resolve merge conflicts

.clang-format

@@ -30,13 +30,13 @@ IncludeCategories:
   - Regex:           '<(musica)\/'
     Priority:        2
   # MICM, TUV-X headers
-  - Regex:           '<(micm|tuvx)[[:alnum:].\Q/-_\E]+>'
+  - Regex:           '<(micm|tuvx)[[:alnum:].(-|_)*]+>'
     Priority:        3
   # External libraries headers
-  - Regex:           '<([[:alnum:].\Q/-_\E]+)\/'
+  - Regex:           '<[[:alnum:].(-|_)*]+\/'
     Priority:        4
   # System headers
-  - Regex:           '<[[:alnum:].\Q/-_\E]+>'
+  - Regex:           '<[[:alnum:].(-|_)*]+>'
     Priority:        5
   # Main, local, private headers
   - Regex:           '".*'

.github/workflows/clang_format.yml

@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - main
+  workflow_dispatch:
 
 jobs:
   format:

.github/workflows/mac.yml

@@ -38,9 +38,28 @@ jobs:
       - run: pip install -r python/requirements.txt --user
 
       - name: Run Cmake 
+        if: matrix.compiler.cpp != 'g++-13'
         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=$PYTHON_PATH
+            PYTHON_PATH=$(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 
+
+      - 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_ENABLE_PYTHON_LIBRARY=ON \
+                -D Python3_EXECUTABLE=$PYTHON_PATH \
+                -D CMAKE_OSX_SYSROOT=""
 
       - name: Build
         run: cmake --build build --verbose
@@ -49,6 +68,7 @@ jobs:
         run: |
           cd build
           ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10
+
   fortran:
     runs-on: macos-latest
     strategy:
@@ -65,7 +85,7 @@ jobs:
         run: brew install netcdf netcdf-fortran
 
       - name: Run Cmake 
-        run: cmake -S . -B build -D CMAKE_CXX_FLAGS=-Wl,-ld_classic -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_BUILD_FORTRAN_INTERFACE=ON
+        run: cmake -S . -B build -D CMAKE_CXX_FLAGS=-Wl,-ld_classic -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_BUILD_FORTRAN_INTERFACE=ON
 
       - name: Build
         run: cmake --build build --verbose --parallel 10

CMakeLists.txt

@@ -125,3 +125,9 @@ endif()
 if(MUSICA_ENABLE_PYTHON_LIBRARY)
   add_subdirectory(python)
 endif()
+
+###
+# Configure and display a summary file for how musica was built.
+###
+include(summary)
+

cmake/dependencies.cmake

@@ -51,7 +51,7 @@ endif()
 if (MUSICA_ENABLE_MICM AND MUSICA_BUILD_C_CXX_INTERFACE)
 
   set_git_default(MICM_GIT_REPOSITORY https://github.com/NCAR/micm.git)
-  set_git_default(MICM_GIT_TAG inline_version)
+  set_git_default(MICM_GIT_TAG 401add1bb3d0db9cd13464ed0566dc2599f02ca9)
 
   FetchContent_Declare(micm
       GIT_REPOSITORY ${MICM_GIT_REPOSITORY}
@@ -74,7 +74,7 @@ if (MUSICA_ENABLE_TUVX AND MUSICA_BUILD_C_CXX_INTERFACE)
   set(TUVX_INSTALL_INCLUDE_DIR ${MUSICA_INSTALL_INCLUDE_DIR} CACHE STRING "" FORCE)
 
   set_git_default(TUVX_GIT_REPOSITORY https://github.com/NCAR/tuv-x.git)
-  set_git_default(TUVX_GIT_TAG pic)
+  set_git_default(TUVX_GIT_TAG f8961c1a6cd66cf619b32fce1f124a78e9a4ea18)
 
