Add MusicBox.to_config() export and round-trip integration test (#355)

Adds to_config() to serialize an in-memory MusicBox to a v1 JSON-compatible
dict so configurations built programmatically can be exported, stored, and
reloaded with loadJson() producing bit-for-bit identical results.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: K20shores

python/acom_music_box/music_box.py

@@ -437,3 +437,64 @@ def mechanism(self):
         if self.__mechanism is None:
             raise ValueError("Mechanism is not loaded.")
         return self.__mechanism
+
+    def to_config(self) -> dict:
+        """
+        Export the current box model state as a v1 JSON-compatible dict.
+
+        Returns:
+            dict: A music-box v1 config with 'box model options', 'mechanism',
+                  and 'conditions' sections. Conditions are exported as inline
+                  data blocks (one per time point) so the result is self-contained.
+
+        Raises:
+            ValueError: If the mechanism has not been loaded.
+        """
+        config = {}
+
+        # Box model options (all times in seconds for unambiguous round-trip)
+        config['box model options'] = {
+            'grid': self.box_model_options.grid,
+            'chemistry time step [sec]': self.box_model_options.chem_step_time,
+            'output time step [sec]': self.box_model_options.output_step_time,
+            'simulation length [sec]': self.box_model_options.simulation_length,
+            'max iterations': self.box_model_options.max_iterations,
+        }
+
+        # Mechanism — musica serialize() returns a v1-compatible dict
+        mech_dict = self.mechanism.serialize()
+        mech_dict['version'] = '1.0.0'
+        config['mechanism'] = mech_dict
+
+        # Conditions — one data block per time point avoids null/sparse issues
+        raw_df = self._conditions_manager.raw
+        conc_events = self._conditions_manager.concentration_events
+        all_times = self._conditions_manager.get_times()
+
+        data_blocks = []
+        for t in all_times:
+            headers = ['time.s']
+            values = [float(t)]
+
+            # ENV and rate parameters from the sparse DataFrame
+            time_mask = raw_df['time.s'] == t
+            if time_mask.any():
+                row = raw_df[time_mask].iloc[0]
+                for col in raw_df.columns:
+                    if col == 'time.s':
+                        continue
+                    val = row[col]
+                    if pd.notna(val):
+                        headers.append(col)
+                        values.append(float(val))
+
+            # Concentration events (applied at exact time, not interpolated)
+            if t in conc_events:
+                for species, value in sorted(conc_events[t].items()):
+                    headers.append(f'CONC.{species}.mol m-3')
+                    values.append(float(value))
+
+            data_blocks.append({'headers': headers, 'rows': [values]})
+
+        config['conditions'] = {'data': data_blocks}
+        return config

