Add support for YAML input. (#322)

* Convert YAML to JSON

* Fix YAML CMake

* Add YAML to JSON to main

CMakeLists.txt

@@ -256,6 +256,10 @@ target_link_libraries(polyfem PUBLIC Glob::Glob)
 include(units)
 target_link_libraries(polyfem PUBLIC units::units)
 
+# YAML library
+include(yaml)
+target_link_libraries(polyfem PUBLIC yaml-cpp::yaml-cpp)
+
 # FCPW
 # include(fcpw)
 # target_link_libraries(polyfem PUBLIC fcpw::fcpw)

cmake/recipes/yaml.cmake

@@ -0,0 +1,11 @@
+# yaml-cpp (https://github.com/jbeder/yaml-cpp)
+# License: MIT
+
+if(TARGET yaml-cpp::yaml-cpp)
+    return()
+endif()
+
+message(STATUS "Third-party: creating target 'yaml-cpp::yaml-cpp'")
+
+include(CPM)
+CPMAddPackage("gh:jbeder/yaml-cpp#0.8.0")

src/polyfem/io/CMakeLists.txt

@@ -1,4 +1,6 @@
 set(SOURCES
+	Evaluator.cpp
+	Evaluator.hpp
 	MatrixIO.cpp
 	MatrixIO.hpp
 	MshReader.cpp
@@ -9,8 +11,10 @@ set(SOURCES
 	OBJReader.hpp
 	OBJWriter.cpp
 	OBJWriter.hpp
-	Evaluator.cpp
 	OutData.cpp
+	OutData.hpp
+	YamlToJson.cpp
+	YamlToJson.hpp
 )
 
 source_group(TREE "${CMAKE_CURRENT_SOURCE_DIR}" PREFIX "Source Files" FILES ${SOURCES})

src/polyfem/io/YamlToJson.cpp

@@ -0,0 +1,67 @@
+// Original source code from https://github.com/mircodezorzi/tojson (MIT License)
+
+#include "YamlToJson.hpp"
+
+#include <yaml-cpp/yaml.h>
+
+namespace polyfem::io
+{
+	namespace
+	{
+		inline nlohmann::json parse_scalar(const YAML::Node &node)
+		{
+			int i;
+			double d;
+			bool b;
+			std::string s;
+
+			if (YAML::convert<int>::decode(node, i))
+				return i;
+			if (YAML::convert<double>::decode(node, d))
+				return d;
+			if (YAML::convert<bool>::decode(node, b))
+				return b;
+			if (YAML::convert<std::string>::decode(node, s))
+				return s;
+
+			return nullptr;
+		}
+
+		/// @todo refactor and pass nlohmann::json down by reference instead of returning it
+		inline nlohmann::json yaml_to_json(const YAML::Node &root)
+		{
+			nlohmann::json j{};
+
+			switch (root.Type())
+			{
+			case YAML::NodeType::Null:
+				break;
+			case YAML::NodeType::Scalar:
+				return parse_scalar(root);
+			case YAML::NodeType::Sequence:
+				for (auto &&node : root)
+					j.emplace_back(yaml_to_json(node));
+				break;
+			case YAML::NodeType::Map:
+				for (auto &&it : root)
+					j[it.first.as<std::string>()] = yaml_to_json(it.second);
+				break;
+			default:
+				break;
+			}
+			return j;
+		}
+	} // namespace
+
+	json yaml_string_to_json(const std::string &yaml_str)
+	{
+		YAML::Node root = YAML::Load(yaml_str);
+		return yaml_to_json(root);
+	}
+
+	json yaml_file_to_json(const std::string &yaml_filepath)
+	{
+		YAML::Node root = YAML::LoadFile(yaml_filepath);
+		return yaml_to_json(root);
+	}
+} // namespace polyfem::io

src/polyfem/io/YamlToJson.hpp

@@ -0,0 +1,12 @@
+#pragma once
+
+#include <polyfem/Common.hpp>
+
+namespace polyfem::io
+{
+	/// @brief Convert YAML string to JSON.
+	json yaml_string_to_json(const std::string &yaml_str);
+
+	/// @brief Load a YAML file to JSON.
+	json yaml_file_to_json(const std::string &yaml_filepath);
+} // namespace polyfem::io

src/polyfem/main.cpp

@@ -9,6 +9,7 @@
 
 #include <polyfem/utils/JSONUtils.hpp>
 #include <polyfem/utils/Logger.hpp>
+#include <polyfem/io/YamlToJson.hpp>
 
 using namespace polyfem;
 using namespace solver;
@@ -37,17 +38,32 @@ bool load_json(const std::string &json_file, json &out)
 	return true;
 }
 
