Replace nlohmann::json with nlohmann::ordered_json to maintain order in input/output. Bumps nanobind_json submodule. Closes #213 (#461)

Griger5 · slayoo · web-flow · commit 1490a37beff7 · 2025-11-09T14:19:36.000Z
Co-authored-by: Sylwester Arabas &lt;sylwester.arabas@agh.edu.pl&gt;
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,4 @@
 examples/tmp*.pdf
 examples/tmp*.svg
 examples/tmp*.gif
+**/__pycache__/
diff --git a/.gitmodules b/.gitmodules
@@ -56,5 +56,5 @@
 	shallow = true
 [submodule "nanobind_json"]
 	path = gitmodules/nanobind_json
-	url = https://github.com/Griger5/nanobind_json
+	url = https://github.com/Griger5/nanobind_json.git
 	shallow = true
diff --git a/gitmodules/nanobind_json b/gitmodules/nanobind_json
@@ -1 +1 @@
-Subproject commit 6e9e15fee7fee798ec3259cb1fa1829c3991b567
+Subproject commit cb8a8565cc3bc7510b448cea6e6ec9cff98a599b
diff --git a/src/aero_data.hpp b/src/aero_data.hpp
@@ -48,7 +48,7 @@ struct AeroData {
         f_aero_data_from_camp(this->ptr.f_arg(), camp_core.ptr.f_arg());
     }
 
-    AeroData(const nlohmann::json &json) :
+    AeroData(const nlohmann::ordered_json &json) :
         ptr(f_aero_data_ctor, f_aero_data_dtor)
     {
         if (!InputJSONResource::unique_keys(json))
diff --git a/src/aero_dist.hpp b/src/aero_dist.hpp
@@ -44,7 +44,7 @@ struct AeroDist {
 
     AeroDist(
         std::shared_ptr<AeroData> aero_data,
-        const nlohmann::json &json
+        const nlohmann::ordered_json &json
     ):
         ptr(f_aero_dist_ctor, f_aero_dist_dtor),
         aero_data(aero_data)
diff --git a/src/aero_mode.hpp b/src/aero_mode.hpp
@@ -138,7 +138,7 @@ struct AeroMode {
         ptr(f_aero_mode_ctor, f_aero_mode_dtor)
     {}
 
-    AeroMode(AeroData &aero_data, const nlohmann::json &json) :
+    AeroMode(AeroData &aero_data, const nlohmann::ordered_json &json) :
         ptr(f_aero_mode_ctor, f_aero_mode_dtor)
     {
         if (json.size() != 1 || !json.is_object() || !json.begin().value().is_object())
@@ -149,7 +149,7 @@ struct AeroMode {
         guard.check_parameters();
     }
 
-    static void check_mode_json(const nlohmann::json &mode) {
+    static void check_mode_json(const nlohmann::ordered_json &mode) {
         for (auto key : std::set<std::string>({"mass_frac", "mode_type"})) // TODO #320: more...
             if (mode.find(key) == mode.end())
                 throw std::runtime_error("mode parameters dict must include key '" + key + "'");
diff --git a/src/env_state.hpp b/src/env_state.hpp
@@ -29,7 +29,7 @@ extern "C" void f_env_state_air_dens(const void *ptr, double *air_density) noexc
 struct EnvState {
     PMCResource ptr;
 
-    EnvState(const nlohmann::json &json) :
+    EnvState(const nlohmann::ordered_json &json) :
         ptr(f_env_state_ctor, f_env_state_dtor)
     {
         JSONResourceGuard<InputJSONResource> guard(json);
diff --git a/src/gas_data.hpp b/src/gas_data.hpp
@@ -11,7 +11,7 @@
 #include "gas_data_parameters.hpp"
 #include "camp_core.hpp"
 #include "nanobind/nanobind.h"
-#include "nanobind_json/nanobind_json.hpp"
+#include "nanobind_json/nanobind_json.h"
 
 extern "C" void f_gas_data_ctor(void *ptr) noexcept;
 extern "C" void f_gas_data_dtor(void *ptr) noexcept;
@@ -26,7 +26,7 @@ extern "C" void f_gas_data_spec_name_by_index(const void *ptr, const int *i_spec
 
 struct GasData {
     PMCResource ptr;
-    const nlohmann::json json;
+    const nlohmann::ordered_json json;
 
