
| tags: ghcr.io/sage-bionetworks/synapsepythonclient:${{ env.RELEASE_VERSION }}-prerelease | |
| file: ./Dockerfile | |
| platforms: linux/amd64 | |
| cache-from: type=registry,ref=ghcr.io/sage-bionetworks/synapsepythonclient:build-cache-prerelease | |
| cache-to: type=registry,mode=max,ref=ghcr.io/sage-bionetworks/synapsepythonclient:build-cache-prerelease | |
| - name: Output image digest (official release) | |
| if: '!github.event.release.prerelease' | |
| run: echo "The image digest for official release is ${{ steps.docker_build.outputs.digest }}" | |
| - name: Output image digest (pre-release) | |
| if: 'github.event.release.prerelease' | |
| run: echo "The image digest for pre-release is ${{ steps.docker_build_prerelease.outputs.digest }}" | |
| # containerize the package and upload to the GHCR upon commit in develop | |
| ghcr-build-and-push-on-develop: | |
| runs-on: ubuntu-latest | |
| if: github.ref == 'refs/heads/develop' | |
| permissions: | |
| contents: read | |
| packages: write | |
| steps: | |
| - name: Check out the repo | |
| uses: actions/checkout@v4 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| - name: Log in to GitHub Container Registry | |
| uses: docker/login-action@v2 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Build and push Docker image for develop | |
| id: docker_build | |
| uses: docker/build-push-action@v5 | |
| with: | |
| push: true | |
| provenance: false | |
| tags: ghcr.io/sage-bionetworks/synapsepythonclient:develop-${{ github.sha }} | |
| file: ./Dockerfile | |
| platforms: linux/amd64 | |
| cache-from: type=registry,ref=ghcr.io/sage-bionetworks/synapsepythonclient:build-cache | |
| cache-to: type=inline | |
| - name: Output image digest | |
| run: echo "The image digest is ${{ steps.docker_build.outputs.digest }}" |