redirect stderr to stdout for better output comparison

Author: FynnBe

example/dataset_creation.ipynb

@@ -11,13 +11,31 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Create `DatasetDescr` object "
+    "#### Setup"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 1,
    "metadata": {},
+   "outputs": [],
+   "source": [
+    "import sys\n",
+    "# redirect stderr to stdout for better output comparison across runs with 'pytest --nbval'\n",
+    "sys.stderr = sys.stdout"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Create `DatasetDescr` object "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -142,7 +160,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
@@ -173,7 +191,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -245,7 +263,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {

example/load_model_and_create_your_own.ipynb

@@ -81,6 +81,9 @@
     "\n",
     "from bioimageio.spec.utils import download\n",
     "\n",
+    "# redirect stderr to stdout for better output comparison across runs with 'pytest --nbval'\n",
+    "sys.stderr = sys.stdout\n",
+    "\n",
     "# enable and configure loguru logging for bioimageio.spec and bioimageio.core\n",
     "logger.enable(\"bioimageio\")\n",
     "logger.remove()\n",
@@ -735,7 +738,7 @@
    },
    "outputs": [
     {
-     "name": "stderr",
+     "name": "stdout",
      "output_type": "stream",
      "text": [
       "Level 35\u001b[0m | \u001b[36mfield_warning\u001b[0m - description: Needs to be filled for FAIR compliance\u001b[0m\n",
@@ -753,7 +756,7 @@
      "traceback": [
       "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
       "\u001b[1;31mValidationError\u001b[0m                           Traceback (most recent call last)",
-      "Cell \u001b[1;32mIn[11], line 4\u001b[0m\n\u001b[0;32m      1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21;01mpydantic\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m ValidationError\n\u001b[0;32m      2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21;01mbioimageio\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mspec\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmodel\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mv0_5\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m ModelDescr\n\u001b[1;32m----> 4\u001b[0m _ \u001b[38;5;241m=\u001b[39m \u001b[43mModelDescr\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m  \u001b[38;5;66;03m# pyright: ignore[reportCallIssue]\u001b[39;00m\n",
+      "Cell \u001b[1;32mIn[11], line 3\u001b[0m\n\u001b[0;32m      1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21;01mbioimageio\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mspec\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmodel\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mv0_5\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m ModelDescr\n\u001b[1;32m----> 3\u001b[0m _ \u001b[38;5;241m=\u001b[39m \u001b[43mModelDescr\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m  \u001b[38;5;66;03m# pyright: ignore[reportCallIssue]\u001b[39;00m\n",
       "\u001b[1;31mValidationError\u001b[0m: 4 validation errors for ModelDescr:\nname\n  Field required [input={'format_version': '0.5.5', 'type': 'model'}]\ninputs\n  Field required [input={'format_version': '0.5.5', 'type': 'model'}]\noutputs\n  Field required [input={'format_version': '0.5.5', 'type': 'model'}]\nweights\n  Field required [input={'format_version': '0.5.5', 'type': 'model'}]"
      ]
     }
@@ -796,7 +799,7 @@
    },
    "outputs": [
     {
-     "name": "stderr",
+     "name": "stdout",
      "output_type": "stream",
      "text": [
       "Level 35\u001b[0m | \u001b[36mfield_warning\u001b[0m - test_tensor: Needs to be filled for FAIR compliance\u001b[0m\n",
@@ -891,7 +894,7 @@
    },
    "outputs": [
     {
-     "name": "stderr",
+     "name": "stdout",
      "output_type": "stream",
      "text": [
       "Level 35\u001b[0m | \u001b[36mfield_warning\u001b[0m - test_tensor: Needs to be filled for FAIR compliance\u001b[0m\n",
@@ -1186,18 +1189,12 @@
     }
    },
    "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Level 35\u001b[0m | \u001b[36mfield_warning\u001b[0m - tags: Needs to be filled for FAIR compliance\u001b[0m\n",
-      "Level 30\u001b[0m | \u001b[36mv0_5\u001b[0m - covers: Failed to generate cover image(s): Failed to construct cover image from shape (1, 2, 256, 256)\u001b[0m\n"
-     ]
-    },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
+      "Level 35\u001b[0m | \u001b[36mfield_warning\u001b[0m - tags: Needs to be filled for FAIR compliance\u001b[0m\n",
+      "Level 30\u001b[0m | \u001b[36mv0_5\u001b[0m - covers: Failed to generate cover image(s): Failed to construct cover image from shape (1, 2, 256, 256)\u001b[0m\n",
       "created 'My cool Model'\n"
      ]
     }
@@ -1344,7 +1341,7 @@
    },
    "outputs": [
     {
-     "name": "stderr",
+     "name": "stdout",
      "output_type": "stream",
      "text": [
       "\u001b[33m\u001b[1mWARNING \u001b[0m | \u001b[36m_get_conda_env\u001b[0m - \u001b[33m\u001b[1mUPDATE NEEDED: Leaving torchvision and torchaudio unpinned for pytorch==2.8.0\u001b[0m\n",