     GasData(const CampCore &CampCore) :
         ptr(f_gas_data_ctor, f_gas_data_dtor)
@@ -38,11 +38,11 @@ struct GasData {
         ptr(f_gas_data_ctor, f_gas_data_dtor),
         json(tpl)
     {
-        auto json_array = nlohmann::json::array();
+        auto json_array = nlohmann::ordered_json::array();
         for (const auto item : tpl)
-            json_array.push_back(nlohmann::json::object({{
+            json_array.push_back(nlohmann::ordered_json::object({{
                 nanobind::cast<std::string>(item),
-                nlohmann::json::array()
+                nlohmann::ordered_json::array()
             }}));
 
         JSONResourceGuard<InputJSONResource> guard(json_array);
diff --git a/src/gas_state.hpp b/src/gas_state.hpp
@@ -115,7 +115,7 @@ struct GasState {
         return data;
     }
 
-    static void set_mix_rats(const GasState &self, const nlohmann::json &json) {
+    static void set_mix_rats(const GasState &self, const nlohmann::ordered_json &json) {
         if (json.size() == 0)
             throw std::runtime_error("Non-empty sequence of mixing ratios expected");
 
diff --git a/src/input_guard.hpp b/src/input_guard.hpp
@@ -6,7 +6,7 @@
 
 struct InputGuard {
   public:
-    InputGuard(const nlohmann::json &j) {
+    InputGuard(const nlohmann::ordered_json &j) {
         process_json(j);
 
         this->dict_key_present = false;
@@ -71,8 +71,8 @@ struct InputGuard {
 
     bool dict_key_present;
 
-    void process_json(const nlohmann::json &j) {
-        nlohmann::json flat = j.flatten();
+    void process_json(const nlohmann::ordered_json &j) {
+        nlohmann::ordered_json flat = j.flatten();
 
         // JSON Pointer, as in a string syntax for identifying a specific value in JSON
         std::vector<std::string> json_pointers;
diff --git a/src/json_resource.hpp b/src/json_resource.hpp
@@ -19,8 +19,8 @@
 struct JSONResource {
   private:
     std::set<std::string> vars;
-    const nlohmann::json *json;
-    std::stack<const nlohmann::json*> json_parent;
+    const nlohmann::ordered_json *json;
+    std::stack<const nlohmann::ordered_json*> json_parent;
 
     std::unique_ptr<InputGuard> input_guard_ptr;
 
@@ -34,7 +34,7 @@ struct JSONResource {
 
     JSONResource() {}
 
-    JSONResource(const nlohmann::json &json) {
+    JSONResource(const nlohmann::ordered_json &json) {
         this->set_current_json_ptr(&json);
         for (auto &entry : this->json->items()) {
             this->vars.insert(entry.key());
@@ -43,7 +43,7 @@ struct JSONResource {
         input_guard_ptr = std::make_unique<InputGuard>(json);
     };
 
-    void set_current_json_ptr(const nlohmann::json *ptr) {
+    void set_current_json_ptr(const nlohmann::ordered_json *ptr) {
         this->json = ptr;
     }
 
