Parse v0 mechanisms

.github/workflows/mac.yml

@@ -39,7 +39,6 @@ jobs:
       - run: pip install numpy --user
 
       - name: Run Cmake 
-        if: matrix.compiler.cpp != 'g++-13'
         run: |
             PYTHON_PATH=$(which python)
             cmake -S . -B build \
@@ -49,23 +48,8 @@ jobs:
                 -D MUSICA_ENABLE_PYTHON_LIBRARY=ON \
                 -D Python3_EXECUTABLE=$PYTHON_PATH 
 
-      - name: Run Cmake 
-        if: matrix.compiler.cpp == 'g++-13'
-        run: |
-            PYTHON_PATH=$(which python)
-            # for some reason gcc 13 was having issues finding the correct osx sdk
-            # it seems it was a known issue: https://github.com/actions/runner-images/issues/9997
-            # for some reason, passing in an empty string for the osx sysroot fixed the issue
-            cmake -S . -B build \
-                -D CMAKE_CXX_FLAGS=-Wl,-ld_classic \
-                -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                -D MUSICA_GIT_TAG=${{ github.sha }} \
-                -D MUSICA_ENABLE_PYTHON_LIBRARY=ON \
-                -D Python3_EXECUTABLE=$PYTHON_PATH \
-                -D CMAKE_OSX_SYSROOT=""
-
       - name: Build
-        run: cmake --build build --verbose --parallel 10
+        run: cmake --build build --verbose
 
       - name: Run tests
         run: |

cmake/dependencies.cmake

@@ -34,14 +34,16 @@ FetchContent_MakeAvailable(yaml-cpp)
 # Mechanism Configuration
 
 set_git_default(MECH_CONFIG_GIT_REPOSITORY https://github.com/open-atmos/MechanismConfiguration.git)
-set_git_default(MECH_CONFIG_GIT_TAG 0835527)
+set_git_default(MECH_CONFIG_GIT_TAG c379f9fa5164112d562a35f96718973acbc3e286)
 
 FetchContent_Declare(mechanism_configuration
     GIT_REPOSITORY ${MECH_CONFIG_GIT_REPOSITORY}
     GIT_TAG ${MECH_CONFIG_GIT_TAG}
     GIT_PROGRESS NOT ${FETCHCONTENT_QUIET}
 )
 
+set(OPEN_ATMOS_ENABLE_PYTHON_LIBRARY OFF CACHE BOOL "" FORCE)
+
 FetchContent_MakeAvailable(mechanism_configuration)
 
 ################################################################################

fortran/test/fetch_content_integration/test_micm_api.F90

@@ -11,6 +11,7 @@ program test_micm_api
   use musica_util, only: assert, error_t, mapping_t, string_t, find_mapping_index
 
 #include "micm/util/error.hpp"
+#include "musica/error.hpp"
 
 #define ASSERT( expr ) call assert( expr, __FILE__, __LINE__ )
 #define ASSERT_EQ( a, b ) call assert( a == b, __FILE__, __LINE__ )
@@ -166,7 +167,7 @@ subroutine test_api()
     ASSERT( error%is_error( MICM_ERROR_CATEGORY_SPECIES, MICM_SPECIES_ERROR_CODE_PROPERTY_NOT_FOUND ) )
     deallocate( micm )
     micm => micm_t( "configs/invalid", solver_type, num_grid_cells, error )
-    ASSERT( error%is_error( MICM_ERROR_CATEGORY_CONFIGURATION, MICM_CONFIGURATION_ERROR_CODE_INVALID_FILE_PATH ) )
+    ASSERT( error%is_error( MUSICA_ERROR_CATEGORY, MUSICA_ERROR_CODE_CONFIG_PARSE_FAILED ) )
     ASSERT( .not. associated( micm ) )
 
     write(*,*) "[test micm fort api] Finished."