python/tests/integration/test_export_round_trip.py

@@ -0,0 +1,197 @@
+"""
+Round-trip export test: build a MusicBox entirely in code with every possible
+option, run it, export to v1 JSON via to_config(), reload with loadJson(), run
+again, and assert the two result DataFrames are exactly equal.
+
+"Every possible option" covers:
+  - All five BoxModelOptions fields (grid, chem_step_time, output_step_time,
+    simulation_length, max_iterations)
+  - Four reaction types: Arrhenius (all A/B/C/D/E params), Photolysis, Emission,
+    FirstOrderLoss
+  - Initial conditions at t=0: temperature, pressure, concentrations for all
+    species, and all rate-parameter types (PHOTO, EMIS, LOSS)
+  - Evolving conditions at t=30: temperature, pressure, concentration reset,
+    and updated rate parameters
+"""
+
+import json
+import os
+import tempfile
+
+import pandas as pd
+import pytest
+
+import musica.mechanism_configuration as mc
+from acom_music_box import MusicBox
+
+
+def _build_model():
+    """Return a fully-configured MusicBox using only the in-code API."""
+    A = mc.Species(name="A")
+    B = mc.Species(name="B")
+    C = mc.Species(name="C")
+    D = mc.Species(name="D")
+    E = mc.Species(name="E")
+    species_list = [A, B, C, D, E]
+    gas = mc.Phase(name="gas", species=species_list)
+
+    # Arrhenius: all five parameters set
+    arr1 = mc.Arrhenius(
+        name="A->B", A=4.0e-3, B=0.0, C=50.0, D=300.0, E=0.0,
+        reactants=[A], products=[B], gas_phase=gas,
+    )
+    arr2 = mc.Arrhenius(
+        name="B->C", A=1.2e-4, B=2.5, C=75.0, D=50.0, E=0.5,
+        reactants=[B], products=[C], gas_phase=gas,
+    )
+    # Photolysis: requires PHOTO rate parameter
+    photo = mc.Photolysis(
+        name="photo_D", scaling_factor=1.0,
+        reactants=[D], products=[E], gas_phase=gas,
+    )
+    # Emission: requires EMIS rate parameter
+    emis = mc.Emission(
+        name="emis_A", scaling_factor=1.0,
+        products=[A], gas_phase=gas,
+    )
+    # FirstOrderLoss: requires LOSS rate parameter
+    loss = mc.FirstOrderLoss(
+        name="loss_E", scaling_factor=1.0,
+        reactants=[E], gas_phase=gas,
+    )
+
+    mechanism = mc.Mechanism(
+        name="all_options_test",
+        species=species_list,
+        phases=[gas],
+        reactions=[arr1, arr2, photo, emis, loss],
+    )
+
+    box = MusicBox()
+    box.load_mechanism(mechanism)
+
+    # All five BoxModelOptions fields
+    box.box_model_options.grid = "box"
+    box.box_model_options.chem_step_time = 2.0
+    box.box_model_options.output_step_time = 6.0
+    box.box_model_options.simulation_length = 60.0
+    box.box_model_options.max_iterations = 100
+
+    # Initial conditions (t=0): temperature, pressure, all species,
+    # and all rate-parameter types
+    (box
+        .set_condition(
+            time=0.0,
+            temperature=298.15,
+            pressure=101325.0,
+            concentrations={"A": 1.0, "B": 0.0, "C": 0.0, "D": 0.5, "E": 0.0},
+            rate_parameters={
+                "PHOTO.photo_D.s-1": 1.0e-4,
+                "EMIS.emis_A.mol m-3 s-1": 1.0e-8,
+                "LOSS.loss_E.s-1": 1.0e-3,
+            },
+        )
+        # Evolving conditions (t=30): temperature, pressure, concentration reset,
+        # and updated rate parameters
+        .set_condition(
+            time=30.0,
+            temperature=300.0,
+            pressure=101000.0,
+            concentrations={"D": 0.3},
+            rate_parameters={
+                "PHOTO.photo_D.s-1": 2.0e-4,
+                "EMIS.emis_A.mol m-3 s-1": 5.0e-9,
+                "LOSS.loss_E.s-1": 2.0e-3,
+            },
+        ))
+
+    return box
+
+
+class TestExportRoundTrip:
+
+    def test_to_config_structure(self):
+        """to_config() produces a well-formed v1 config dict."""
+        box = _build_model()
+        config = box.to_config()
+
+        assert "box model options" in config
+        assert "mechanism" in config
+        assert "conditions" in config
+
+        opts = config["box model options"]
+        assert opts["grid"] == "box"
+        assert opts["chemistry time step [sec]"] == 2.0
+        assert opts["output time step [sec]"] == 6.0
+        assert opts["simulation length [sec]"] == 60.0
+        assert opts["max iterations"] == 100
+
+        mech = config["mechanism"]
+        assert mech["version"] == "1.0.0"
+        reaction_types = {r["type"] for r in mech["reactions"]}
+        assert reaction_types == {"ARRHENIUS", "PHOTOLYSIS", "EMISSION", "FIRST_ORDER_LOSS"}
+
+        conds = config["conditions"]
+        assert "data" in conds
+        # Two time points → two data blocks
+        assert len(conds["data"]) == 2
+
+        # t=0 block must contain all condition types
+        t0_block = conds["data"][0]
+        assert "CONC.A.mol m-3" in t0_block["headers"]
+        assert "CONC.D.mol m-3" in t0_block["headers"]
+        assert "ENV.temperature.K" in t0_block["headers"]
+        assert "ENV.pressure.Pa" in t0_block["headers"]
+        assert "PHOTO.photo_D.s-1" in t0_block["headers"]
+        assert "EMIS.emis_A.mol m-3 s-1" in t0_block["headers"]
+        assert "LOSS.loss_E.s-1" in t0_block["headers"]
+
+        # t=30 block must contain updated evolving conditions
+        t30_block = conds["data"][1]
+        assert "ENV.temperature.K" in t30_block["headers"]
+        assert "CONC.D.mol m-3" in t30_block["headers"]
+        assert "PHOTO.photo_D.s-1" in t30_block["headers"]
+
+    def test_round_trip_results_exactly_equal(self):
+        """
+        Solve in code, export, reload via loadJson, solve again.
+        Both result DataFrames must be exactly equal (bit-for-bit).
+        """
+        # --- Step 1: build and solve in code ---
+        box1 = _build_model()
+        df1 = box1.solve()
+
+        # --- Step 2: export to v1 JSON dict ---
+        config = box1.to_config()
+
+        # Verify it is JSON-serializable (no NaN/inf that would break JSON)
+        config_json = json.dumps(config)
+
+        # --- Step 3: reload from exported JSON ---
+        with tempfile.NamedTemporaryFile(
+            mode="w", suffix=".json", delete=False
+        ) as f:
+            f.write(config_json)
+            tmp_path = f.name
+
+        try:
+            box2 = MusicBox()
+            box2.loadJson(tmp_path)
+            df2 = box2.solve()
+        finally:
+            os.unlink(tmp_path)
+
+        # --- Step 4: compare exactly equal ---
+        assert df1.shape == df2.shape, (
+            f"Result shapes differ: {df1.shape} vs {df2.shape}"
+        )
+
+        # Sort columns so ordering differences don't cause false failures
+        df1_sorted = df1.reindex(sorted(df1.columns), axis=1)
+        df2_sorted = df2.reindex(sorted(df2.columns), axis=1)
+
+        pd.testing.assert_frame_equal(
+            df1_sorted, df2_sorted,
+            check_exact=True,
+            obj="solve() results after export/reload round-trip",
+        )