Update tests, CI and pre-commit

.clang-format

@@ -0,0 +1,88 @@
+---
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+AlignAfterOpenBracket: AlwaysBreak
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlinesLeft: true
+AlignOperands:   false
+AlignTrailingComments: false
+AllowAllParametersOfDeclarationOnNextLine: false
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: Empty
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: true
+AlwaysBreakTemplateDeclarations: true
+BinPackArguments: false
+BinPackParameters: false
+BraceWrapping:
+  AfterClass:      false
+  AfterControlStatement: false
+  AfterEnum:       false
+  AfterFunction:   false
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  BeforeCatch:     false
+  BeforeElse:      false
+  IndentBraces:    false
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Attach
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: false
+ColumnLimit:     120
+CommentPragmas:  '^ IWYU pragma:'
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: false
+DisableFormat:   false
+ForEachMacros:   [ FOR_EACH_RANGE, FOR_EACH, ]
+IncludeCategories:
+  - Regex:           '^<.*\.h(pp)?>'
+    Priority:        1
+  - Regex:           '^<.*'
+    Priority:        2
+  - Regex:           '.*'
+    Priority:        3
+IndentCaseLabels: true
+IndentWidth:     2
+IndentWrappedFunctionNames: false
+KeepEmptyLinesAtTheStartOfBlocks: false
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBlockIndentWidth: 2
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: false
+PenaltyBreakBeforeFirstCallParameter: 1
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 2000000
+PointerAlignment: Left
+ReflowComments:  true
+SortIncludes:    true
+SpaceAfterCStyleCast: false
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: ControlStatements
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard:        Cpp11
+TabWidth:        8
+UseTab:          Never
+...

.deepsource.toml

@@ -0,0 +1,22 @@
+version = 1
+
+test_patterns = ["tests/**"]
+
+[[analyzers]]
+name = "python"
+enabled = true
+
+  [analyzers.meta]
+  runtime_version = "3.x.x"
+
+[[analyzers]]
+name = "test-coverage"
+enabled = true
+
+[[analyzers]]
+name = "docker"
+enabled = true
+
+[[analyzers]]
+name = "shell"
+enabled = true

