Migrate off Anaconda to Poetry and create dedicated RMG-Py builder image

.env.dev

@@ -1,6 +1,4 @@
 # environment configuration for vscode
-RMGpy=../RMG-Py
-PYTHONPATH=${RMGpy}:${PYTHONPATH}
 POSTGRES_DB=postgres
 POSTGRES_USER=postgres
 POSTGRES_PASSWORD=postgres

.github/workflows/docker-builds.yml

@@ -0,0 +1,40 @@
+name: Docker Builds
+on:
+  push:
+    branches: [ master ]
+jobs:
+  docker_builds:
+    name: Docker Builds
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout main
+      - uses: actions/checkout@v2
+        with:
+          path: main
+      - name: Checkout RMG-models
+      - uses: actions/checkout@v2
+        with:
+          repository: comocheng/RMG-models
+          token: ${{ secrets.PAT }}
+          path: rmg-models
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      - name: Login to Docker Hub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+      - name: Build RMG Image
+        uses: docker/build-push-action@v2
+        with:
+          file: main/Dockerfile.rmg
+          push: true
+          tags: comocheng/kms-rmg:latest
+      - name: Build Application Image
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          push: true
+          tags: comocheng/kms:latest

.github/workflows/main.yml

@@ -1,21 +1,16 @@
-name: CI/CD
+name: CI
 on:
   push:
     branches: [ master ]
   pull_request:
     branches: [ master ]
     types: [ opened, synchronize, ready_for_review ]
 jobs:
-  testing:
-    name: Testing
+  tests:
+    name: Tests
     runs-on: ubuntu-latest
     if: github.event.pull_request.draft == false
     steps:
       - uses: actions/checkout@v2
-      - name: Run Tests
-        run: |
-          echo ${{ secrets.CR_PAT }} | docker login ghcr.io -u $GITHUB_ACTOR --password-stdin
-          docker pull ghcr.io/comocheng/kineticmodelssite/kms-build:latest
-          cp .env.dev .env
-          docker volume create rmg-models
-          docker-compose run web ./bin/test.sh --rm
+      - name: Tests
+        run: docker-compose run web ./bin/test.sh --rm

Dockerfile

@@ -1,11 +1,27 @@
-FROM ghcr.io/comocheng/kineticmodelssite/kms-build:latest
+# Fetch RMG-Py build
+FROM comocheng/kms-rmg:latest as rmg
 
-COPY environment.yml /app/
-RUN conda config --set channel_priority strict
-RUN conda env update --prefix $ENV_PREFIX --file environment.yml
-RUN conda clean -afy
-ENV PATH /kms_env/bin:$PATH
-ENV CONDA_DEFAULT_ENV /kms_env
-RUN source activate /kms_env
+# Application
+FROM python:3.9-alpine
 
-COPY . /app/
+ENV PYTHONUNBUFFERED=1 \
+  PYTHONDONTWRITEBYTECODE=1 \
+  POETRY_HOME="/opt/poetry" \
+  POETRY_NO_INTERACTION=1
+
+COPY --from=rmg /rmg/RMG-Py/rmgpy /rmgpy
+
+RUN apk add --no-cache curl \
+  && (curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python -)
+ENV PATH="$POETRY_HOME/bin:$PATH" \
+  PYTHONPATH="/rmgpy:$PYTHONPATH"
+
+WORKDIR /app
+
+COPY main/pyproject.toml poetry.lock ./
+RUN poetry install --no-dev --no-interaction
+
+COPY rmg-models/ /rmg-models
+COPY main/ .
+
+CMD [ "./bin/entrypoint.sh" ]

Dockerfile.rmg

@@ -0,0 +1,21 @@
+# Builds RMG-Py from source to /rmg/RMG-Py/rmgpy
+FROM continuumio/miniconda3:latest
+
+RUN apt update && apt -y install \
+  g++ \
+  gcc \
+  git \
+  make
+
+WORKDIR /rmg
+RUN git clone https://github.com/ReactionMechanismGenerator/RMG-Py.git \
+  && git clone https://github.com/ReactionMechanismGenerator/RMG-database.git
+
+WORKDIR /rmg/RMG-Py
+ENV PYTHONUNBUFFERED=1
+
+RUN conda env create -v --file environment.yml
+SHELL ["conda", "run", "-n", "rmg_env", "/bin/bash", "-c"]
+RUN make
+
+WORKDIR /rmg/RMG-Py/rmgpy

bin/entrypoint.sh

@@ -1,5 +1,3 @@
 #!/bin/bash
-
-python manage.py collectstatic --noinput
-python manage.py migrate --noinput
-gunicorn kms.wsgi --bind 0.0.0.0:8000
+poetry run python manage.py migrate --noinput
+poetry run gunicorn kms.wsgi --bind 0.0.0.0:8000

bin/test.sh

@@ -2,5 +2,5 @@
 
 set -e
 
-python -m flake8
-python manage.py test --settings=kms.test_settings --pattern="test_*unit.py" --noinput
+poetry run python -m flake8
+poetry run python manage.py test --settings=kms.test_settings --pattern="test_*unit.py" --noinput

database/scripts/import_rmg_models.py

@@ -88,7 +88,7 @@ def import_rmg_models(apps, schema_editor):
     logger.info(datetime.now().strftime("%Y-%m-%d %H:%M:%S"))
     for name in model_names:
         setattr(models, name, apps.get_model("database", name))
-    path = os.getenv("RMGMODELSPATH", "./rmg-models/")
+    path = os.getenv("RMGMODELSPATH", "/rmg-models/")
     skip_list = ["PCI2011/193-Mehl"]
     model_paths = get_models(path, skip_list)
 

docker-compose.debug.yml

@@ -1,28 +1,24 @@
-version: "3.8"
+version: "3.7"
 
 services:
   db:
     image: postgres
+    env_file: .env.dev
     ports:
       - "5432:5432"
-    env_file:
-      - ./.env.dev
   debug:
     build: .
     tty: true
-    env_file:
-      - ./.env.dev
+    env_file: .env.dev
     volumes:
       - .:/app
       - rmg-models:/app/rmg-models
-      - conda:/kms_env
     ports:
       - "5678:5678"
       - "8080:8080"
     depends_on:
       - db
+
 volumes:
   rmg-models:
     external: true
-  conda:
-    external: true

docker-compose.yml

@@ -1,26 +1,17 @@
-version: "3.8"
+version: "3.7"
 
 services:
   db:
     image: postgres
-    expose:
-      - 5432
-    env_file:
-      - ./.env
+    env_file: .env
   web:
-    build: .
-    command: ./bin/entrypoint.sh
+    build: comocheng/kms
+    env_file: .env
     volumes:
-      - .:/app
       - static:/app/static
       - media:/app/media
-      - rmg-models:/app/rmg-models
-    expose:
-      - 8000
     depends_on:
       - db
-    env_file:
-      - ./.env
   nginx:
     build: ./nginx
     volumes:
@@ -30,8 +21,7 @@ services:
       - "8000:80"
     depends_on:
       - web
+
 volumes:
   static:
   media:
-  rmg-models:
-    external: true