Merge pull request SimVascular#45 from mrp089/refactor_patch

Refactoring .hpp -> .h, .cpp and remove class templates

.github/workflows/codechecks.yml

@@ -12,4 +12,4 @@ jobs:
  - name: Run clang-format
  run: |
  cd src
- find **/*.hpp **/*.cpp | xargs clang-format --dry-run --style=Google --Werror
+ find **/*.h **/*.cpp | xargs clang-format --dry-run --style=Google --Werror

CMakeLists.txt

@@ -1,10 +1,41 @@
+# Copyright (c) Stanford University, The Regents of the University of
+# California, and others.
+#
+# All Rights Reserved.
+#
+# See Copyright-SimVascular.txt for additional details.
+#
+# Permission is hereby granted, free of charge, to any person obtaining
+# a copy of this software and associated documentation files (the
+# "Software"), to deal in the Software without restriction, including
+# without limitation the rights to use, copy, modify, merge, publish,
+# distribute, sublicense, and/or sell copies of the Software, and to
+# permit persons to whom the Software is furnished to do so, subject
+# to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included
+# in all copies or substantial portions of the Software.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
 cmake_minimum_required(VERSION 3.22)
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED True)
+
 project(svZeroDSolver)
+
 include(FetchContent)
 
-# -----------------------------------------------------------------------------
 # Enable code coverage
 # -----------------------------------------------------------------------------
 set(ENABLE_COVERAGE OFF CACHE BOOL "Enable code coverage")
@@ -26,30 +57,51 @@ if(ENABLE_COVERAGE)
  WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
 endif()
 
+# -----------------------------------------------------------------------------
+# Set the location to store the binaries and libraries created by this project.
+# -----------------------------------------------------------------------------
+#
+#set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+#set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+#set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
+
+# Need to add the -fPIC flag to build the interface shared library.
+if(CMAKE_CXX_COMPILER_ID MATCHES "GNU")
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC")
+endif()
+
 # -----------------------------------------------------------------------------
 # Fetch Eigen
 # -----------------------------------------------------------------------------
+# Eigen is a header-only C++ template library for linear algebra.
+#
 FetchContent_Declare(
  Eigen
  GIT_REPOSITORY https://gitlab.com/libeigen/eigen.git
  GIT_TAG master
  GIT_SHALLOW TRUE
  GIT_PROGRESS TRUE)
+
 set(EIGEN_BUILD_DOC OFF)
 set(BUILD_TESTING OFF)
 set(EIGEN_BUILD_PKGCONFIG OFF)
 set( OFF)
+
 FetchContent_MakeAvailable(Eigen)
 
 # -----------------------------------------------------------------------------
 # Fetch pybind11
 # -----------------------------------------------------------------------------
+# pybind11 is a library used to create Python bindings of existing C++ code.
+#
 FetchContent_Declare(
  pybind11
  GIT_REPOSITORY https://github.com/pybind/pybind11
  GIT_TAG master
 )
+
 FetchContent_GetProperties(pybind11)
+
 if(NOT pybind11_POPULATED)
  FetchContent_Populate(pybind11)
  add_subdirectory(${pybind11_SOURCE_DIR} ${pybind11_BINARY_DIR})
@@ -58,38 +110,101 @@ endif()
 # -----------------------------------------------------------------------------
 # Fetch nlohmann/json
 # -----------------------------------------------------------------------------
+# This is a C++ header-only library for reading JSON files.
+#
 FetchContent_Declare(
  json
  URL https://github.com/nlohmann/json/releases/download/v3.11.2/json.tar.xz
 )
+
 FetchContent_MakeAvailable(json)
 
 # -----------------------------------------------------------------------------
 # Fetch pybind11_json
 # -----------------------------------------------------------------------------
+# pybind11_json is an nlohmann::json to pybind11 bridge that converts 
+# between nlohmann::json and py::object objects. 
+#
 FetchContent_Declare(
  pybind11_json
  GIT_REPOSITORY https://github.com/pybind/pybind11_json.git
  GIT_TAG master
 )
+
 FetchContent_MakeAvailable(pybind11_json)
 