@@ -86,8 +86,8 @@ struct JSONResource {
 
     void zoom_in(const bpstd::string_view &sub) noexcept {
         auto it = this->json->is_array() 
-            ? this->json->at(this->json->size()-1).find(sub)
-            : this->json->find(sub);
+            ? this->json->at(this->json->size()-1).find(sub.to_string())
+            : this->json->find(sub.to_string());
 
         assert(*it != NULL);
         this->json_parent.push(this->json);
@@ -157,15 +157,15 @@ struct JSONResource {
         const bpstd::string_view name,
         T *var
     ) {
-        *var = this->find(name)->get<T>();
+        *var = this->find(name.to_string())->get<T>();
     }
 
     void read_str(
         const bpstd::string_view &name,
         char* var_data,
         int* var_size
     ) noexcept {
-        auto it = this->find(name);
+        auto it = this->find(name.to_string());
         if (it == this->json->end())
         {
             assert(false);
@@ -240,7 +240,7 @@ struct InputJSONResource: JSONResource {
 
   public:
     InputJSONResource(
-        const nlohmann::json &json,
+        const nlohmann::ordered_json &json,
         const std::string key_cond = "",
         const std::string key_name = "",
         const std::size_t max_zoom_level = 3
@@ -290,7 +290,7 @@ struct InputJSONResource: JSONResource {
         return 1;
     }
 
-    static bool unique_keys(const nlohmann::json &json) {
+    static bool unique_keys(const nlohmann::ordered_json &json) {
         std::set<std::string> keys;
         for (auto i=0u; i<json.size(); ++i) {
             for (auto &entry : json.at(i).items()) {
@@ -304,9 +304,9 @@ struct InputJSONResource: JSONResource {
 };
 
 struct OutputJSONResource: JSONResource {
-    std::unique_ptr<nlohmann::json> guard;
+    std::unique_ptr<nlohmann::ordered_json> guard;
 
-    OutputJSONResource() : guard(std::make_unique<nlohmann::json>()) {
+    OutputJSONResource() : guard(std::make_unique<nlohmann::ordered_json>()) {
         this->set_current_json_ptr(this->guard.get());
     }
 
@@ -331,20 +331,20 @@ struct JSONResourceGuard {
         json_resource_ptr() = std::make_unique<T>();
     }
 
-    JSONResourceGuard(const nlohmann::json & json) {
+    JSONResourceGuard(const nlohmann::ordered_json & json) {
         json_resource_ptr() = std::make_unique<T>(json);
     }
 
     JSONResourceGuard(
-        const nlohmann::json & json,
+        const nlohmann::ordered_json & json,
         const std::string key_cond,
         const std::string key_name
     ) {
         json_resource_ptr() = std::make_unique<T>(json, key_cond, key_name);
     }
 
