make all C++ headers self contained and add a CMake check to ensure it remains this way. closes #25

CMakeLists.txt

@@ -44,7 +44,8 @@ set(PyPartMC_sources
   pypartmc.cpp gimmicks.cpp fake_netcdf.cpp fake_spec_file.cpp sys.cpp
   run_part.F90 run_part_opt.F90 util.F90 aero_data.F90 aero_state.F90 env_state.F90 gas_data.F90 
   gas_state.F90 scenario.F90 condense.F90 aero_particle.F90 bin_grid.F90
-  camp_core.F90 photolysis.F90 aero_mode.F90 aero_dist.F90
+  camp_core.F90 photolysis.F90 aero_mode.F90 aero_dist.F90 bin_grid.cpp condense.cpp run_part.cpp
+  scenario.cpp util.cpp
 )
 add_prefix(src/ PyPartMC_sources)
 
@@ -291,12 +292,13 @@ target_link_libraries(partmclib PRIVATE klulib)
 add_subdirectory(gitmodules/pybind11)
 pybind11_add_module(_PyPartMC ${PyPartMC_sources})
 add_dependencies(_PyPartMC partmclib)
-target_include_directories(_PyPartMC PRIVATE 
-  ${CMAKE_SOURCE_DIR}/gitmodules/json/include 
-  ${CMAKE_SOURCE_DIR}/gitmodules/pybind11_json/include
-  ${CMAKE_SOURCE_DIR}/gitmodules/span/include
-  ${CMAKE_SOURCE_DIR}/gitmodules/string_view-standalone/include
+set(PYPARTMC_INCLUDE_DIRS 
+  "${CMAKE_SOURCE_DIR}/gitmodules/json/include;"
+  "${CMAKE_SOURCE_DIR}/gitmodules/pybind11_json/include;"
+  "${CMAKE_SOURCE_DIR}/gitmodules/span/include;"
+  "${CMAKE_SOURCE_DIR}/gitmodules/string_view-standalone/include;"
 )
+target_include_directories(_PyPartMC PRIVATE ${PYPARTMC_INCLUDE_DIRS})
 target_compile_definitions(_PyPartMC PRIVATE VERSION_INFO=${VERSION_INFO})
 target_link_libraries(_PyPartMC PRIVATE partmclib)
 if (APPLE)
@@ -319,3 +321,24 @@ foreach(target _PyPartMC)
   )
 endforeach()
 
+include(CheckCXXSourceCompiles)
+file(GLOB PyPartMC_headers ${CMAKE_SOURCE_DIR}/src/*.hpp)
+if (NOT "${CMAKE_REQUIRED_INCLUDES}" STREQUAL "")
+  message("CMAKE_REQUIRED_INCLUDES not empty! (${CMAKE_REQUIRED_INCLUDES})")
+endif()
+foreach(file ${PyPartMC_headers})
+  set(CMAKE_REQUIRED_INCLUDES "${PYPARTMC_INCLUDE_DIRS};${pybind11_INCLUDE_DIRS}")
+  check_cxx_source_compiles("
+      // https://github.com/nlohmann/json/issues/1408
+      #define HAVE_SNPRINTF 
+      #include \"${file}\"
+      int main() { return 0;}
+    "
+    _header_self_contained_${file}
+  )
+  unset(CMAKE_REQUIRED_INCLUDES)
+  if (NOT _header_self_contained_${file})
+    message(SEND_ERROR "non-self-contained header: ${file}")
+  endif()
+endforeach()
+

src/aero_mode.hpp

@@ -8,6 +8,8 @@
 
 #include "pmc_resource.hpp"
 #include "pybind11/stl.h"
+#include "aero_data.hpp"
+#include "bin_grid.hpp"
 
