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v4.6.1

v4.6.1 #3343

Workflow file for this run

# 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: '3.12'
- 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-13, windows-2022]
# if changing the below change the run-integration-tests versions and the check-deploy versions
# Make sure that we are running the integration tests on the first and last versions of the matrix
python: ['3.9', '3.10', '3.11', '3.12']
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 sysconfig import get_path; print(get_path('purelib'))")
SITE_BIN_DIR=$(python3 -c "import os; import platform; import sysconfig; pre = sysconfig.get_config_var('prefix'); bindir = os.path.join(pre, 'Scripts' if platform.system() == 'Windows' else 'bin'); print(bindir)")
echo "site_packages_loc=$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') }}-v20
- 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: ${{ contains(fromJSON('["3.9"]'), matrix.python) || contains(fromJSON('["3.12"]'), matrix.python) }}
# perform secret check & put boolean result as an output
shell: bash
run: |
if [ -z "${{ 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) || contains(fromJSON('["3.12"]'), 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 [ ${{ steps.otel-check.outputs.run_opentelemetry }} == "true" ]; then
# Set to 'file' to enable OpenTelemetry export to file
export SYNAPSE_OTEL_INTEGRATION_TEST_EXPORTER="file"
fi
# use loadscope to avoid issues running tests concurrently that share scoped fixtures
pytest -sv --reruns 3 --cov-append --cov=. --cov-report xml tests/integration -n 8 --ignore=tests/integration/synapseclient/test_command_line_client.py --dist loadscope
# Execute the CLI tests in a non-dist way because they were causing some test instability when being run concurrently
pytest -sv --reruns 3 --cov-append --cov=. --cov-report xml tests/integration/synapseclient/test_command_line_client.py
- name: Upload otel spans
uses: actions/upload-artifact@v4
if: always()
with:
name: otel_spans_integration_testing_${{ 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('["3.12"]'), 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: ${{ steps.build-package.outputs.bdist-package-name }}
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: 3.9
- name: set-release-env
shell: bash
run: |
RELEASE_TAG="${{ 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-13, windows-2022]
# python versions should be consistent with the strategy matrix and the runs-integration-tests versions
python: ['3.9', '3.10', '3.11', '3.12']
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 }}"