Merge pull request #424 from bioimage-io/collections_abc_fix

Collections abc fix

.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

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",