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ci: build and push dev images from the master branch
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5 files changed

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‎.github/workflows/docker.yaml‎

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@@ -6,12 +6,58 @@ on:
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pull_request:
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branches: [ master ]
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jobs:
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build:
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env:
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DOCKER_IMAGE_NAME: cogstacksystems/cogstack-modelserve
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jobs:
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lint:
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runs-on: ubuntu-latest
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container: hadolint/hadolint:latest-debian
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v4
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- name: Lint
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run: hadolint --ignore DL3008 --ignore DL3013 --ignore DL3003 --ignore DL4006 docker/**/Dockerfile* docker/mlflow/**/Dockerfile*
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run: hadolint --ignore DL3008 --ignore DL3013 --ignore DL3003 --ignore DL4006 docker/Dockerfile* docker/**/Dockerfile* docker/mlflow/**/Dockerfile*
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build-and-push:
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needs: lint
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if: |
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github.repository == 'CogStack/CogStack-ModelServe' &&
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github.ref == 'refs/heads/master' &&
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github.event_name == 'push'
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runs-on: ubuntu-latest
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concurrency: build-and-push
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steps:
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- uses: actions/checkout@v4
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- name: Set up QEMU
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uses: docker/setup-qemu-action@v3
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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- name: Login to Docker Hub
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uses: docker/login-action@v3
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with:
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username: ${{ secrets.DOCKERHUB_USERNAME }}
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password: ${{ secrets.DOCKERHUB_TOKEN }}
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- name: Cache Docker layers
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uses: actions/cache@v4
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with:
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path: /tmp/.buildx-cache
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key: ${{ runner.os }}-buildx-${{ github.sha }}
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restore-keys: |
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${{ runner.os }}-buildx-
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- name: Build and push
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uses: docker/build-push-action@v6
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with:
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platforms: linux/amd64,linux/arm64
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context: .
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file: docker/Dockerfile
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push: true
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tags: |
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${{ env.DOCKER_IMAGE_NAME }}:dev
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cache-from: type=local,src=/tmp/.buildx-cache
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cache-to: type=local,dest=/tmp/.buildx-cache,mode=max

