Execute all notebooks / clear notebook output

.readthedocs.yml

@@ -26,4 +26,4 @@ build:
     - libhdf5-serial-dev
     - swig
   tools:
-    python: "3.10"
+    python: "3.11"

doc/example/amici.ipynb

@@ -11,19 +11,14 @@
    "source": [
     "# AMICI in pyPESTO\n",
     "\n",
-    "---\n",
-    "---\n",
     "**After this notebook you can...**\n",
+    "\n",
     "* ...create a pyPESTO problem directly from an AMICI model or through PEtab.\n",
     "* ...perform parameter estimation of your amici model and adjust advanced settings for this.\n",
     "* ...evaluate an optimization through basic visualizations.\n",
     "* ...inspect parameter uncertainties through profile likelihoods and MCMC sampling.\n",
     "\n",
-    "---\n",
-    "---\n",
-    "\n",
-    "\n",
-    "In order to run optimizations and/or uncertainty analysis, we turn to pyPESTO (**P**arameter **ES**timation **TO**olbox for python).\n",
+    "To run optimizations and/or uncertainty analysis, we turn to pyPESTO (**P**arameter **ES**timation **TO**olbox for python).\n",
     "\n",
     "pyPESTO is a Python tool for parameter estimation. It provides an interface to the model simulation tool [AMICI](https://github.com/AMICI-dev/AMICI) for the simulation of Ordinary Differential Equation (ODE) models specified in the SBML format. With it, we can optimize our model parameters given measurement data, we can do uncertainty analysis via profile likelihoods and/or through sampling methods. pyPESTO provides an interface to many optimizers, global and local, such as e.g. SciPy optimizers, Fides and Pyswarm. Additionally, it interfaces samplers such as pymc, emcee and some of its own samplers."
    ]

doc/example/censored_data.ipynb

@@ -261,7 +261,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.10"
+   "version": "3.11.2"
   },
   "vscode": {
    "interpreter": {