chore: replace mamba by pixi

.github/workflows/ci.yml

@@ -23,35 +23,19 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - name: Cache
-        uses: actions/cache@v3
+      - uses: prefix-dev/[email protected]
         with:
-          path: |
-            ~/.cache/ccache
-            ~/micromamba/envs/samurai-env
-          key: cppcheck
+          pixi-version: v0.10.0
+          cache: false
 
-      - name: Mamba and samurai env installation
-        uses: mamba-org/setup-micromamba@v1
-        with:
-          environment-file: conda/environment.yml
-          environment-name: samurai-env
-          cache-environment: true
-
-      - name: cppcheck installation
-        shell: bash -el {0}
-        run: |
-          conda install -y cppcheck cxx-compiler
+      - name: Remove petsc
+        run: pixi remove -p linux-64 petsc
 
       - name: Configure
-        shell: bash -el {0}
-        run: |
-          cmake . -Bbuild -DCMAKE_EXPORT_COMPILE_COMMANDS=ON -DCMAKE_BUILD_TYPE=Debug -DBUILD_DEMOS=ON
-
-      - name: Run cppcheck on samurai
-        shell: bash -el {0}
+        shell: pixi run bash {0}
         run: |
-          cppcheck --enable=all -q --project=./build/compile_commands.json --suppressions-list=.cppcheck --inline-suppr 2> cppcheck_err.txt
+          cmake -S . -B .build -DCMAKE_EXPORT_COMPILE_COMMANDS=ON -DCMAKE_BUILD_TYPE=Debug -DBUILD_DEMOS=ON
+          cppcheck --enable=all -q --project=.build/compile_commands.json --inline-suppr --suppressions-list=.cppcheck 2> cppcheck_err.txt
 
       - name: Check for errors
         run: |
@@ -116,74 +100,30 @@ jobs:
             package: "clang-15"
             cc: "clang-15"
             cxx: "clang++-15"
+
+    env:
+      CC: ${{ matrix.cc }}
+      CXX: ${{ matrix.cxx }}
+
     steps:
       - uses: actions/checkout@v3
 
-      - name: Cache
-        uses: actions/cache@v3
-        with:
-          path: |
-            ~/.cache/ccache
-            ~/micromamba-root/envs/samurai-env
-          key: linux-${{ matrix.cpp-version }}
-          restore-keys: |
-            linux-${{ matrix.cpp-version }}
-
-      - name: Compiler and dev tools installation
+      - name: Compiler installation
         run: |
           sudo apt update
           sudo apt install ${{ matrix.package }}
 
-      # - name: Information about ccache
-      #   run: |
-      #     ccache -s -v
-
-      - name: Mamba and samurai env installation
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/[email protected]
         with:
-          environment-file: conda/environment.yml
-          environment-name: samurai-env
-          cache-environment: true
-
-      - name: Petsc installation
-        shell: bash -l {0}
-        run: |
-          conda install -y petsc=3.18 pkg-config
-
-      - name: Conda informations
-        shell: bash -l {0}
-        run: |
-          conda info
-          conda list
+          pixi-version: v0.10.0
+          cache: true
 
-      - name: Configure
-        shell: bash -l {0}
-        run: |
-          export LDFLAGS="${LDFLAGS} -L$CONDA_PREFIX/lib"
-          CC=${{ matrix.cc }} CXX=${{ matrix.cxx }} cmake \
-              . \
-              -Bbuild \
-              -GNinja \
-              -DCMAKE_BUILD_TYPE=Release \
-              -DBUILD_DEMOS=ON \
-              -DBUILD_TESTS=ON
-
-      - name: Build
-        shell: bash -l {0}
-        run: |
-          cmake --build build --target all
-
-      - name: Test with googletest
-        shell: bash -l {0}
-        run: |
-          export LD_LIBRARY_PATH="$CONDA_PREFIX/lib:$LD_LIBRARY_PATH"
-          cd build
-          ./tests/test_samurai_lib
+      - name: Run tests
+        run: pixi run test
 
       - name: Test with pytest
-        shell: bash -l {0}
+        shell: pixi run bash {0}
         run: |
-          export LD_LIBRARY_PATH="$CONDA_PREFIX/lib:$LD_LIBRARY_PATH"
           cd tests
           pytest -v -s --h5diff
 
