CMake build from pip

.github/workflows/cmake_build_and_test.yml

@@ -0,0 +1,45 @@
+name: cmake_build_and_test
+
+on: 
+  push:
+    branches: [ main, develop ]
+  pull_request:
+    branches: [ main, develop ]
+
+jobs:
+  build_and_test:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Install Dependencies
+      run: |
+        sudo apt-get install g++ cmake libhdf5-dev
+    - name: Install OpenMC
+      run: |
+        cd /opt
+        git clone https://github.com/openmc-dev/openmc.git
+        cd openmc
+        git checkout develop
+        mkdir build && cd build
+        cmake -DCMAKE_INSTALL_PREFIX=.. ..
+        make
+        make install
+    - name: Build plasma source
+      run: |
+        mkdir build && cd build
+        cmake ..
+        make
+    - name: Test plasma source
+      run: |
+        cd build
+        ./tests
+    - name: Check Source Generator
+      run: |
+        cd build
+        ./source_generator -l "$PWD/source_sampling.so" -i "major_radius=9.06, minor_radius=2.92258, elongation=1.557, \
+          triangularity=0.27, shafranov_shift=0.44789, pedestal_radius=2.33806, ion_density_pedestal=1.09e+20, \
+          ion_density_separatrix=3e+19, ion_density_origin=1.09e+20, ion_density_alpha=1, ion_temperature_pedestal=6.09, \
+          ion_temperature_separatrix=0.1, ion_temperature_origin=45.9, ion_temperature_alpha=8.06, ion_temperature_beta=6, \
+          plasma_type=plasma, plasma_id=1, number_of_bins=100, minimum_toroidal_angle=0, maximum_toroidal_angle=360"

.github/workflows/python.yml → .github/workflows/python_package.yml

@@ -13,44 +13,22 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
-    container: quay.io/pypa/manylinux2014_x86_64
-    strategy:
-      matrix:
-        python-version: [3.6, 3.7, 3.8]
 
     steps:
     - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
       with:
-        fetch-depth: 0  # Get the repo history so we can version by number of commits
-    - name: Install OpenMC
-      run: |
-        yum install -y gcc-c++ cmake3 hdf5-devel
-        alternatives --install /usr/local/bin/cmake cmake /usr/bin/cmake3 20 \
-        --slave /usr/local/bin/ctest ctest /usr/bin/ctest3 \
-        --slave /usr/local/bin/cpack cpack /usr/bin/cpack3 \
-        --slave /usr/local/bin/ccmake ccmake /usr/bin/ccmake3 \
-        --family cmake
-        git clone --recurse-submodules https://github.com/openmc-dev/openmc.git
-        cd openmc
-        git checkout
-        mkdir build && cd build
-        cmake ..
-        make
-        make install
+        python-version: 3.8
     - name: Build plasma source
       run: |
-        export PYVER=${{ matrix.python-version }}
-        alias python=$(ls -d /opt/python/* | grep ${PYVER//.})/bin/python
-        python -m pip install -r requirements-develop.txt
-        python -m pip install auditwheel
-        python setup.py bdist_wheel
-        python -m auditwheel show dist/*.whl
-        python -m auditwheel repair dist/*.whl
+        pip install -r requirements-develop.txt
+        python -m build --sdist .
     - name: Upload wheel artifact
       uses: actions/upload-artifact@v2
       with:
         name: dist
-        path: wheelhouse
+        path: dist
 
   test:
     runs-on: ubuntu-latest
@@ -72,16 +50,57 @@ jobs:
         path: dist
     - name: Install plasma source
       run: |
-        python -m pip install --no-index --find-links=file:dist parametric-plasma-source
+        python -m pip install dist/parametric_plasma_source-*.tar.gz
+    - name: Run tests
+      run: |
+        python -m pip install -r requirements-develop.txt
+        cd tests
+        python -m pytest
+
+  test_openmc:
+    runs-on: ubuntu-latest
+    needs: build
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Download build
+      uses: actions/download-artifact@v2
+      with:
+        name: dist
+        path: dist
+    - name: Install OpenMC
+      run: |
+        cd /opt
+        sudo apt install g++ cmake libhdf5-dev
+        git clone https://github.com/openmc-dev/openmc.git
+        cd openmc
+        git checkout develop
+        mkdir build && cd build
+        cmake -DCMAKE_INSTALL_PREFIX=.. ..
+        make
+        make install
+        cd ..
+        python -m pip install .
+    - name: Install plasma source
+      run: |
+        python -m pip install dist/parametric_plasma_source-*.tar.gz
     - name: Run tests
       run: |
         python -m pip install -r requirements-develop.txt
         cd tests
         python -m pytest
 
   publish:
+    if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags')}}
     runs-on: ubuntu-latest
-    needs: test
+    needs: [test, test_openmc]
 
     steps:
     - name: Download build
@@ -90,6 +109,7 @@ jobs:
         name: dist
         path: dist
     - name: Publish wheel artifact to TestPyPI
+      if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
       env:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}

