Add decompression preprocessing step to TotalSegmentator2D for more efficient slice loading
#819
Workflow file for this run
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| --- | |
| name: CI | |
| on: | |
| pull_request: | |
| branches: | |
| jobs: | |
| quality: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| - name: Setting up PDM | |
| uses: pdm-project/setup-pdm@568ddd69406b30de1774ec0044b73ae06e716aa4 # v4 | |
| with: | |
| python-version: "3.10" | |
| architecture: x64 | |
| - name: Setting up nox | |
| uses: wntrblm/nox@5656fcedc31a1ea37d016e4d94d00185330cc528 # 2024.04.15 | |
| with: | |
| python-versions: "3.10" | |
| - name: Performing lint checks | |
| run: nox -s lint | |
| - name: Performing static type checks | |
| run: nox -s check | |
| tests: | |
| strategy: | |
| matrix: | |
| os: | |
| - ubuntu-latest | |
| python-version: | |
| - "3.10" | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Install OS dependencies | |
| run: | | |
| sudo apt update | |
| sudo apt install -y software-properties-common | |
| sudo add-apt-repository ppa:openslide/openslide | |
| sudo apt install -y openslide-tools | |
| - name: Checkout | |
| uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| with: | |
| lfs: true | |
| - name: Setting up PDM | |
| uses: pdm-project/setup-pdm@568ddd69406b30de1774ec0044b73ae06e716aa4 # v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| architecture: x64 | |
| - name: Setting up nox | |
| uses: wntrblm/nox@5656fcedc31a1ea37d016e4d94d00185330cc528 # 2024.04.15 | |
| with: | |
| python-versions: ${{ matrix.python-version }} | |
| - name: Executing unit tests | |
| run: nox -s test | |
| docs: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| - name: Setting up PDM | |
| uses: pdm-project/setup-pdm@568ddd69406b30de1774ec0044b73ae06e716aa4 # v4 | |
| with: | |
| python-version: "3.10" | |
| architecture: x64 | |
| - name: Setting up nox | |
| uses: wntrblm/nox@5656fcedc31a1ea37d016e4d94d00185330cc528 # 2024.04.15 | |
| with: | |
| python-versions: "3.10" | |
| - name: Configure Git Credentials | |
| run: | | |
| git config user.email "[email protected]" | |
| git config user.name "GitHub Action" | |
| - name: Building docs | |
| run: nox -s docs -- deploy --update-aliases dev | |
| security: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| - name: Perform gitleaks checks | |
| run: | | |
| # Download and check | |
| curl -LJO https://github.com/gitleaks/gitleaks/releases/download/v8.18.2/gitleaks_8.18.2_linux_x64.tar.gz | |
| curl -LJO https://github.com/gitleaks/gitleaks/releases/download/v8.18.2/gitleaks_8.18.2_checksums.txt | |
| shasum -a 256 --ignore-missing --quiet -c gitleaks_8.18.2_checksums.txt | |
| if [ $? != 0 ]; then exit 1; fi | |
| # Extract gitleaks | |
| tar -zxvf gitleaks_8.18.2_linux_x64.tar.gz gitleaks | |
| # Run gitleaks | |
| ./gitleaks detect \ | |
| --config .gitleaks.toml \ | |
| --gitleaks-ignore-path .gitleaksignore \ | |
| --no-git |