Hook up CI

.clang-tidy

@@ -0,0 +1,66 @@
+---
+Checks: 'bugprone-*,
+         -bugprone-exception-escape,
+         clang-diagnostic-*,
+         clang-analyzer-*,
+         corecppguidelines-*,
+         modernize-*,
+         -modernize-use-nodiscard,
+         readability-*,
+         -readability-magic-numbers,
+         -readability-identifier-naming,
+         -readability-isolate-declaration,
+         -readability-avoid-const-params-in-decls,
+         -readability-identifier-length,
+         -readability-function-cognitive-complexity'
+WarningsAsErrors: ''
+HeaderFilterRegex: '.*'
+AnalyzeTemporaryDtors: false
+FormatStyle:     none
+User:            user
+CheckOptions:
+  - key:             cert-dcl16-c.NewSuffixes
+    value:           'L;LL;LU;LLU'
+  - key:             cert-oop54-cpp.WarnOnlyIfThisHasSuspiciousField
+    value:           '0'
+  - key:             cert-str34-c.DiagnoseSignedUnsignedCharComparisons
+    value:           '0'
+  - key:             cppcoreguidelines-explicit-virtual-functions.IgnoreDestructors
+    value:           '1'
+  - key:             cppcoreguidelines-non-private-member-variables-in-classes.IgnoreClassesWithAllMemberVariablesBeingPublic
+    value:           '1'
+  - key:             google-readability-braces-around-statements.ShortStatementLines
+    value:           '1'
+  - key:             google-readability-function-size.StatementThreshold
+    value:           '800'
+  - key:             google-readability-namespace-comments.ShortNamespaceLines
+    value:           '10'
+  - key:             google-readability-namespace-comments.SpacesBeforeComments
+    value:           '2'
+  - key:             llvm-else-after-return.WarnOnConditionVariables
+    value:           '0'
+  - key:             llvm-else-after-return.WarnOnUnfixable
+    value:           '0'
+  - key:             llvm-qualified-auto.AddConstToQualified
+    value:           '0'
+  - key:             modernize-loop-convert.MaxCopySize
+    value:           '16'
+  - key:             modernize-loop-convert.MinConfidence
+    value:           reasonable
+  - key:             modernize-loop-convert.NamingStyle
+    value:           CamelCase
+  - key:             modernize-pass-by-value.IncludeStyle
+    value:           llvm
+  - key:             modernize-replace-auto-ptr.IncludeStyle
+    value:           llvm
+  - key:             modernize-use-nullptr.NullMacros
+    value:           'NULL'
+  - { key: readability-identifier-naming.NamespaceCase,       value: lower_case }
+  - { key: readability-identifier-naming.ClassCase,           value: CamelCase  }
+  - { key: readability-identifier-naming.PrivateMemberPrefix, value: m_         }
+  - { key: readability-identifier-naming.ProtectedMemberPrefix, value: m_         }
+  - { key: readability-identifier-naming.StructCase,          value: CamelCase  }
+  - { key: readability-identifier-naming.FunctionCase,        value: lower_case }
+  - { key: readability-identifier-naming.VariableCase,        value: lower_case }
+  - { key: readability-identifier-naming.GlobalConstantCase,  value: UPPER_CASE }
+...

.codespell-ignore-words

@@ -0,0 +1,2 @@
+inout
+nd

.codespellrc

@@ -0,0 +1,3 @@
+[codespell]
+skip = .git,*.ipynb,*.bib,*.ps,*.patch,spack-build-*,*/build,,__pycache__,.ccls,.ccls-cache,*.pdf,*.f90,*.f,*.bak
+ignore-words = .codespell-ignore-words

.github/codeql/codeql-config.yml

@@ -0,0 +1,6 @@
+name: "AMR-Wind CodeQL config"
+
+query-filters:
+  - exclude:
+      id: cpp/poorly-documented-function
+

.github/problem-matchers/gcc.json

@@ -0,0 +1,18 @@
+{
+     "__comment": "Taken from vscode-cpptools's Extension/package.json gcc rule",
+     "problemMatcher": [
+         {
+             "owner": "gcc-problem-matcher",
+             "pattern": [
+                 {
+                     "regexp": "^(.*):(\\d+):(\\d+):\\s+(?:fatal\\s+)?(warning|error):\\s+(.*)$",
+                     "file": 1,
+                     "line": 2,
+                     "column": 3,
+                     "severity": 4,
+                     "message": 5
+                 }
+             ]
+         }
+     ]
+} 

.github/workflows/ci.yml

@@ -3,53 +3,237 @@ name: TIOGA CI
 on:
   push:
     branches:
-      - master
       - exawind
   pull_request:
     branches:
-      - master
       - exawind
 
