Merge pull request #495 from bioimage-io/bump_version

bump to 0.4.9

Author: FynnBe

README.md

@@ -147,8 +147,10 @@ As a dependency it is included in [bioimageio.core](https://github.com/bioimage-
 | BIOIMAGEIO_CACHE_WARNINGS_LIMIT | "3" | Maximum number of warnings generated for simple cache hits. |
 
 ## Changelog
-#### bioimageio.spec tbd
-- make pre-/postprocessing kwargs `mode` and `axes` always optional for model RDF 0.3 and 0.4
+#### bioimageio.spec 0.4.9
+- small bugixes
+- better type hints
+- improved tests 
 
 #### bioimageio.spec 0.4.8post1
 - add `axes` and `eps` to `scale_mean_var`
@@ -237,6 +239,10 @@ As a dependency it is included in [bioimageio.core](https://github.com/bioimage-
 
 
 ### RDF Format Versions
+#### bioimageio.spec 0.4.9
+- Non-breaking changes
+  - make pre-/postprocessing kwargs `mode` and `axes` always optional for model RDF 0.3 and 0.4
+
 #### model RDF 0.4.8
 - Non-breaking changes
   - `cite` field is now optional

bioimageio/spec/VERSION

@@ -1,3 +1,3 @@
 {
-    "version": "0.4.8post1"
+    "version": "0.4.9"
 }

bioimageio/spec/model/v0_4/converters.py

@@ -99,6 +99,9 @@ def maybe_convert(data: Dict[str, Any]) -> Dict[str, Any]:
     if data["format_version"] == "0.4.7":
         data["format_version"] = "0.4.8"
 
+    if data["format_version"] == "0.4.8":
+        data["format_version"] = "0.4.9"
+
     # remove 'future' from config if no other than the used future entries exist
     config = data.get("config", {})
     if config.get("future") == {}:

bioimageio/spec/model/v0_4/raw_nodes.py

@@ -50,7 +50,7 @@
 PreprocessingName = PreprocessingName
 
 FormatVersion = Literal[
-    "0.4.0", "0.4.1", "0.4.2", "0.4.3", "0.4.4", "0.4.5", "0.4.6", "0.4.7", "0.4.8"
+    "0.4.0", "0.4.1", "0.4.2", "0.4.3", "0.4.4", "0.4.5", "0.4.6", "0.4.7", "0.4.8", "0.4.9"
 ]  # newest format needs to be last (used in __init__.py)
 WeightsFormat = Literal[
     "pytorch_state_dict", "torchscript", "keras_hdf5", "tensorflow_js", "tensorflow_saved_model_bundle", "onnx"

example_specs/models/unet2d_nuclei_broad/rdf.yaml

@@ -1,5 +1,5 @@
 # TODO physical scale of the data
-format_version: 0.4.8
+format_version: 0.4.9
 
 name: UNet 2D Nuclei Broad
 description: A 2d U-Net trained on the nuclei broad dataset.

tests/conftest.py

@@ -9,7 +9,7 @@ def unet2d_nuclei_broad_base_path():
 
 
 def get_unet2d_nuclei_broad(unet2d_nuclei_broad_base_path, request) -> dict:
-    if request.param == "v0_4_7":
+    if request.param == "v0_4_9":
         v = ""
     else:
         v = f"_{request.param}"
@@ -18,7 +18,7 @@ def get_unet2d_nuclei_broad(unet2d_nuclei_broad_base_path, request) -> dict:
     return unet2d_nuclei_broad_base_path / f_name
 
 
-@pytest.fixture(params=["v0_3_0", "v0_3_1", "v0_3_2", "v0_3_3", "v0_3_6", "v0_4_0", "v0_4_7"])
+@pytest.fixture(params=["v0_3_0", "v0_3_1", "v0_3_2", "v0_3_3", "v0_3_6", "v0_4_0", "v0_4_9"])
 def unet2d_nuclei_broad_any(unet2d_nuclei_broad_base_path, request):
     yield get_unet2d_nuclei_broad(unet2d_nuclei_broad_base_path, request)
 
@@ -28,12 +28,12 @@ def unet2d_nuclei_broad_before_latest(unet2d_nuclei_broad_base_path, request):
     yield get_unet2d_nuclei_broad(unet2d_nuclei_broad_base_path, request)
 
 
-@pytest.fixture(params=["v0_4_7"])
+@pytest.fixture(params=["v0_4_9"])
 def unet2d_nuclei_broad_latest(unet2d_nuclei_broad_base_path, request):
     yield get_unet2d_nuclei_broad(unet2d_nuclei_broad_base_path, request)
 
 
-@pytest.fixture(params=["v0_3_6", "v0_4_7"])
+@pytest.fixture(params=["v0_3_6", "v0_4_9"])
 def unet2d_nuclei_broad_any_minor(unet2d_nuclei_broad_base_path, request):
     yield get_unet2d_nuclei_broad(unet2d_nuclei_broad_base_path, request)