update to test build action workflow

biosimulators · Nov 1, 2024 · 37064d7 · 37064d7
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commit 37064d7
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Showing 5 changed files with 142 additions and 7 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -26,3 +26,63 @@ jobs:
       - name: Test build base image
         run: |
           docker build --no-cache -f ./Dockerfile-base -t ghcr.io/biosimulations/bio-check-base:${{ env.BASE_VERSION }} .
+
+  get-microservice-versions:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      # Step 5: Extract API container version
+      - name: Extract API container version
+        id: extract_api_version
+        run: |
+          API_VERSION=$(python3 .github/parse_container_version.py api)
+          echo "API_VERSION=$API_VERSION" >> $GITHUB_ENV
+          echo "API Version: $API_VERSION"
+
+      # Step 6: Extract worker container version
+      - name: Extract worker container version
+        id: extract_worker_version
+        run: |
+          WORKER_VERSION=$(python3 .github/parse_container_version.py worker)
+          echo "WORKER_VERSION=$WORKER_VERSION" >> $GITHUB_ENV
+          echo "WORKER Version: $WORKER_VERSION"
+
+      # Step 7: Debug output of extracted versions
+      - name: Debug output of extracted versions
+        run: |
+          echo "API_VERSION=${{ env.API_VERSION }}"
+          echo "WORKER_VERSION=${{ env.WORKER_VERSION }}"
+
+  build-microservice-images:
+    needs: get-microservice-versions
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.10'
+
+      - name: Log in to GHCR
+        run: echo "${{ secrets.REPO_ADMIN_GHCR_TOKEN }}" | docker login ghcr.io -u "${{ secrets.REPO_ADMIN_GH_USERNAME }}" --password-stdin
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r assets/configs/requirements.github.txt
+
+      - name: Install Docker Compose
+        run: |
+          sudo curl -L "https://github.com/docker/compose/releases/download/$(curl -s https://api.github.com/repos/docker/compose/releases/latest | grep 'tag_name' | cut -d\" -f4)/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose
+          sudo chmod +x /usr/local/bin/docker-compose
+          docker-compose --version  # Check if Docker Compose is installed correctly
+
+      - name: Build Docker containers with Docker Compose
+        run: docker-compose build
diff --git a/.github/workflows/test-build-microservices.yml b/.github/workflows/test-build-microservices.yml
@@ -0,0 +1,68 @@
+name: Test Build Microservices
+
+# TODO: add main here
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  get-microservice-versions:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      # Step 5: Extract API container version
+      - name: Extract API container version
+        id: extract_api_version
+        run: |
+          API_VERSION=$(python3 .github/parse_container_version.py api)
+          echo "API_VERSION=$API_VERSION" >> $GITHUB_ENV
+          echo "API Version: $API_VERSION"
+
+      # Step 6: Extract worker container version
+      - name: Extract worker container version
+        id: extract_worker_version
+        run: |
+          WORKER_VERSION=$(python3 .github/parse_container_version.py worker)
+          echo "WORKER_VERSION=$WORKER_VERSION" >> $GITHUB_ENV
+          echo "WORKER Version: $WORKER_VERSION"
+
+      # Step 7: Debug output of extracted versions
+      - name: Debug output of extracted versions
+        run: |
+          echo "API_VERSION=${{ env.API_VERSION }}"
+          echo "WORKER_VERSION=${{ env.WORKER_VERSION }}"
+
+  build-microservice-images:
+    needs: get-microservice-versions
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.10'
+
+      - name: Log in to GHCR
+        run: echo "${{ secrets.REPO_ADMIN_GHCR_TOKEN }}" | docker login ghcr.io -u "${{ secrets.REPO_ADMIN_GH_USERNAME }}" --password-stdin
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r assets/configs/requirements.github.txt
+
+      - name: Install Docker Compose
+        run: |
+          sudo curl -L "https://github.com/docker/compose/releases/download/$(curl -s https://api.github.com/repos/docker/compose/releases/latest | grep 'tag_name' | cut -d\" -f4)/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose
+          sudo chmod +x /usr/local/bin/docker-compose
+          docker-compose --version  # Check if Docker Compose is installed correctly
+
+      - name: Build Docker containers with Docker Compose
+        run: docker-compose build
diff --git a/api/Dockerfile-api b/api/Dockerfile-api
@@ -10,14 +10,16 @@ COPY . /app/api
 EXPOSE 3001
 
 # RUN /app/assets/install_deps.sh /app/api/requirements.api.txt
+# ENV PATH="/root/.local/bin:$PATH"
 
-ENV PATH="/root/.local/bin:$PATH"
+SHELL ["/usr/bin/env", "bash", "-c"]
 
-RUN poetry install --only=api
+# RUN source ~/.bashrc \
+#     && poetry install --only=api
 
 WORKDIR /app/api
 
-RUN python3 -c "import os;files=os.listdir();import shutil;[shutil.rmtree(f) if '__pycache__' in f else None for f in files]"
+# RUN python3 -c "import os;files=os.listdir();import shutil;[shutil.rmtree(f) if '__pycache__' in f else None for f in files]"
 
-ENTRYPOINT ["poetry", "run", "uvicorn", "main:app", "--host", "0.0.0.0", "--port", "3001", "--reload"]
+# ENTRYPOINT ["/usr/bin/env", "bash", "-c", "&&", "source", "~/.bashrc", "&&", "poetry", "run", "uvicorn", "main:app", "--host", "0.0.0.0", "--port", "3001", "--reload"]
 
diff --git a/docker-compose.yaml b/docker-compose.yaml
@@ -32,7 +32,7 @@ services:
   worker:
     build:
       context: ./worker
-      dockerfile: worker/_Dockerfile-worker1
+      dockerfile: ./Dockerfile-worker
     image: ghcr.io/biosimulators/bio-check-worker:1.12.0  # ghcr.io/biosimulators/bio-check-compose_worker:1.11.9  # .7
     container_name: worker
     environment:

diff --git a/worker/Dockerfile-worker b/worker/Dockerfile-worker
@@ -24,13 +24,18 @@ RUN apt-get update && apt-get install -y libatlas-base-dev \
 COPY environment.worker.yml /tmp/environment.worker.yml
 COPY . /app/worker
 
-RUN conda install -c conda-forge -c pysces pysces -y \
+SHELL ["/usr/bin/env", "bash", "-c"]
+
+RUN source ~/.bashrc \
+    && conda install -c conda-forge -c pysces pysces -y \
     && conda env update -n conda-env -f /tmp/environment.worker.yml \
-    && /usr/bin/env bash -c "source ~/.bashrc && conda activate conda-env && poetry install --only=worker --no-cache" \
+    && poetry install --only=worker --no-cache \
     && rm -rf /var/lib/apt/lists/* \
     && apt-get autoremove -y  \
     && apt-get clean
 
+# && /usr/bin/env bash -c "source ~/.bashrc && conda activate conda-env && poetry install --only=worker --no-cache" \
+
 ENV TEST_SBML_FP="test_fixtures/Elowitz-Nature-2000-Repressilator/BIOMD0000000012_url.xml" \
     TEST_PSC_FP="/Pysces/psc/BIOMD0000000012_url.xml.psc" \
     TEST_OMEX_FP="test_fixtures/Elowitz-Nature-2000-Repressilator.omex"