Merge pull request #34 from CogStack/production

release: Prepare release 0.2.0
chore: post release tidy up

Author: baixiac

.github/workflows/release.yaml

@@ -42,6 +42,7 @@ jobs:
       - name: Install dependencies
         run: |
           uv sync --extra dev --extra docs --extra llm
+          uv run python -m ensurepip
       - name: Run unit tests
         run: |
           uv run pytest -v tests/app --cov --cov-report=html:coverage_reports #--random-order

README.md

@@ -34,7 +34,7 @@ cms train --help
 
 ## Download models:
 
-CMS runs the NLP model packaged in a ZIP file or a Gzipped tarball. To download pretrained GA models, please follow the [instructions](https://github.com/CogStack/MedCAT#available-models). Contact [Cogstack]([email protected])
+CMS runs the NLP model packaged in a ZIP file or a Gzipped tarball. To download pretrained GA models, please follow the [instructions](https://medcat.readthedocs.io/en/latest/main.html#models). Contact [Cogstack]([email protected])
 if you are interested in trying out Alpha release such as the de-identification model. To serve or train existing HuggingFace NER models, you can
 package the model, either downloaded from the Hugging Face Hub or cached locally, as a ZIP or Gzipped tarball by running:
 ```commandline

docker-compose-mlflow.yml

@@ -65,7 +65,7 @@ services:
         condition: "service_healthy"
 
   mlflow-ui:
-    image: cogstacksystems/cogstack-mlflow-ui:0.1.1
+    image: cogstacksystems/cogstack-mlflow-ui:0.2.0
     restart: always
     networks:
       - cogstack-model-serve_cms

docker-compose.yml

@@ -5,7 +5,7 @@ name: cms
 services:
 
   medcat-snomed:
-    image: cogstacksystems/cogstack-modelserve:0.1.1
+    image: cogstacksystems/cogstack-modelserve:0.2.0
     labels:
       - org.cogstack.model-serve=medcat_snomed
       - org.cogstack.model-name=SNOMED MedCAT model
@@ -40,6 +40,7 @@ services:
       - http_proxy=$HTTP_PROXY
       - https_proxy=$HTTPS_PROXY
       - no_proxy=mlflow-ui,minio,graylog,auth-db,localhost
+      - COLUMNS=200
     expose:
       - 8000
     ports:
@@ -52,7 +53,7 @@ services:
       start_period: 60s
 
   medcat-icd10:
-    image: cogstacksystems/cogstack-modelserve:0.1.1
+    image: cogstacksystems/cogstack-modelserve:0.2.0
     labels:
       - org.cogstack.model-serve=medcat_icd10
       - org.cogstack.model-name=ICD-10 MedCAT model
@@ -87,6 +88,7 @@ services:
       - http_proxy=$HTTP_PROXY
       - https_proxy=$HTTPS_PROXY
       - no_proxy=mlflow-ui,minio,graylog,auth-db,localhost
+      - COLUMNS=200
     expose:
       - 8000
     ports:
@@ -99,7 +101,7 @@ services:
       start_period: 60s
 
   medcat-opcs4:
-    image: cogstacksystems/cogstack-modelserve:0.1.1
+    image: cogstacksystems/cogstack-modelserve:0.2.0
     labels:
       - org.cogstack.model-serve=medcat_opcs4
       - org.cogstack.model-name=OPCS-4 MedCAT model
@@ -134,6 +136,7 @@ services:
       - http_proxy=$HTTP_PROXY
       - https_proxy=$HTTPS_PROXY
       - no_proxy=mlflow-ui,minio,graylog,auth-db,localhost
+      - COLUMNS=200
     expose:
       - 8000
     ports:
@@ -146,7 +149,7 @@ services:
       start_period: 60s
 
   medcat-deid:
-    image: cogstacksystems/cogstack-modelserve:0.1.1
+    image: cogstacksystems/cogstack-modelserve:0.2.0
     labels:
       - org.cogstack.model-serve=medcat_deid
       - org.cogstack.model-name=De-Identification MedCAT model
@@ -181,6 +184,7 @@ services:
       - http_proxy=$HTTP_PROXY
       - https_proxy=$HTTPS_PROXY
       - no_proxy=mlflow-ui,minio,graylog,auth-db,localhost
+      - COLUMNS=200
     expose:
       - 8000
     ports:
@@ -193,7 +197,7 @@ services:
       start_period: 60s
 
   medcat-umls:
-    image: cogstacksystems/cogstack-modelserve:0.1.1
+    image: cogstacksystems/cogstack-modelserve:0.2.0
     labels:
       - org.cogstack.model-serve=medcat_umls
       - org.cogstack.model-name=UMLS MedCAT model
@@ -228,6 +232,7 @@ services:
       - http_proxy=$HTTP_PROXY
       - https_proxy=$HTTPS_PROXY
       - no_proxy=mlflow-ui,minio,graylog,auth-db,localhost
+      - COLUMNS=200
     expose:
       - 8000
     ports:
@@ -240,7 +245,7 @@ services:
       start_period: 60s
 
   huggingface-ner:
-    image: cogstacksystems/cogstack-modelserve:0.1.1
+    image: cogstacksystems/cogstack-modelserve:0.2.0
     labels:
       - org.cogstack.model-serve=huggingface_ner
       - org.cogstack.model-name=HuggingFace NER model
@@ -275,6 +280,7 @@ services:
       - http_proxy=$HTTP_PROXY
       - https_proxy=$HTTPS_PROXY
       - no_proxy=mlflow-ui,minio,graylog,auth-db,localhost
+      - COLUMNS=200
     expose:
       - 8000
     ports:
@@ -287,7 +293,7 @@ services:
       start_period: 60s
 
   huggingface-llm:
-    image: cogstacksystems/cogstack-modelserve:0.1.0
+    image: cogstacksystems/cogstack-modelserve:0.2.0
     labels:
       - org.cogstack.model-serve=huggingface_llm
       - org.cogstack.model-name=HuggingFace LLM model
@@ -301,8 +307,8 @@ services:
       - ./docker/huggingface-llm/.env:/app/envs/.env:ro
     environment:
       - BASE_MODEL_FULL_PATH=$MODEL_PACKAGE_FULL_PATH
-      - CMS_MODEL_TYPE=huggingface_ner
-      - CMS_MODEL_NAME=HuggingFace NER model
+      - CMS_MODEL_TYPE=huggingface_llm
+      - CMS_MODEL_NAME=HuggingFace LLM model
       - CMS_STREAMABLE=${CMS_STREAMABLE:-false}
       - AWS_ACCESS_KEY_ID=$AWS_ACCESS_KEY_ID
       - AWS_SECRET_ACCESS_KEY=$AWS_SECRET_ACCESS_KEY
@@ -322,6 +328,7 @@ services:
       - http_proxy=$HTTP_PROXY
       - https_proxy=$HTTPS_PROXY
       - no_proxy=mlflow-ui,minio,graylog,auth-db,localhost
+      - COLUMNS=200
     expose:
       - 8000
     ports: