refactor(serif): refactored entire codebase into serif and sub namespaces

src/probe/private/probe.cpp

@@ -42,7 +42,7 @@
 #include "warning_control.h"
 
 
-namespace Probe {
+namespace serif::probe {
 
 void pause() {
   std::cout << "Execution paused. Please press enter to continue..."
@@ -56,7 +56,7 @@ void wait(int seconds) {
 
 void glVisView(mfem::GridFunction& u, mfem::Mesh& mesh,
                const std::string& windowTitle, const std::string& keyset) {
-  Config& config = Config::getInstance();
+  serif::config::Config& config = serif::config::Config::getInstance();
   quill::Logger* logger = LogManager::getInstance().getLogger("log");
   if (config.get<bool>("Probe:GLVis:Visualization", true)) {
     std::string usedKeyset;
@@ -108,8 +108,8 @@ double getMeshRadius(mfem::Mesh& mesh) {
 std::pair<std::vector<double>, std::vector<double>> getRaySolution(mfem::GridFunction& u, mfem::Mesh& mesh,
                                    const std::vector<double>& rayDirection,
                                    int numSamples, std::string filename) {
-  Config& config = Config::getInstance();
-  Probe::LogManager& logManager = Probe::LogManager::getInstance();
+  serif::config::Config& config = serif::config::Config::getInstance();
+  serif::probe::LogManager& logManager = serif::probe::LogManager::getInstance();
   quill::Logger* logger = logManager.getLogger("log");
   LOG_INFO(logger, "Getting ray solution...");
   // Check if the directory to write to exists
@@ -204,7 +204,7 @@ std::pair<std::vector<double>, std::vector<double>> getRaySolution(mfem::Vector
 }
 
 LogManager::LogManager() {
-  Config& config = Config::getInstance();
+  serif::config::Config& config = serif::config::Config::getInstance();
   quill::Backend::start();
   auto CLILogger = quill::Frontend::create_or_get_logger(
       "root",

src/probe/public/probe.h

@@ -32,7 +32,7 @@
 /**
  * @brief The Probe namespace contains utility functions for debugging and logging.
  */
-namespace Probe {
+namespace serif::probe {
   /**
    * @brief Pause the execution and wait for user input.
    */