include/musica/error.hpp

@@ -0,0 +1,13 @@
+#if 0
+// Copyright (C) 2023-2025 National Center for Atmospheric Research
+// SPDX-License-Identifier: Apache-2.0
+#endif
+
+#define MUSICA_ERROR_CATEGORY                       "MUSICA Error"
+#define MUSICA_ERROR_CODE_SPECIES_NOT_FOUND         1
+#define MUSICA_ERROR_CODE_SOLVER_TYPE_NOT_FOUND     2
+#define MUSICA_ERROR_CODE_MAPPING_NOT_FOUND         3
+#define MUSICA_ERROR_CODE_PARSING_FAILED            4
+#define MUSICA_ERROR_CODE_MAPPING_OPTIONS_UNDEFINED 5
+#define MUSICA_ERROR_CODE_CONFIG_PARSE_FAILED       6
+#define MUSICA_ERROR_CODE_VERSION_NOT_SUPPORTED     7

include/musica/micm/chemistry.hpp

@@ -0,0 +1,12 @@
+#pragma once
+
+#include <micm/process/process.hpp>
+#include <micm/system/system.hpp>
+
+namespace musica
+{
+  struct Chemistry {
+    micm::System system;
+    std::vector<micm::Process> processes;
+  };
+}

include/musica/micm/micm.hpp

@@ -6,6 +6,8 @@
 #pragma once
 
 #include <musica/util.hpp>
+#include <musica/micm/parse.hpp>
+#include <musica/micm/chemistry.hpp>
 
 #include <micm/configure/solver_config.hpp>
 #include <micm/process/process_set.hpp>
@@ -31,7 +33,6 @@
 
 namespace musica
 {
-
   class MICM;
 
 #ifdef __cplusplus
@@ -169,25 +170,25 @@ namespace musica
   class MICM
   {
    public:
-    /// @brief Create a Rosenbrock solver of vector-ordered matrix type by reading and parsing configuration file
-    /// @param config_path Path to configuration file or directory containing configuration file
+    /// @brief Create a Rosenbrock solver of vector-ordered matrix type using the provided chemistry configuration
+    /// @param chemistry Chemistry configuration
     /// @param error Error struct to indicate success or failure
-    void CreateRosenbrock(const std::string &config_path, Error *error);
+    void CreateRosenbrock(const Chemistry &chemistry, Error *error);
 
-    /// @brief Create a Rosenbrock solver of standard-ordered matrix type by reading and parsing configuration file
-    /// @param config_path Path to configuration file or directory containing configuration file
+    /// @brief Create a Rosenbrock solver of standard-ordered matrix type using the provided chemistry configuration
+    /// @param chemistry Chemistry configuration
     /// @param error Error struct to indicate success or failure
-    void CreateRosenbrockStandardOrder(const std::string &config_path, Error *error);
+    void CreateRosenbrockStandardOrder(const Chemistry &chemistry, Error *error);
 
     /// @brief Create a BackwardEuler solver of vector-ordered matrix type by reading and parsing configuration file
-    /// @param config_path Path to configuration file or directory containing configuration file
+    /// @param chemistry Chemistry configuration
     /// @param error Error struct to indicate success or failure
-    void CreateBackwardEuler(const std::string &config_path, Error *error);
+    void CreateBackwardEuler(const Chemistry &chemistry, Error *error);
 
     /// @brief Create a BackwardEuler solver of standard-ordered matrix type by reading and parsing configuration file
-    /// @param config_path Path to configuration file or directory containing configuration file
+    /// @param chemistry Chemistry configuration
     /// @param error Error struct to indicate success or failure
-    void CreateBackwardEulerStandardOrder(const std::string &config_path, Error *error);
+    void CreateBackwardEulerStandardOrder(const Chemistry &chemistry, Error *error);
 
     /// @brief Solve the system
     /// @param solver_state_pair A pair containing a pointer to a solver and a state for that solver (temporary fix)
@@ -223,6 +224,11 @@ namespace musica
     {
       num_grid_cells_ = num_grid_cells;
     }
+
+    void SetChemistry(Chemistry chemistry)
+    {
+      chemistry_ = std::make_unique<Chemistry>(chemistry);
+    }
 