     JSONResourceGuard(
-        const nlohmann::json & json,
+        const nlohmann::ordered_json & json,
         const std::string key_cond,
         const std::string key_name,
         const int max_zoom_level
diff --git a/src/pypartmc.cpp b/src/pypartmc.cpp
@@ -14,7 +14,7 @@
 #include "nanobind/ndarray.h"
 #undef snprintf // required to fix an issue with std::snprintf in nlohmann::json
 #include "nlohmann/json.hpp"
-#include "nanobind_json/nanobind_json.hpp"
+#include "nanobind_json/nanobind_json.h"
 #include "sundials/sundials_config.h"
 #include "camp/version.h"
 #include "tl/optional.hpp"
@@ -174,7 +174,7 @@ NB_MODULE(_PyPartMC, m) {
         )pbdoc"
     )
         .def(nb::init<const CampCore&>())
-        .def(nb::init<const nlohmann::json&>())
+        .def(nb::init<const nlohmann::ordered_json&>())
         .def("spec_by_name", AeroData::spec_by_name,
              "Return the number of the species in AeroData with the given name.")
         .def("__len__", AeroData::__len__, "Return number of aerosol species.")
@@ -409,7 +409,7 @@ NB_MODULE(_PyPartMC, m) {
             scenario_t.
         )pbdoc"
     )
-        .def(nb::init<const nlohmann::json&>())
+        .def(nb::init<const nlohmann::ordered_json&>())
         .def("set_temperature", EnvState::set_temperature,
             "Set the temperature of the environment state.")
         .def_prop_ro("temp", EnvState::temp,
@@ -468,7 +468,7 @@ NB_MODULE(_PyPartMC, m) {
             nb::init<
                 const GasData&,
                 const AeroData&,
-                const nlohmann::json&
+                const nlohmann::ordered_json&
             >(),
             "instantiates and initializes from a JSON object"
         )
@@ -530,7 +530,7 @@ NB_MODULE(_PyPartMC, m) {
         "RunPartOpt",
         "Options controlling the execution of run_part()."
     )
-        .def(nb::init<const nlohmann::json&>())
+        .def(nb::init<const nlohmann::ordered_json&>())
         .def_prop_ro("t_max", RunPartOpt::t_max, "Total simulation time.")
         .def_prop_ro("del_t", RunPartOpt::del_t, "Time step.")
     ;
@@ -539,7 +539,7 @@ NB_MODULE(_PyPartMC, m) {
         "RunSectOpt",
         "Options controlling the execution of run_sect()."
     )
-        .def(nb::init<const nlohmann::json&, EnvState&>())
+        .def(nb::init<const nlohmann::ordered_json&, EnvState&>())
         .def_prop_ro("t_max", RunSectOpt::t_max, "Total simulation time.")
         .def_prop_ro("del_t", RunSectOpt::del_t, "Time step.")
     ;
@@ -548,7 +548,7 @@ NB_MODULE(_PyPartMC, m) {
         "RunExactOpt",
         "Options controlling the execution of run_exact()."
     )
-        .def(nb::init<const nlohmann::json&, EnvState&>())
+        .def(nb::init<const nlohmann::ordered_json&, EnvState&>())
         .def_prop_ro("t_max", RunExactOpt::t_max, "Total simulation time.")
     ;
 
@@ -561,9 +561,8 @@ NB_MODULE(_PyPartMC, m) {
         .def_prop_ro("widths", BinGrid::widths, "Return bin widths.")
     ;
 
-    nb::class_<AeroMode>(m,"AeroMode",
-        "An aerosol size distribution mode.")
-        .def(nb::init<AeroData&, const nlohmann::json&>())
+    nb::class_<AeroMode>(m,"AeroMode")
+        .def(nb::init<AeroData&, const nlohmann::ordered_json&>())
         .def_prop_rw("num_conc", &AeroMode::get_num_conc, &AeroMode::set_num_conc,
              "Provide access (read or write) to the total number concentration of a mode.")
         .def("num_dist", &AeroMode::num_dist,
@@ -589,7 +588,7 @@ NB_MODULE(_PyPartMC, m) {
     ;
 
     nb::class_<AeroDist>(m,"AeroDist")
-        .def(nb::init<std::shared_ptr<AeroData>, const nlohmann::json&>())
+        .def(nb::init<std::shared_ptr<AeroData>, const nlohmann::ordered_json&>())
         .def_prop_ro("n_mode", &AeroDist::get_n_mode,
             "Number of aerosol modes in the distribution.")
         .def_prop_ro("num_conc", &AeroDist::get_total_num_conc,
diff --git a/src/run_exact_opt.hpp b/src/run_exact_opt.hpp
@@ -18,10 +18,10 @@ extern "C" void f_run_exact_opt_t_max(const void *ptr, double *t_max) noexcept;
 struct RunExactOpt {
     PMCResource ptr;
 
-    RunExactOpt(const nlohmann::json &json, EnvState &env_state) :
+    RunExactOpt(const nlohmann::ordered_json &json, EnvState &env_state) :
         ptr(f_run_exact_opt_ctor, f_run_exact_opt_dtor)
     {
-        nlohmann::json json_copy(json);
+        nlohmann::ordered_json json_copy(json);
 
         for (auto key : std::set<std::string>({
             "t_output"
diff --git a/src/run_part_opt.hpp b/src/run_part_opt.hpp
@@ -19,10 +19,10 @@ struct RunPartOpt {
     PMCResource ptr;
     bool allow_halving, allow_doubling;
 