 # -----------------------------------------------------------------------------
-# Set executable and python library
+# Set executables for each application.
+# -----------------------------------------------------------------------------
+# There are two executables
+# 1) svzerodsolver
+# 2) svzerodcalibrator 
+#
+add_executable(svzerodsolver applications/svzerodsolver.cpp 
+ $<TARGET_OBJECTS:svzero_algebra_library> 
+ $<TARGET_OBJECTS:svzero_model_library> 
+ $<TARGET_OBJECTS:svzero_solve_library> 
+)
+
+add_executable(svzerodcalibrator applications/svzerodcalibrator.cpp
+ $<TARGET_OBJECTS:svzero_optimize_library> 
+ $<TARGET_OBJECTS:svzero_model_library> 
+)
+
+# -----------------------------------------------------------------------------
+# Setup building of the svzerodplus Python extension module.
 # -----------------------------------------------------------------------------
-include_directories(src)
-add_executable(svzerodsolver applications/svzerodsolver.cpp)
-add_executable(svzerodcalibrator applications/svzerodcalibrator.cpp)
 pybind11_add_module(svzerodplus EXCLUDE_FROM_ALL applications/svzerodplus.cpp)
+
+# -----------------------------------------------------------------------------
+# Add source sub-directories.
+# -----------------------------------------------------------------------------
+add_subdirectory("src/algebra")
 add_subdirectory("src/interface")
+add_subdirectory("src/model")
+add_subdirectory("src/optimize")
+add_subdirectory("src/solve")
 
 # -----------------------------------------------------------------------------
-# Link libraries
+# Set header file include directories.
 # -----------------------------------------------------------------------------
+#
+target_include_directories(svzerodsolver PUBLIC
+ ${CMAKE_SOURCE_DIR}/src/algebra
+ ${CMAKE_SOURCE_DIR}/src/model
+ ${CMAKE_SOURCE_DIR}/src/solve
+)
+
+target_include_directories(svzerodcalibrator PUBLIC 
+ ${CMAKE_SOURCE_DIR}/src/algebra
+ ${CMAKE_SOURCE_DIR}/src/model 
+ ${CMAKE_SOURCE_DIR}/src/optimize
+ ${CMAKE_SOURCE_DIR}/src/solve 
+)
+
+target_include_directories(svzerodplus PUBLIC 
+ ${CMAKE_SOURCE_DIR}/src/algebra
+ ${CMAKE_SOURCE_DIR}/src/model 
+ ${CMAKE_SOURCE_DIR}/src/optimize
+ ${CMAKE_SOURCE_DIR}/src/solve 
+)
+
+# -----------------------------------------------------------------------------
+# Set the libraries each application needs to link to.
+# -----------------------------------------------------------------------------
+# These are needed only for the header-only applications.
+#
 target_link_libraries(svzerodsolver PRIVATE Eigen3::Eigen)
 target_link_libraries(svzerodsolver PRIVATE nlohmann_json::nlohmann_json)
+
 target_link_libraries(svzerodcalibrator PRIVATE Eigen3::Eigen)
 target_link_libraries(svzerodcalibrator PRIVATE nlohmann_json::nlohmann_json)
+
 target_link_libraries(svzerodplus PRIVATE Eigen3::Eigen)
 target_link_libraries(svzerodplus PRIVATE nlohmann_json::nlohmann_json)
 target_link_libraries(svzerodplus PRIVATE pybind11_json)
+target_link_libraries(svzerodplus PRIVATE svzero_algebra_library)
+target_link_libraries(svzerodplus PRIVATE svzero_model_library)
+target_link_libraries(svzerodplus PRIVATE svzero_optimize_library)
+target_link_libraries(svzerodplus PRIVATE svzero_solve_library)
+

applications/svzerodcalibrator.cpp

@@ -31,10 +31,9 @@
  * @file svzerodcalibrator.cpp
  * @brief Main routine for svZeroDCalibrator
  */
-#include "optimize/calibrate.hpp"
+#include "calibrate.h"
 
 // Setting scalar type to double
-typedef double T;
 
 int main(int argc, char* argv[]) {
  DEBUG_MSG("Starting svZeroDCalibrator");
@@ -56,7 +55,7 @@ int main(int argc, char* argv[]) {
  std::ifstream ifs(input_file);
  const auto& config = nlohmann::json::parse(ifs);
 
- auto output_config = OPT::calibrate<T>(config);
+ auto output_config = optimize::calibrate(config);
 
  // Write optimized simulation config
  std::ofstream o(output_file);

applications/svzerodplus.cpp

@@ -36,14 +36,14 @@
 #include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
 
-#include "optimize/calibrate.hpp"
+#include "Solver.h"
+#include "calibrate.h"
 #include "pybind11_json/pybind11_json.hpp"
-#include "solve/solver.hpp"
 
 namespace py = pybind11;
 
