91 remove submodules (#92)

* correcting fortran build

* install stuff

* correcting python build

* what

* adding lapack to containers

* installating lapack on ubuntu action

* Rename CMakelists.txt to CMakeLists.txt

.github/workflows/ubuntu.yml

@@ -29,6 +29,11 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y liblapack-dev libblas-dev
+
       - uses: actions/setup-python@v5
       - run: pip install -r python/requirements.txt
 

CMakeLists.txt

@@ -89,11 +89,6 @@ endif()
 ################################################################################
 # Dependencies
 
-include(musica_util)
-
-# Add submodules
-checkout_submodules()
-
 include(dependencies)
 
 ################################################################################

cmake/dependencies.cmake

@@ -31,28 +31,37 @@ endif()
 # MICM
 
 if (MUSICA_ENABLE_MICM)
-  FetchContent_Declare(json
-      GIT_REPOSITORY https://github.com/nlohmann/json.git
-      GIT_TAG v3.11.2
+  FetchContent_Declare(micm
+      GIT_REPOSITORY https://github.com/NCAR/micm.git
+      GIT_TAG v3.5.0-release-candidate
   )
-  FetchContent_MakeAvailable(json)
+  FetchContent_MakeAvailable(micm)
 endif()
 
 ################################################################################
 # TUV-x
 
 if (MUSICA_ENABLE_TUVX)
-  FetchContent_Declare(
-    yaml-cpp
-    GIT_REPOSITORY https://github.com/jbeder/yaml-cpp/
-    GIT_TAG 0.8.0
+  FetchContent_Declare(tuvx
+    GIT_REPOSITORY https://github.com/NCAR/tuv-x.git
+    GIT_TAG v0.8.0
   )
-  FetchContent_MakeAvailable(yaml-cpp)
+  FetchContent_MakeAvailable(tuvx)
 endif()
 
 ################################################################################
 # pybind11
 if(MUSICA_ENABLE_PYTHON_LIBRARY)
   set(PYBIND11_NEWPYTHON ON)
-  add_subdirectory(${CMAKE_SOURCE_DIR}/lib/pybind11)
+
+  FetchContent_Declare(pybind11
+      GIT_REPOSITORY https://github.com/pybind/pybind11
+      GIT_TAG        v2.12.0
+  )
+
+  FetchContent_GetProperties(pybind11)
+  if(NOT pybind11_POPULATED)
+      FetchContent_Populate(pybind11)
+      add_subdirectory(${pybind11_SOURCE_DIR} ${pybind11_BINARY_DIR})
+  endif()
 endif()

docker/Dockerfile.fortran-gcc

@@ -6,16 +6,17 @@ RUN dnf -y update \
     curl \
     gcc \
     gcc-c++ \
-    gdb \
     gcc-gfortran \
+    gdb \
     git \
+    hdf5-devel \
+    json-devel \
+    lapack-devel \
     lcov \
     libcurl-devel \
-    hdf5-devel \
-    netcdf-fortran-devel \
     m4 \
     make \
-    json-devel \
+    netcdf-fortran-devel \
     valgrind \ 
     vim \
     zlib-devel \
@@ -35,7 +36,6 @@ RUN cd musica \
     && cmake -S . \
              -B build \
              -D CMAKE_BUILD_TYPE=Release \
-             -D MUSICA_ENABLE_TESTS=ON \
              -D MUSICA_BUILD_FORTRAN_INTERFACE=ON \
              -D MUSICA_ENABLE_MICM=ON \
     && cd build \

docker/Dockerfile.fortran-gcc.integration

@@ -6,16 +6,17 @@ RUN dnf -y update \
     curl \
     gcc \
     gcc-c++ \
-    gdb \
     gcc-gfortran \
+    gdb \
     git \
+    hdf5-devel \
+    json-devel \
+    lapack-devel \
     lcov \
     libcurl-devel \
-    hdf5-devel \
-    netcdf-fortran-devel \
     m4 \
     make \
-    json-devel \
+    netcdf-fortran-devel \
     valgrind \ 
     vim \
     zlib-devel \

fortran/CMakeLists.txt

@@ -35,7 +35,7 @@ target_include_directories(musica-fortran
 )
 
 target_link_libraries(musica-fortran
-  INTERFACE
+  PUBLIC
     musica::musica
 )
 
