added skeleton path length example to docs #2981
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: CI | |
| on: | |
| push: | |
| branches: | |
| - master | |
| tags: | |
| - "**" | |
| pull_request: {} | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: ${{ github.ref != 'refs/heads/master' }} | |
| jobs: | |
| changes: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| webknossos: ${{ steps.filter.outputs.webknossos || github.ref == 'refs/heads/master' }} | |
| cluster_tools: ${{ steps.filter.outputs.cluster_tools || github.ref == 'refs/heads/master' }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: dorny/paths-filter@v2 | |
| id: filter | |
| with: | |
| filters: | | |
| webknossos: | |
| - 'webknossos/**' | |
| cluster_tools: | |
| - 'cluster_tools/**' | |
| cluster_tools: | |
| needs: changes | |
| if: ${{ needs.changes.outputs.cluster_tools == 'true' }} | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 30 | |
| strategy: | |
| max-parallel: 4 | |
| matrix: | |
| executors: [multiprocessing, slurm, kubernetes] | |
| python-version: ["3.11", "3.10", "3.9", "3.8"] | |
| defaults: | |
| run: | |
| working-directory: cluster_tools | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| architecture: "x64" | |
| - name: Build/pull dockered-slurm image | |
| if: ${{ matrix.executors == 'slurm' }} | |
| run: | | |
| cd ./dockered-slurm | |
| echo docker-compose up | |
| docker-compose up -d | |
| # Register cluster (with retry) | |
| for i in {1..5}; do | |
| echo register_cluster | |
| ./register_cluster.sh && s=0 && break || s=$? | |
| sleep 10 | |
| done | |
| # Show log output for debugging | |
| docker logs slurmctld | |
| docker logs c1 | |
| docker logs c2 | |
| # Run setup.py on all three nodes | |
| docker exec -w /cluster_tools slurmctld bash -c "poetry install" & | |
| docker exec -w /cluster_tools c1 bash -c "poetry install" & | |
| docker exec -w /cluster_tools c2 bash -c "poetry install" & | |
| wait | |
| - name: Setup Kubernetes-in-Docker | |
| if: ${{ matrix.executors == 'kubernetes' }} | |
| run: | | |
| curl -Lo ./kind https://kind.sigs.k8s.io/dl/v0.11.1/kind-linux-amd64 | |
| chmod +x ./kind | |
| sed -i "s#__PATH__#$(pwd)#g" tests/cluster-config.yaml | |
| ./kind create cluster --config=tests/cluster-config.yaml | |
| ./kind export kubeconfig | |
| docker build -f tests/Dockerfile -t scalableminds/cluster-tools:latest . | |
| ./kind load docker-image scalableminds/cluster-tools:latest | |
| - name: Install dependencies (without docker) | |
| if: ${{ matrix.executors == 'multiprocessing' || matrix.executors == 'kubernetes' }} | |
| run: | | |
| pip install -r ../requirements.txt | |
| poetry install | |
| - name: Check typing | |
| if: ${{ matrix.executors == 'multiprocessing' }} | |
| run: ./typecheck.sh | |
| - name: Check formatting | |
| if: ${{ matrix.executors == 'multiprocessing' }} | |
| run: ./format.sh check | |
| - name: Lint code | |
| if: ${{ matrix.executors == 'multiprocessing' }} | |
| run: ./lint.sh | |
| - name: Run multiprocessing tests | |
| if: ${{ matrix.executors == 'multiprocessing' }} | |
| run: | | |
| cd tests | |
| PYTEST_EXECUTORS=multiprocessing,sequential,test_pickling,debug_sequential \ | |
| poetry run python -m pytest -sv test_all.py test_multiprocessing.py | |
| - name: Run slurm tests | |
| if: ${{ matrix.executors == 'slurm' }} | |
| run: | | |
| cd ./dockered-slurm | |
| docker exec \ | |
| -w /cluster_tools/tests \ | |
| -e PYTEST_EXECUTORS=slurm \ | |
