90 allow api users to create and destroy instances of tuvx

.github/workflows/mac.yml

@@ -35,10 +35,10 @@ jobs:
       - name: Run Cmake 
         run: |
           PYTHON_PATH=$(which python)
-          cmake -S . -B build -D CMAKE_CXX_FLAGS=-Wl,-ld_classic -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D Python3_EXECUTABLE=${PYTHON_PATH}
+          cmake -S . -B build -D CMAKE_CXX_FLAGS=-Wl,-ld_classic -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D Python3_EXECUTABLE=$PYTHON_PATH
 
       - name: Build
-        run: cmake --build build --parallel
+        run: cmake --build build --verbose --parallel 10
 
       - name: Run tests
         run: |
@@ -63,9 +63,9 @@ jobs:
         run: cmake -S . -B build -D CMAKE_CXX_FLAGS=-Wl,-ld_classic -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_BUILD_FORTRAN_INTERFACE=ON
 
       - name: Build
-        run: cmake --build build --parallel
+        run: cmake --build build --verbose --parallel 10
 
       - name: Run tests
         run: |
           cd build
-          ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10
+          ctest -E "tuvx_c_api|tuvx_fortran_api" -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10

.github/workflows/ubuntu.yml

@@ -41,7 +41,7 @@ jobs:
         run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}  -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
 
       - name: Build
-        run: cmake --build build --verbose --parallel
+        run: cmake --build build --verbose --parallel 10
 
       - name: Run tests
         run: |
@@ -68,7 +68,7 @@ jobs:
         run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_BUILD_FORTRAN_INTERFACE=ON
 
       - name: Build
-        run: cmake --build build --parallel
+        run: cmake --build build --verbose --parallel 10
 
       - name: Run tests
         run: |

CMakeLists.txt

@@ -62,28 +62,30 @@ set(MUSICA_MOD_DIR ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_INCLUDEDIR})
 set(MUSICA_LIB_DIR ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR})
 set(MUSICA_FORTRAN_SRC_DIR ${CMAKE_SOURCE_DIR}/fortran)
 
+set(musica_compile_definitions "")
+
 # Add flags for various compilers
 if(${CMAKE_Fortran_COMPILER_ID} MATCHES "Intel")
-  add_definitions(-DMUSICA_USING_INTEL)
+  list(APPEND musica_compile_definitions MUSICA_USING_INTEL)
 elseif(${CMAKE_Fortran_COMPILER_ID} MATCHES "GNU")
-  add_definitions(-DMUSICA_USING_GNU)
+  list(APPEND musica_compile_definitions MUSICA_USING_GNU)
 elseif(${CMAKE_Fortran_COMPILER_ID} MATCHES "PGI")
-  add_definitions(-DMUSICA_USING_PGI)
-endif()
-
-# Add flags when using the ClangCL toolset
-if(CMAKE_GENERATOR_TOOLSET STREQUAL "ClangCL")
-  add_definitions(-DMUSICA_USING_CLANGCL)
+  list(APPEND musica_compile_definitions MUSICA_USING_PGI)
 endif()
 
 if(MUSICA_BUILD_C_CXX_INTERFACE)
+  # must be global so that it also applies to dependencies like google test, unless we want
+  # to set it for each target
   # on ubuntu with clang, an incorrect version of the c++ standard library was being linked
   if (${CMAKE_HOST_SYSTEM_NAME} MATCHES "Linux" AND "${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
       # If the compiler is Clang, use libc++
       set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
   endif()
+endif()
 
-  set(CMAKE_CXX_STANDARD 20)
+# Add flags when using the ClangCL toolset
+if(CMAKE_GENERATOR_TOOLSET STREQUAL "ClangCL")
+  list(APPEND musica_compile_definitions MUSICA_USING_CLANGCL)
 endif()
 
 ################################################################################

cmake/dependencies.cmake

@@ -42,6 +42,7 @@ endif()
 # TUV-x
 
 if (MUSICA_ENABLE_TUVX)
+  set(ENABLE_TESTS OFF CACHE BOOL "" FORCE)
   FetchContent_Declare(tuvx
     GIT_REPOSITORY https://github.com/NCAR/tuv-x.git
     GIT_TAG v0.8.0

cmake/test_util.cmake

@@ -63,6 +63,7 @@ function(add_musica_test test_name test_binary test_args working_dir)
     add_test(NAME ${test_name}
              COMMAND ${test_binary} ${test_args}
              WORKING_DIRECTORY ${working_dir})
+    set_tests_properties(${test_name} PROPERTIES TIMEOUT 20)
   endif()
   set(MEMORYCHECK_COMMAND_OPTIONS "--error-exitcode=1 --trace-children=yes --leak-check=full --gen-suppressions=all ${MEMCHECK_SUPPRESS}")
   set(memcheck "${MEMORYCHECK_COMMAND} ${MEMORYCHECK_COMMAND_OPTIONS}")

fortran/CMakeLists.txt

@@ -42,29 +42,14 @@ target_link_libraries(musica-fortran
 target_sources(musica-fortran
   PRIVATE
     micm_core.F90
-    util.F90
+    tuvx_core.F90
 )
 