@@ -53,40 +53,15 @@ endif()
 ####################
 # TUV-x
 if (MUSICA_ENABLE_TUVX)
-  set(TUVX_MOD_DIR ${MUSICA_MOD_DIR})
-  set(TUVX_LIB_DIR ${MUSICA_LIB_DIR})
-
-  add_subdirectory(${CMAKE_SOURCE_DIR}/lib/tuv-x/src ${MUSICA_LIB_DIR}/tuv-x/src)
-
-  # for yaml-cpp
-  target_compile_features(tuvx_object PRIVATE cxx_std_20)
-
-  set_target_properties(tuvx_object PROPERTIES
-    ARCHIVE_OUTPUT_DIRECTORY ${MUSICA_LIB_DIR}
-    Fortran_MODULE_DIRECTORY ${MUSICA_MOD_DIR}
-  )
-
-  target_include_directories(tuvx_object
-    PUBLIC  
-      $<BUILD_INTERFACE:${MUSICA_MOD_DIR}>
-      $<INSTALL_INTERFACE:${MUSICA_INSTALL_INCLUDE_DIR}>
-  )
-
-  target_link_libraries(tuvx_object 
-    PUBLIC
-      musicacore_object
-  )
-
-  target_link_libraries(musica-fortran 
-    PUBLIC
-      yaml-cpp::yaml-cpp
-  )
-
   # add the sources to musica
   target_sources(musica-fortran
     PRIVATE
       $<TARGET_OBJECTS:tuvx_object>
   )
+  target_link_libraries(musica-fortran
+    PUBLIC
+      tuvx
+  )
 endif()
 
 
@@ -95,4 +70,11 @@ endif()
 
 if(MUSICA_ENABLE_TESTS)
   add_subdirectory(test)
+endif()
+
+################################################################################
+# installation
+
+if(MUSICA_ENABLE_INSTALL AND NOT MUSICA_ENABLE_PYTHON_LIBRARY)
+  add_subdirectory(packaging)
 endif()

fortran/packaging/CMakelists.txt → fortran/packaging/CMakeLists.txt

@@ -3,6 +3,8 @@ include(CMakePackageConfigHelpers)
 install(
   TARGETS
     musica-fortran
+    tuvx
+    yaml-cpp
   EXPORT
     musica_fortran_Exports
   LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
@@ -13,6 +15,7 @@ install(
 install(
   DIRECTORY
     ${MUSICA_MOD_DIR}/
+    ${tuvx_BINARY_DIR}/include
   DESTINATION
     ${MUSICA_INSTALL_INCLUDE_DIR}/musica/fortran
   FILES_MATCHING PATTERN "*.mod"
@@ -62,4 +65,4 @@ if(NOT TARGET uninstall)
 
   add_custom_target(uninstall
     COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake)
-endif()
+endif()

python/CMakeLists.txt

@@ -11,7 +11,7 @@ set_target_properties(musica_python PROPERTIES OUTPUT_NAME musica)
 
 target_include_directories(musica_python
   PUBLIC  
-    $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/lib/micm/include>
+    $<BUILD_INTERFACE:${micm_SOURCE_DIR}/include>
     $<INSTALL_INTERFACE:${MUSICA_INSTALL_INCLUDE_DIR}>
 )
 

src/CMakeLists.txt

@@ -62,15 +62,7 @@ target_sources(musica
 ####################
 # MICM
 if(MUSICA_ENABLE_MICM)
-  target_compile_features(musica PUBLIC cxx_std_20)
-
-  target_include_directories(musica
-    PUBLIC  
-      $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/lib/micm/include>
-      $<INSTALL_INTERFACE:${MUSICA_INSTALL_INCLUDE_DIR}>
-  )
-
-  target_link_libraries(musica PUBLIC nlohmann_json::nlohmann_json)
+  target_link_libraries(musica PUBLIC musica::micm)
 
   add_subdirectory(micm)
 endif()

src/packaging/CMakeLists.txt

@@ -4,6 +4,7 @@ install(
   TARGETS
     musica
     nlohmann_json
+    micm
   EXPORT
     musica_Exports
   LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
@@ -28,7 +29,7 @@ install(
 if (MUSICA_ENABLE_MICM)
   install(
     DIRECTORY
-      ${CMAKE_SOURCE_DIR}/lib/micm/include/
+      ${micm_SOURCE_DIR}/include/
     DESTINATION 
       ${MUSICA_INSTALL_INCLUDE_DIR}/musica
   )

src/test/connections/micm_c_api.cpp

@@ -68,12 +68,8 @@ TEST_F(MicmCApiTest, GetSpeciesProperty) {
             ASSERT_STREQ(e.what(), "Species 'bad species' not found");
             throw;
         }}, std::runtime_error);
-    ASSERT_THROW({
-        try {
-            get_species_property_double(micm, "O3", "bad property");
-        } catch (const std::runtime_error& e) {
-            ASSERT_STREQ(e.what(), "Species property 'bad property' not found for species 'O3'");
-            throw;
-        }}, std::runtime_error);
+    EXPECT_ANY_THROW(
+        get_species_property_double(micm, "O3", "bad property")
+    );
 #endif
 }