+concurrency:
+  group: ${{github.ref}}-${{github.head_ref}}-ci
+  cancel-in-progress: true
+
 jobs:
-  build:
+  Formatting:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Clone
+      uses: actions/checkout@v4
+    - name: Check formatting
+      uses: DoozyX/[email protected]
+      with:
+        source: './src'
+        exclude: '.'
+        extensions: 'h,cpp'
+        clangFormatVersion: 16
+  CPU:
+    needs: Formatting
     runs-on: ${{matrix.os}}
     strategy:
       matrix:
-        #os: [ubuntu-latest, macos-latest]
-        os: [ ubuntu-latest ]
+        os: [ubuntu-latest, macos-latest]
         build_type: [Release, Debug]
         include:
-          # - os: macos-latest
-          #   build_deps: brew install open-mpi && brew link gcc
+          - os: macos-latest
+            install_deps: brew install mpich ccache
+            comp: llvm
+            procs: $(sysctl -n hw.ncpu)
+            ccache_cache: /Users/runner/Library/Caches/ccache
+            ccache_size: 50M
           - os: ubuntu-latest
-            build_deps: sudo apt-get install mpich libmpich-dev
-    name: ${{matrix.os}} - ${{matrix.build_type}}
+            install_deps: sudo apt-get install -y mpich libmpich-dev
+            comp: gnu
+            procs: $(nproc)
+            ccache_cache: ~/.cache/ccache
+            ccache_size: 50M
+    steps:
+    - name: Clone
+      uses: actions/checkout@v4
+      with: 
+        submodules: true
+    - name: Dependencies
+      run: ${{matrix.install_deps}}
+    - name: Setup
+      run: |
+        echo "NPROCS=${{matrix.procs}}" >> $GITHUB_ENV
+        echo "CCACHE_COMPRESS=1" >> $GITHUB_ENV
+        echo "CCACHE_COMPRESSLEVEL=1" >> $GITHUB_ENV
+        echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV
+        echo "CCACHE_MAXSIZE=${{matrix.ccache_size}}" >> $GITHUB_ENV
+    - name: Install Ccache
+      run: |
+        if [ "${RUNNER_OS}" != "macOS" ]; then
+          wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
+          tar xvf ccache-4.8-linux-x86_64.tar.xz
+          sudo cp -f ccache-4.8-linux-x86_64/ccache /usr/local/bin/
+        fi
+    - name: Set Up Ccache
+      uses: actions/cache@v4
+      with:
+        path: ${{matrix.ccache_cache}}
+        key: ccache-${{github.workflow}}-${{github.job}}-${{matrix.os}}-${{matrix.build_type}}-git-${{github.sha}}
+        restore-keys: |
+             ccache-${{github.workflow}}-${{github.job}}-${{matrix.os}}-${{matrix.build_type}}-git-
+    - name: Configure
+      run: |
+        cmake -B ${{runner.workspace}}/build-ci-${{matrix.build_type}} \
+          -DCMAKE_INSTALL_PREFIX:PATH=${{runner.workspace}}/install-${{matrix.build_type}} \
+          -DCMAKE_BUILD_TYPE:STRING=${{matrix.build_type}} \
+          -DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
+          ${{github.workspace}}
+    - name: Build
+      run: |
+        echo "::add-matcher::.github/problem-matchers/gcc.json"
+        ccache -z
+        set -eu -o pipefail
+        cmake --build ${{runner.workspace}}/build-ci-${{matrix.build_type}} --parallel ${{env.NPROCS}} 2>&1 | \
+          tee -a ${{runner.workspace}}/build-ci-${{matrix.build_type}}/build-output.txt
+    - name: Ccache Report
+      run: |
+        ccache -s
+        ls ${{matrix.ccache_cache}}
+        du -hs ${{matrix.ccache_cache}}
+    - name: Report
+      working-directory: ${{runner.workspace}}/build-ci-${{matrix.build_type}}
+      run: |
+        echo "::add-matcher::.github/problem-matchers/gcc.json"
+        egrep "warning:|error:" build-output.txt | egrep -v "submods" \
+          | egrep -v "ld: warning:" | egrep -v "lto-wrapper: warning:" | sort | uniq \
+          | awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' > build-output-warnings.txt
+        cat build-output-warnings.txt
+        exit $(tail -n 1 build-output-warnings.txt | awk '{print $2}')
+  Lint-clang-tidy:
+    needs: Formatting
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - name: Install dependencies
-        run: ${{matrix.build_deps}}
-      - name: Configure and build
+      - name: Clone
+        uses: actions/checkout@v4
+        with:
+          submodules: true
+      - name: Setup
         run: |
-          cmake -Bbuild -DCMAKE_Fortran_COMPILER=$(which mpif90) .
-          cmake --build build -- -j $(nproc)
-
-  # analyze:
-  #   name: CodeQL analysis
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - name: Checkout
-  #       uses: actions/checkout@v2
-
-  #     - name: Install dependencies
-  #       run: sudo apt-get install mpich libmpich-dev
-
-  #     - name: Initialize CodeQL
-  #       uses: github/codeql-action/init@v1
-  #       with:
-  #         languages: cpp
-
-  #     - name: Configure and build
-  #       uses: github/codeql-action/autobuild@v1
-
-  #     - name: Analyze
-  #       uses: github/codeql-action/analyze@v1