@@ -192,42 +132,17 @@ jobs:
     runs-on: macos-12
     steps:
       - uses: actions/checkout@v3
-      - name: Mamba and samurai env installation
-        uses: mamba-org/setup-micromamba@v1
-        with:
-          environment-file: conda/environment.yml
-          environment-name: samurai-env
-          cache-environment: true
 
-      # - name: Petsc installation
-      #   shell: bash -l {0}
-      #   run: |
-      #     micromamba install -y petsc=3.18 pkg-config
-
-      - name: micromamba informations
-        shell: bash -l {0}
-        run: |
-          micromamba info
-          micromamba list
-
-      - name: Configure
-        shell: bash -l {0}
-        run: |
-          cmake \
-              . \
-              -Bbuild \
-              -GNinja \
-              -DCMAKE_BUILD_TYPE=Release \
-              -DBUILD_DEMOS=ON \
-              -DBUILD_TESTS=ON
-
-      - name: Build
-        shell: bash -l {0}
-        run: |
-          cmake --build ./build --config Release
+      - uses: prefix-dev/[email protected]
+        with:
+          pixi-version: v0.10.0
+          cache: true
 
       - name: Run tests
-        shell: bash -l {0}
+        run: pixi run test
+
+      - name: Test with pytest
+        shell: pixi run bash {0}
         run: |
-          ./build/tests/test_samurai_lib
-          cd tests; pytest --h5diff
+          cd tests
+          pytest -v -s --h5diff

CMakeLists.txt

@@ -85,10 +85,13 @@ set_target_properties(samurai
         CXX_EXTENSIONS NO
 )
 
+set(CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
+include(addHighFive)
+
 # Includes
 set(INCLUDE_DIR "include") # must be relative paths
 target_include_directories(samurai INTERFACE "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/${INCLUDE_DIR}>"
-  "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>")
+"$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>")
 
 # Find dependencies:
 set(DEPENDENCIES_CONFIGURED xtensor HighFive pugixml fmt)
@@ -112,12 +115,11 @@ target_link_system_libraries(
   HighFive
   pugixml::pugixml
   fmt::fmt
-)
+  )
 
-target_compile_features(samurai INTERFACE cxx_std_17)
+  target_compile_features(samurai INTERFACE cxx_std_17)
 
-# target_compile_definitions(samurai INTERFACE _HAS_AUTO_PTR_ETC=0)
-set(CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
+  # target_compile_definitions(samurai INTERFACE _HAS_AUTO_PTR_ETC=0)
 
 OPTION(BUILD_BENCHMARKS "samurai benchmark suite" OFF)
 OPTION(BUILD_DEMOS "samurai build all demos" OFF)

cmake/addHighFive.cmake

@@ -0,0 +1,11 @@
+include(FetchContent)
+FetchContent_Declare(HighFive
+    GIT_REPOSITORY      https://github.com/BlueBrain/HighFive
+    GIT_TAG             v2.8.0)
+FetchContent_GetProperties(highfive)
+if(NOT HighFive_POPULATED)
+    FetchContent_Populate(HighFive)
+    set(CMAKE_SUPPRESS_DEVELOPER_WARNINGS 1 CACHE BOOL "")
+    add_subdirectory(${HighFive_SOURCE_DIR} ${HighFive_BINARY_DIR} EXCLUDE_FROM_ALL)
+    unset(CMAKE_SUPPRESS_DEVELOPER_WARNINGS)
+endif()

include/samurai/field.hpp

@@ -567,7 +567,7 @@ namespace samurai
     }
 
     template <class mesh_t, class value_t, std::size_t size_, bool SOA>
-    inline auto Field<mesh_t, value_t, size_, SOA>::operator=(const Field& field) -> Field&
+    inline auto Field<mesh_t, value_t, size_, SOA>::operator=(const Field& field) -> Field& // cppcheck-suppress operatorEqRetRefThis
     {
         inner_mesh_t::operator=(field.mesh());
         m_name = field.m_name;

include/samurai/numeric/gauss_legendre.hpp

@@ -9,6 +9,7 @@ namespace samurai
     {
       private:
 
+        // cppcheck-suppress unusedPrivateFunction
         static constexpr std::size_t n_required_points(int degree)
         {
             return degree < 0 ? N_IMPLEMENTED_POINTS : static_cast<std::size_t>(ce_ceil((degree + 1.) / 2.));