diff --git a/doc/example/example_petablint.ipynb b/doc/example/example_petablint.ipynb
index ed20b0d9..6925a433 100644
--- a/doc/example/example_petablint.ipynb
+++ b/doc/example/example_petablint.ipynb
@@ -16,75 +16,26 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "usage: petablint [-h] [-v] [-s SBML_FILE_NAME] [-m MEASUREMENT_FILE_NAME]\r\n",
-      "                 [-c CONDITION_FILE_NAME] [-p PARAMETER_FILE_NAME]\r\n",
-      "                 [-y YAML_FILE_NAME | -n MODEL_NAME] [-d DIRECTORY]\r\n",
-      "\r\n",
-      "Check if a set of files adheres to the PEtab format.\r\n",
-      "\r\n",
-      "optional arguments:\r\n",
-      "  -h, --help            show this help message and exit\r\n",
-      "  -v, --verbose         More verbose output\r\n",
-      "  -s SBML_FILE_NAME, --sbml SBML_FILE_NAME\r\n",
-      "                        SBML model filename\r\n",
-      "  -m MEASUREMENT_FILE_NAME, --measurements MEASUREMENT_FILE_NAME\r\n",
-      "                        Measurement table\r\n",
-      "  -c CONDITION_FILE_NAME, --conditions CONDITION_FILE_NAME\r\n",
-      "                        Conditions table\r\n",
-      "  -p PARAMETER_FILE_NAME, --parameters PARAMETER_FILE_NAME\r\n",
-      "                        Parameter table\r\n",
-      "  -y YAML_FILE_NAME, --yaml YAML_FILE_NAME\r\n",
-      "                        PEtab YAML problem filename\r\n",
-      "  -n MODEL_NAME, --model-name MODEL_NAME\r\n",
-      "                        Model name where all files are in the working\r\n",
-      "                        directory and follow PEtab naming convention.\r\n",
-      "                        Specifying -[smcp] will override defaults\r\n",
-      "  -d DIRECTORY, --directory DIRECTORY\r\n"
-     ]
-    }
-   ],
    "source": [
     "!petablint -h"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "markdown",
    "metadata": {},
-   "source": [
-    "Let's look at an example: In the example_Fujita folder, we have a PEtab configuration file `Fujita.yaml` telling which files belong to the Fujita model:"
-   ]
+   "source": "Let's look at an example: In the `example_Fujita/` directory, we have a PEtab problem configuration file `Fujita.yaml` telling which files belong to the \"Fujita\" problem:"
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "parameter_file: Fujita_parameters.tsv\r\n",
-      "petab_version: 0.0.0a17\r\n",
-      "problems:\r\n",
-      "- condition_files:\r\n",
-      "  - Fujita_experimentalCondition.tsv\r\n",
-      "  measurement_files:\r\n",
-      "  - Fujita_measurementData.tsv\r\n",
-      "  sbml_files:\r\n",
-      "  - Fujita_model.xml\r\n"
-     ]
-    }
-   ],
    "source": [
     "!cat example_Fujita/Fujita.yaml"
-   ]
+   ],
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "markdown",
@@ -95,20 +46,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\u001b[0m"
-     ]
-    }
-   ],
-   "source": [
-    "!petablint -y example_Fujita/Fujita.yaml"
-   ]
+   "source": "!petablint example_Fujita/Fujita.yaml",
+   "outputs": [],
+   "execution_count": null
   },
   {
    "cell_type": "markdown",