 PYBIND11_MODULE(svzerodplus, m) {
- using Solver = SOLVE::Solver<double>;
+ using Solver = solve::Solver;
  py::class_<Solver>(m, "Solver")
  .def(py::init([](py::dict& config) {
  const nlohmann::json& config_json = config;
@@ -83,7 +83,7 @@ PYBIND11_MODULE(svzerodplus, m) {
  });
  m.def("calibrate", [](py::dict& config) {
  const nlohmann::json& config_json = config;
- return OPT::calibrate<double>(config);
+ return optimize::calibrate(config);
  });
  m.def("run_simulation_cli", []() {
  py::module_ sys = py::module_::import("sys");
@@ -96,7 +96,7 @@ PYBIND11_MODULE(svzerodplus, m) {
  }
  std::ifstream ifs(argv[1]);
  const auto& config = nlohmann::json::parse(ifs);
- auto solver = SOLVE::Solver<double>(config);
+ auto solver = solve::Solver(config);
  solver.run();
  solver.write_result_to_csv(argv[2]);
  });
@@ -111,7 +111,7 @@ PYBIND11_MODULE(svzerodplus, m) {
  }
  std::ifstream ifs(argv[1]);
  const auto& config = nlohmann::json::parse(ifs);
- auto output_config = OPT::calibrate<double>(config);
+ auto output_config = optimize::calibrate(config);
  std::ofstream o(argv[2]);
  o << std::setw(4) << output_config << std::endl;
  });

applications/svzerodsolver.cpp

@@ -31,7 +31,9 @@
  * @file svzerodsolver.cpp
  * @brief Main routine of svZeroDSolver
  */
-#include "solve/solver.hpp"
+#include <fstream>
+
+#include "Solver.h"
 
 /**
  *
@@ -59,26 +61,31 @@ int main(int argc, char* argv[]) {
  "Usage: svzerodsolver path/to/config.json "
  "(optional:path/to/output.csv)");
  }
+
  std::string input_file = argv[1];
  std::string output_file;
+
  if (argc == 3) {
  output_file = argv[2];
+
  } else {
  // If output file is not provided, default is <path to .json>+"output.csv"
+
  std::size_t end_of_path = input_file.rfind("/");
  if (end_of_path == std::string::npos) {
  end_of_path = input_file.rfind("\\"); // For Windows paths (?)
  if (end_of_path == std::string::npos) {
  std::runtime_error("Could not find path to .json file.");
  }
  }
+
  output_file = input_file.substr(0, end_of_path) + "output.csv";
  }
 
  std::ifstream ifs(input_file);
  const auto& config = nlohmann::json::parse(ifs);
 
- auto solver = SOLVE::Solver<double>(config);
+ auto solver = solve::Solver(config);
  solver.run();
  solver.write_result_to_csv(output_file);
 

docs/Doxyfile

@@ -109,7 +109,7 @@ INPUT = "src" \
  "docs/pages"
 INPUT_ENCODING = UTF-8
 FILE_PATTERNS = *.cpp \
- *.hpp \
+ *.h \
  *.inc \
  *.markdown \
  *.md \
@@ -122,7 +122,7 @@ EXCLUDE_SYMBOLS =
 EXAMPLE_PATH = 
 EXAMPLE_PATTERNS = *
 EXAMPLE_RECURSIVE = NO
-IMAGE_PATH = images
+IMAGE_PATH = "docs"
 INPUT_FILTER =
 FILTER_PATTERNS =
 FILTER_SOURCE_FILES = NO
@@ -159,7 +159,6 @@ HTML_EXTRA_FILES =
 HTML_COLORSTYLE_HUE = 220
 HTML_COLORSTYLE_SAT = 100
 HTML_COLORSTYLE_GAMMA = 80
-HTML_TIMESTAMP = YES
 HTML_DYNAMIC_SECTIONS = NO
 HTML_INDEX_NUM_ENTRIES = 100
 GENERATE_DOCSET = NO

docs/pages/developer_guide.md

@@ -44,15 +44,15 @@ comment to format all your files:
 
 ```bash
 cd src
-find **/*.hpp **/*.cpp | xargs clang-format -i --style=Google
+find **/*.h **/*.cpp | xargs clang-format -i --style=Google
 ```
 
 You can also just check **if** a file would be formatted without actually formatting
 it with:
 
 ```bash
 cd src
-find **/*.hpp **/*.cpp | xargs clang-format --dry-run --style=Google --Werror
+find **/*.h **/*.cpp | xargs clang-format --dry-run --style=Google --Werror
 ```
 
 The latter check is also performed in the GitHub CI/CD (a.k.a. Actions) and