| slurmctld bash -c "poetry run python -m pytest -sv test_all.py test_slurm.py" | |
| docker exec \ | |
| -w /cluster_tools/tests \ | |
| slurmctld bash -c "poetry run python test_deref_main.py" | |
| - name: Run kubernetes tests | |
| if: ${{ matrix.executors == 'kubernetes' }} | |
| run: | | |
| cd tests | |
| PYTEST_EXECUTORS=kubernetes poetry run python -m pytest -sv test_all.py test_kubernetes.py | |
| webknossos_linux: | |
| needs: changes | |
| if: | | |
| ${{ needs.changes.outputs.cluster_tools == 'true' }} || | |
| ${{ needs.changes.outputs.webknossos == 'true' }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 4 | |
| matrix: | |
| python-version: ["3.11", "3.10", "3.9", "3.8"] | |
| group: [1, 2, 3] | |
| fail-fast: false | |
| defaults: | |
| run: | |
| working-directory: webknossos | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| architecture: "x64" | |
| - name: Install dependencies | |
| run: | | |
| pip install -r ../requirements.txt | |
| poetry install --extras all | |
| - name: Check formatting | |
| if: matrix.group == 1 | |
| run: ./format.sh check | |
| - name: Lint code | |
| if: matrix.group == 1 | |
| run: ./lint.sh | |
| - name: Check typing | |
| if: matrix.group == 1 | |
| run: ./typecheck.sh | |
| - name: Python tests | |
| timeout-minutes: 30 | |
| env: | |
| WK_TOKEN: ${{ secrets.WK_TOKEN }} | |
| run: ./test.sh -vv -p no:faulthandler --splits 3 --group ${{ matrix.group }} --splitting-algorithm least_duration | |
| - name: Check if git is dirty | |
| run: | | |
| git diff --no-ext-diff --quiet --exit-code | |
| [[ -z $(git status -s) ]] | |
| webknossos_cli_docker: | |
| needs: [cluster_tools, webknossos_linux] | |
| if: | | |
| always() && | |
| !contains(needs.*.result, 'failure') && | |
| !contains(needs.*.result, 'cancelled') && | |
| !github.event.pull_request.head.repo.fork | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Write version file | |
| run: | | |
| pip install -r requirements.txt | |
| pushd webknossos | |
| PKG_VERSION="$(dunamai from git)" | |
| echo "__version__ = '$PKG_VERSION'" > ./webknossos/version.py | |
| poetry version "$PKG_VERSION" | |
| popd | |
| - name: Build docker image | |
| run: docker build -t scalableminds/webknossos-cli:$GITHUB_SHA -f webknossos/Dockerfile . | |
| - name: Smoke test docker | |
| run: | | |
| docker run --rm \ | |
| -v$(pwd)/webknossos/testdata:/webknossos/testdata \ | |
| scalableminds/webknossos-cli:$GITHUB_SHA \ | |
| webknossos convert \ | |
| --jobs 2 \ | |
| --voxel-size 1,1,1 \ | |
| testdata/tiff testoutput/tiff | |
| - name: Login to docker | |
| env: | |
| DOCKER_USER: ${{ secrets.DOCKER_USER }} | |
| DOCKER_PASS: ${{ secrets.DOCKER_PASS }} | |
| run: | | |
| echo $DOCKER_PASS | docker login -u $DOCKER_USER --password-stdin | |
| - name: Push docker images | |
| run: | | |
| docker push scalableminds/webknossos-cli:$GITHUB_SHA | |
| - name: Push docker images (for tag) | |
| if: github.ref_type == 'tag' | |
| run: | | |
| CI_TAG=$(git describe --tags) | |
| docker tag \ | |
| scalableminds/webknossos-cli:$GITHUB_SHA \ | |
| scalableminds/webknossos-cli:$CI_TAG | |
| docker push scalableminds/webknossos-cli:$CI_TAG | |
| docker tag \ | |
| scalableminds/webknossos-cli:$GITHUB_SHA \ | |
| scalableminds/webknossos-cli:latest | |
| docker push scalableminds/webknossos-cli:latest | |
| - name: Push docker images (for branch) | |
| if: github.ref_type == 'branch' | |
| run: | | |
| CI_BRANCH=${GITHUB_HEAD_REF:-$GITHUB_REF_NAME} | |
