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biosimulators · Oct 24, 2024 · 8ee086c · 8ee086c
1 parent ddc1aa4
commit 8ee086c
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diff --git a/.github/workflows/cd.yaml b/.github/workflows/cd.yaml
@@ -4,7 +4,7 @@ on:
   workflow_dispatch:
 
 jobs:
-  build-and-deploy-microservices:
+  configure-environment:
     runs-on: ubuntu-latest
     steps:
       # Step 1: Checkout repository
@@ -28,6 +28,31 @@ jobs:
           sudo apt-get install -y python3 python3-pip
           pip install pyyaml
 
+  build-base-image:
+    needs: configure-environment
+    runs-on: ubuntu-latest
+    steps:
+      - name: Get base image version
+        run: |
+          BASE_VERSION=$(echo ./assets/.BASE_VERSION)
+          echo "BASE_VERSION=$BASE_VERSION" >> $GITHUB_ENV
+          echo "Base Version: $BASE_VERSION"
+
+      - name: Build base image
+        run: |
+          sudo chmod +x ./assets/scripts/build_base.sh
+          ./assets/scripts/build_base.sh ${{ env.BASE_VERSION }}
+
+      - name: Push base image to GHCR
+        run: |
+          sudo chmod +x ./assets/scripts/push_base.sh
+          sudo chmod +x ./assets/scripts/push_image.sh
+          ./assets/scripts/push_base.sh ${{ env.BASE_VERSION }} ${{ secrets.REPO_ADMIN_GH_USERNAME }}
+
+  get-microservice-versions:
+    needs: build-base-image
+    runs-on: ubuntu-latest
+    steps:
       # Step 5: Extract API container version
       - name: Extract API container version
         id: extract_api_version
@@ -50,6 +75,10 @@ jobs:
           echo "API_VERSION=${{ env.API_VERSION }}"
           echo "WORKER_VERSION=${{ env.WORKER_VERSION }}"
 
+  build-microservice-images:
+    needs: get-microservice-versions
+    runs-on: ubuntu-latest
+    steps:
       # Step 8: Set up Docker Buildx
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v2
@@ -58,6 +87,10 @@ jobs:
       - name: Build Docker containers with Docker Compose
         run: docker-compose build --no-cache
 
+  deploy-microservice-images:
+    needs: build-microservice-images
+    runs-on: ubuntu-latest
+    steps:
       # Step 10: Change permissions for push script
       - name: Change push script permissions
         run: chmod +x ./assets/scripts/push_image.sh

diff --git a/compose_worker/Dockerfile-compose_worker b/compose_worker/Dockerfile-compose_worker
@@ -53,7 +53,7 @@ COPY . /app/worker
 ENV PATH="/root/.local/bin:$PATH"
 
 # Install only worker deps TODO: include toml in base deps
-RUN poetry add toml --group=worker --lock && poetry install --only=worker --no-cache
+RUN poetry install --only=worker --no-cache
 
 # Install Assimulo from source for Pysces
 RUN apt-get update \
@@ -71,14 +71,16 @@ RUN apt-get update \
 # && rm -rf build \
 # && poetry run python3 setup.py install --sundials-home=/usr/local --blas-home=/usr/lib/x86_64-linux-gnu
 
-# install masspy TODO: do this
-# RUN poetry run pip install biosimulators-masspy
-
 # revert numpy back to original spec
 RUN poetry remove numpy
 # RUN poetry run pip install numpy==$(poetry run python3 -c "import toml; print(toml.load('/app/pyproject.toml')['tool']['poetry']['group']['worker']['dependencies']['numpy'].strip('<'))") \
 #     && poetry lock
 
+# install masspy TODO: implement this
+RUN git clone https://github.com/biosimulators/Biosimulators_MASSpy.git \
+    && cd Biosimulators_MASSpy \
+    && rm pyproject.toml
+
 WORKDIR /app/worker
 
 RUN python3 -c "import os;files=os.listdir();import shutil;[shutil.rmtree(f) if '__pycache__' in f else None for f in files]"