-    RunPartOpt(const nlohmann::json &json) :
+    RunPartOpt(const nlohmann::ordered_json &json) :
         ptr(f_run_part_opt_ctor, f_run_part_opt_dtor)
     {
-        nlohmann::json json_copy(json);
+        nlohmann::ordered_json json_copy(json);
 
         if (json_copy.find("do_parallel") != json_copy.end() && json_copy["do_parallel"])
             throw std::runtime_error("setting do_parallel=true not supported in PyPartMC");
diff --git a/src/run_sect_opt.hpp b/src/run_sect_opt.hpp
@@ -19,10 +19,10 @@ extern "C" void f_run_sect_opt_del_t(const void *ptr, double *del_t) noexcept;
 struct RunSectOpt {
     PMCResource ptr;
 
-    RunSectOpt(const nlohmann::json &json, EnvState &env_state) :
+    RunSectOpt(const nlohmann::ordered_json &json, EnvState &env_state) :
         ptr(f_run_sect_opt_ctor, f_run_sect_opt_dtor)
     {
-        nlohmann::json json_copy(json);
+        nlohmann::ordered_json json_copy(json);
 
         for (auto key : std::set<std::string>({
             "t_output", "t_progress"
diff --git a/src/scenario.hpp b/src/scenario.hpp
@@ -85,12 +85,12 @@ extern "C" void f_scenario_aero_background_time(
 
 struct Scenario {
     PMCResource ptr;
-    const nlohmann::json json;
+    const nlohmann::ordered_json json;
 
     Scenario(
         const GasData &gas_data,
         const AeroData &aero_data,
-        const nlohmann::json &json
+        const nlohmann::ordered_json &json
     ) :
         ptr(f_scenario_ctor, f_scenario_dtor),
         json(json)
diff --git a/tests/test_aero_dist.py b/tests/test_aero_dist.py
diff --git a/tests/test_aero_mode.py b/tests/test_aero_mode.py
diff --git a/tests/test_scenario.py b/tests/test_scenario.py

Original file line number	Diff line number	Diff line change
`@@ -48,7 +48,7 @@ struct AeroData {`
`48`	`48`	`f_aero_data_from_camp(this->ptr.f_arg(), camp_core.ptr.f_arg());`
`49`	`49`	`}`
`50`	`50`
`51`		`- AeroData(const nlohmann::json &json) :`
	`51`	`+ AeroData(const nlohmann::ordered_json &json) :`
`52`	`52`	`ptr(f_aero_data_ctor, f_aero_data_dtor)`
`53`	`53`	`{`
`54`	`54`	`if (!InputJSONResource::unique_keys(json))`
Original file line number	Diff line number	Diff line change
`@@ -29,7 +29,7 @@ extern "C" void f_env_state_air_dens(const void ptr, double air_density) noexc`
`29`	`29`	`struct EnvState {`
`30`	`30`	`PMCResource ptr;`
`31`	`31`
`32`		`- EnvState(const nlohmann::json &json) :`
	`32`	`+ EnvState(const nlohmann::ordered_json &json) :`
`33`	`33`	`ptr(f_env_state_ctor, f_env_state_dtor)`
`34`	`34`	`{`
`35`	`35`	`JSONResourceGuard<InputJSONResource> guard(json);`
Original file line number	Diff line number	Diff line change
`@@ -115,7 +115,7 @@ struct GasState {`
`115`	`115`	`return data;`
`116`	`116`	`}`
`117`	`117`
`118`		`- static void set_mix_rats(const GasState &self, const nlohmann::json &json) {`
	`118`	`+ static void set_mix_rats(const GasState &self, const nlohmann::ordered_json &json) {`
`119`	`119`	`if (json.size() == 0)`
`120`	`120`	`throw std::runtime_error("Non-empty sequence of mixing ratios expected");`
`121`	`121`