Auto-format code using Clang-Format, Prettier, autopep8, and JuliaFormatter (#756)

Co-authored-by: GitHub Actions <actions@github.com>

Author: github-actions[bot]

include/musica/micm/parse.hpp

@@ -67,7 +67,9 @@ namespace musica
       bool ignore_non_gas_phases = false);
   Chemistry ParserV1(const mechanism_configuration::ParserResult<>& result);
 
-  mechanism_configuration::v1::types::Mechanism ConvertV0MechanismToV1(const std::string& config_path, bool convert_reaction_units = true);
+  mechanism_configuration::v1::types::Mechanism ConvertV0MechanismToV1(
+      const std::string& config_path,
+      bool convert_reaction_units = true);
   mechanism_configuration::v1::types::Mechanism ConvertV0MechanismToV1(
       const mechanism_configuration::v0::types::Mechanism& v0_mechanism,
       bool convert_reaction_units = true);

python/bindings/mechanism_configuration/mechanism_configuration.cpp

@@ -492,9 +492,11 @@ void bind_mechanism_configuration(py::module_ &mechanism_configuration)
           "parse_and_convert_v0",
           [](V1Parser &self, const std::string &path, bool convert_reaction_units)
           {
-            mechanism_configuration::v1::types::Mechanism mechanism = musica::ConvertV0MechanismToV1(path, convert_reaction_units);
+            mechanism_configuration::v1::types::Mechanism mechanism =
+                musica::ConvertV0MechanismToV1(path, convert_reaction_units);
             return mechanism;
           },
-          py::arg("path"), py::arg("convert_reaction_units") = true,
+          py::arg("path"),
+          py::arg("convert_reaction_units") = true,
           "Parse a v0 mechanism configuration file");
 }

python/musica/examples/ts1_box_model.py

@@ -36,7 +36,8 @@
 initial_concentrations = conditions[conditions['parameter'].str.contains(
     'CONC')]
 # remove CONC. from the parameter names
-initial_concentrations.loc[:, 'parameter'] = initial_concentrations.loc[:, 'parameter'].str.replace('CONC.', '', regex=False)
+initial_concentrations.loc[:, 'parameter'] = initial_concentrations.loc[:,
+                                                                        'parameter'].str.replace('CONC.', '', regex=False)
 
 # grab the environmental conditions, anything prefixed with ENV.
 environmental_conditions = conditions[conditions['parameter'].str.contains('ENV')]
@@ -77,26 +78,26 @@
 times = [0]
 concentrations = [state.get_concentrations()]
 time_step = 30  # seconds
-simulation_length = 1 * 60 * 60 # 1 hour in seconds
+simulation_length = 1 * 60 * 60  # 1 hour in seconds
 current_time = 0
 last_printed_percent = -5  # Track last printed percentage
 
 while current_time < simulation_length:
     elapsed = 0
     while elapsed < time_step:
-      remaining_time = time_step - elapsed
-      result = solver.solve(state, remaining_time)
-      elapsed += result.stats.final_time
-      current_time += result.stats.final_time
-      if result.state != SolverState.Converged:
-        print(f"Solver state: {result.state}, time: {current_time}")
-    
+        remaining_time = time_step - elapsed
+        result = solver.solve(state, remaining_time)
+        elapsed += result.stats.final_time
+        current_time += result.stats.final_time
+        if result.state != SolverState.Converged:
+            print(f"Solver state: {result.state}, time: {current_time}")
+
     # Print progress every 5%
     current_percent = (current_time / simulation_length) * 100
     if int(current_percent // 5) * 5 > last_printed_percent:
         last_printed_percent = int(current_percent // 5) * 5
         print(f"Simulation progress: {last_printed_percent}%")
-      
+
     times.append(current_time)
     concentrations.append(state.get_concentrations())
 

python/musica/main.py

@@ -84,7 +84,7 @@ def convert_configuration(logger, configuration, output_path):
     parser = musica.mechanism_configuration.Parser()
     # the mechanism configuration automatically converts pre exponential factors to SI units
     # so we don't need to convert units again here.
-    convert_units=False
+    convert_units = False
     mechanism = parser.parse_and_convert_v0(configuration, convert_units)
     mechanism.export(output_path)
 

src/micm/convert_v0_to_v1.cpp

@@ -17,7 +17,8 @@ namespace musica
     // remove USER. SURF. PHOTO. from name
     std::string stripped_name = name;
     const std::string prefixes[] = { "USER.", "SURF.", "PHOTO." };
-    for (const auto& prefix : prefixes) {
+    for (const auto& prefix : prefixes)
+    {
       if (stripped_name.find(prefix) == 0)
       {
         stripped_name = stripped_name.substr(prefix.length());
@@ -69,15 +70,18 @@ namespace musica
       const std::vector<mechanism_configuration::v0::types::Species>& v0_species);
 
   mechanism_configuration::v1::types::Reactions convert_reactions_v0_to_v1(
-      const mechanism_configuration::v0::types::Reactions& v0_reactions, bool convert_reaction_units);
+      const mechanism_configuration::v0::types::Reactions& v0_reactions,
+      bool convert_reaction_units);
 
   std::vector<mechanism_configuration::v1::types::ReactionComponent> convert_reaction_components_v0_to_v1(
       const std::vector<mechanism_configuration::v0::types::ReactionComponent>& v0_components);
 
   mechanism_configuration::v1::types::ReactionComponent convert_reaction_component_v0_to_v1(
       const mechanism_configuration::v0::types::ReactionComponent& v0_component);
 