   FetchContent_Declare(tuvx
     GIT_REPOSITORY ${TUVX_GIT_REPOSITORY}

cmake/musica.settings.in

@@ -0,0 +1,41 @@
+# MUSICA Configuration Summary
+
+## General
+----------
+MUSICA Version:     @musica-distribution_VERSION@
+Configured On:	    @BUILD_CONFIG_DATE@
+Host System:	    @CMAKE_SYSTEM_PROCESSOR@-@CMAKE_SYSTEM_NAME@-@CMAKE_SYSTEM_VERSION@
+Build Directory:    @CMAKE_BINARY_DIR@
+Install Prefix:     @CMAKE_INSTALL_PREFIX@
+
+## Compilers and Flags
+----------------------
+
+C Compiler:         @C_COMPILER_NAME_INFO@
+C++ Compiler:       @CXX_COMPILER_NAME_INFO@
+Fortran Compiler:   @Fortran_COMPILER_NAME_INFO@
+
+CFLAGS:		@CMAKE_C_FLAGS@
+CXXFLAGS:	@CMAKE_CXX_FLAGS@
+Fortran Flags: @CMAKE_Fortran_FLAGS@
+LDFLAGS:	@CMAKE_EXE_LINKER_FLAGS@
+
+## Parallel I/O
+---------------
+
+MPI:    @MUSICA_ENABLE_MPI@
+OPENMP: @MUSICA_ENABLE_OPENMP@
+
+## Interfaces:
+--------------
+
+CXX Interface:      @MUSICA_BUILD_C_CXX_INTERFACE@
+Fortran Interface:  @MUSICA_BUILD_FORTRAN_INTERFACE@
+Python Library:     @MUSICA_ENABLE_PYTHON_LIBRARY@
+
+## Dependencies:
+----------------
+
+MICM:               @MUSICA_ENABLE_MICM_INFO@
+TUV-X:              @MUSICA_ENABLE_TUVX_INFO@
+PyBind11:           @MUSICA_ENABLE_PYTHON_LIBRARY_INFO@

cmake/summary.cmake

@@ -0,0 +1,51 @@
+# Parse out a few individual variables
+string(TIMESTAMP BUILD_CONFIG_DATE "%Y-%m-%d %H:%M:%S")
+get_filename_component(C_COMPILER_NAME ${CMAKE_C_COMPILER} NAME)
+set(C_COMPILER_NAME_INFO "${C_COMPILER_NAME} (${CMAKE_C_COMPILER_VERSION})")
+
+if(MUSICA_BUILD_C_CXX_INTERFACE)
+  get_filename_component(CXX_COMPILER_NAME ${CMAKE_CXX_COMPILER} NAME)
+  set(CXX_COMPILER_NAME_INFO "${CXX_COMPILER_NAME} (${CMAKE_CXX_COMPILER_VERSION})")
+else()
+  set(CXX_COMPILER_NAME_INFO " ")
+endif()
+
+if(MUSICA_BUILD_FORTRAN_INTERFACE)
+  get_filename_component(Fortran_COMPILER_NAME ${CMAKE_Fortran_COMPILER} NAME)
+  set(Fortran_COMPILER_NAME_INFO "${Fortran_COMPILER_NAME}")
+  if(${CMAKE_Fortran_COMPILER_VERSION})
+    set(Fortran_COMPILER_NAME_INFO "${Fortran_COMPILER_NAME_INFO} (${CMAKE_Fortran_COMPILER_VERSION})")
+  endif()
+else()
+  set(Fortran_COMPILER_NAME " ")
+endif()
+
+if(MUSICA_ENABLE_MICM)
+  set(MUSICA_ENABLE_MICM_INFO "ON (repo: ${MICM_GIT_REPOSITORY} tag: ${MICM_GIT_TAG})")
+else()
+  set(MUSICA_ENABLE_MICM_INFO "OFF")
+endif()
+
+if(MUSICA_ENABLE_TUVX)
+  set(MUSICA_ENABLE_TUVX_INFO "ON (repo: ${TUVX_GIT_REPOSITORY} tag: ${TUVX_GIT_TAG})")
+else()
+  set(MUSICA_ENABLE_TUVX_INFO "OFF")
+endif()
+
+if(MUSICA_ENABLE_PYTHON_LIBRARY)
+  set(MUSICA_ENABLE_PYTHON_LIBRARY_INFO "ON (repo: ${PYBIND11_GIT_REPOSITORY} tag: ${PYBIND11_GIT_TAG})")
+else()
+  set(MUSICA_ENABLE_PYTHON_LIBRARY_INFO "OFF")
+endif()
+
+# Configure musica.settings file
+configure_file("${CMAKE_SOURCE_DIR}/cmake/musica.settings.in"
+  "${CMAKE_BINARY_DIR}/musica.settings"
+  @ONLY)
+
+# Read in settings file, print out.
+# Avoid using system-specific calls so that this
+# might also work on Windows.
+file(READ "${CMAKE_BINARY_DIR}/musica.settings"
+  MUSICA_SETTINGS)
+message(STATUS ${MUSICA_SETTINGS})

docker/Dockerfile.fortran-nvhpc

@@ -7,6 +7,7 @@
 FROM nvcr.io/nvidia/nvhpc:23.7-devel-cuda12.2-ubuntu22.04
 
 ARG MUSICA_GIT_TAG=main
+ARG BUILD_TYPE=release
 
 RUN apt update \
     && apt -y install \
@@ -50,7 +51,7 @@ COPY . musica
 RUN cd musica \
     && cmake -S . \
              -B build \
-             -D CMAKE_BUILD_TYPE=Release \
+             -D CMAKE_BUILD_TYPE=${BUILD_TYPE} \
     && cd build \
     && make install -j
 