| NORMALIZED_CI_BRANCH=${CI_BRANCH//[\/-]/_} | |
| docker tag \ | |
| scalableminds/webknossos-cli:$GITHUB_SHA \ | |
| scalableminds/webknossos-cli:$NORMALIZED_CI_BRANCH | |
| docker push scalableminds/webknossos-cli:$NORMALIZED_CI_BRANCH | |
| docs: | |
| needs: [cluster_tools, webknossos_linux] | |
| runs-on: ubuntu-latest | |
| if: | | |
| always() && | |
| !contains(needs.*.result, 'failure') && | |
| !contains(needs.*.result, 'cancelled') && | |
| !github.event.pull_request.head.repo.fork | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/checkout@v3 | |
| with: | |
| repository: scalableminds/webknossos | |
| path: docs/wk-repo | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.8 | |
| architecture: "x64" | |
| - name: Install dependencies | |
| run: | | |
| pip3 install -r requirements.txt | |
| - name: Build Docs | |
| run: | | |
| docs/generate.sh --persist | |
| - name: Push docs (for branch) | |
| if: github.ref_type == 'branch' | |
| env: | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| AWS_DEFAULT_REGION: "eu-west-1" | |
| run: | | |
| CI_BRANCH=${GITHUB_HEAD_REF:-$GITHUB_REF_NAME} | |
| NORMALIZED_CI_BRANCH=${CI_BRANCH//[\/-]/_} | |
| aws s3 sync --acl public-read docs/out s3://static.webknossos.org/docs/${NORMALIZED_CI_BRANCH} | |
| - name: Push docs (for tag) | |
| if: github.ref_type == 'tag' | |
| env: | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| AWS_DEFAULT_REGION: "eu-west-1" | |
| run: | | |
| CI_TAG=$(git describe --tags) | |
| aws s3 sync --acl public-read docs/out s3://static.webknossos.org/docs/${CI_TAG} | |
| - name: Check links (on master) | |
| if: github.ref == 'refs/heads/master' | |
| env: # Or as an environment variable | |
| SLACK_HOOK: ${{ secrets.LINK_CHECKER_SLACK_HOOK }} | |
| run: | | |
| cd docs | |
| poetry run linkchecker https://docs.webknossos.org > link_status || \ | |
| curl -X POST --data-urlencode "payload={\"text\": \":warning: Broken Links on doc.webknossos.org :warning:\n"'```'"\n$(cat link_status)\n"'```"}' \ | |
| "$SLACK_HOOK" | |
| pypi_and_gh_release: | |
| needs: [cluster_tools, webknossos_linux] | |
| if: | | |
| always() && | |
| !contains(needs.*.result, 'failure') && | |
| !contains(needs.*.result, 'cancelled') && | |
| github.ref_type == 'tag' && | |
| !github.event.pull_request.head.repo.fork | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.8 | |
| architecture: "x64" | |
| - name: Install dependencies | |
| run: pip3 install -r requirements.txt | |
| - name: Publish python packages | |
| env: | |
| POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_PASSWORD }} | |
| run: _tooling/publish.sh | |
| - name: Prepare github release | |
| run: | | |
| VERSION="$(dunamai from git)" | |
| _tooling/changelog_for_version.sh $VERSION > Changelog.md | |
| - name: Publish github release | |
| id: create_release | |
| uses: actions/create-release@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| tag_name: ${{ github.ref }} | |
| release_name: ${{ github.ref }} | |
| body_path: Changelog.md | |
| draft: false | |
| prerelease: false | |
| complete: | |
| needs: | |
| [ | |
| cluster_tools, | |
| webknossos_linux, | |
| webknossos_cli_docker, | |
| docs, | |
| pypi_and_gh_release, | |
| ] | |
| if: always() | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check failure | |
| if: | | |
| contains(needs.*.result, 'failure') || | |
| contains(needs.*.result, 'cancelled') | |
| run: exit 1 | |
| - name: Success | |
| run: echo Success! |