[INFRA] Update CI

.clang-format

@@ -0,0 +1,186 @@
+# Format all files in include folder, including std module, excluding contrib module
+# find . \( -path "./include/seqan3/std/*" -or -iname "*.hpp" \) -and -not -path "./submodules/*" -and -not -path "./build/*" -and -not -path "./include/seqan3/contrib/*" -and -not -path "./test/*" | xargs clang-format-15 --style=file -i
+---
+Language:        Cpp
+AccessModifierOffset: -4
+AlignAfterOpenBracket: Align
+AlignArrayOfStructures: None
+AlignConsecutiveMacros: None
+AlignConsecutiveAssignments: None
+AlignConsecutiveBitFields: None
+AlignConsecutiveDeclarations: None
+AlignEscapedNewlines: Right
+AlignOperands:   AlignAfterOperator
+AlignTrailingComments: true
+AllowAllArgumentsOnNextLine: false
+AllowAllParametersOfDeclarationOnNextLine: false
+AllowShortEnumsOnASingleLine: true
+AllowShortBlocksOnASingleLine: Never
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: None
+AllowShortLambdasOnASingleLine: Empty
+AllowShortIfStatementsOnASingleLine: Never
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: Yes
+AttributeMacros:
+BinPackArguments: false
+BinPackParameters: false
+BraceWrapping:
+  AfterCaseLabel:  true
+  AfterClass:      true
+  AfterControlStatement: Always
+  AfterEnum:       true
+  AfterFunction:   true
+  AfterNamespace:  true
+  AfterObjCDeclaration: false
+  AfterStruct:     true
+  AfterUnion:      true
+  AfterExternBlock: true
+  BeforeCatch:     true
+  BeforeElse:      true
+  BeforeLambdaBody: true
+  BeforeWhile:     true
+  IndentBraces:    false
+  SplitEmptyFunction: false
+  SplitEmptyRecord: false
+  SplitEmptyNamespace: false
+BreakBeforeBinaryOperators: NonAssignment
+BreakBeforeConceptDeclarations: true
+BreakBeforeBraces: Custom
+BreakBeforeInheritanceComma: false
+BreakInheritanceList: AfterColon
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakConstructorInitializers: AfterColon
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
+ColumnLimit:     120
+CommentPragmas:  '^ IWYU pragma:'
+QualifierAlignment: Custom
+QualifierOrder: ['static', 'inline', 'constexpr', 'volatile', 'type', 'const']
+CompactNamespaces: false
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DeriveLineEnding: true
+DerivePointerAlignment: false
+DisableFormat:   false
+EmptyLineAfterAccessModifier: Never
+EmptyLineBeforeAccessModifier: Always
+ExperimentalAutoDetectBinPacking: false
+PackConstructorInitializers: CurrentLine
+BasedOnStyle:    ''
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+AllowAllConstructorInitializersOnNextLine: true
+FixNamespaceComments: true
+ForEachMacros:
+IfMacros:
+IncludeBlocks:   Regroup
+IncludeCategories:
+  - Regex:           '(<gtest/.*|<benchmark/.*)'
+    Priority:        1
+  - Regex:           '(<[[:alnum:]._]+>|<seqan3/std/.*>)'
+    Priority:        2
+  - Regex:           '<sdsl/'
+    Priority:        3
+  - Regex:           '<seqan3/'
+    Priority:        4
+  - Regex:           '<cereal/'
+    Priority:        5
+  - Regex:           '<lemon/'
+    Priority:        6
+  - Regex:           '.*'
+    Priority:        7
+IncludeIsMainRegex: '(Test)?$'
+IncludeIsMainSourceRegex: ''
+IndentAccessModifiers: false
+IndentCaseLabels: false
+IndentCaseBlocks: false
+IndentGotoLabels: true
+IndentPPDirectives: AfterHash
+IndentExternBlock: AfterExternBlock
+IndentRequiresClause :  true
+IndentWidth:     4
+IndentWrappedFunctionNames: false
+InsertTrailingCommas: None
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: true
+LambdaBodyIndentation: Signature
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBinPackProtocolList: Never
+ObjCBlockIndentWidth: 2
+ObjCBreakBeforeNestedBlockParam: true
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: true
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 19
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakOpenParenthesis: 0
+PenaltyBreakString: 1000
+PenaltyBreakTemplateDeclaration: 10
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 60
+PenaltyIndentedWhitespace: 0
+PointerAlignment: Middle
+PPIndentWidth:   -1
+ReferenceAlignment: Pointer
+ReflowComments:  false
+RemoveBracesLLVM: false
+RequiresClausePosition : OwnLine
+SeparateDefinitionBlocks: Leave
+ShortNamespaceLines: 1
+SortIncludes:    true
+SortJavaStaticImport: Before
+SortUsingDeclarations: true
+SpaceAfterCStyleCast: false
+SpaceAfterLogicalNot: false
+SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCaseColon: false
+SpaceBeforeCpp11BracedList: false
+SpaceBeforeCtorInitializerColon: true
+SpaceBeforeInheritanceColon: true
+SpaceBeforeParens: Custom
+SpaceBeforeParensOptions:
+  AfterControlStatements: true
+  AfterForeachMacros: true
+  AfterFunctionDefinitionName: false
+  AfterFunctionDeclarationName: false
+  AfterIfMacros:   true
+  AfterOverloadedOperator: false
+  AfterRequiresInClause : true
+  AfterRequiresInExpression : true
+  BeforeNonEmptyParentheses: false
+SpaceAroundPointerQualifiers: Default
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceInEmptyBlock: false
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  Never
+SpacesInConditionalStatement: false
+SpacesInContainerLiterals: false
+SpacesInCStyleCastParentheses: false
+SpacesInLineCommentPrefix:
+  Minimum:         1
+  Maximum:         -1
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+SpaceBeforeSquareBrackets: false
+BitFieldColonSpacing: Both
+Standard:        c++20
+StatementAttributeLikeMacros:
+StatementMacros:
+TabWidth:        4
+UseCRLF:         false
+UseTab:          Never
+WhitespaceSensitiveMacros:
+  - SHARG_DEPRECATED_HEADER
+...