.gitignore

@@ -31,6 +31,7 @@
 *.out
 *.app
 source_generator
+testprog
 
 # Build path
 build/

.gitmodules

@@ -1,6 +1,3 @@
 [submodule "pybind11"]
 	path = pybind11
 	url = https://github.com/pybind/pybind11
-[submodule "pugixml"]
-	path = pugixml
-	url = https://github.com/zeux/pugixml.git

CMakeLists.txt

@@ -1,92 +1,5 @@
 cmake_minimum_required(VERSION 3.3 FATAL_ERROR)
 project(parametric_plasma_source)
 
-set(CMAKE_VERBOSE_MAKEFILE OFF)
-
-set(SRC_DIR parametric_plasma_source)
-
-if(NOT CMAKE_BUILD_TYPE)
-  set(CMAKE_BUILD_TYPE Release)
-endif()
-
-set(CMAKE_CXX_FLAGS "-Wall")
-set(CMAKE_CXX_FLAGS_DEBUG "-g")
-set(CMAKE_CXX_FLAGS_RELEASE "-O3")
-
-# Ensure submodules are available and up to date
-find_package(Git QUIET)
-if(GIT_FOUND AND EXISTS "${PROJECT_SOURCE_DIR}/.git")
-  # Update submodules as needed
-  option(GIT_SUBMODULE "Check submodules during build" ON)
-  if(GIT_SUBMODULE)
-    message(STATUS "Submodule update")
-    execute_process(COMMAND ${GIT_EXECUTABLE} submodule update --init --recursive
-                    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-                    RESULT_VARIABLE GIT_SUBMOD_RESULT)
-    if(NOT GIT_SUBMOD_RESULT EQUAL "0")
-      message(FATAL_ERROR "git submodule update --init failed with ${GIT_SUBMOD_RESULT}, please checkout submodules")
-    endif()
-  endif()
-endif()
-
-if(NOT EXISTS "${PROJECT_SOURCE_DIR}/pybind11/CMakeLists.txt")
-  message(FATAL_ERROR "The submodules were not downloaded! GIT_SUBMODULE was turned off or failed. Please update submodules and try again.")
-endif()
-
-# Build source_sampling
-list(APPEND source_sampling_SOURCES
-  ${SRC_DIR}/source_sampling.cpp
-  ${SRC_DIR}/plasma_source.cpp
-)
-
-# Use output paths from OpenMC install
-# If OpenMC isn't available then we won't be able to build the plugin
-# However, the package can still be run by using the sampling methods directly
-# So don't terminate the build
-find_package(OpenMC QUIET)
-
-if(OpenMC_FOUND)
-  # Build the source_sampling OpenMC plugin if OpenMC is available
-  set(OPENMC_INC_DIR ${OpenMC_DIR}/../../../include/openmc)
-  set(OPENMC_LIB_DIR ${OpenMC_DIR}/../../../lib)
-
-  add_library(source_sampling SHARED ${source_sampling_SOURCES})
-
-  find_library(OPENMC_LIB openmc HINTS ${OPENMC_LIB_DIR} OPTIONAL)
-
-  if (OPENMC_LIB)
-    set_target_properties(source_sampling PROPERTIES PREFIX "")
-    set_target_properties(source_sampling PROPERTIES POSITION_INDEPENDENT_CODE ON)
-    target_include_directories(source_sampling PUBLIC ${OPENMC_INC_DIR})
-    target_link_libraries(source_sampling ${OPENMC_LIB} gfortran)
-  endif()
-else()
-  message(WARNING "Unable to find OpenMC installation - the source_sampling plugin will not be built.")
-endif()
-
-# Build plasma_source Python bindings
-list(APPEND plasma_source_pybind_SOURCES
-  ${SRC_DIR}/plasma_source.cpp
-  ${SRC_DIR}/plasma_source_pybind.cpp
-)
-
-add_subdirectory(pybind11)
-
-pybind11_add_module(plasma_source ${plasma_source_pybind_SOURCES})
-
-add_subdirectory(pugixml)
-
-# Build source_generator
-list(APPEND source_generator_SOURCES
-  ${SRC_DIR}/source_generator.cpp
-)
-
-add_executable(source_generator ${source_generator_SOURCES})
-
-find_package(HDF5 REQUIRED)
-
-set_target_properties(source_generator PROPERTIES POSITION_INDEPENDENT_CODE ON)
-target_include_directories(source_generator PUBLIC ${OPENMC_INC_DIR})
-target_include_directories(source_generator PUBLIC ${HDF5_INCLUDE_DIRS})
-target_include_directories(source_generator PUBLIC ${OPENMC_DIR}/vendor/pugixml)
-target_link_libraries(source_generator ${OPENMC_LIB} ${HDF5_LIBRARIES} stdc++fs)
+include(parametric_plasma_source/CMakeLists.txt)
+include(tests/src/CMakeLists.txt)