Devel (#156)

Recent work on geometric algorithm bug fixes, CMFD spectral radius computation, and Knudsen number based mesh generation.
KyleVaughn · Jul 1, 2024 · 42330aa · 42330aa
1 parent 3980452
commit 42330aa
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diff --git a/.clang-tidy b/.clang-tidy
@@ -1,4 +1,4 @@
-Checks: 'bugprone-*,\
+Checks: 'bugprone-*,
 cert-*,
 clang-analyzer-*,
 cppcoreguidelines-*,
@@ -11,22 +11,21 @@ portability-*,
 -*-avoid-c-arrays,
 -*-magic-numbers,
 -bugprone-easily-swappable-parameters,
--bugprone-exception-escape,
 -clang-analyzer-osx*,
 -cppcoreguidelines-avoid-do-while,
 -cppcoreguidelines-macro-usage,
 -cppcoreguidelines-no-malloc,
 -cppcoreguidelines-owning-memory,
+-cppcoreguidelines-pro-bounds-array-to-pointer-decay,
+-cppcoreguidelines-pro-bounds-constant-array-index,
 -cppcoreguidelines-pro-bounds-pointer-arithmetic,
 -cppcoreguidelines-pro-type-member-init,
 -cppcoreguidelines-pro-type-reinterpret-cast,
 -cppcoreguidelines-pro-type-vararg,
--cppcoreguidelines-pro-bounds-array-to-pointer-decay,
--cppcoreguidelines-pro-bounds-constant-array-index,
 -cppcoreguidelines-pro-type-union-access,
 -readability-identifier-length,
+-misc-confusable-identifiers,
 -misc-non-private-member-variables-in-classes
--misc-confusable-identifiers
 '
 HeaderFilterRegex: '.*'
 WarningsAsErrors: '*'
@@ -134,7 +133,7 @@ CheckOptions:
   - key: 'readability-identifier-naming.PrivateMemberPrefix'
     value: '_'
   - key: 'readability-identifier-naming.PrivateMethodCase'
-    value: 'lower_case'
+    value: 'camelBack'
   - key: 'readability-identifier-naming.ProtectedMemberCase'
     value: 'lower_case'
   - key: 'readability-identifier-naming.ProtectedMemberPrefix'

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -9,26 +9,20 @@ on:
       - main
 
 env:
-  HDF5_ROOT: /usr
   OMP_NUM_THREADS: 2
-  ENABLE_COVERAGE: OFF
-  COVERALLS_PARALLEL: true
-  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
   main:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     strategy:
       fail-fast: true
       matrix:
         compiler: [gcc, clang]
         build_type: [Debug, Release]
-        dev_mode: [ON]
-        gmsh: [ON]
-        int64: [OFF, ON]
-        float64: [OFF, ON]
+        asserts: [ON, OFF]
+        gmsh: [ON, OFF]
 
-    name: "${{matrix.compiler}}-${{matrix.build_type}},Dev=${{matrix.dev_mode}},Gmsh=${{matrix.gmsh}},I64=${{matrix.int64}},F64=${{matrix.float64}}"
+    name: "${{matrix.compiler}}-${{matrix.build_type}},asserts=${{matrix.asserts}},gmsh=${{matrix.gmsh}}"
 
     steps:
       - uses: actions/checkout@v3
@@ -37,88 +31,47 @@ jobs:
         shell: bash
         run: |
           sudo apt -y update
-          sudo apt install -y libhdf5-dev libpugixml-dev libtbb-dev
+          sudo apt install -y cmake clang-format clang-tidy libomp-dev
+          sudo apt install -y libhdf5-dev libpugixml-dev
 
       - name: gcc
         shell: bash
         if: matrix.compiler == 'gcc'
         run: |
-          sudo apt install -y gcc-12 g++-12
-          sudo rm /usr/bin/gcov
-          sudo ln -s /usr/bin/gcov-12 /usr/bin/gcov
-          echo "CC=gcc-12" >> $GITHUB_ENV
-          echo "CXX=g++-12" >> $GITHUB_ENV
-
-      - name: Dev mode dependencies
-        shell: bash
-        if: matrix.dev_mode == 'ON'
-        run: |
-          sudo apt install -y clang-tidy-15 clang-format-15 cppcheck libomp-15-dev
-          sudo rm /usr/bin/clang-tidy
-          sudo ln -s /usr/bin/clang-tidy-15 /usr/bin/clang-tidy
-          sudo rm /usr/bin/clang-format
-          sudo ln -s /usr/bin/clang-format-15 /usr/bin/clang-format
+          sudo apt install -y gcc
+          echo "CC=gcc" >> $GITHUB_ENV
+          echo "CXX=g++" >> $GITHUB_ENV
 