.github/workflows/ci_linux.yml

@@ -3,8 +3,16 @@ name: CI on Linux
 on:
   push:
     branches:
+      # Push events to branches matching refs/heads/master
       - 'master'
+      # Push events to branches matching refs/heads/release*
+      - 'release*'
+  # Trigger after PR was unlabeled
   pull_request:
+    types:
+      - unlabeled
+  # Enables a manual trigger, may run on any branch
+  workflow_dispatch:
 
 concurrency:
   group: linux-${{ github.event.pull_request.number || github.ref }}
@@ -22,46 +30,57 @@ defaults:
 jobs:
   build:
     name: ${{ matrix.name }}
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     timeout-minutes: 120
+    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'clang-format'
     strategy:
       fail-fast: true
       matrix:
         include:
-          - name: "Coverage gcc11"
-            cxx: "g++-11"
-            cc: "gcc-11"
-            build_type: Coverage
+          - name: "Coverage gcc12"
+            cxx: "g++-12"
+            cc: "gcc-12"
+            build: coverage
+            build_type: Debug
+
+          - name: "Unit gcc12"
+            cxx: "g++-12"
+            cc: "gcc-12"
+            build: unit
+            build_type: Release
 
           - name: "Unit gcc11"
             cxx: "g++-11"
             cc: "gcc-11"
+            build: unit
             build_type: Release
 
           - name: "Unit gcc10"
             cxx: "g++-10"
             cc: "gcc-10"
+            build: unit
             build_type: Release
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           path: sharg
           fetch-depth: 2
           submodules: recursive
 
       # To reuse scripts
       - name: Checkout SeqAn3
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           repository: seqan/seqan3
-          ref: 383e8f8d638f8a727a79136ce96ae7642befe39f
+          ref: df3f29a00543f02cc8cb5e05f40ea8057cf36c5d
           path: seqan3
-          fetch-depth: 2
+          fetch-depth: 1
           submodules: false
 
