Changelog

Version 3.0.0

Version 3.0.0 introduces breaking changes compared to the 2.x series. The following changes may require updates to existing configurations and code:

• The Conditions and EvolvingConditions classes have been removed.

• The callback functionality has been removed from solve().

• CSV files now require a time.s column.

• Column naming conventions have changed from square brackets to dots, e.g.:

  CONC.A [mol m-3]  ->  CONC.A.mol m-3
  

• A unified conditions API is now provided via set_condition(), set_conditions(), and add_conditions().

Users upgrading from 2.x should update their input files, analysis scripts, and any direct uses of the old conditions or callback APIs to the new interfaces described above.

JSON Configuration Changes

The JSON configuration format has been simplified. The old sections environmental conditions, initial conditions, and evolving conditions have been replaced with a single unified conditions section.

Old format (2.x):

{
  "environmental conditions": {
    "temperature": {"initial value [K]": 298.15},
    "pressure": {"initial value [Pa]": 101325.0}
  },
  "initial conditions": {
    "filepaths": ["initial_concentrations.csv"]
  },
  "evolving conditions": {
    "filepaths": ["evolving_conditions.csv"]
  }
}

New format (3.x):

{
  "conditions": {
    "data": [
      {
        "headers": ["time.s", "ENV.temperature.K", "ENV.pressure.Pa"],
        "rows": [[0.0, 298.15, 101325.0]]
      }
    ],
    "filepaths": ["conditions.csv"]
  }
}

CSV Column Naming

All CSV files must use dot-separated column names with units as the final component:

Python API Changes

Old API (2.x):

from acom_music_box import MusicBox, Conditions, EvolvingConditions

box = MusicBox()
box.loadJson("config.json")

# Old way to set conditions
box.initial_conditions.temperature = 298.15
box.initial_conditions.concentrations["A"] = 1.0
box.add_evolving_condition(3600, Conditions(temperature=310))

# Old solve with callback
result = box.solve(callback=my_callback)

New API (3.x):

from acom_music_box import MusicBox

box = MusicBox()
box.loadJson("config.json")

# New unified conditions API
box.set_condition(time=0, temperature=298.15, concentrations={"A": 1.0})
box.set_condition(time=3600, temperature=310)

# Or use DataFrame input
import pandas as pd
df = pd.DataFrame({
    "time.s": [0, 3600],
    "ENV.temperature.K": [298.15, 310],
    "CONC.A.mol m-3": [1.0, None]
})
box.set_conditions(df)

# Solve without callback
result = box.solve()