 # Add flags for gfortran
 if(${CMAKE_Fortran_COMPILER_ID} MATCHES "GNU")
   add_compile_options($<$<COMPILE_LANGUAGE:Fortran>:-ffree-line-length-none>)
 endif()
 
-####################
-# TUV-x
-if (MUSICA_ENABLE_TUVX)
-  # add the sources to musica
-  target_sources(musica-fortran
-    PRIVATE
-      $<TARGET_OBJECTS:tuvx_object>
-  )
-  target_link_libraries(musica-fortran
-    PUBLIC
-      tuvx
-  )
-endif()
-
-
 ################################################################################
 # testing
 

fortran/micm_core.F90

@@ -1,4 +1,5 @@
-module micm_core
+module musica_micm_core
+
    use iso_c_binding, only: c_ptr, c_char, c_int, c_bool, c_double, c_null_char, &
                             c_size_t, c_f_pointer, c_funptr, c_null_ptr, c_associated
    use musica_util, only: error_t_c, is_success
@@ -224,4 +225,4 @@ subroutine finalize(this)
       this%ptr = c_null_ptr
    end subroutine finalize
 
-end module micm_core
+end module musica_micm_core

fortran/test/CMakeLists.txt

@@ -1,3 +1 @@
-create_standard_test_fortran(NAME musica_fortran_interface SOURCES fetch_content_integration/test_micm_fort_api.F90)
-create_standard_test_fortran(NAME musica_fortran_interface_invalid SOURCES fetch_content_integration/test_micm_fort_api_invalid.F90)
 add_subdirectory(unit)

fortran/test/fetch_content_integration/CMakeLists.txt

@@ -28,7 +28,7 @@ pkg_check_modules(netcdff IMPORTED_TARGET REQUIRED netcdf-fortran)
 enable_testing()
 
 # API Test
-add_executable(test_micm_fort_api test_micm_fort_api.F90)
+add_executable(test_micm_core_api test_micm_api.F90)
 
 target_link_libraries(test_micm_fort_api
   PRIVATE
@@ -46,20 +46,21 @@ add_test(
   WORKING_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}
 )
 
-add_executable(test_micm_fort_api_invalid test_micm_fort_api_invalid.F90)
+# API Test
+add_executable(test_tuvx_core_api test_tuvx_api.F90)
 
-target_link_libraries(test_micm_fort_api_invalid
+target_link_libraries(test_tuvx_fort_api
   PRIVATE
     musica::musica-fortran
 )
 
-add_test(
-  NAME test_micm_fort_api_invalid
-  COMMAND $<TARGET_FILE:test_micm_fort_api_invalid>
-  WORKING_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}
-)
-
-set_target_properties(test_micm_fort_api_invalid
+set_target_properties(test_tuvx_fort_api
   PROPERTIES
     LINKER_LANGUAGE Fortran
+)
+
+add_test(
+  NAME test_tuvx_fort_api
+  COMMAND $<TARGET_FILE:test_tuvx_fort_api>
+  WORKING_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}
 )