@@ -62,7 +63,7 @@ ENV FC=nvfortran
 RUN cd musica/fortran/test/fetch_content_integration \
     && mkdir build && cd build \
     && cmake .. \
-        -D CMAKE_BUILD_TYPE=Release \
+        -D CMAKE_BUILD_TYPE=${BUILD_TYPE} \
         -D CMAKE_EXE_LINKER_FLAGS="-Wl,--copy-dt-needed-entries" \
         -D MUSICA_GIT_TAG=${MUSICA_GIT_TAG} \
     && make -j

fortran/test/fetch_content_integration/test_tuvx_api.F90

@@ -44,12 +44,12 @@ end subroutine test_tuvx_api
   subroutine test_tuvx_api_invalid_config()
     type(tuvx_t), pointer :: tuvx
     type(error_t)         :: error
-    character(len=256)     :: config_path
+    character(len=256)    :: config_path
 
     config_path = "invalid_config"
 
     tuvx => tuvx_t(config_path, error)
-    ! ASSERT( .not. error%is_success() )
+    ASSERT( .not. error%is_success() )
 
   end subroutine test_tuvx_api_invalid_config
 
@@ -75,23 +75,15 @@ subroutine test_tuvx_solve()
     grids = tuvx%get_grids( error )
     ASSERT( error%is_success() )
 
-    ! profiles = tuvx%create_profiles( )
-    ! radiators = tuvx%create_radiators( )
-
-    ! update conditions for each time step
     grid => grids%get( "height", "km", error )
-    ! ASSERT( error%is_success() )
+    ASSERT( error%is_success() )
 
     call grid%set_edges( edges, error )
     ASSERT( error%is_success() )
 
     call grid%set_midpoints( midpoints, error )
     ASSERT( error%is_success() )
 
-    ! profile => profiles%get( "O3", "mol m-3" )
-
-    ! call tuvx%solve( grids, profiles, radiators, photo_rates )
-
     deallocate( tuvx )
     deallocate( grid )
 

fortran/tuvx.F90

@@ -18,7 +18,7 @@ module musica_tuvx
       function create_tuvx_c(config_path, error) bind(C, name="CreateTuvx")
          use musica_util, only: error_t_c
          import c_ptr, c_int, c_char
-         character(kind=c_char), intent(in) :: config_path(*)
+         character(len=1, kind=c_char), intent(in) :: config_path(*)
          type(error_t_c), intent(inout)     :: error
          type(c_ptr)                        :: create_tuvx_c
       end function create_tuvx_c

include/musica/component_versions.hpp

@@ -1,7 +1,5 @@
-/* Copyright (C) 2023-2024 National Center for Atmospheric Research
- *
- * SPDX-License-Identifier: Apache-2.0
- */
+// Copyright (C) 2023-2024 National Center for Atmospheric Research
+// SPDX-License-Identifier: Apache-2.0
 #pragma once
 
 #ifdef __cplusplus

include/musica/micm.hpp

@@ -1,20 +1,18 @@
-/* Copyright (C) 2023-2024 National Center for Atmospheric Research
- *
- * SPDX-License-Identifier: Apache-2.0
- *
- * This file contains the defintion of the MICM class, which represents a multi-component reactive transport model.
- * It also includes functions for creating and deleting MICM instances with c bindings.
- */
+// Copyright (C) 2023-2024 National Center for Atmospheric Research
+// SPDX-License-Identifier: Apache-2.0
+//
+// This file contains the defintion of the MICM class, which represents a multi-component reactive transport model.
+// It also includes functions for creating and deleting MICM instances with c bindings.
 #pragma once
 
 #include <musica/util.hpp>
 
 #include <micm/configure/solver_config.hpp>
+#include <micm/process/process_set.hpp>
 #include <micm/solver/rosenbrock.hpp>
 #include <micm/solver/rosenbrock_solver_parameters.hpp>
 #include <micm/solver/solver.hpp>
 #include <micm/util/matrix.hpp>
-#include <micm/process/process_set.hpp>
 