-  mechanism_configuration::v1::types::Mechanism ConvertV0MechanismToV1(const std::string& config_path, bool convert_reaction_units)
+  mechanism_configuration::v1::types::Mechanism ConvertV0MechanismToV1(
+      const std::string& config_path,
+      bool convert_reaction_units)
   {
     mechanism_configuration::v0::Parser parser;
     auto parsed = parser.Parse(config_path);
@@ -160,7 +164,8 @@ namespace musica
   }
 
   mechanism_configuration::v1::types::Reactions convert_reactions_v0_to_v1(
-      const mechanism_configuration::v0::types::Reactions& v0_reactions, bool convert_reaction_units)
+      const mechanism_configuration::v0::types::Reactions& v0_reactions,
+      bool convert_reaction_units)
   {
     mechanism_configuration::v1::types::Reactions v1_reactions;
 
@@ -187,7 +192,8 @@ namespace musica
       v1_branched.reactants = convert_reaction_components_v0_to_v1(branched.reactants);
       v1_branched.alkoxy_products = convert_reaction_components_v0_to_v1(branched.alkoxy_products);
       v1_branched.nitrate_products = convert_reaction_components_v0_to_v1(branched.nitrate_products);
-      v1_branched.X = convert_reaction_units ? convert_molecules_cm3_to_moles_m3(v1_branched.reactants, branched.X) : branched.X;
+      v1_branched.X =
+          convert_reaction_units ? convert_molecules_cm3_to_moles_m3(v1_branched.reactants, branched.X) : branched.X;
       v1_branched.Y = branched.Y;
       v1_branched.a0 = branched.a0;
       v1_branched.n = branched.n;
@@ -215,8 +221,10 @@ namespace musica
       mechanism_configuration::v1::types::Troe v1_troe;
       v1_troe.reactants = convert_reaction_components_v0_to_v1(troe.reactants);
       v1_troe.products = convert_reaction_components_v0_to_v1(troe.products);
-      v1_troe.k0_A = convert_reaction_units ? k0_A_convert_molecules_cm3_to_moles_m3(v1_troe.reactants, troe.k0_A) : troe.k0_A;
-      v1_troe.kinf_A = convert_reaction_units ? convert_molecules_cm3_to_moles_m3(v1_troe.reactants, troe.kinf_A) : troe.kinf_A;
+      v1_troe.k0_A =
+          convert_reaction_units ? k0_A_convert_molecules_cm3_to_moles_m3(v1_troe.reactants, troe.k0_A) : troe.k0_A;
+      v1_troe.kinf_A =
+          convert_reaction_units ? convert_molecules_cm3_to_moles_m3(v1_troe.reactants, troe.kinf_A) : troe.kinf_A;
       v1_troe.k0_B = troe.k0_B;
       v1_troe.k0_C = troe.k0_C;
       v1_troe.kinf_B = troe.kinf_B;
@@ -234,8 +242,10 @@ namespace musica
       mechanism_configuration::v1::types::TernaryChemicalActivation v1_ternary;
       v1_ternary.reactants = convert_reaction_components_v0_to_v1(ternary.reactants);
       v1_ternary.products = convert_reaction_components_v0_to_v1(ternary.products);
-      v1_ternary.k0_A = convert_reaction_units ? convert_molecules_cm3_to_moles_m3(v1_ternary.reactants, ternary.k0_A) : ternary.k0_A;
-      v1_ternary.kinf_A = convert_reaction_units ? convert_molecules_cm3_to_moles_m3(v1_ternary.reactants, ternary.kinf_A) : ternary.kinf_A;
+      v1_ternary.k0_A =
+          convert_reaction_units ? convert_molecules_cm3_to_moles_m3(v1_ternary.reactants, ternary.k0_A) : ternary.k0_A;
+      v1_ternary.kinf_A =
+          convert_reaction_units ? convert_molecules_cm3_to_moles_m3(v1_ternary.reactants, ternary.kinf_A) : ternary.kinf_A;
       v1_ternary.k0_B = ternary.k0_B;
       v1_ternary.k0_C = ternary.k0_C;
       v1_ternary.kinf_B = ternary.kinf_B;
@@ -253,7 +263,8 @@ namespace musica
       mechanism_configuration::v1::types::Tunneling v1_tunneling;
       v1_tunneling.reactants = convert_reaction_components_v0_to_v1(tunneling.reactants);
       v1_tunneling.products = convert_reaction_components_v0_to_v1(tunneling.products);
-      v1_tunneling.A = convert_reaction_units ? convert_molecules_cm3_to_moles_m3(v1_tunneling.reactants, tunneling.A) : tunneling.A;
+      v1_tunneling.A =
+          convert_reaction_units ? convert_molecules_cm3_to_moles_m3(v1_tunneling.reactants, tunneling.A) : tunneling.A;
       v1_tunneling.B = tunneling.B;
       v1_tunneling.C = tunneling.C;
       v1_tunneling.gas_phase = "gas";