-      - name: Add package source
+      - name: Configure APT
+        continue-on-error: true
         run: bash ./seqan3/.github/workflows/scripts/configure_apt.sh
 
       - name: Install CMake
@@ -75,16 +94,16 @@ jobs:
       - name: Install compiler ${{ matrix.cxx }}
         run: sudo apt-get install --yes ${{ matrix.cxx }}
 
-      - name: Install lcov
-        if: matrix.build_type == 'Coverage'
+      - name: Install gcovr
+        if: matrix.build == 'coverage'
         env:
           CC: ${{ matrix.cc }}
         run: |
-          sudo apt-get install --yes lcov
           sudo update-alternatives --install /usr/bin/gcov gcov /usr/bin/${CC/gcc/gcov} 100
+          pip install gcovr==5.0
 
       - name: Load ccache
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: .ccache
           key: ${{ runner.os }}-${{ matrix.name }}-ccache-${{ github.ref }}-${{ github.run_number }}
@@ -104,11 +123,11 @@ jobs:
           CXX: ${{ matrix.cxx }}
           CC: ${{ matrix.cc }}
         run: |
-          mkdir build
-          cd build
-          cmake ../sharg/test/unit -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                                   -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" \
-                                   -DSHARG_VERBOSE_TESTS=OFF
+          mkdir sharg-build
+          cd sharg-build
+          cmake ../sharg/test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
+                                                  -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" \
+                                                  -DSHARG_VERBOSE_TESTS=OFF
           make -j2 gtest_build
 
       - name: Build tests
@@ -117,39 +136,24 @@ jobs:
           CCACHE_DIR: ${{ github.workspace }}/.ccache
           CCACHE_COMPRESS: true
           CCACHE_COMPRESSLEVEL: 12
-          CCACHE_MAXSIZE: ${{ matrix.build_type == 'Coverage' && '125M' || '50M' }}
+          CCACHE_MAXSIZE: ${{ matrix.build != 'coverage' && '125M' || '50M' }}
+          CCACHE_IGNOREOPTIONS: "-fprofile-abs-path"
+          GCOV: ${{ github.workspace }}/seqan3/.github/workflows/scripts/gcov.sh
         run: |
           ccache -z
-          cd build
+          cd sharg-build
           make -k -j2
           ccache -sv
 
-      - name: Generate coverage baseline
-        if: matrix.build_type == 'Coverage'
-        run: |
-          lcov --directory ./build/ --zerocounters
-          lcov --directory ./build/ --capture --initial --output-file ./build/coverage_report.baseline
-
       - name: Run tests
+        if: matrix.build != 'coverage'
         run: |
-          cd build
+          cd sharg-build
           ctest . -j2 --output-on-failure
 
-      - name: Generate coverage report
-        if: matrix.build_type == 'Coverage'
-        run: |
-          lcov --directory ./build/ --capture --output-file ./build/coverage_report.captured
-          lcov -a ./build/coverage_report.baseline -a ./build/coverage_report.captured --output-file ./build/coverage_report.total
-          lcov --remove ./build/coverage_report.total \
-                        '/usr/*' \
-                        '${{ github.workspace }}/sharg/lib/*' \
-                        '${{ github.workspace }}/sharg/test/*' \
-                        '${{ github.workspace }}/build/vendor/*' \
-               --output-file ./build/coverage_report
-
-      - name: Submit coverage report
-        if: matrix.build_type == 'Coverage'
-        uses: codecov/codecov-action@v1
+      - name: Submit coverage build
+        if: matrix.build == 'coverage'
+        uses: codecov/codecov-action@v2
         with:
-          files: ${{ github.workspace }}/build/coverage_report
+          files: ${{ github.workspace }}/sharg-build/sharg_coverage.xml
           root_dir: ${{ github.workspace }}/sharg