 extern "C" void f_aero_mode_ctor(
     void *ptr

src/bin_grid.cpp

@@ -0,0 +1,72 @@
+/*##################################################################################################
+# This file is a part of PyPartMC licensed under the GNU General Public License v3 (LICENSE file)  #
+# Copyright (C) 2022 University of Illinois Urbana-Champaign                                       #
+# Authors: https://github.com/open-atmos/PyPartMC/graphs/contributors                              #
+##################################################################################################*/
+
+#include "bin_grid.hpp"
+
+std::valarray<double> histogram_1d(
+    const BinGrid &bin_grid,
+    std::valarray<double> values,
+    std::valarray<double> weights
+) {
+    int len;
+    f_bin_grid_size(
+        bin_grid.ptr.f_arg(),
+        &len
+    );
+    int data_size = values.size();
+    std::valarray<double> data(len);
+    f_bin_grid_histogram_1d(
+        bin_grid.ptr.f_arg(),
+        begin(values),
+        begin(weights),
+        &data_size,
+        begin(data),
+        &len
+    );
+
+    return data;
+}
+
+std::vector<std::vector<double>> histogram_2d(
+    const BinGrid &x_bin_grid,
+    std::valarray<double> x_values,
+    const BinGrid &y_bin_grid,
+    std::valarray<double> y_values,
+    std::valarray<double> weights
+) {
+    int x_len;
+    f_bin_grid_size(x_bin_grid.ptr.f_arg(), &x_len);
+
+    int y_len;
+    f_bin_grid_size(y_bin_grid.ptr.f_arg(), &y_len);
+
+    const int data_size = x_values.size();
+
+    std::vector<std::vector<double>> data(
+        x_len,
+        std::vector<double>(y_len, 0)
+    );
+    std::valarray<double> data_flat(x_len * y_len);
+    f_bin_grid_histogram_2d(
+        x_bin_grid.ptr.f_arg(),
+        begin(x_values),
+        y_bin_grid.ptr.f_arg(),
+        begin(y_values),
+        begin(weights),
+        &data_size, 
+        begin(data_flat),
+        &x_len,
+        &y_len
+    );
+
+    for(int i = 0; i < x_len; i++) {
+        for(int j = 0; j < y_len; j++) {
+            data[i][j] = data_flat[i*y_len + j];
+        }
+    }
+
+    return data;
+}

src/bin_grid.hpp

@@ -117,67 +117,16 @@ struct BinGrid {
     }
 };
 
-auto histogram_1d(
+std::valarray<double> histogram_1d(
     const BinGrid &bin_grid,
     std::valarray<double> values,
     std::valarray<double> weights
-) {
-    int len;
-    f_bin_grid_size(
-        bin_grid.ptr.f_arg(),
-        &len
-    );
-    int data_size = values.size();
-    std::valarray<double> data(len);
-    f_bin_grid_histogram_1d(
-        bin_grid.ptr.f_arg(),
-        begin(values),
-        begin(weights),
-        &data_size,
-        begin(data),
-        &len
-    );
-
-    return data;
-}
-
-auto histogram_2d(
+);
+
+std::vector<std::vector<double>> histogram_2d(
     const BinGrid &x_bin_grid,
     std::valarray<double> x_values,
     const BinGrid &y_bin_grid,
     std::valarray<double> y_values,
     std::valarray<double> weights
-) {
-    int x_len;
-    f_bin_grid_size(x_bin_grid.ptr.f_arg(), &x_len);
-
-    int y_len;
-    f_bin_grid_size(y_bin_grid.ptr.f_arg(), &y_len);
-
-    const int data_size = x_values.size();
-
-    std::vector<std::vector<double>> data(
-        x_len,
-        std::vector<double>(y_len, 0)
-    );
-    std::valarray<double> data_flat(x_len * y_len);
-    f_bin_grid_histogram_2d(
-        x_bin_grid.ptr.f_arg(),
-        begin(x_values),
-        y_bin_grid.ptr.f_arg(),
-        begin(y_values),
-        begin(weights),
-        &data_size, 
-        begin(data_flat),
-        &x_len,
-        &y_len
-    );
-
-    for(int i = 0; i < x_len; i++) {
-        for(int j = 0; j < y_len; j++) {
-            data[i][j] = data_flat[i*y_len + j];
-        }
-    }
-
-    return data;
-}
+);

src/condense.cpp

@@ -0,0 +1,31 @@
+/*##################################################################################################
+# This file is a part of PyPartMC licensed under the GNU General Public License v3 (LICENSE file)  #
+# Copyright (C) 2022 University of Illinois Urbana-Champaign                                       #
+# Authors: https://github.com/open-atmos/PyPartMC/graphs/contributors                              #
+##################################################################################################*/
+
+#include "condense.hpp"
+
+void condense_equilib_particle(
+    const EnvState &env_state,
+    const AeroData &aero_data,
+    const AeroParticle &aero_particle
+) {
+    f_condense_equilib_particle(
+        env_state.ptr.f_arg(),
+        aero_data.ptr.f_arg(),
+        aero_particle.ptr.f_arg()
+    );
+}
+
+void condense_equilib_particles(
+    const EnvState &env_state,
+    const AeroData &aero_data,
+    const AeroState &aero_state
+) {
+    f_condense_equilib_particles(
+        env_state.ptr.f_arg(),
+        aero_data.ptr.f_arg(),
+        aero_state.ptr.f_arg()
+    );
+}