 #include <memory>
 #include <string>
@@ -130,7 +128,8 @@ namespace musica
    private:
     using DenseMatrixPolicy = micm::Matrix<double>;
     using SparseMatrixPolicy = micm::SparseMatrix<double, micm::SparseMatrixStandardOrdering>;
-    using SolverPolicy = typename micm::RosenbrockSolverParameters::template SolverType<micm::ProcessSet, micm::LinearSolver<SparseMatrixPolicy, micm::LuDecomposition>>;
+    using SolverPolicy = typename micm::RosenbrockSolverParameters::
+        template SolverType<micm::ProcessSet, micm::LinearSolver<SparseMatrixPolicy, micm::LuDecomposition>>;
     using Rosenbrock = micm::Solver<SolverPolicy, micm::State<DenseMatrixPolicy, SparseMatrixPolicy>>;
 
     std::unique_ptr<Rosenbrock> solver_;

include/musica/tuvx.hpp

@@ -1,10 +1,8 @@
-/* Copyright (C) 2023-2024 National Center for Atmospheric Research
- *
- * SPDX-License-Identifier: Apache-2.0
- *
- * This file contains the defintion of the TUVX class, which represents a photolysis calculator.
- * It also includes functions for creating and deleting TUVX instances with c binding.
- */
+// Copyright (C) 2023-2024 National Center for Atmospheric Research
+// SPDX-License-Identifier: Apache-2.0
+//
+// This file contains the defintion of the TUVX class, which represents a photolysis calculator.
+// It also includes functions for creating and deleting TUVX instances with c binding.
 #pragma once
 
 #include <musica/util.hpp>
@@ -82,10 +80,16 @@ namespace musica
     // for use by musica interanlly. If tuvx ever gets rewritten in C++, these functions will
     // go away but the C API will remain the same and downstream projects (like CAM-SIMA) will
     // not need to change
-    void *InternalCreateTuvx(const char* config_path, std::size_t config_path_length, int *error_code);
+    void *InternalCreateTuvx(const char *config_path, std::size_t config_path_length, int *error_code);
     void InternalDeleteTuvx(void *tuvx, int *error_code);
     void *InternalGetGridMap(void *tuvx, int *error_code);
-    void *InternalGetGrid(void *grid_map, const char* grid_name, std::size_t grid_name_length, const char* grid_units, std::size_t grid_units_length, int *error_code);
+    void *InternalGetGrid(
+        void *grid_map,
+        const char *grid_name,
+        std::size_t grid_name_length,
+        const char *grid_units,
+        std::size_t grid_units_length,
+        int *error_code);
     void InternalDeleteGrid(void *grid, int *error_code);
     void InternalSetEdges(void *grid, double edges[], std::size_t num_edges, int *error_code);
     void InternalSetMidpoints(void *grid, double midpoints[], std::size_t num_midpoints, int *error_code);
@@ -99,11 +103,10 @@ namespace musica
    public:
     TUVX();
 
-    /// @brief Create an instance ove tuvx from a configuration file
+    /// @brief Create an instance of tuvx from a configuration file
     /// @param config_path Path to configuration file or directory containing configuration file
     /// @param error Error struct to indicate success or failure
-    /// @return 0 on success, 1 on failure in parsing configuration file
-    void Create(const char* config_path, Error *error);
+    void Create(const char *config_path, Error *error);
 
     /// @brief Create a grid map. For now, this calls the interal tuvx fortran api, but will allow the change to c++ later on
     /// to be transparent to downstream projects

include/musica/util.hpp

@@ -1,7 +1,5 @@
-/* Copyright (C) 2023-2024 National Center for Atmospheric Research
- *
- * SPDX-License-Identifier: Apache-2.0
- */
+// Copyright (C) 2023-2024 National Center for Atmospheric Research
+// SPDX-License-Identifier: Apache-2.0
 #pragma once
 
 #include <cstddef>

include/musica/version.hpp

@@ -1,7 +1,5 @@
-/* Copyright (C) 2023-2024 National Center for Atmospheric Research
- *
- * SPDX-License-Identifier: Apache-2.0
- */
+// Copyright (C) 2023-2024 National Center for Atmospheric Research
+// SPDX-License-Identifier: Apache-2.0
 #pragma once
 
 #ifdef __cplusplus