Merge branch 'develop' into update_julia_objective

ICB-DCM · Oct 23, 2024 · d0f7ff0 · d0f7ff0
2 parents 251299f + 47ae5d5
commit d0f7ff0
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Showing 4 changed files with 16 additions and 15 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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():