src/condense.hpp

@@ -26,23 +26,10 @@ void condense_equilib_particle(
     const EnvState &env_state,
     const AeroData &aero_data,
     const AeroParticle &aero_particle
-) {
-    f_condense_equilib_particle(
-        env_state.ptr.f_arg(),
-        aero_data.ptr.f_arg(),
-        aero_particle.ptr.f_arg()
-    );
-}
+);
 
 void condense_equilib_particles(
     const EnvState &env_state,
     const AeroData &aero_data,
     const AeroState &aero_state
-) {
-    f_condense_equilib_particles(
-        env_state.ptr.f_arg(),
-        aero_data.ptr.f_arg(),
-        aero_state.ptr.f_arg()
-    );
-}
-
+);

src/gas_data.hpp

@@ -8,6 +8,8 @@
 
 #include "gimmicks.hpp" // TODO #119: rename to something like json_resource.hpp?
 #include "pmc_resource.hpp"
+#include "pybind11/stl.h"
+#include "pybind11_json/pybind11_json.hpp"
 
 extern "C" void f_gas_data_ctor(void *ptr) noexcept;
 extern "C" void f_gas_data_dtor(void *ptr) noexcept;
@@ -21,7 +23,7 @@ struct GasData {
     PMCResource ptr;
     const nlohmann::json json;
 
-    GasData(const py::tuple &tpl) :
+    GasData(const pybind11::tuple &tpl) :
         ptr(f_gas_data_ctor, f_gas_data_dtor),
         json(tpl)
     {

src/run_part.cpp

@@ -0,0 +1,89 @@
+/*##################################################################################################
+# This file is a part of PyPartMC licensed under the GNU General Public License v3 (LICENSE file)  #
+# Copyright (C) 2022 University of Illinois Urbana-Champaign                                       #
+# Authors: https://github.com/open-atmos/PyPartMC/graphs/contributors                              #
+##################################################################################################*/
+
+#include "run_part.hpp"
+
+void run_part(
+    const Scenario &scenario,
+    EnvState &env_state,
+    const AeroData &aero_data,
+    AeroState &aero_state,
+    const GasData &gas_data,
+    GasState &gas_state,
+    const RunPartOpt &run_part_opt,
+    const CampCore &camp_core,
+    const Photolysis &photolysis
+) {
+    f_run_part(
+        scenario.ptr.f_arg(),
+        env_state.ptr.f_arg_non_const(),
+        aero_data.ptr.f_arg(),
+        aero_state.ptr.f_arg_non_const(),
+        gas_data.ptr.f_arg(),
+        gas_state.ptr.f_arg_non_const(),
+        run_part_opt.ptr.f_arg(),
+        camp_core.ptr.f_arg(),
+        photolysis.ptr.f_arg()
+    );
+}
+
+void run_part_timestep(
+    const Scenario &scenario,
+    EnvState &env_state,
+    const AeroData &aero_data,
+    AeroState &aero_state,
+    const GasData &gas_data,
+    GasState &gas_state,
+    const RunPartOpt &run_part_opt,
+    const CampCore &camp_core,
+    const Photolysis &photolysis,
+    const int &i_time,
+    const double &t_start
+) {
+    f_run_part_timestep(
+        scenario.ptr.f_arg(),
+        env_state.ptr.f_arg_non_const(),
+        aero_data.ptr.f_arg(),
+        aero_state.ptr.f_arg_non_const(),
+        gas_data.ptr.f_arg(),
+        gas_state.ptr.f_arg_non_const(),
+        run_part_opt.ptr.f_arg(),
+        camp_core.ptr.f_arg(),
+        photolysis.ptr.f_arg(),
+        &i_time,
+        &t_start
+    );
+}
+
+void run_part_timeblock(
+    const Scenario &scenario,
+    EnvState &env_state,
+    const AeroData &aero_data,
+    AeroState &aero_state,
+    const GasData &gas_data,
+    GasState &gas_state,
+    const RunPartOpt &run_part_opt,
+    const CampCore &camp_core,
+    const Photolysis &photolysis,
+    const int &i_time,
+    const int &i_next,
+    const double &t_start
+) {
+    f_run_part_timeblock(
+        scenario.ptr.f_arg(),
+        env_state.ptr.f_arg_non_const(),
+        aero_data.ptr.f_arg(),
+        aero_state.ptr.f_arg_non_const(),
+        gas_data.ptr.f_arg(),
+        gas_state.ptr.f_arg_non_const(),
+        run_part_opt.ptr.f_arg(),
+        camp_core.ptr.f_arg(),
+        photolysis.ptr.f_arg(),
+        &i_time,
+        &i_next,
+        &t_start
+    );
+}