Add quick links within model_usage.ipynb

.github/workflows/build.yaml

@@ -77,11 +77,12 @@ jobs:
         cache-environment: true
         environment-file: dev/env-py38.yaml
         post-cleanup: 'all'
-    - name: additional setup
+    - name: additional setup spec
       run: |
         conda remove --yes --force bioimageio.spec || true  # allow failure for cached env
         pip install --no-deps git+https://github.com/bioimage-io/spec-bioimage-io
-        pip install --no-deps -e .
+    - name: additional setup core
+      run: pip install --no-deps -e .
     - name: pytest-spec-main
       run: pytest --disable-pytest-warnings
 

bioimageio/core/VERSION

@@ -1,3 +1,3 @@
 {
-    "version": "0.6.9"
+    "version": "0.6.10"
 }

bioimageio/core/prediction.py

@@ -161,7 +161,7 @@ def predict_many(
                 f"Missing `{{member_id}}` in save_output_path={save_output_path}"
             )
 
-        if not isinstance(inputs, collections.Mapping) and "{sample_id}" not in str(
+        if not isinstance(inputs, collections.abc.Mapping) and "{sample_id}" not in str(
             save_output_path
         ):
             raise ValueError(
@@ -179,7 +179,7 @@ def predict_many(
 
         pp = create_prediction_pipeline(model)
 
-    if not isinstance(inputs, collections.Mapping):
+    if not isinstance(inputs, collections.abc.Mapping):
         sample_id = str(sample_id)
         if "{i}" not in sample_id and "{i:" not in sample_id:
             sample_id += "{i:03}"

dev/env-py38.yaml

@@ -4,7 +4,7 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - bioimageio.spec>=0.5.3.2
+  - bioimageio.spec>=0.5.3.3
   - black
   - crick # uncommented
   - filelock

dev/env-tf.yaml

@@ -4,7 +4,7 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - bioimageio.spec>=0.5.3.2
+  - bioimageio.spec>=0.5.3.3
   - black
   # - crick  # currently requires python<=3.9
   - filelock

dev/env-wo-python.yaml

@@ -4,7 +4,7 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - bioimageio.spec>=0.5.3.2
+  - bioimageio.spec>=0.5.3.3
   - black
   # - crick  # currently requires python<=3.9
   - filelock

dev/env.yaml

@@ -2,7 +2,7 @@ name: core
 channels:
   - conda-forge
 dependencies:
-  - bioimageio.spec>=0.5.3.2
+  - bioimageio.spec>=0.5.3.3
   - black
   # - crick  # currently requires python<=3.9
   - filelock

example/model_usage.ipynb

@@ -6,7 +6,11 @@
    "source": [
     "# Bioimage Model Zoo Core  Example notebook\n",
     "\n",
-    "This notebook shows how to interact with the `bioimageio.core` programmatically to explore, load, use, and export content from the [BioImage Model Zoo](https://bioimage.io)."
+    "This notebook shows how to interact with the `bioimageio.core` programmatically to explore, load, use, and export content from the [BioImage Model Zoo](https://bioimage.io).\n",
+    "\n",
+    "\n",
+    "quick links:\n",
+    "- [Create an input sample for a given model](#create_sample_for_model)"
    ]
   },
   {
@@ -30,9 +34,10 @@
    "outputs": [],
    "source": [
     "try:\n",
-    "    import bioimageio.core\n",
-    "    import torch\n",
     "    import matplotlib\n",
+    "    import torch\n",
+    "\n",
+    "    import bioimageio.core\n",
     "except ImportError:\n",
     "    %pip install bioimageio.core==0.6.7 torch==2.3.1 matplotlib==3.9.0"
    ]
@@ -73,11 +78,13 @@
    "outputs": [],
    "source": [
     "# Load general dependencies\n",
-    "from imageio.v2 import imread\n",
-    "from bioimageio.spec.utils import download\n",
     "from pprint import pprint\n",
+    "\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
+    "from imageio.v2 import imread\n",
+    "\n",
+    "from bioimageio.spec.utils import download\n",
     "\n",
     "\n",
     "# Function to display input and prediction output images\n",
@@ -300,8 +307,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from bioimageio.spec.utils import load_array\n",
     "from bioimageio.spec.model import v0_5\n",
+    "from bioimageio.spec.utils import load_array\n",
     "\n",
     "assert isinstance(model, v0_5.ModelDescr)\n",
     "input_image = load_array(model.inputs[0].test_tensor)\n",
@@ -359,7 +366,8 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "`bioimageio.core` provides the helper function `create_sample_for_model` to automatically create the `Sample` for the given model."
+    "`bioimageio.core` provides the helper function `create_sample_for_model` to automatically create the `Sample` for the given model.\n",
+    "<a id='create_sample_for_model'></a>"
    ]
   },
   {

setup.py

@@ -29,7 +29,7 @@
     ],
     packages=find_namespace_packages(exclude=["tests"]),
     install_requires=[
-        "bioimageio.spec ==0.5.3.2",
+        "bioimageio.spec ==0.5.3.3",
         "imageio>=2.10",
         "loguru",
         "numpy",