+          echo "NPROCS=$(nproc)" >> $GITHUB_ENV
+          echo "CCACHE_COMPRESS=1" >> $GITHUB_ENV
+          echo "CCACHE_COMPRESSLEVEL=1" >> $GITHUB_ENV
+          echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV
+          echo "CCACHE_EXTRAFILES=${{github.workspace}}/.clang-tidy" >> $GITHUB_ENV
+          echo "CCACHE_MAXSIZE=50M" >> $GITHUB_ENV
+          echo "CTCACHE_DIR=~/.cache/ctcache" >> $GITHUB_ENV
+      - name: Install Ccache
+        run: |
+          wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
+          sudo curl https://raw.githubusercontent.com/matus-chochlik/ctcache/7fd516e91c17779cbc6fc18bd119313d9532dd90/clang-tidy-cache -Lo /usr/bin/clang-tidy-cache
+          tar xvf ccache-4.8-linux-x86_64.tar.xz
+          sudo cp -f ccache-4.8-linux-x86_64/ccache /usr/local/bin/
+          sudo chmod +x /usr/bin/clang-tidy-cache
+          mkdir -p ~/.cache/ctcache
+      - name: Set Up Ccache
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache
+          key: ccache-${{github.workflow}}-${{github.job}}-git-${{github.sha}}
+          restore-keys: |
+               ccache-${{github.workflow}}-${{github.job}}-git-
+      - name: Dependencies
+        run: sudo apt-get install -y mpich libmpich-dev
+      - name: Configure
+        run: |
+          export MPICH_CXX=$(which clang++)
+          export MPICH_CC=$(which clang)
+          cmake \
+          -B ${{runner.workspace}}/build-clang-tidy \
+          -DCMAKE_BUILD_TYPE:STRING=Release \
+          -DCMAKE_CXX_COMPILER:STRING=mpicxx \
+          -DCMAKE_C_COMPILER:STRING=mpicc \
+          -DTIOGA_ENABLE_CLANG_TIDY:BOOL=ON \
+          -DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
+          ${{github.workspace}}
+      - name: Check
+        working-directory: ${{runner.workspace}}/build-clang-tidy
+        run: |
+          cmake --build . --parallel ${{env.NPROCS}} 2>&1 | tee -a clang-tidy-full-report.txt
+          cat clang-tidy-full-report.txt | grep "warning:" | grep -v "submods" | sort | uniq | \
+            awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' > clang-tidy-ci-report.txt
+      - name: Ccache Report
+        run: |
+          ls ~/.cache
+          ls ~/.cache/ccache
+          du -hs ~/.cache/ccache
+          ls ~/.cache/ctcache
+          du -hs ~/.cache/ctcache
+          ccache -s
+      - name: Full report
+        working-directory: ${{runner.workspace}}/build-clang-tidy
+        run: cat clang-tidy-full-report.txt
+      - name: Short report
+        working-directory: ${{runner.workspace}}/build-clang-tidy
+        run: |
+          echo "::add-matcher::.github/problem-matchers/gcc.json"
+          cat clang-tidy-ci-report.txt
+          exit $(tail -n 1 clang-tidy-ci-report.txt | awk '{print $2}')
+  Lint-codeql:
+    needs: Formatting
+    runs-on: ubuntu-latest
+    steps:
+      - name: Clone
+        uses: actions/checkout@v4
+        with:
+          submodules: true
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v2
+        with:
+          languages: cpp
+          queries: +security-and-quality
+          config-file: ./.github/codeql/codeql-config.yml
+      - name: Dependencies
+        run: sudo apt-get install -y mpich libmpich-dev
+      - name: Configure
+        run: |
+          echo "NPROCS=$(nproc)" >> $GITHUB_ENV
+          export MPICH_CXX=$(which clang++)
+          export MPICH_CC=$(which clang)
+          cmake \
+            -B ${{runner.workspace}}/build-ci-codeql \
+            -DCMAKE_INSTALL_PREFIX:PATH=${{runner.workspace}}/install-codeql \
+            -DCMAKE_BUILD_TYPE:STRING=Debug \
+            -DCMAKE_CXX_COMPILER:STRING=mpicxx \
+            -DCMAKE_C_COMPILER:STRING=mpicc \
+            ${{github.workspace}}
+      - name: Build
+        run: |
+          cmake --build ${{runner.workspace}}/build-ci-codeql --parallel ${{env.NPROCS}}
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v2
+        with:
+          category: "/language:cpp"
+          upload: False
+          output: sarif-results
+      - name: Filter CodeQL sarif
+        uses: advanced-security/filter-sarif@v1
+        with:
+          patterns: |
+            -**/submods/**
+          input: sarif-results/cpp.sarif
+          output: sarif-results/cpp.sarif
+      - name: Upload CodeQL sarif
+        uses: github/codeql-action/upload-sarif@v2
+        with:
+          sarif_file: sarif-results/cpp.sarif
+  Lint-codespell:
+    needs: Formatting
+    runs-on: ubuntu-latest
+    steps:
+      - name: Clone
+        uses: actions/checkout@v4
+        with:
+          submodules: false
+      - name: Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+      - name: Dependencies
+        run: |
+          # Install Python packages
+          python -m pip install --upgrade pip
+          pip install codespell
+      - name: Run codespell
+        run: codespell