add clear error printing in cell matching nb

Author: rcpeene

docs/embargoed/cell_matching.ipynb

@@ -259,41 +259,12 @@
    "metadata": {
     "scrolled": true
    },
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "WARNING:root:many=True not supported from argparse\n",
-      "INFO:NwayMatching:NWAY_COMMIT_SHA None\n",
-      "INFO:NwayMatching:Nway matching version 0.6.0\n",
-      "WARNING:root:many=True not supported from argparse\n",
-      "WARNING:root:many=True not supported from argparse\n",
-      "INFO:PairwiseMatching:Matching 1193675753 to 1194754135\n",
-      "INFO:PairwiseMatching:Matching 1193675753 to 1194754135: best registration was ['Crop', 'CLAHE', 'PhaseCorrelate']\n",
-      "INFO:NwayMatching:registration success(1) or failure (0):\n",
-      "   0  1\n",
-      "0  1  1\n",
-      "1  1  1\n",
-      "id map{\n",
-      "  \"0\": 1193675753,\n",
-      "  \"1\": 1194754135\n",
-      "}\n",
-      "INFO:NwayMatching:Nway matching is done!\n",
-      "INFO:NwayMatching:Creating match summary plots\n",
-      "WARNING:root:setting Dict fields not supported from argparse\n",
-      "c:\\Users\\carter.peene\\AppData\\Local\\Programs\\Python\\Python39\\lib\\site-packages\\argschema\\utils.py:346: FutureWarning: '--nway_output.nway_matches' is using old-style command-line syntax with each element as a separate argument. This will not be supported in argschema after 2.0. See http://argschema.readthedocs.io/en/master/user/intro.html#command-line-specification for details.\n",
-      "  warnings.warn(warn_msg, FutureWarning)\n",
-      "WARNING:root:many=True not supported from argparse\n",
-      "INFO:NwayMatching:wrote matching_output\\nway_match_fraction_plot_2025_06_24_16_15_42.png\n",
-      "INFO:NwayMatching:wrote matching_output\\nway_warp_overlay_plot_2025_06_24_16_15_42.png\n",
-      "INFO:NwayMatching:wrote matching_output\\nway_warp_summary_plot_2025_06_24_16_15_42.png\n",
-      "INFO:NwayMatching:wrote ./output.json\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
-    "!python -m nway.nway_matching --input_json input.json --output_json \"./output.json\" --output_dir matching_output"
+    "res = !python -m nway.nway_matching --input_json input.json --output_json \"./output.json\" --output_dir matching_output\n",
+    "\n",
+    "if not os.path.exists(\"output.json\"):\n",
+    "    raise RuntimeError(\"output.json was not created!\\nCommand output:\\n\" + \"\\n\".join(res))"
    ]
   },
   {
@@ -364,7 +335,7 @@
     {
      "data": {
       "text/plain": [
-       "<matplotlib.image.AxesImage at 0x1690c1a3280>"
+       "<matplotlib.image.AxesImage at 0x1b146645640>"
       ]
      },
      "execution_count": 13,
@@ -400,7 +371,7 @@
     {
      "data": {
       "text/plain": [
-       "<matplotlib.image.AxesImage at 0x1690bdcc580>"
+       "<matplotlib.image.AxesImage at 0x1b146632250>"
       ]
      },
      "execution_count": 14,