Doc: Clear petab notebook output (#1271)

* Doc: Clear petab notebook output A subset of #1246. Co-authored-by: Doresic <[email protected]> * some cleanup * fix name collision for Boehm model (used with different observation model in different notebooks) * pin ipykernel to avoid `zmq.error.ZMQError: Too many open files` issues
ICB-DCM · Jan 9, 2024 · 8d6f5a0 · 8d6f5a0
1 parent 9e27528
commit 8d6f5a0
Show file tree

Hide file tree

Showing 3 changed files with 65 additions and 223 deletions.
diff --git a/doc/example/hierarchical.ipynb b/doc/example/hierarchical.ipynb
@@ -165,15 +165,23 @@
    "outputs": [],
    "source": [
     "# Create a pypesto problem with hierarchical optimization (`problem`)\n",
-    "importer = PetabImporter(petab_problem_hierarchical, hierarchical=True)\n",
+    "importer = PetabImporter(\n",
+    "    petab_problem_hierarchical,\n",
+    "    hierarchical=True,\n",
+    "    model_name=\"Boehm_JProteomeRes2014_hierarchical\",\n",
+    ")\n",
     "problem = importer.create_problem(verbose=False)\n",
     "# set option to compute objective function gradients using adjoint sensitivity analysis\n",
     "problem.objective.amici_solver.setSensitivityMethod(\n",
     "    amici.SensitivityMethod.adjoint\n",
     ")\n",
     "\n",
     "# ... and create another pypesto problem without hierarchical optimization (`problem2`)\n",
-    "importer2 = PetabImporter(petab_problem, hierarchical=False)\n",
+    "importer2 = PetabImporter(\n",
+    "    petab_problem,\n",
+    "    hierarchical=False,\n",
+    "    model_name=\"Boehm_JProteomeRes2014_hierarchical\",\n",
+    ")\n",
     "problem2 = importer2.create_problem(verbose=False)\n",
     "problem2.objective.amici_solver.setSensitivityMethod(\n",
     "    amici.SensitivityMethod.adjoint\n",