Merge pull request #53 from open-atmos/main-formatting

Auto-format code changes
open-atmos · Jan 16, 2025 · 0a6d1ad · 0a6d1ad
2 parents dae56fd + f4874c0
commit 0a6d1ad
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Showing 14 changed files with 71 additions and 69 deletions.
diff --git a/include/open_atmos/constants.hpp b/include/open_atmos/constants.hpp
@@ -10,5 +10,5 @@ namespace open_atmos
     static constexpr double boltzmann = 1.380649e-23;  // J K^{-1}
     static constexpr double avogadro = 6.02214076e23;  // # mol^{-1}
     static constexpr double R = boltzmann * avogadro;  // J K^{-1} mol^{-1}
-  }                                                    // namespace constants
+  }  // namespace constants
 }  // namespace open_atmos
diff --git a/include/open_atmos/mechanism_configuration/utils.hpp b/include/open_atmos/mechanism_configuration/utils.hpp
@@ -4,15 +4,15 @@
 
 #pragma once
 
-#include <open_atmos/mechanism_configuration/parse_status.hpp>
-#include <open_atmos/types.hpp>
-#include <open_atmos/mechanism_configuration/validation.hpp>
+#include <yaml-cpp/yaml.h>
 
 #include <iostream>
+#include <open_atmos/mechanism_configuration/parse_status.hpp>
+#include <open_atmos/mechanism_configuration/validation.hpp>
+#include <open_atmos/types.hpp>
 #include <string>
 #include <unordered_map>
 #include <vector>
-#include <yaml-cpp/yaml.h>
 
 namespace open_atmos
 {
@@ -34,10 +34,12 @@ namespace open_atmos
 
     ConfigParseStatus
     ValidateSchema(const YAML::Node& object, const std::vector<std::string>& required_keys, const std::vector<std::string>& optional_keys);
-    
+
     std::pair<ConfigParseStatus, std::vector<types::Species>> ParseSpecies(const YAML::Node& objects);
 
-    std::pair<ConfigParseStatus, std::vector<types::Phase>> ParsePhases(const YAML::Node& objects, const std::vector<types::Species> existing_species);
+    std::pair<ConfigParseStatus, std::vector<types::Phase>> ParsePhases(
+        const YAML::Node& objects,
+        const std::vector<types::Species> existing_species);
 
     std::pair<ConfigParseStatus, types::ReactionComponent> ParseReactionComponent(const YAML::Node& object);
 

diff --git a/include/open_atmos/mechanism_configuration/validation.hpp b/include/open_atmos/mechanism_configuration/validation.hpp
@@ -168,7 +168,6 @@ namespace open_atmos
       // aerosol phase
       // aerosol-phase water
       // aerosol-phase species
-
     };
 
     struct Mechanism

diff --git a/include/open_atmos/types.hpp b/include/open_atmos/types.hpp
@@ -5,10 +5,10 @@
 #pragma once
 
 #include <array>
+#include <map>
 #include <optional>
 #include <string>
 #include <unordered_map>
-#include <map>
 #include <vector>
 
 namespace open_atmos

diff --git a/src/aqueous_equilibrium_parser.cpp b/src/aqueous_equilibrium_parser.cpp
@@ -1,7 +1,7 @@
 #include <open_atmos/constants.hpp>
 #include <open_atmos/mechanism_configuration/parser.hpp>
-#include <open_atmos/mechanism_configuration/utils.hpp>
 #include <open_atmos/mechanism_configuration/parser_types.hpp>
+#include <open_atmos/mechanism_configuration/utils.hpp>
 
 namespace open_atmos
 {

diff --git a/src/arrhenius_parser.cpp b/src/arrhenius_parser.cpp
@@ -1,7 +1,7 @@
 #include <open_atmos/constants.hpp>
 #include <open_atmos/mechanism_configuration/parser.hpp>
-#include <open_atmos/mechanism_configuration/utils.hpp>
 #include <open_atmos/mechanism_configuration/parser_types.hpp>
+#include <open_atmos/mechanism_configuration/utils.hpp>
 
 namespace open_atmos
 {

diff --git a/src/branched_parser.cpp b/src/branched_parser.cpp
@@ -1,7 +1,7 @@
 #include <open_atmos/constants.hpp>
-#include <open_atmos/mechanism_configuration/utils.hpp>
 #include <open_atmos/mechanism_configuration/parser.hpp>
 #include <open_atmos/mechanism_configuration/parser_types.hpp>
+#include <open_atmos/mechanism_configuration/utils.hpp>
 
 namespace open_atmos
 {
@@ -13,62 +13,61 @@ namespace open_atmos
         const std::vector<types::Phase>& existing_phases,
         open_atmos::types::Reactions& reactions)
     {
-        ConfigParseStatus status = ConfigParseStatus::Success;
-        types::Branched branched;
-
-        status = ValidateSchema(object, validation::branched.required_keys, validation::branched.optional_keys);
-        if (status == ConfigParseStatus::Success)
-        {
-          auto alkoxy_products = ParseReactantsOrProducts(validation::keys.alkoxy_products, object, status);
-          auto nitrate_products = ParseReactantsOrProducts(validation::keys.nitrate_products, object, status);
-          auto reactants = ParseReactantsOrProducts(validation::keys.reactants, object, status);
+      ConfigParseStatus status = ConfigParseStatus::Success;
+      types::Branched branched;
 
