fix(clang): fixed a few compiler warnings in clang

Doxyfile

@@ -48,7 +48,7 @@ PROJECT_NAME           = GridFire
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = v0.7.1_rc2
+PROJECT_NUMBER         = v0.7.2_rc2
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewers a

meson.build

@@ -18,7 +18,7 @@
 #   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 #
 # *********************************************************************** #
-project('GridFire', ['c', 'cpp', 'fortran'], version: 'v0.7.1_rc2', default_options: ['cpp_std=c++23'], meson_version: '>=1.5.0')
+project('GridFire', ['c', 'cpp', 'fortran'], version: 'v0.7.2_rc2', default_options: ['cpp_std=c++23'], meson_version: '>=1.5.0')
 
 # Add default visibility for all C++ targets
 add_project_arguments('-fvisibility=default', language: 'cpp')

pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "mesonpy"
 
 [project]
 name = "gridfire"  # Choose your Python package name
-version = "0.7.1_rc2" # Your project's version
+version = "0.7.2_rc2" # Your project's version
 description = "Python interface to the GridFire nuclear network code"
 readme = "README.md"
 license = { file = "LICENSE.txt" } # Reference your license file [cite: 2]

src/lib/engine/engine_graph.cpp

@@ -813,42 +813,7 @@ namespace gridfire::engine {
 
     // --- Generate Stoichiometry Matrix ---
     void GraphEngine::generateStoichiometryMatrix() {
-        LOG_TRACE_L1(m_logger, "Generating stoichiometry matrix...");
+        return; // Deprecated
-
-        // Task 1: Set dimensions and initialize the matrix
-        // size_t numSpecies = m_networkSpecies.size();
-        // size_t numReactions = m_reactions.size();
-        // m_stoichiometryMatrix.resize(numSpecies, numReactions, false);
-
-        LOG_TRACE_L1(m_logger, "Stoichiometry matrix initialized with dimensions: {} rows (species) x {} columns (reactions).",
-                 numSpecies, numReactions);
-
-        // Task 2: Populate the stoichiometry matrix
-        // Iterate through all reactions, assign them a column index, and fill in their stoichiometric coefficients.
-        size_t reactionColumnIndex = 0;
-        for (const auto& reaction : m_reactions) {
-            // Get the net stoichiometry for the current reaction
-            std::unordered_map<fourdst::atomic::Species, int> netStoichiometry = reaction->stoichiometry();
-
-            // Iterate through the species and their coefficients in the stoichiometry map
-            for (const auto& [species, coefficient] : netStoichiometry) {
-                // Find the row index for this species
-                auto it = m_speciesToIndexMap.find(species);
-                if (it != m_speciesToIndexMap.end()) {
-                    // const size_t speciesRowIndex = it->second;
-                    // Set the matrix element. Boost.uBLAS handles sparse insertion.
-                    // m_stoichiometryMatrix(speciesRowIndex, reactionColumnIndex) = coefficient;
-                } else {
-                    // This scenario should ideally not happen if m_networkSpeciesMap and m_speciesToIndexMap are correctly synced
-                    LOG_ERROR(m_logger, "CRITICAL ERROR: Species '{}' from reaction '{}' stoichiometry not found in species to index map.",
-                             species.name(), reaction->id());
-                    m_logger -> flush_log();
-                    throw std::runtime_error("Species not found in species to index map: " + std::string(species.name()));
-                }
-            }
-            reactionColumnIndex++; // Move to the next column for the next reaction
-        }
-
     }
 
     void GraphEngine::setScreeningModel(const screening::ScreeningType model) {

src/python/gridfire/__init__.py

@@ -16,5 +16,5 @@ sys.modules['gridfire.io'] = io
 
 __all__ = ['type', 'utils', 'engine', 'solver', 'exceptions', 'partition', 'reaction', 'screening', 'io', 'policy']
 
-__version__ = "v0.7.1_rc2"
+__version__ = "v0.7.2_rc2"