From 47ae5d56c2f99ad88cc342cc1cef8d2ec528b30d Mon Sep 17 00:00:00 2001
From: Paul Jonas Jost <70631928+PaulJonasJost@users.noreply.github.com>
Date: Wed, 23 Oct 2024 13:50:00 +0200
Subject: [PATCH] Updated PEtab.jl to work with version 3.x (#1489)

* Updated Julia version and PEtab.jl version to latest non breaking version

* Updated strings and functions. Changed to version 3.x. Slightly adjusted tolerances in a test

* removed specified version from petab.jl

* remove caching as a test
---
 .github/workflows/ci.yml                     |  7 ++-----
 pypesto/objective/julia/petabJl.py           | 16 ++++++++--------
 pypesto/objective/julia/petab_jl_importer.py |  2 +-
 test/julia/test_pyjulia.py                   |  6 +++++-
 4 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b274e2a61..4db56ab55 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -199,17 +199,14 @@ jobs:
     - name: Install julia
       uses: julia-actions/setup-julia@v2
       with:
-        version: 1.9
-
-    - name: Cache Julia
-      uses: julia-actions/cache@v2
+        version: 1.11
 
     - name: Install dependencies
       run: .github/workflows/install_deps.sh
 
     - name: Install PEtabJL dependencies
       run: >
-        julia -e 'using Pkg; Pkg.add(Pkg.PackageSpec(;name="PEtab", version="2.5.0"));
+        julia -e 'using Pkg; Pkg.add("PEtab");
         Pkg.add("OrdinaryDiffEq"); Pkg.add("Sundials")'
 
     - name: Run tests
diff --git a/pypesto/objective/julia/petabJl.py b/pypesto/objective/julia/petabJl.py
index 84de76999..f9ddefb22 100644
--- a/pypesto/objective/julia/petabJl.py
+++ b/pypesto/objective/julia/petabJl.py
@@ -62,10 +62,10 @@ def __init__(
         self.petab_jl_problem = petab_jl_problem
 
         # get functions
-        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)
+        fun = self.petab_jl_problem.nllh
+        grad = self.petab_jl_problem.grad
+        hess = self.petab_jl_problem.hess
+        x_names = np.asarray(self.petab_jl_problem.xnames)
 
         # call the super super super constructor
         super(JuliaObjective, self).__init__(
@@ -105,10 +105,10 @@ def __setstate__(self, state):
         self.petab_jl_problem = petab_jl_problem
 
         # get functions
-        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)
+        fun = self.petab_jl_problem.nllh
+        grad = self.petab_jl_problem.grad
+        hess = self.petab_jl_problem.hess
+        x_names = np.asarray(self.petab_jl_problem.xnames)
 
         # 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
index 3d76900b5..b5b0b444e 100644
--- a/pypesto/objective/julia/petab_jl_importer.py
+++ b/pypesto/objective/julia/petab_jl_importer.py
@@ -309,7 +309,7 @@ def _write_julia_file(
         f"found at {link_to_options}\n"
         f"petabProblem = PEtabODEProblem(\n\t"
         f"petabModel,\n\t"
-        f"ode_solver=ODESolver({odeSolvOpt_str}),\n\t"
+        f"odesolver=ODESolver({odeSolvOpt_str}),\n\t"
         f"gradient_method=:{options['gradient_method']},\n\t"
         f"hessian_method=:{options['hessian_method']},\n\t"
         f"sparse_jacobian={options['sparse_jacobian']},\n\t"
diff --git a/test/julia/test_pyjulia.py b/test/julia/test_pyjulia.py
index dc0abcdef..8325a44e8 100644
--- a/test/julia/test_pyjulia.py
+++ b/test/julia/test_pyjulia.py
@@ -59,7 +59,11 @@ def test_pyjulia_pipeline():
 
     # check with analytical value
     p_opt = obj.get("p_opt")
-    assert np.allclose(result.optimize_result[0].x, p_opt)  # noqa: S101
+    assert np.allclose(
+        result.optimize_result[0].x,
+        p_opt,
+        atol=1e-6,  # noqa:  S101
+    )
 
 
 def test_petabJL_interface():