v0.1.1

.github/workflows/mac.yml

@@ -26,7 +26,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Run Cmake 
-        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
       - name: Build
         run: cmake --build build --parallel 10

.github/workflows/release.yml

@@ -1,6 +1,10 @@
 name: Publish Python Package
 
 on:
+  push:
+    branches:
+      - main
+  pull_request:
   workflow_dispatch:
   release:
     types:
@@ -63,6 +67,7 @@ jobs:
   upload_all:
     name: Upload release
     needs: [build_wheels, build_sdist]
+    if: github.event_name == 'release' && github.event.action == 'published'
     runs-on: ubuntu-latest
     environment:
       name: pypi

.github/workflows/ubuntu.yml

@@ -31,7 +31,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Run Cmake 
-        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_POLICY_VERSION_MINIMUM=3.5
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
       - name: Build
         run: cmake --build build --config ${{ matrix.build_type }} --parallel 10

.github/workflows/windows.yml

@@ -14,6 +14,7 @@ concurrency:
 jobs:
   build-and-test:
     runs-on: windows-latest
+    continue-on-error: true
     strategy:
       matrix:
         build_type: [Release]
@@ -38,13 +39,8 @@ jobs:
           architecture: 'x64'
 
       - name: Run Cmake
-        if: matrix.architecture == 'Win32'
-        run: cmake -S . -B build -A ${{ matrix.architecture }} -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -DOPEN_ATMOS_ENABLE_PYTHON_LIBRARY=ON -DCMAKE_POLICY_VERSION_MINIMUM=3.5
+        run: cmake -S . -B build -A ${{ matrix.architecture }} -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_POLICY_VERSION_MINIMUM="3.5"
 
-      - name: Run Cmake
-        if: matrix.architecture == 'x64'
-        run: cmake -S . -B build -A ${{ matrix.architecture }} -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_POLICY_VERSION_MINIMUM=3.5
-
       - name: Build
         run: cmake --build build --config ${{ matrix.build_type }} --parallel 10
 

CMakeLists.txt

@@ -3,7 +3,7 @@
 cmake_minimum_required(VERSION 3.21)
 
 # must be on the same line so that pyproject.toml can correctly identify the version
-project(mechanism_configuration VERSION 0.1.0 LANGUAGES CXX)
+project(mechanism_configuration VERSION 0.1.1 LANGUAGES CXX)
 
 if(NOT CMAKE_BUILD_TYPE)
   set(CMAKE_BUILD_TYPE "Release" CACHE STRING
@@ -13,6 +13,8 @@ endif()
 
 message(STATUS "CMake build configuration for ${PROJECT_NAME} (${CMAKE_BUILD_TYPE}) ${PROJECT_VERSION}")
 
+include(GNUInstallDirs)
+
 ################################################################################
 # Projet wide setup options
 
@@ -21,6 +23,10 @@ set(CMAKE_MODULE_PATH "${CMAKE_MODULE_PATH};${PROJECT_SOURCE_DIR}/cmake")
 
 option(OPEN_ATMOS_ENABLE_TESTS "Build the tests" ON)
 option(OPEN_ATMOS_ENABLE_PYTHON_LIBRARY "Build the python library" ON)
+option(OPEN_ATMOS_ENABLE_PIC "Build the library with position independent code" ON)
+
+set(OPEN_ATMOS_INSTALL_INCLUDE_DIR ${CMAKE_INSTALL_INCLUDEDIR})
+set(OPEN_ATMOS_LIB_DIR ${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR})
 
 ################################################################################
 # Dependencies

include/mechanism_configuration/version.hpp

@@ -9,7 +9,7 @@ extern "C" {
 
   const char* getVersionString()
   {
-    return "0.1.0";
+    return "0.1.1";
   }
   unsigned getVersionMajor()
   {
@@ -21,7 +21,7 @@ extern "C" {
   }
   unsigned getVersionPatch()
   {
-    return 0+0;
+    return 1+0;
   }
   unsigned getVersionTweak()
   {

python/CMakeLists.txt

@@ -32,4 +32,4 @@ else()
   set(PYTHON_MODULE_PATH "${CMAKE_CURRENT_BINARY_DIR}")
 endif()
 
-install(TARGETS mechanism_configuration_python LIBRARY DESTINATION .)
+install(TARGETS mechanism_configuration_python mechanism_configuration LIBRARY DESTINATION .)

