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

Dockerfile

@@ -1,11 +1,26 @@
-FROM ghcr.io/comocheng/kineticmodelssite/kms-build:latest
+# Fetch RMG-Py build
+FROM comocheng/kms-rmgpy:latest as rmgpy
 
-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=rmgpy /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 pyproject.toml poetry.lock ./
+RUN poetry install --no-dev --no-interaction
+
+COPY . .
+
+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

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 +1,18 @@
-version: "3.8"
+version: "3.7"
 
 services:
   db:
     image: postgres
-    expose:
-      - 5432
-    env_file:
-      - ./.env
+    env_file: .env
   web:
     build: .
-    command: ./bin/entrypoint.sh
+    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:
@@ -30,6 +22,7 @@ services:
       - "8000:80"
     depends_on:
       - web
+
 volumes:
   static:
   media: