review: remove notebook outputs

doc/examples/README.md

@@ -0,0 +1 @@
+These notebooks need to be run to see the output. Pre-computed output can be viewed in the documentation, at https://petab-select.readthedocs.io/en/stable/examples.html

doc/examples/example_cli_famos.ipynb

@@ -22,7 +22,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "1f04dce0",
    "metadata": {},
    "outputs": [],
@@ -44,7 +44,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "a81560e6",
    "metadata": {},
    "outputs": [],
@@ -109,83 +109,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "bb1a5144",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Executing iteration 1\n",
-      "Executing iteration 2\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "petab_select/petab_select/candidate_space.py:1143: RuntimeWarning: Model `model_subspace_1-1100110111000111` has been previously excluded from the candidate space so is skipped here.\n",
-      "  return_value = self.inner_candidate_space.consider(model)\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Executing iteration 3\n",
-      "Executing iteration 4\n",
-      "Executing iteration 5\n",
-      "Executing iteration 6\n",
-      "Executing iteration 7\n",
-      "Executing iteration 8\n",
-      "Executing iteration 9\n",
-      "Executing iteration 10\n",
-      "Executing iteration 11\n",
-      "Executing iteration 12\n",
-      "Executing iteration 13\n",
-      "Executing iteration 14\n",
-      "Executing iteration 15\n",
-      "Executing iteration 16\n",
-      "Executing iteration 17\n",
-      "Executing iteration 18\n",
-      "Executing iteration 19\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "petab_select/petab_select/candidate_space.py:1143: RuntimeWarning: Model `model_subspace_1-0001011010010010` has been previously excluded from the candidate space so is skipped here.\n",
-      "  return_value = self.inner_candidate_space.consider(model)\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Executing iteration 20\n",
-      "Executing iteration 21\n",
-      "Executing iteration 22\n",
-      "Executing iteration 23\n",
-      "Executing iteration 24\n",
-      "Executing iteration 25\n",
-      "Executing iteration 26\n",
-      "Executing iteration 27\n",
-      "Executing iteration 28\n",
-      "Executing iteration 29\n",
-      "Executing iteration 30\n",
-      "Executing iteration 31\n",
-      "Executing iteration 32\n",
-      "Executing iteration 33\n",
-      "Executing iteration 34\n",
-      "Executing iteration 35\n",
-      "Executing iteration 36\n",
-      "Executing iteration 37\n",
-      "Model selection has terminated.\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "%%bash -s \"$petab_select_problem_yaml\" \"$output_path_str\"\n",
     "petab_select_problem_yaml=$1\n",
@@ -231,7 +158,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "id": "93caf071",
    "metadata": {},
    "outputs": [],
@@ -241,7 +168,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "id": "cb61d0f7",
    "metadata": {},
    "outputs": [],