     /// @brief Get a property for a chemical species
     /// @param species_name Name of the species
@@ -275,14 +281,14 @@ namespace musica
 
    private:
     int num_grid_cells_;
-    std::unique_ptr<micm::SolverParameters> solver_parameters_;
+    std::unique_ptr<Chemistry> chemistry_;
   };
 
   template<class T>
   inline T MICM::GetSpeciesProperty(const std::string &species_name, const std::string &property_name, Error *error)
   {
     *error = NoError();
-    for (const auto &species : solver_parameters_->system_.gas_phase_.species_)
+    for (const auto &species : chemistry_->system.gas_phase_.species_)
     {
       if (species.name_ == species_name)
       {

include/musica/micm/parse.hpp

@@ -0,0 +1,19 @@
+#pragma once
+
+#include <musica/micm/chemistry.hpp>
+#include <musica/micm/micm.hpp>
+#include <musica/util.hpp>
+
+#include <mechanism_configuration/parser.hpp>
+
+namespace musica
+{
+  Chemistry ReadConfiguration(const std::string& config_path, Error* error);
+  Chemistry ParserV0(const mechanism_configuration::ParserResult<>& result, Error* error);
+  Chemistry ParserV1(const mechanism_configuration::ParserResult<>& result, Error* error);
+
+  // Utility functions to check types and perform conversions
+  bool IsBool(const std::string& value);
+  bool IsInt(const std::string& value);
+  bool IsFloatingPoint(const std::string& value);
+}  // namespace musica

include/musica/util.hpp

@@ -1,15 +1,10 @@
+
 // Copyright (C) 2023-2025 National Center for Atmospheric Research
 // SPDX-License-Identifier: Apache-2.0
 #pragma once
 
 #include <cstddef>
-
-#define MUSICA_ERROR_CATEGORY                       "MUSICA Error"
-#define MUSICA_ERROR_CODE_SPECIES_NOT_FOUND         1
-#define MUSICA_ERROR_CODE_SOLVER_TYPE_NOT_FOUND     2
-#define MUSICA_ERROR_CODE_MAPPING_NOT_FOUND         3
-#define MUSICA_ERROR_CODE_PARSING_FAILED            4
-#define MUSICA_ERROR_CODE_MAPPING_OPTIONS_UNDEFINED 5
+#include <musica/error.hpp>
 
 #ifdef __cplusplus
   #include <yaml-cpp/yaml.h>

pyproject.toml

@@ -7,8 +7,6 @@ name = "musica"
 dynamic = ["version"]
 readme = "README.md"
 description = "MUSICA is a Python library for performing computational simulations in atmospheric chemistry."
-long_description = "MUSICA (Multiscale Interface for Chemistry and Aerosols) is a powerful tool for modeling atmospheric chemistry processes. It provides a flexible interface for running simulations and analyzing results."
-long_description_content_type = "text/plain"
 authors = [
     { name = "Matthew Dawsom", email = "[email protected]" },
     { name = "Jiwon Gim", email = "[email protected]" },

python/CMakeLists.txt

@@ -1,12 +1,22 @@
+# we specify the sources by hand because sometimes musica builds with tuvx
+# it is hard to guarantee there is a fortran compiler on windows
 pybind11_add_module(musica_python 
   wrapper.cpp
   ${PROJECT_SOURCE_DIR}/src/micm/micm.cpp
+  ${PROJECT_SOURCE_DIR}/src/micm/parse.cpp
+  ${PROJECT_SOURCE_DIR}/src/micm/v0_parse.cpp
+  ${PROJECT_SOURCE_DIR}/src/micm/v1_parse.cpp
   ${PROJECT_SOURCE_DIR}/src/component_versions.cpp
   ${PROJECT_SOURCE_DIR}/src/util.cpp
   ${CMAKE_BINARY_DIR}/version.cpp
 )
 
-target_link_libraries(musica_python PRIVATE yaml-cpp)
+target_link_libraries(musica_python 
+  PUBLIC 
+    open_atmos::mechanism_configuration
+  PRIVATE 
+    yaml-cpp
+)
 
 target_compile_features(musica_python PUBLIC cxx_std_20)
 
@@ -39,7 +49,7 @@ elseif(UNIX)
   )
 endif()
 
-install(TARGETS musica_python yaml-cpp
+install(TARGETS musica_python yaml-cpp mechanism_configuration
   LIBRARY DESTINATION .
 )
 

src/micm/CMakeLists.txt

@@ -1,5 +1,8 @@
 target_sources(musica
   PRIVATE
     micm.cpp
+    parse.cpp
+    v0_parse.cpp
+    v1_parse.cpp
 )