Improve speed and RAM consumption of buffered slice writer #2926
Workflow file for this run
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| 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! |