ENH: Use Latest Monai GridPatch to filter both threshold and count (#834

)

Temporary fix until next release of MONAI
Include fixes: 
Project-MONAI/MONAI#6095
Project-MONAI/MONAI#6055

Install dev version of MONAI pointing at commit
Project-MONAI/MONAI@958aac7

hi-ml-cpath/environment.yml

@@ -96,7 +96,7 @@ dependencies:
       - aiohttp==3.8.4
       - aiosignal==1.3.1
       - alabaster==0.7.13
-      - alembic==1.10.1
+      - alembic==1.10.2
       - applicationinsights==0.11.10
       - argcomplete==2.1.1
       - astroid==2.15.0
@@ -114,8 +114,8 @@ dependencies:
       - azure-mgmt-resource==21.2.1
       - azure-mgmt-storage==20.1.0
       - azure-storage-blob==12.10.0
-      - azure-storage-file-datalake==12.10.0
-      - azure-storage-file-share==12.11.0
+      - azure-storage-file-datalake==12.10.1
+      - azure-storage-file-share==12.11.1
       - azureml-core==1.47.0
       - azureml-dataprep==4.5.7
       - azureml-dataprep-native==38.0.0
@@ -144,7 +144,7 @@ dependencies:
       - cryptography==39.0.2
       - cucim==22.10.0
       - cycler==0.11.0
-      - databricks-cli==0.17.4
+      - databricks-cli==0.17.5
       - dataclasses-json==0.5.2
       - debugpy==1.6.6
       - dill==0.3.6
@@ -171,9 +171,9 @@ dependencies:
       - gunicorn==20.1.0
       - hi-ml==0.2.19
       - hi-ml-azure==0.2.19
-      - huggingface-hub==0.12.1
+      - huggingface-hub==0.13.1
       - humanfriendly==10.0
-      - identify==2.5.18
+      - identify==2.5.19
       - imageio==2.26.0
       - imagesize==1.4.1
       - importlib-metadata==4.2.0
@@ -210,7 +210,7 @@ dependencies:
       - mdit-py-plugins==0.2.8
       - mlflow==2.2.1
       - mlflow-skinny==2.2.1
-      - monai==1.0.1
+      - monai-weekly==1.2.dev2310
       - more-itertools==8.10.0
       - msal==1.21.0
       - msal-extensions==0.3.1
@@ -274,7 +274,7 @@ dependencies:
       - rsa==4.9
       - ruamel-yaml==0.16.12
       - scikit-image==0.19.3
-      - scikit-learn==1.2.1
+      - scikit-learn==1.2.2
       - scipy==1.7.3
       - seaborn==0.10.1
       - secretstorage==3.3.3
@@ -296,7 +296,7 @@ dependencies:
       - sphinxcontrib-serializinghtml==1.1.5
       - sqlalchemy==2.0.5.post1
       - sqlparse==0.4.3
-      - strictyaml==1.6.2
+      - strictyaml==1.7.3
       - stringcase==1.2.0
       - tabulate==0.9.0
       - tensorboard==2.6.0

hi-ml-cpath/requirements_run.txt

@@ -4,7 +4,7 @@ girder-client==3.1.14
 hi-ml
 ipykernel==6.21.2
 lightning-bolts==0.4.0
-monai==1.0.1
+monai-weekly==1.2.dev2310
 more-itertools==8.10.0
 numpy==1.22.0
 pillow==9.3.0