diff --git a/sbmltoodejax/modulegeneration.py b/sbmltoodejax/modulegeneration.py index 2afd37d..fa448b1 100644 --- a/sbmltoodejax/modulegeneration.py +++ b/sbmltoodejax/modulegeneration.py @@ -14,7 +14,7 @@ def GenerateModel(modelData, outputFilePath, atol: float=1e-6, rtol: float = 1e-12, mxstep: int = 5000000, - solver_type: str = 'odeint', + solver_type: str = 'diffrax', diffrax_solver: str = 'Tsit5' ): """ @@ -591,14 +591,4 @@ def ParseRHS(rawRateLaw, extended_param_names=[], reaction_name=None, yvar="y", outputFile.write("\t\treturn ys, ws, ts\n\n") # ================================================================================================================================ - outputFile.close() - - - - - - - - - - + outputFile.close() \ No newline at end of file diff --git a/sbmltoodejax/utils.py b/sbmltoodejax/utils.py index 46bfc55..a30fdad 100644 --- a/sbmltoodejax/utils.py +++ b/sbmltoodejax/utils.py @@ -6,7 +6,7 @@ def generate_biomodel(model_idx, model_fp="jax_model.py", vary_constant_reactants=False, vary_boundary_reactants=False, deltaT=0.1, atol=1e-6, rtol=1e-12, mxstep=5000000, - solver_type='odeint', diffrax_solver='Tsit5'): + solver_type='diffrax', diffrax_solver='Tsit5'): """Calls the `sbmltoodejax.modulegeneration_3.GenerateModel` for a SBML model hosted on the BioModel website and indexed by the provided `model_idx`. Args: @@ -16,7 +16,7 @@ def generate_biomodel(model_idx, model_fp="jax_model.py", atol (float, optional): parameter passed to `sbmltoodejax.modulegeneration.GenerateModel`. Default to 1e-6. rtol (float, optional): parameter passed to `sbmltoodejax.modulegeneration.GenerateModel`. Default to 1e-12. mxstep (int, optional): parameter passed to `sbmltoodejax.modulegeneration.GenerateModel`. Default to 5000000. - solver_type (str, optional): parameter passed to `sbmltoodejax.modulegeneration.GenerateModel`. Default to 'odeint'. + solver_type (str, optional): parameter passed to `sbmltoodejax.modulegeneration.GenerateModel`. Default to 'diffrax'. diffrax_solver (str, optional): parameter passed to `sbmltoodejax.modulegeneration.GenerateModel`. Default to 'Tsit5'. Returns: @@ -35,7 +35,7 @@ def generate_biomodel(model_idx, model_fp="jax_model.py", def load_biomodel(model_idx, model_fp="jax_model.py", vary_constant_reactants=False, vary_boundary_reactants=False, deltaT=0.1, atol=1e-6, rtol=1e-12, mxstep=5000000, - solver_type='odeint', diffrax_solver='Tsit5'): + solver_type='diffrax', diffrax_solver='Tsit5'): """Calls the generate_biomodel function for a SBML model hosted on the BioModel website and indexed by the provided `model_idx`, then loads and returns the generated `model` module and `y0`, `w0`, `c` variables. @@ -46,6 +46,8 @@ def load_biomodel(model_idx, model_fp="jax_model.py", atol (float, optional): parameter passed to `generate_biomodel`. Default to 1e-6. rtol (float, optional): parameter passed to `generate_biomodel`. Default to 1e-12. mxstep (int, optional): parameter passed to `generate_biomodel`. Default to 5000000. + solver_type (str, optional): parameter passed to `sbmltoodejax.modulegeneration.GenerateModel`. Default to 'diffrax'. + diffrax_solver (str, optional): parameter passed to `sbmltoodejax.modulegeneration.GenerateModel`. Default to 'Tsit5'. Returns: tuple containing