.github/workflows/pythonapp-min.yml

@@ -0,0 +1,171 @@
+# Jenkinsfile.monai-premerge
+name: premerge-min
+
+on:
+  # quick tests for pull requests and the releasing branches
+  push:
+    branches:
+      - main
+  pull_request:
+
+concurrency:
+  # automatically cancel the previously triggered workflows when there's a newer version
+  group: build-min-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  # caching of these jobs:
+  #   - docker-py3-pip- (shared)
+  #   - ubuntu py37 pip-
+  #   - os-latest-pip- (shared)
+  min-dep-os:  # min dependencies installed tests for different OS
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [windows-latest, macOS-latest, ubuntu-latest]
+    timeout-minutes: 40
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.8'
+    - name: Prepare pip wheel
+      run: |
+        which python
+        python -m pip install --upgrade pip wheel
+    - name: cache weekly timestamp
+      id: pip-cache
+      run: |
+        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
+        echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
+      shell: bash
+    - name: cache for pip
+      uses: actions/cache@v3
+      id: cache
+      with:
+        path: ${{ steps.pip-cache.outputs.dir }}
+        key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
+    - if: runner.os == 'windows'
+      name: Install torch cpu from pytorch.org (Windows only)
+      run: |
+        python -m pip install torch==1.13.1+cpu -f https://download.pytorch.org/whl/torch_stable.html
+    - name: Install the dependencies
+      run: |
+        # min. requirements
+        python -m pip install torch==1.13.1
+        python -m pip install -r requirements-min.txt
+        python -m pip list
+        BUILD_MONAI=0 python setup.py develop  # no compile of extensions
+      shell: bash
+    - name: Run quick tests (CPU ${{ runner.os }})
+      run: |
+        python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
+        python -c "import monai; monai.config.print_config()"
+        ./runtests.sh --min
+      shell: bash
+      env:
+        QUICKTEST: True
+
+  min-dep-py3:  # min dependencies installed tests for different python
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+    timeout-minutes: 40
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Prepare pip wheel
+      run: |
+        which python
+        python -m pip install --user --upgrade pip setuptools wheel
+    - name: cache weekly timestamp
+      id: pip-cache
+      run: |
+        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
+        echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
+      shell: bash
+    - name: cache for pip
+      uses: actions/cache@v3
+      id: cache
+      with:
+        path: ${{ steps.pip-cache.outputs.dir }}
+        key: ubuntu-latest-latest-pip-${{ steps.pip-cache.outputs.datew }}
+    - name: Install the dependencies
+      run: |
+        # min. requirements
+        python -m pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
+        python -m pip install -r requirements-min.txt
+        python -m pip list
+        BUILD_MONAI=0 python setup.py develop  # no compile of extensions
+      shell: bash
+    - name: Run quick tests (CPU ${{ runner.os }})
+      run: |
+        python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
+        python -c "import monai; monai.config.print_config()"
+        ./runtests.sh --min
+      env:
+        QUICKTEST: True
+
+  min-dep-pytorch:  # min dependencies installed tests for different pytorch
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        pytorch-version: ['1.8.2', '1.9.1', '1.10.2', '1.11.0', '1.12.1', 'latest']
+    timeout-minutes: 40
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.8'
+    - name: Prepare pip wheel
+      run: |
+        which python
+        python -m pip install --user --upgrade pip setuptools wheel
+    - name: cache weekly timestamp
+      id: pip-cache
+      run: |
+        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
+        echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
+      shell: bash
+    - name: cache for pip
+      uses: actions/cache@v3
+      id: cache
+      with:
+        path: ${{ steps.pip-cache.outputs.dir }}
+        key: ubuntu-latest-latest-pip-${{ steps.pip-cache.outputs.datew }}
+    - name: Install the dependencies
+      run: |
+        # min. requirements
+        if [ ${{ matrix.pytorch-version }} == "latest" ]; then
+          python -m pip install torch
+        elif [ ${{ matrix.pytorch-version }} == "1.8.2" ]; then
+          python -m pip install torch==1.8.2 --extra-index-url https://download.pytorch.org/whl/lts/1.8/cpu
+        elif [ ${{ matrix.pytorch-version }} == "1.9.1" ]; then
+          python -m pip install torch==1.9.1
+        elif [ ${{ matrix.pytorch-version }} == "1.10.2" ]; then
+          python -m pip install torch==1.10.2
+        elif [ ${{ matrix.pytorch-version }} == "1.11.0" ]; then
+          python -m pip install torch==1.11.0
+        elif [ ${{ matrix.pytorch-version }} == "1.12.1" ]; then
+          python -m pip install torch==1.12.1
+        fi
+        python -m pip install -r requirements-min.txt
+        python -m pip list
+        BUILD_MONAI=0 python setup.py develop  # no compile of extensions
+      shell: bash
+    - name: Run quick tests (pytorch ${{ matrix.pytorch-version }})
+      run: |
+        python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
+        python -c "import monai; monai.config.print_config()"
+        ./runtests.sh --min
+      env:
+        QUICKTEST: True

.pre-commit-config.yaml

@@ -1,6 +1,15 @@
+default_language_version:
+  python: python3.8
+
+ci:
+  autofix_prs: true
+  autoupdate_commit_msg: '[pre-commit.ci] pre-commit suggestions'
+  autoupdate_schedule: quarterly
+  # submodules: true
+
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.4.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
@@ -17,24 +26,49 @@ repos:
         args: ['--autofix', '--no-sort-keys', '--indent=4']
       - id: end-of-file-fixer
       - id: mixed-line-ending
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.3.1
+    hooks:
+      - id: pyupgrade
+        args: [--py37-plus]
+        name: Upgrade code
+        exclude: |
+          (?x)^(
+              versioneer.py|
+              monai/_version.py
+          )$
+
+  - repo: https://github.com/asottile/yesqa
+    rev: v1.4.0
+    hooks:
+      - id: yesqa
+        name: Unused noqa
+        additional_dependencies:
+          - flake8>=3.8.1
+          - flake8-bugbear
+          - flake8-comprehensions
+          - flake8-executable
+          - flake8-pyi
+          - pep8-naming
+        exclude: |
+          (?x)^(
+              generative/__init__.py|
+              docs/source/conf.py
+          )$
+
+  - repo: https://github.com/hadialqattan/pycln
+    rev: v2.1.2
+    hooks:
+      - id: pycln
+        args: [--config=pyproject.toml]
+
   - repo: https://github.com/psf/black
     rev: 22.3.0
     hooks:
       - id: black
+
   - repo: https://github.com/PyCQA/isort
     rev: 5.9.3
     hooks:
       - id: isort
-  - repo: https://github.com/PyCQA/flake8
-    rev: 3.9.2
-    hooks:
-      - id: flake8
-        args: # arguments to configure flake8
-          # these are errors that will be ignored by flake8
-          # check out their meaning here
-          # https://flake8.pycqa.org/en/latest/user/error-codes.html
-          - "--ignore=E203,E266,E501,W503,E731,F541,F841"
-          # Adding args to work with black format
-          - "--max-line-length=120"
-          - "--max-complexity=18"
-          - "--per-file-ignores=__init__.py:F401"