Prospective test fixes

Author: C-Achard

.github/workflows/test_and_deploy.yml

@@ -51,6 +51,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           python -m pip install setuptools tox tox-gh-actions
+          python -m pip install monai[nibabel,einops, tifffile]
 #         pip install git+https://github.com/lucasb-eyer/pydensecrf.git@master#egg=pydensecrf
 
 # this runs the platform-specific tests declared in tox.ini

napari_cellseg3d/code_models/models/model_SwinUNetR.py

@@ -45,7 +45,7 @@ def __init__(
         except TypeError as e:
             logger.warning(f"Caught TypeError: {e}")
             super().__init__(
-                # img_size=input_img_size,
+                img_size=input_img_size, # hack for compatibility, latest MONAI for py3.9 does not have img_size but py3.8 does
                 in_channels=1,
                 out_channels=1,
                 feature_size=48,

tox.ini

@@ -40,6 +40,7 @@ deps =
     git+https://github.com/lucasb-eyer/pydensecrf.git@master#egg=pydensecrf
     onnx
     onnxruntime
+    monai[tifffile]
 ;    pyopencl[pocl]
 ;    opencv-python
 extras = crf