Adhere to new petabl.jl 2.0 version syntax

ICB-DCM · Oct 10, 2023 · beb8b9e · beb8b9e
1 parent d28fa0e
commit beb8b9e
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Showing 3 changed files with 19 additions and 21 deletions.
diff --git a/doc/example/conversion_reaction/PEtabJl_module.jl b/doc/example/conversion_reaction/PEtabJl_module.jl
@@ -5,15 +5,14 @@ using Sundials
 using PEtab
 
 pathYaml = "/Users/pauljonasjost/Documents/GitHub_Folders/pyPESTO/test/julia/../../doc/example/conversion_reaction/conversion_reaction.yaml"
-petabModel = readPEtabModel(pathYaml, verbose=true)
+petabModel = PEtabModel(pathYaml, verbose=true)
 
 # A full list of options for createPEtabODEProblem can be found at https://sebapersson.github.io/PEtab.jl/dev/API_choosen/#PEtab.setupPEtabODEProblem
-petabProblem = createPEtabODEProblem(
+petabProblem = PEtabODEProblem(
 	petabModel,
-	odeSolverOptions=ODESolverOptions(Rodas5P(), abstol=1e-08, reltol=1e-08, maxiters=Int64(1e4)),
-	gradientMethod=:ForwardDiff,
-	hessianMethod=:ForwardDiff,
-	sparseJacobian=nothing,
+	ode_solver=ODESolver(Rodas5P(), abstol=1e-08, reltol=1e-08, maxiters=Int64(1e4)),
+	gradient_method=:ForwardDiff,
+	hessian_method=:ForwardDiff,
 	verbose=true
 )
 

diff --git a/pypesto/objective/julia/petabJl.py b/pypesto/objective/julia/petabJl.py
@@ -61,10 +61,10 @@ def __init__(
         self.petab_jl_problem = petab_jl_problem
 
         # get functions
-        fun = self.petab_jl_problem.computeCost
-        grad = self.petab_jl_problem.computeGradient
-        hess = self.petab_jl_problem.computeHessian
-        x_names = np.asarray(self.petab_jl_problem.θ_estNames)
+        fun = self.petab_jl_problem.compute_cost
+        grad = self.petab_jl_problem.compute_gradient
+        hess = self.petab_jl_problem.compute_hessian
+        x_names = np.asarray(self.petab_jl_problem.θ_names)
 
         # call the super super super constructor
         super(JuliaObjective, self).__init__(
@@ -102,10 +102,10 @@ def __setstate__(self, state):
         self.petab_jl_problem = petab_jl_problem
 
         # get functions
-        fun = self.petab_jl_problem.computeCost
-        grad = self.petab_jl_problem.computeGradient
-        hess = self.petab_jl_problem.computeHessian
-        x_names = np.asarray(self.petab_jl_problem.θ_estNames)
+        fun = self.petab_jl_problem.compute_cost
+        grad = self.petab_jl_problem.compute_gradient
+        hess = self.petab_jl_problem.compute_hessian
+        x_names = np.asarray(self.petab_jl_problem.θ_names)
 
         # call the super super constructor
         super(JuliaObjective, self).__init__(fun, grad, hess, x_names)

diff --git a/pypesto/objective/julia/petab_jl_importer.py b/pypesto/objective/julia/petab_jl_importer.py
@@ -304,15 +304,14 @@ def _write_julia_file(
         f"using Sundials\n"
         f"using PEtab\n\n"
         f"pathYaml = \"{yaml_file}\"\n"
-        f"petabModel = readPEtabModel(pathYaml, verbose=true)\n\n"
-        f"# A full list of options for createPEtabODEProblem can be "
+        f"petabModel = PEtabModel(pathYaml, verbose=true)\n\n"
+        f"# A full list of options for PEtabODEProblem can be "
         f"found at {link_to_options}\n"
-        f"petabProblem = createPEtabODEProblem(\n\t"
+        f"petabProblem = PEtabODEProblem(\n\t"
         f"petabModel,\n\t"
-        f"odeSolverOptions=ODESolverOptions({odeSolvOpt_str}),\n\t"
-        f"gradientMethod=:{options['gradientMethod']},\n\t"
-        f"hessianMethod=:{options['hessianMethod']},\n\t"
-        f"sparseJacobian={options['sparseJacobian']},\n\t"
+        f"ode_solver=ODESolver({odeSolvOpt_str}),\n\t"
+        f"gradient_method=:{options['gradientMethod']},\n\t"
+        f"hessian_method=:{options['hessianMethod']},\n\t"
         f"verbose={options['verbose']}\n)\n\nend\n"
     )
     # write file