       - name: clang
         shell: bash
         if: matrix.compiler == 'clang'
         run: |
-          sudo apt install -y clang-15 libomp-15-dev
-          echo "CC=clang-15" >> $GITHUB_ENV
-          echo "CXX=clang++-15" >> $GITHUB_ENV
+          sudo apt install -y clang
+          echo "CC=clang" >> $GITHUB_ENV
+          echo "CXX=clang++" >> $GITHUB_ENV
 
       - name: Gmsh
         shell: bash
         if: matrix.gmsh == 'ON'
-        run: |
-          sudo apt install -y libglu1-mesa
-          wget https://gmsh.info/bin/Linux/gmsh-4.11.1-Linux64-sdk.tgz
-          tar -xzvf gmsh-4.11.1-Linux64-sdk.tgz
-          echo "GMSH_ROOT=${PWD}/gmsh-4.11.1-Linux64-sdk" >> $GITHUB_ENV
-
-      - name: Configure with coverage
-        if: matrix.dev_mode == 'ON' && matrix.build_type == 'Debug'  && matrix.compiler == 'gcc'
-        run: |
-          echo "ENABLE_COVERAGE=ON" >> $GITHUB_ENV
+        run: sudo apt install -y libgmsh-dev
 
       - name: Configure
         run: |
           cmake -S . -B build \
                 -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                -DUM2_BUILD_TUTORIAL=OFF \
-                -DUM2_DEV_MODE=${{ matrix.dev_mode }} \
-                -DUM2_USE_GMSH=${{ matrix.gmsh }} \
-                -DUM2_ENABLE_INT64=${{ matrix.int64 }} \
-                -DUM2_ENABLE_FLOAT64=${{ matrix.float64}} \
+                -DUM2_ENABLE_ASSERTS=${{ matrix.asserts }} \
+                -DUM2_ENABLE_NATIVE=OFF \
+                -DUM2_USE_CLANG_FORMAT=ON \
+                -DUM2_USE_CLANG_TIDY=ON \
                 -DUM2_USE_COVERAGE=${ENABLE_COVERAGE} \
-                -DUM2_USE_CUDA=OFF
+                -DUM2_USE_GMSH=${{ matrix.gmsh }} \
+                -DUM2_USE_MPACT_XSLIBS=OFF
 
       - name: Format check
-        if: matrix.dev_mode == 'ON'
         run: make -C build format-check
 
       - name: Build
-        run: make -j -C build
+        run: make -C build
 
       - name: Run tests
-        run: make -j -C build test
-
-      - name: coverage
-        if: matrix.dev_mode == 'ON' && matrix.build_type == 'Debug'  && matrix.compiler == 'gcc'
-        run: |
-          sudo apt install -y python3 python3-pip
-          python3 -m pip install --upgrade pip
-          python3 -m pip install cpp-coveralls
-          python3 -m pip install coveralls
-          cpp-coveralls -i include -i src -e /usr --gcov /usr/bin/gcov-12 --dump cpp_cov.json
-          coveralls --merge=cpp_cov.json --service=github
-
-  finish:
-    needs: main
-    runs-on: ubuntu-22.04
-    steps:
-      - name: Coveralls finished
-        uses: coverallsapp/github-action@master
-        with:
-          github-token: ${{ secrets.github_token }}
-          parallel-finished: true
+        run: CTEST_OUTPUT_ON_FAILURE=ON make -C build test
diff --git a/.gitignore b/.gitignore
@@ -1,18 +1,9 @@
-.idea/
-.vs/
-.vscode/
+# Build directory
 build/
-cmake-build-*/
-prefix/
-**/.DS_Store
-CMakeLists.txt.user
-CMakeUserPresets.json
+
+# MPACT data
+MPACT_Extras/
+MPACT_Extras
+
+# config files
 include/um2/config.hpp
-.cache/    
-env/    
-docs/_build/    
-docs/_static/    
-docs/_templates/    
-docs/html/    
-docs/latex/    
-docs/Doxyfile.bak
diff --git a/.gitmodules b/.gitmodules
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -1,9 +1,9 @@
 version: 2
 
 build:
-  os: "ubuntu-22.04"
+  os: "ubuntu-24.04"
   tools:
-    python: "3.10"
+    python: "3.12"
 
 sphinx:
   configuration: docs/source/conf.py