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WarvitoWarvito
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Update tests, CI and pre-commit (#193)
* Add initial runtests.sh * Duplicate utils to remove necessity to clone MONAI in order to run tests * Add note * [WIP] Add tests runners * Update min_tests list and reduce tests scope * Use all environments tested in monai core * Update pre-commit and requirements for tests * Remove duplicated tqdm and move lpips to dev * Remove test_latent_diffusion_inferer.py from min tests * Try to fix requirements for min tests * Fix dependencies * Add test_diffusion_inferer to excluded min-tests * Update CONTRIBUTING.md * Fix typos, remove formatting from unit tests and add black and isort to pre-commit Signed-off-by: Walter Hugo Lopez Pinaya <[email protected]>
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‎.clang-format

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AlwaysBreakBeforeMultilineStrings: true
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BinPackParameters: false
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BreakBeforeBinaryOperators: None
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BreakBeforeBraces: Attach
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BreakBeforeTernaryOperators: true
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BreakAfterJavaFieldAnnotations: false
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BreakStringLiterals: false
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CommentPragmas: '^ IWYU pragma:'
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ConstructorInitializerAllOnOneLineOrOnePerLine: true
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ConstructorInitializerIndentWidth: 4
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ContinuationIndentWidth: 4
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Cpp11BracedListStyle: true
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DerivePointerAlignment: false
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DisableFormat: false
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ForEachMacros: [ FOR_EACH_RANGE, FOR_EACH, ]
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IncludeCategories:
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- Regex: '^<.*\.h(pp)?>'
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- Regex: '^<.*'
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IndentCaseLabels: true
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IndentWrappedFunctionNames: false
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KeepEmptyLinesAtTheStartOfBlocks: false
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MacroBlockBegin: ''
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MacroBlockEnd: ''
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NamespaceIndentation: None
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ObjCBlockIndentWidth: 2
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ObjCSpaceAfterProperty: false
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ObjCSpaceBeforeProtocolList: false
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PenaltyBreakBeforeFirstCallParameter: 1
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SpaceInEmptyParentheses: false
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SpacesBeforeTrailingComments: 1
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SpacesInAngles: false
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SpacesInContainerLiterals: true
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SpacesInCStyleCastParentheses: false
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SpacesInParentheses: false
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SpacesInSquareBrackets: false
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Standard: Cpp11
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TabWidth: 8
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UseTab: Never
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...

‎.deepsource.toml

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version = 1
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test_patterns = ["tests/**"]
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[[analyzers]]
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name = "python"
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enabled = true
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[analyzers.meta]
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runtime_version = "3.x.x"
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[[analyzers]]
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name = "test-coverage"
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enabled = true
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[[analyzers]]
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name = "docker"
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enabled = true
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[[analyzers]]
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name = "shell"
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enabled = true