fortran/test/fetch_content_integration/test_micm_api.F90

@@ -0,0 +1,131 @@
+program combined_micm_tests
+  use iso_c_binding
+  use musica_micm_core, only: micm_t, mapping_t
+  use musica_util, only: assert, error_t_c, is_error, is_success
+
+  implicit none
+
+#include "micm/util/error.hpp"
+
+#define ASSERT( expr ) call assert( expr, __FILE__, __LINE__ )
+#define ASSERT_EQ( a, b ) call assert( a == b, __FILE__, __LINE__ )
+#define ASSERT_NE( a, b ) call assert( a /= b, __FILE__, __LINE__ )
+
+  ! Declarations
+  type(micm_t), pointer         :: micm
+  real(c_double)                :: time_step
+  real(c_double)                :: temperature
+  real(c_double)                :: pressure
+  integer(c_int)                :: num_concentrations, num_user_defined_reaction_rates
+  real(c_double), dimension(5)  :: concentrations 
+  real(c_double), dimension(3)  :: user_defined_reaction_rates 
+  integer                       :: errcode
+
+  ! Main program
+  time_step = 200
+  temperature = 272.5
+  pressure = 101253.4
+  num_concentrations = 5
+  concentrations = (/ 0.75, 0.4, 0.8, 0.01, 0.02 /)
+  num_user_defined_reaction_rates = 3
+  user_defined_reaction_rates = (/ 0.1, 0.2, 0.3 /)
+
+  ! Call the valid test subroutine
+  call test_micm_fort_api()
+
+  ! Call the invalid test subroutine
+  call test_micm_fort_api_invalid()
+
+contains
+
+  ! Valid MICM solver creation test
+  subroutine test_micm_fort_api()
+    type(mapping_t)               :: the_mapping
+    character(len=:), allocatable :: string_value
+    real(c_double)                :: double_value
+    integer(c_int)                :: int_value
+    logical(c_bool)               :: bool_value
+    type(error_t_c)               :: error
+    character(len=256)            :: config_path
+    integer                       :: i
+
+    config_path = "configs/chapman"
+
+    write(*,*) "[test micm fort api] Creating MICM solver..."
+    micm => micm_t(config_path, error)
+    ASSERT( is_success( error ) )
+
+    do i = 1, micm%species_ordering_length
+      the_mapping = micm%species_ordering(i)
+      print *, "Species Name:", the_mapping%name(:the_mapping%string_length), ", Index:", the_mapping%index
+    end do
+    do i = 1, micm%user_defined_reaction_rates_length
+      the_mapping = micm%user_defined_reaction_rates(i)
+      print *, "User Defined Reaction Rate Name:", the_mapping%name(:the_mapping%string_length), ", Index:", the_mapping%index
+    end do
+
+    write(*,*) "[test micm fort api] Initial concentrations", concentrations
+
+    write(*,*) "[test micm fort api] Solving starts..."
+    call micm%solve(time_step, temperature, pressure, num_concentrations, concentrations, &
+                    num_user_defined_reaction_rates, user_defined_reaction_rates, error)
+    ASSERT( is_success( error ) )
+
+    write(*,*) "[test micm fort api] After solving, concentrations", concentrations
+
+    string_value = micm%get_species_property_string( "O3", "__long name", error )
+    ASSERT( is_success( error ) )
+    ASSERT_EQ( string_value, "ozone" )
+    double_value = micm%get_species_property_double( "O3", "molecular weight [kg mol-1]", error )
+    ASSERT( is_success( error ) )
+    ASSERT_EQ( double_value, 0.048_c_double )
+    int_value = micm%get_species_property_int( "O3", "__atoms", error )
+    ASSERT( is_success( error ) )
+    ASSERT_EQ( int_value, 3_c_int )
+    bool_value = micm%get_species_property_bool( "O3", "__do advect", error )
+    ASSERT( is_success( error ) )
+    ASSERT( logical( bool_value ) )
+
+    string_value = micm%get_species_property_string( "O3", "missing property", error )
+    ASSERT( is_error( error, MICM_ERROR_CATEGORY_SPECIES, \
+                      MICM_SPECIES_ERROR_CODE_PROPERTY_NOT_FOUND ) )
+    double_value = micm%get_species_property_double( "O3", "missing property", error )
+    ASSERT( is_error( error, MICM_ERROR_CATEGORY_SPECIES, \
+                      MICM_SPECIES_ERROR_CODE_PROPERTY_NOT_FOUND ) )
+    int_value = micm%get_species_property_int( "O3", "missing property", error )
+    ASSERT( is_error( error, MICM_ERROR_CATEGORY_SPECIES, \
+                      MICM_SPECIES_ERROR_CODE_PROPERTY_NOT_FOUND ) )
+    bool_value = micm%get_species_property_bool( "O3", "missing property", error )
+    ASSERT( is_error( error, MICM_ERROR_CATEGORY_SPECIES, \
+                      MICM_SPECIES_ERROR_CODE_PROPERTY_NOT_FOUND ) )
+    deallocate( micm )
+    micm => micm_t( "configs/invalid", error )
+    ASSERT( is_error( error, MICM_ERROR_CATEGORY_CONFIGURATION, \
+                      MICM_CONFIGURATION_ERROR_CODE_INVALID_FILE_PATH ) )
+    ASSERT( .not. associated( micm ) )
+
+    write(*,*) "[test micm fort api] Finished."
+
+  end subroutine test_micm_fort_api
+
+  ! Invalid MICM solver creation test
+  subroutine test_micm_fort_api_invalid()
+    use musica_util, only: error_t_c
+    use musica_micm_core, only: micm_t
+
+    implicit none
+
+    type(micm_t), pointer         :: micm
+    character(len=7)              :: config_path
+    type(error_t_c)               :: error
+
+    config_path = "invalid_config"
+
+    write(*,*) "[test micm fort api] Creating MICM solver..."
+    micm => micm_t(config_path, error)
+    ASSERT( is_error( error, MICM_ERROR_CATEGORY_CONFIGURATION, \
+                      MICM_CONFIGURATION_ERROR_CODE_INVALID_FILE_PATH ) )
+
+  end subroutine test_micm_fort_api_invalid
+
+end program combined_micm_tests