-          branched.X = object[validation::keys.X].as<double>();
-          branched.Y = object[validation::keys.Y].as<double>();
-          branched.a0 = object[validation::keys.a0].as<double>();
-          branched.n = object[validation::keys.n].as<double>();
+      status = ValidateSchema(object, validation::branched.required_keys, validation::branched.optional_keys);
+      if (status == ConfigParseStatus::Success)
+      {
+        auto alkoxy_products = ParseReactantsOrProducts(validation::keys.alkoxy_products, object, status);
+        auto nitrate_products = ParseReactantsOrProducts(validation::keys.nitrate_products, object, status);
+        auto reactants = ParseReactantsOrProducts(validation::keys.reactants, object, status);
 
-          if (object[validation::keys.name])
-          {
-            branched.name = object[validation::keys.name].as<std::string>();
-          }
+        branched.X = object[validation::keys.X].as<double>();
+        branched.Y = object[validation::keys.Y].as<double>();
+        branched.a0 = object[validation::keys.a0].as<double>();
+        branched.n = object[validation::keys.n].as<double>();
 
-          std::vector<std::string> requested_species;
-          for (const auto& spec : nitrate_products)
-          {
-            requested_species.push_back(spec.species_name);
-          }
-          for (const auto& spec : alkoxy_products)
-          {
-            requested_species.push_back(spec.species_name);
-          }
-          for (const auto& spec : reactants)
-          {
-            requested_species.push_back(spec.species_name);
-          }
+        if (object[validation::keys.name])
+        {
+          branched.name = object[validation::keys.name].as<std::string>();
+        }
 
-          if (status == ConfigParseStatus::Success && RequiresUnknownSpecies(requested_species, existing_species))
-          {
-            status = ConfigParseStatus::ReactionRequiresUnknownSpecies;
-          }
+        std::vector<std::string> requested_species;
+        for (const auto& spec : nitrate_products)
+        {
+          requested_species.push_back(spec.species_name);
+        }
+        for (const auto& spec : alkoxy_products)
+        {
+          requested_species.push_back(spec.species_name);
+        }
+        for (const auto& spec : reactants)
+        {
+          requested_species.push_back(spec.species_name);
+        }
 
-          std::string gas_phase = object[validation::keys.gas_phase].as<std::string>();
-          auto it = std::find_if(existing_phases.begin(), existing_phases.end(), [&gas_phase](const auto& phase) { return phase.name == gas_phase; });
-          if (status == ConfigParseStatus::Success && it == existing_phases.end())
-          {
-            status = ConfigParseStatus::UnknownPhase;
-          }
+        if (status == ConfigParseStatus::Success && RequiresUnknownSpecies(requested_species, existing_species))
+        {
+          status = ConfigParseStatus::ReactionRequiresUnknownSpecies;
+        }
 
-          branched.gas_phase = gas_phase;
-          branched.nitrate_products = nitrate_products;
-          branched.alkoxy_products = alkoxy_products;
-          branched.reactants = reactants;
-          branched.unknown_properties = GetComments(object, validation::branched.required_keys, validation::branched.optional_keys);
-          reactions.branched.push_back(branched);
+        std::string gas_phase = object[validation::keys.gas_phase].as<std::string>();
+        auto it = std::find_if(existing_phases.begin(), existing_phases.end(), [&gas_phase](const auto& phase) { return phase.name == gas_phase; });
+        if (status == ConfigParseStatus::Success && it == existing_phases.end())
+        {
+          status = ConfigParseStatus::UnknownPhase;
         }
 
-        return status;
+        branched.gas_phase = gas_phase;
+        branched.nitrate_products = nitrate_products;
+        branched.alkoxy_products = alkoxy_products;
+        branched.reactants = reactants;
+        branched.unknown_properties = GetComments(object, validation::branched.required_keys, validation::branched.optional_keys);
+        reactions.branched.push_back(branched);
+      }
 