src/CMakeLists.txt

@@ -7,12 +7,20 @@ add_library(open_atmos::mechanism_configuration ALIAS mechanism_configuration)
 
 target_compile_features(mechanism_configuration PUBLIC cxx_std_20)
 
-if(OPEN_ATMOS_ENABLE_PYTHON_LIBRARY)
-  # Add the -fPIC flag for position-independent code if we are building the python library
-  # so that it links correctly on linux
+if(OPEN_ATMOS_ENABLE_PYTHON_LIBRARY OR OPEN_ATMOS_ENABLE_PIC)
+  # Add the -fPIC flag for position-independent code if we are building shared libraries
+  # or the python library so that it links correctly on linux
   set_target_properties(mechanism_configuration PROPERTIES POSITION_INDEPENDENT_CODE ON)
 endif()
 
+set_target_properties(mechanism_configuration PROPERTIES
+  ARCHIVE_OUTPUT_DIRECTORY ${OPEN_ATMOS_LIB_DIR}
+  LIBRARY_OUTPUT_DIRECTORY ${OPEN_ATMOS_LIB_DIR}
+  RUNTIME_OUTPUT_DIRECTORY ${OPEN_ATMOS_LIB_DIR}
+  VERSION ${PROJECT_VERSION}
+  SOVERSION ${PROJECT_VERSION_MAJOR}
+)
+
 target_sources(mechanism_configuration
   PRIVATE
     parse_status.cpp
@@ -32,3 +40,17 @@ target_link_libraries(mechanism_configuration
   PUBLIC 
     yaml-cpp::yaml-cpp
 )
+
+if (APPLE)
+  # set the rpath for the shared library
+  set_target_properties(mechanism_configuration PROPERTIES
+    INSTALL_RPATH "@loader_path"
+    BUILD_WITH_INSTALL_RPATH TRUE
+  )
+elseif(UNIX)
+  # set the rpath for the shared library
+  set_target_properties(mechanism_configuration PROPERTIES
+    INSTALL_RPATH "$ORIGIN"
+    BUILD_WITH_INSTALL_RPATH TRUE
+  )
+endif()

src/v0/first_order_loss_parser.cpp

@@ -23,7 +23,8 @@ namespace mechanism_configuration
         YAML::Node products_object{};
         std::vector<types::ReactionComponent> reactants;
         std::vector<types::ReactionComponent> products;
-        products.push_back({ .species_name = species, .coefficient = 1.0 });
+
+        reactants.push_back({ .species_name = species, .coefficient = 1.0 });
         double scaling_factor = object[validation::SCALING_FACTOR] ? object[validation::SCALING_FACTOR].as<double>() : 1.0;
 
         std::string name = "LOSS." + object[validation::MUSICA_NAME].as<std::string>();

test/unit/v0/test_first_order_loss_config.cpp

@@ -50,18 +50,18 @@ TEST(FirstOrderLossConfig, ParseConfig)
 
     // first reaction
     {
-      EXPECT_EQ(process_vector[0].reactants.size(), 0);
-      EXPECT_EQ(process_vector[0].products.size(), 1);
-      EXPECT_EQ(process_vector[0].products[0].species_name, "foo");
+      EXPECT_EQ(process_vector[0].reactants.size(), 1);
+      EXPECT_EQ(process_vector[0].products.size(), 0);
+      EXPECT_EQ(process_vector[0].reactants[0].species_name, "foo");
       EXPECT_EQ(process_vector[0].name, "LOSS.foo");
       EXPECT_EQ(process_vector[0].scaling_factor, 1.0);
     }
 
     // second reaction
     {
-      EXPECT_EQ(process_vector[1].reactants.size(), 0);
-      EXPECT_EQ(process_vector[1].products.size(), 1);
-      EXPECT_EQ(process_vector[1].products[0].species_name, "bar");
+      EXPECT_EQ(process_vector[1].reactants.size(), 1);
+      EXPECT_EQ(process_vector[1].products.size(), 0);
+      EXPECT_EQ(process_vector[1].reactants[0].species_name, "bar");
       EXPECT_EQ(process_vector[1].name, "LOSS.bar");
       EXPECT_EQ(process_vector[1].scaling_factor, 2.5);
     }