‎docker-compose-dev.yml‎

Lines changed: 104 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -9,9 +9,18 @@ services:
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extends:
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file: ./docker-compose.yml
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service: medcat-snomed
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image: cogstack-model-serve_medcat-snomed:dev
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volumes:
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- ${MODEL_PACKAGE_FULL_PATH}:/app/model/model.zip:ro
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build:
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context: ./
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dockerfile: ./docker/medcat-snomed/Dockerfile
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args:
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- CMS_MODEL_NAME=SNOMED MedCAT model
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- CMS_UID=${CMS_UID:-1000}
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- CMS_GID=${CMS_GID:-1000}
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- HTTP_PROXY=$HTTP_PROXY
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- HTTPS_PROXY=$HTTPS_PROXY
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- NO_PROXY=$NO_PROXY
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image: local-cms-medcat-snomed:do-not-push
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container_name: dev-cms-medcat-snomed
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environment:
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- BASE_MODEL_FULL_PATH=$MODEL_PACKAGE_FULL_PATH
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- AWS_ACCESS_KEY_ID=
@@ -31,13 +40,24 @@ services:
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- NO_PROXY=localhost
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- http_proxy=$HTTP_PROXY
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- https_proxy=$HTTPS_PROXY
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- NO_PROXY=localhost
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- no_proxy=localhost
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medcat-icd10:
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extends:
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file: ./docker-compose.yml
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service: medcat-icd10
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image: cogstack-model-serve_medcat-icd10:dev
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build:
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context: ./
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dockerfile: ./docker/medcat-icd10/Dockerfile
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args:
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- CMS_MODEL_NAME=ICD-10 MedCAT model
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- CMS_UID=${CMS_UID:-1000}
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- CMS_GID=${CMS_GID:-1000}
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- HTTP_PROXY=$HTTP_PROXY
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- HTTPS_PROXY=$HTTPS_PROXY
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- NO_PROXY=$NO_PROXY
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image: local-cms-medcat-icd10:do-not-push
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container_name: dev-cms-medcat-icd10
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environment:
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- BASE_MODEL_FULL_PATH=$MODEL_PACKAGE_FULL_PATH
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- AWS_ACCESS_KEY_ID=
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- NO_PROXY=localhost
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- http_proxy=$HTTP_PROXY
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- https_proxy=$HTTPS_PROXY
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- NO_PROXY=localhost
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- no_proxy=localhost
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de-identification:
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extends:
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file: ./docker-compose.yml
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service: de-identification
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image: cogstack-model-serve_de-identification:dev
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build:
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context: ./
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dockerfile: ./docker/trf-deid/Dockerfile
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args:
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- CMS_MODEL_NAME=De-identification model
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- CMS_UID=${CMS_UID:-1000}
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- CMS_GID=${CMS_GID:-1000}
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- HTTP_PROXY=$HTTP_PROXY
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- HTTPS_PROXY=$HTTPS_PROXY
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- NO_PROXY=$NO_PROXY
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image: local-cms-trf-deid:do-not-push
97+
container_name: dev-cms-trf-deid
6798
environment:
6899
- BASE_MODEL_FULL_PATH=$MODEL_PACKAGE_FULL_PATH
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- AWS_ACCESS_KEY_ID=
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- NO_PROXY=localhost
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- http_proxy=$HTTP_PROXY
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- https_proxy=$HTTPS_PROXY
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- NO_PROXY=localhost
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- no_proxy=localhost
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88119
medcat-deid:
89120
extends:
90121
file: ./docker-compose.yml
91122
service: medcat-deid
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image: cogstack-model-serve_medcat-deid:dev
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build:
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context: ./
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dockerfile: ./docker/medcat-deid/Dockerfile
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args:
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- CMS_MODEL_NAME=De-Identification MedCAT model
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- CMS_UID=${CMS_UID:-1000}
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- CMS_GID=${CMS_GID:-1000}
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- HTTP_PROXY=$HTTP_PROXY
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- HTTPS_PROXY=$HTTPS_PROXY
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- NO_PROXY=$NO_PROXY
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image: local-cms-medcat-deid:do-not-push
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container_name: dev-cms-medcat-deid
93135
environment:
94136
- BASE_MODEL_FULL_PATH=$MODEL_PACKAGE_FULL_PATH
95137
- AWS_ACCESS_KEY_ID=
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- NO_PROXY=localhost
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- http_proxy=$HTTP_PROXY
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- https_proxy=$HTTPS_PROXY
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- NO_PROXY=localhost
154+
- no_proxy=localhost
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medcat-umls:
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extends:
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file: ./docker-compose.yml
117159
service: medcat-umls
118-
image: cogstack-model-serve_medcat-umls:dev
160+
build:
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context: ./
162+
dockerfile: ./docker/medcat-umls/Dockerfile
163+
args:
164+
- CMS_MODEL_NAME=UMLS MedCAT model
165+
- CMS_UID=${CMS_UID:-1000}
166+
- CMS_GID=${CMS_GID:-1000}
167+
- HTTP_PROXY=$HTTP_PROXY
168+
- HTTPS_PROXY=$HTTPS_PROXY
169+
- NO_PROXY=$NO_PROXY
170+
image: local-cms-medcat-umls:do-not-push
171+
container_name: dev-cms-medcat-umls
119172
environment:
120173
- BASE_MODEL_FULL_PATH=$MODEL_PACKAGE_FULL_PATH
121174
- AWS_ACCESS_KEY_ID=
@@ -135,7 +188,47 @@ services:
135188
- NO_PROXY=localhost
136189
- http_proxy=$HTTP_PROXY
137190
- https_proxy=$HTTPS_PROXY
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- no_proxy=localhost
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huggingface-ner:
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extends:
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file: ./docker-compose.yml
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service: huggingface-ner
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build:
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context: ./
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dockerfile: ./docker/huggingface-ner/Dockerfile
200+
args:
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- CMS_MODEL_NAME=Hugging Face NER model
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- CMS_UID=${CMS_UID:-1000}
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- CMS_GID=${CMS_GID:-1000}
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- HTTP_PROXY=$HTTP_PROXY
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- HTTPS_PROXY=$HTTPS_PROXY
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- NO_PROXY=$NO_PROXY
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image: local-cms-huggingface-ner:do-not-push
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container_name: dev-cms-huggingface-ner
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restart: always
210+
networks:
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- cms
212+
environment:
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- BASE_MODEL_FULL_PATH=$MODEL_PACKAGE_FULL_PATH
214+
- AWS_ACCESS_KEY_ID=
215+
- AWS_SECRET_ACCESS_KEY=
216+
- MLFLOW_S3_ENDPOINT_URL=
217+
- MLFLOW_TRACKING_URI=${MLFLOW_TRACKING_URI:-file:/tmp/mlruns}
218+
- MLFLOW_TRACKING_USERNAME=
219+
- MLFLOW_TRACKING_PASSWORD=
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- MLFLOW_ENABLE_SYSTEM_METRICS_LOGGING=${MLFLOW_ENABLE_SYSTEM_METRICS_LOGGING:-false}
221+
- GELF_INPUT_URI=
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- AUTH_USER_ENABLED=${AUTH_USER_ENABLED:-false}
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- AUTH_JWT_SECRET=$AUTH_JWT_SECRET
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- AUTH_ACCESS_TOKEN_EXPIRE_SECONDS=${AUTH_ACCESS_TOKEN_EXPIRE_SECONDS:-3600}
225+
- AUTH_DATABASE_URL=${AUTH_DATABASE_URL:-sqlite+aiosqlite:///./cms-users.db}
226+
- HTTP_PROXY=$HTTP_PROXY
227+
- HTTPS_PROXY=$HTTPS_PROXY
138228
- NO_PROXY=localhost
229+
- http_proxy=$HTTP_PROXY
230+
- https_proxy=$HTTPS_PROXY
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- no_proxy=localhost
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volumes:
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retrained-models:

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