+bool load_yaml(const std::string &yaml_file, json &out)
+{
+	try
+	{
+		out = io::yaml_file_to_json(yaml_file);
+		if (!out.contains("root_path"))
+			out["root_path"] = yaml_file;
+	}
+	catch (...)
+	{
+		return false;
+	}
+	return true;
+}
+
 int forward_simulation(const CLI::App &command_line,
 					   const std::string &hdf5_file,
 					   const std::string output_dir,
-					   const size_t max_threads,
+					   const unsigned max_threads,
 					   const bool is_strict,
 					   const bool fallback_solver,
 					   const spdlog::level::level_enum &log_level,
 					   json &in_args);
 
 int optimization_simulation(const CLI::App &command_line,
-							const size_t max_threads,
+							const unsigned max_threads,
 							const bool is_strict,
 							const spdlog::level::level_enum &log_level,
 							json &opt_args);
@@ -62,14 +78,21 @@ int main(int argc, char **argv)
 	command_line.ignore_underscore();
 
 	// Eigen::setNbThreads(1);
-	size_t max_threads = std::numeric_limits<size_t>::max();
+	unsigned max_threads = std::numeric_limits<unsigned>::max();
 	command_line.add_option("--max_threads", max_threads, "Maximum number of threads");
 
+	auto input = command_line.add_option_group("input");
+
 	std::string json_file = "";
-	command_line.add_option("-j,--json", json_file, "Simulation JSON file")->check(CLI::ExistingFile);
+	input->add_option("-j,--json", json_file, "Simulation JSON file")->check(CLI::ExistingFile);
+
+	std::string yaml_file = "";
+	input->add_option("-y,--yaml", yaml_file, "Simulation YAML file")->check(CLI::ExistingFile);
 
 	std::string hdf5_file = "";
-	command_line.add_option("--hdf5", hdf5_file, "Simulation hdf5 file")->check(CLI::ExistingFile);
+	input->add_option("--hdf5", hdf5_file, "Simulation HDF5 file")->check(CLI::ExistingFile);
+
+	input->require_option(1);
 
 	std::string output_dir = "";
 	command_line.add_option("-o,--output_dir", output_dir, "Directory for output files")->check(CLI::ExistingDirectory | CLI::NonexistentPath);
@@ -78,7 +101,7 @@ int main(int argc, char **argv)
 	command_line.add_flag("-s,--strict_validation,!--ns,!--no_strict_validation", is_strict, "Disables strict validation of input JSON");
 
 	bool fallback_solver = false;
-	command_line.add_flag("--enable_overwrite_solver", fallback_solver, "If solver in json is not present, falls back to default");
+	command_line.add_flag("--enable_overwrite_solver", fallback_solver, "If solver in input is not present, falls back to default.");
 
 	const std::vector<std::pair<std::string, spdlog::level::level_enum>>
 		SPDLOG_LEVEL_NAMES_TO_LEVELS = {
@@ -97,9 +120,9 @@ int main(int argc, char **argv)
 
 	json in_args = json({});
 
-	if (!json_file.empty())
+	if (!json_file.empty() || !yaml_file.empty())
 	{
-		const bool ok = load_json(json_file, in_args);
+		const bool ok = !json_file.empty() ? load_json(json_file, in_args) : load_yaml(yaml_file, in_args);
 
 		if (!ok)
 			log_and_throw_error(fmt::format("unable to open {} file", json_file));
@@ -118,7 +141,7 @@ int main(int argc, char **argv)
 int forward_simulation(const CLI::App &command_line,
 					   const std::string &hdf5_file,
 					   const std::string output_dir,
-					   const size_t max_threads,
+					   const unsigned max_threads,
 					   const bool is_strict,
 					   const bool fallback_solver,
 					   const spdlog::level::level_enum &log_level,
@@ -148,7 +171,7 @@ int forward_simulation(const CLI::App &command_line,
 		cells.resize(names.size());
 		vertices.resize(names.size());
 
-		for (size_t i = 0; i < names.size(); ++i)
+		for (int i = 0; i < names.size(); ++i)
 		{
 			const std::string &name = names[i];
 			cells[i] = file.readDataset<MatrixXl>("/meshes/" + name + "/c").cast<int>();
@@ -202,7 +225,7 @@ int forward_simulation(const CLI::App &command_line,
 }
 
 int optimization_simulation(const CLI::App &command_line,
-							const size_t max_threads,
+							const unsigned max_threads,
 							const bool is_strict,
 							const spdlog::level::level_enum &log_level,
 							json &opt_args)