‎.github/workflows/pythonapp-min.yml

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# Jenkinsfile.monai-premerge
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name: premerge-min
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on:
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# quick tests for pull requests and the releasing branches
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push:
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branches:
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- main
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pull_request:
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concurrency:
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# automatically cancel the previously triggered workflows when there's a newer version
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group: build-min-${{ github.event.pull_request.number || github.ref }}
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cancel-in-progress: true
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jobs:
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# caching of these jobs:
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# - docker-py3-pip- (shared)
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# - ubuntu py37 pip-
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# - os-latest-pip- (shared)
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min-dep-os: # min dependencies installed tests for different OS
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [windows-latest, macOS-latest, ubuntu-latest]
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timeout-minutes: 40
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python 3.8
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uses: actions/setup-python@v4
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with:
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python-version: '3.8'
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- name: Prepare pip wheel
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run: |
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which python
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python -m pip install --upgrade pip wheel
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- name: cache weekly timestamp
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id: pip-cache
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run: |
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echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
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echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
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shell: bash
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- name: cache for pip
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uses: actions/cache@v3
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id: cache
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with:
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path: ${{ steps.pip-cache.outputs.dir }}
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key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
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- if: runner.os == 'windows'
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name: Install torch cpu from pytorch.org (Windows only)
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run: |
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python -m pip install torch==1.13.1+cpu -f https://download.pytorch.org/whl/torch_stable.html
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- name: Install the dependencies
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run: |
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# min. requirements
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python -m pip install torch==1.13.1
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python -m pip install -r requirements-min.txt
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python -m pip list
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BUILD_MONAI=0 python setup.py develop # no compile of extensions
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shell: bash
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- name: Run quick tests (CPU ${{ runner.os }})
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run: |
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python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
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python -c "import monai; monai.config.print_config()"
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./runtests.sh --min
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shell: bash
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env:
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QUICKTEST: True
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min-dep-py3: # min dependencies installed tests for different python
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
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timeout-minutes: 40
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Prepare pip wheel
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run: |
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which python
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python -m pip install --user --upgrade pip setuptools wheel
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- name: cache weekly timestamp
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id: pip-cache
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run: |
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echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
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echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
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shell: bash
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- name: cache for pip
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uses: actions/cache@v3
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id: cache
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with:
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path: ${{ steps.pip-cache.outputs.dir }}
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key: ubuntu-latest-latest-pip-${{ steps.pip-cache.outputs.datew }}
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- name: Install the dependencies
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run: |
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# min. requirements
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python -m pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
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python -m pip install -r requirements-min.txt
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python -m pip list
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BUILD_MONAI=0 python setup.py develop # no compile of extensions
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shell: bash
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- name: Run quick tests (CPU ${{ runner.os }})
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run: |
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python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
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python -c "import monai; monai.config.print_config()"
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./runtests.sh --min
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env:
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QUICKTEST: True
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min-dep-pytorch: # min dependencies installed tests for different pytorch
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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pytorch-version: ['1.8.2', '1.9.1', '1.10.2', '1.11.0', '1.12.1', 'latest']
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timeout-minutes: 40
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python 3.8
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uses: actions/setup-python@v4
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with:
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python-version: '3.8'
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- name: Prepare pip wheel
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run: |
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which python
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python -m pip install --user --upgrade pip setuptools wheel
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- name: cache weekly timestamp
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id: pip-cache
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run: |
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echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
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echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
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shell: bash
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- name: cache for pip
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uses: actions/cache@v3
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id: cache
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with:
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path: ${{ steps.pip-cache.outputs.dir }}
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key: ubuntu-latest-latest-pip-${{ steps.pip-cache.outputs.datew }}
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- name: Install the dependencies
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run: |
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# min. requirements
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if [ ${{ matrix.pytorch-version }} == "latest" ]; then
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python -m pip install torch
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elif [ ${{ matrix.pytorch-version }} == "1.8.2" ]; then
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python -m pip install torch==1.8.2 --extra-index-url https://download.pytorch.org/whl/lts/1.8/cpu
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elif [ ${{ matrix.pytorch-version }} == "1.9.1" ]; then
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python -m pip install torch==1.9.1
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elif [ ${{ matrix.pytorch-version }} == "1.10.2" ]; then
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python -m pip install torch==1.10.2
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elif [ ${{ matrix.pytorch-version }} == "1.11.0" ]; then
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python -m pip install torch==1.11.0
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elif [ ${{ matrix.pytorch-version }} == "1.12.1" ]; then
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python -m pip install torch==1.12.1
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fi
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python -m pip install -r requirements-min.txt
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python -m pip list
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BUILD_MONAI=0 python setup.py develop # no compile of extensions
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shell: bash
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- name: Run quick tests (pytorch ${{ matrix.pytorch-version }})
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run: |
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python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
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python -c "import monai; monai.config.print_config()"
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./runtests.sh --min
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env:
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QUICKTEST: True

‎.pre-commit-config.yaml

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default_language_version:
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python: python3.8
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ci:
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autofix_prs: true
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autoupdate_commit_msg: '[pre-commit.ci] pre-commit suggestions'
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autoupdate_schedule: quarterly
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# submodules: true
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.3.0
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rev: v4.4.0
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hooks:
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- id: end-of-file-fixer
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- id: trailing-whitespace
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args: ['--autofix', '--no-sort-keys', '--indent=4']
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- id: end-of-file-fixer
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- id: mixed-line-ending
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- repo: https://github.com/asottile/pyupgrade
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rev: v3.3.1
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hooks:
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- id: pyupgrade
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args: [--py37-plus]
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name: Upgrade code
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exclude: |
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(?x)^(
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versioneer.py|
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monai/_version.py
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)$
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- repo: https://github.com/asottile/yesqa
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rev: v1.4.0
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hooks:
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- id: yesqa
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name: Unused noqa
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additional_dependencies:
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- flake8>=3.8.1
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- flake8-bugbear
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- flake8-comprehensions
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- flake8-executable
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- flake8-pyi
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- pep8-naming
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exclude: |
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(?x)^(
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generative/__init__.py|
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docs/source/conf.py
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)$
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- repo: https://github.com/hadialqattan/pycln
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rev: v2.1.2
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hooks:
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- id: pycln
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args: [--config=pyproject.toml]
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- repo: https://github.com/psf/black
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rev: 22.3.0
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hooks:
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- id: black
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- repo: https://github.com/PyCQA/isort
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rev: 5.9.3
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hooks:
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- id: isort
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- repo: https://github.com/PyCQA/flake8
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rev: 3.9.2
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hooks:
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- id: flake8
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args: # arguments to configure flake8
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# these are errors that will be ignored by flake8
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# check out their meaning here
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# https://flake8.pycqa.org/en/latest/user/error-codes.html
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- "--ignore=E203,E266,E501,W503,E731,F541,F841"
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# Adding args to work with black format
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- "--max-line-length=120"
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- "--max-complexity=18"
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- "--per-file-ignores=__init__.py:F401"

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