Merge pull request #552 from bioimage-io/cosmetic_updates

Cosmetic updates
bioimage-io · Mar 12, 2024 · e89bf57 · e89bf57
2 parents 859f5bd + b363a25
commit e89bf57
Show file tree

Hide file tree

Showing 10 changed files with 14 additions and 110 deletions.
diff --git a/bioimageio/spec/model/v0_5.py b/bioimageio/spec/model/v0_5.py
@@ -333,8 +333,6 @@ class AxisBase(NodeWithExplicitlySetFields):
 
     description: Annotated[str, MaxLen(128)] = ""
 
-    __hash__ = NodeWithExplicitlySetFields.__hash__
-
 
 class WithHalo(Node):
     halo: Annotated[int, Ge(0)] = 0

diff --git a/...dels/stardist_example_model/rdf_v0_4.yaml → ...ardist_example_model/v0_4.bioimageio.yaml b/...dels/stardist_example_model/rdf_v0_4.yaml → ...ardist_example_model/v0_4.bioimageio.yaml
diff --git a/...ls/unet2d_diff_output_shape/rdf_v0_4.yaml → ...2d_diff_output_shape/v0_4.bioimageio.yaml b/...ls/unet2d_diff_output_shape/rdf_v0_4.yaml → ...2d_diff_output_shape/v0_4.bioimageio.yaml
diff --git a/...s/models/unet2d_fixed_shape/rdf_v0_4.yaml → ...s/unet2d_fixed_shape/v0_4.bioimageio.yaml b/...s/models/unet2d_fixed_shape/rdf_v0_4.yaml → ...s/unet2d_fixed_shape/v0_4.bioimageio.yaml
diff --git a/...ions/models/unet2d_keras_tf/rdf_v0_4.yaml → ...dels/unet2d_keras_tf/v0_4.bioimageio.yaml b/...ions/models/unet2d_keras_tf/rdf_v0_4.yaml → ...dels/unet2d_keras_tf/v0_4.bioimageio.yaml
diff --git a/...ons/models/unet2d_keras_tf2/rdf_v0_4.yaml → ...els/unet2d_keras_tf2/v0_4.bioimageio.yaml b/...ons/models/unet2d_keras_tf2/rdf_v0_4.yaml → ...els/unet2d_keras_tf2/v0_4.bioimageio.yaml
diff --git a/.../models/unet2d_multi_tensor/rdf_v0_4.yaml → .../unet2d_multi_tensor/v0_4.bioimageio.yaml b/.../models/unet2d_multi_tensor/rdf_v0_4.yaml → .../unet2d_multi_tensor/v0_4.bioimageio.yaml
diff --git a/example_descriptions/models/unet2d_nuclei_broad/rdf.yaml.wip b/example_descriptions/models/unet2d_nuclei_broad/rdf.yaml.wip
diff --git a/example_use/load_model_and_create_your_own.ipynb b/example_use/load_model_and_create_your_own.ipynb
@@ -45,11 +45,13 @@
     "else:\n",
     "    raise NotImplementedError(example_model_id)\n",
     "\n",
-    "model = load_description(url, format_version=\"latest\")\n",
-    "if isinstance(model, InvalidDescr):\n",
-    "    raise ValueError(f\"Failed to load {example_model_id}:\\n{model.validation_summary.format()}\")\n",
-    "elif not isinstance(model, ModelDescr):\n",
+    "loaded_descr = load_description(url, format_version=\"latest\")\n",
+    "if isinstance(loaded_descr, InvalidDescr):\n",
+    "    raise ValueError(f\"Failed to load {example_model_id}:\\n{loaded_descr.validation_summary.format()}\")\n",
+    "elif not isinstance(loaded_descr, ModelDescr):\n",
     "    raise ValueError(\"This notebook expects a model description\")\n",
+    "else:\n",
+    "    model = loaded_descr\n",
     "\n",
     "print(f\"loaded '{model.name}'\")\n"
    ]
@@ -264,12 +266,12 @@
    "source": [
     "output_axes = [\n",
     "    BatchAxis(),\n",
-    "    ChannelAxis(channel_names=[\"membrane\"])]\n",
+    "    ChannelAxis(channel_names=[Identifier(\"membrane\")])]\n",
     "if example_model_id == \"impartial-shrimp\":\n",
     "    output_axes += [\n",
-    "        SpaceInputAxis(id=AxisId(\"z\"), size=ParameterizedSize(min=16, step=8)),  # implicitly same size as raw.z as it is parametrized the same.\n",
-    "        SpaceInputAxis(id=AxisId('y'), size=ParameterizedSize(min=144, step=72)),\n",
-    "        SpaceInputAxis(id=AxisId('x'), size=ParameterizedSize(min=144, step=72))\n",
+    "        SpaceOutputAxis(id=AxisId(\"z\"), size=ParameterizedSize(min=16, step=8)),  # implicitly same size as raw.z as it is parametrized the same.\n",
+    "        SpaceOutputAxis(id=AxisId('y'), size=ParameterizedSize(min=144, step=72)),\n",
+    "        SpaceOutputAxis(id=AxisId('x'), size=ParameterizedSize(min=144, step=72))\n",
     "    ]\n",
     "elif example_model_id == \"pioneering-rhino\":\n",
     "    output_axes += [\n",
@@ -320,12 +322,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from bioimageio.spec.model.v0_5 import LicenseId\n",
+    "\n",
     "my_model_descr = ModelDescr(\n",
     "    name=\"My cool model\",\n",
     "    description=\"A test model for demonstration purposes only\",\n",
     "    authors=[Author(name=\"me\", affiliation=\"my institute\", github_user=\"bioimageiobot\")],  # change github_user to your GitHub account name\n",
     "    cite=[CiteEntry(text=\"for model training see my paper\", doi=Doi(\"10.1234something\"))],\n",
-    "    license=\"MIT\",\n",
+    "    license=LicenseId(\"MIT\"),\n",
     "    documentation=HttpUrl(\"https://raw.githubusercontent.com/bioimage-io/spec-bioimage-io/main/README.md\"),\n",
     "    git_repo=HttpUrl(\"https://github.com/bioimage-io/spec-bioimage-io\"),  # change to repo where your model is developed\n",
     "    inputs=[input_descr],\n",

diff --git a/tests/test_example_specs.py b/tests/test_example_specs.py
@@ -3,8 +3,6 @@
 
 import pytest
 
-from bioimageio.spec._description import DISCOVER, LATEST
-from bioimageio.spec._internal.types import FormatVersionPlaceholder
 from tests.conftest import EXAMPLE_DESCRIPTIONS
 from tests.utils import ParameterSet, check_bioimageio_yaml
 
@@ -48,18 +46,16 @@ def yield_invalid_descr_paths() -> Iterable[ParameterSet]:
 }
 
 
-@pytest.mark.parametrize("format_version", [DISCOVER, LATEST])
 @pytest.mark.parametrize("descr_path,key", list(yield_valid_descr_paths()))
 def test_example_descr_paths(
     descr_path: Path,
     key: str,
-    format_version: FormatVersionPlaceholder,
     bioimageio_json_schema: Mapping[Any, Any],
 ):
     check_bioimageio_yaml(
         descr_path,
         root=descr_path.parent,
-        as_latest=format_version == LATEST,
+        as_latest=False,
         exclude_fields_from_roundtrip=EXCLUDE_FIELDS_FROM_ROUNDTRIP.get(key, set()),
         bioimageio_json_schema=bioimageio_json_schema,
     )