tidying up

README.md

@@ -49,6 +49,7 @@ def get_steady_state_from_params(parameters: PyTree):
 jacobian = jax.jacrev(get_steady_state_from_params)(model.parameters)
 
 ```
+
 ### Load a kinetic model from an sbml file
 
 ```python

scripts/sbml_demo.py

@@ -1,19 +1,22 @@
+from pathlib import Path
+
 import jax
 import jax.numpy as jnp
-from enzax.sbml import load_libsbml_model, sbml_to_enzax
+
+from enzax.sbml import load_libsbml_model_from_file, sbml_to_enzax
 from enzax.steady_state import get_kinetic_model_steady_state
 
 jax.config.update("jax_enable_x64", True)
 
-file_path = "tests/data/brusselator.xml"
-model_libsbml = load_libsbml_model(file_path)
+file_path = Path("tests") / "data" / "exampleode.xml"
+model_libsbml = load_libsbml_model_from_file(file_path)
 model = sbml_to_enzax(model_libsbml)
 
 y0 = jnp.array([2.0, 4])
-model.flux(y0)
+print(f"Flux at {str(y0)}: " + str(model.flux(y0)))
 
-model.dcdt(t=1, conc=y0)
+print(f"dcdt at {str(y0)}, t=1: " + str(model.dcdt(t=1, conc=y0)))
 
 guess = jnp.full((2), 0.01)
 steady_state = get_kinetic_model_steady_state(model, guess)
-print(steady_state)
+print("Steady state: " + str(steady_state))

tests/test_sbml.py

@@ -17,7 +17,7 @@
     ],
 )
 def test_load_libsbml_model(file_path):
-    sbml.load_libsbml_model(file_path)
+    sbml.load_libsbml_model_from_file(file_path)
 
 
 @pytest.mark.parametrize(
@@ -31,7 +31,7 @@ def test_load_libsbml_model(file_path):
     ],
 )
 def test_sbml_to_enzax(path, expected, guess):
-    libsbml_model = sbml.load_libsbml_model(path)
+    libsbml_model = sbml.load_libsbml_model_from_file(path)
     model = sbml.sbml_to_enzax(libsbml_model)
     steady_state = get_kinetic_model_steady_state(model, guess)
     assert jnp.isclose(steady_state, expected).all()