+      return status;
     }
   }  // namespace mechanism_configuration
 }  // namespace open_atmos
diff --git a/src/condensed_phase_arrhenius_parser.cpp b/src/condensed_phase_arrhenius_parser.cpp
@@ -1,7 +1,7 @@
 #include <open_atmos/constants.hpp>
-#include <open_atmos/mechanism_configuration/utils.hpp>
 #include <open_atmos/mechanism_configuration/parser.hpp>
 #include <open_atmos/mechanism_configuration/parser_types.hpp>
+#include <open_atmos/mechanism_configuration/utils.hpp>
 
 namespace open_atmos
 {

diff --git a/src/henrys_law_parser.cpp b/src/henrys_law_parser.cpp
@@ -1,7 +1,7 @@
 #include <open_atmos/constants.hpp>
 #include <open_atmos/mechanism_configuration/parser.hpp>
-#include <open_atmos/mechanism_configuration/utils.hpp>
 #include <open_atmos/mechanism_configuration/parser_types.hpp>
+#include <open_atmos/mechanism_configuration/utils.hpp>
 
 namespace open_atmos
 {

diff --git a/src/parser.cpp b/src/parser.cpp
@@ -5,10 +5,10 @@
 #include <yaml-cpp/yaml.h>
 
 #include <open_atmos/constants.hpp>
-#include <open_atmos/mechanism_configuration/validation.hpp>
-#include <open_atmos/mechanism_configuration/version.hpp>
 #include <open_atmos/mechanism_configuration/parser.hpp>
 #include <open_atmos/mechanism_configuration/parser_types.hpp>
+#include <open_atmos/mechanism_configuration/validation.hpp>
+#include <open_atmos/mechanism_configuration/version.hpp>
 
 namespace open_atmos
 {

diff --git a/src/troe_parser.cpp b/src/troe_parser.cpp
@@ -1,7 +1,7 @@
 #include <open_atmos/constants.hpp>
 #include <open_atmos/mechanism_configuration/parser.hpp>
-#include <open_atmos/mechanism_configuration/utils.hpp>
 #include <open_atmos/mechanism_configuration/parser_types.hpp>
+#include <open_atmos/mechanism_configuration/utils.hpp>
 
 namespace open_atmos
 {

diff --git a/src/wet_deposition_parser.cpp b/src/wet_deposition_parser.cpp
@@ -1,7 +1,7 @@
 #include <open_atmos/constants.hpp>
 #include <open_atmos/mechanism_configuration/parser.hpp>
-#include <open_atmos/mechanism_configuration/utils.hpp>
 #include <open_atmos/mechanism_configuration/parser_types.hpp>
+#include <open_atmos/mechanism_configuration/utils.hpp>
 
 namespace open_atmos
 {
@@ -31,8 +31,8 @@ namespace open_atmos
 
         std::string aerosol_phase = object[validation::keys.aerosol_phase].as<std::string>();
 
-        auto it = std::find_if(
-            existing_phases.begin(), existing_phases.end(), [&aerosol_phase](const auto& phase) { return phase.name == aerosol_phase; });
+        auto it =
+            std::find_if(existing_phases.begin(), existing_phases.end(), [&aerosol_phase](const auto& phase) { return phase.name == aerosol_phase; });
         if (status == ConfigParseStatus::Success && it == existing_phases.end())
         {
           status = ConfigParseStatus::UnknownPhase;

diff --git a/test/unit/test_parse_condensed_phase_photolysis.cpp b/test/unit/test_parse_condensed_phase_photolysis.cpp
@@ -90,7 +90,8 @@ TEST(Parser, CondensedPhasePhotolysisDetectsWhenRequestedSpeciesAreNotInAerosolP
   std::vector<std::string> extensions = { ".json", ".yaml" };
   for (auto& extension : extensions)
   {
-    auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/condensed_phase_photolysis/species_not_in_aerosol_phase") + extension);
+    auto [status, mechanism] =
+        parser.Parse(std::string("unit_configs/reactions/condensed_phase_photolysis/species_not_in_aerosol_phase") + extension);
     EXPECT_EQ(status, ConfigParseStatus::RequestedAerosolSpeciesNotIncludedInAerosolPhase);
   }
 }

diff --git a/test/unit/test_parse_simpol_phase_transfer.cpp b/test/unit/test_parse_simpol_phase_transfer.cpp
@@ -78,7 +78,8 @@ TEST(Parser, SimpolPhaseTransferDetectsUnknownGasPhaseSpeciesNotInGasPhase)
   std::vector<std::string> extensions = { ".json", ".yaml" };
   for (auto& extension : extensions)
   {
-    auto [status, mechanism] = parser.Parse(std::string("unit_configs/reactions/simpol_phase_transfer/missing_gas_phase_species_in_gas_phase") + extension);
+    auto [status, mechanism] =
+        parser.Parse(std::string("unit_configs/reactions/simpol_phase_transfer/missing_gas_phase_species_in_gas_phase") + extension);
     EXPECT_EQ(status, ConfigParseStatus::ReactionRequiresUnknownSpecies);
   }
 }