update to workflows

biosimulators · Oct 30, 2024 · 7e0bcd0 · 7e0bcd0
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commit 7e0bcd0
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diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml
@@ -37,4 +37,83 @@ jobs:
       - name: Deploy new latest base version
         run: |
           docker tag ${{ env.BASE_IMG }}:${{ env.BASE_VERSION }} ${{ env.BASE_IMG }}:latest
-          docker push ${{ env.BASE_IMG }}:latest
+          docker push ${{ env.BASE_IMG }}:latest
+
+  get-microservice-versions:
+    needs: deploy-base-image
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      # Step 5: Extract API container version
+      - name: Extract API container version
+        id: extract_api_version
+        run: |
+          API_VERSION=$(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=${{ env.WORKER_VERSION }}"
+
+  build-microservice-images:
+    needs: get-microservice-versions
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.10'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r assets/configs/requirements.github.txt
+
+      - name: Install Docker Compose
+        run: |
+          sudo curl -L "https://github.com/docker/compose/releases/download/$(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 --no-cache
+
+      - name: Authorize push script
+        run: chmod +x ./assets/scripts/push_image.sh
+
+      - name: Deploy API microservice container to GHCR
+        run: |
+          rm compose_api/spec/openapi_3_1_0_generated.yaml
+          python3 compose_api/openapi_spec.py
+          sudo rm -r compose_api/__pycache__
+          ./assets/scripts/push_image.sh compose_api ${{ env.API_VERSION }}
+        env:
+          REPO_ADMIN_GH_USERNAME: ${{ secrets.REPO_ADMIN_GH_USERNAME }}
+          REPO_ADMIN_GHCR_TOKEN: ${{ secrets.REPO_ADMIN_GHCR_TOKEN }}
+
+      - name: Deploy worker microservice container to GHCR
+        run: |
+          sudo rm -r compose_api/__pycache__
+          ./assets/scripts/push_image.sh compose_worker ${{ env.WORKER_VERSION }}
+        env:
+          REPO_ADMIN_GH_USERNAME: ${{ secrets.REPO_ADMIN_GH_USERNAME }}
+          REPO_ADMIN_GHCR_TOKEN: ${{ secrets.REPO_ADMIN_GHCR_TOKEN }}
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -18,7 +18,7 @@ jobs:
           sudo chmod +x /usr/local/bin/docker-compose
           docker-compose --version  # Check if Docker Compose is installed correctly
 
-      - name: Get base image version
+      - name: Get new base image version
         run: |
           BASE_VERSION=$(cat ./assets/.BASE_VERSION)
           echo "BASE_VERSION=$BASE_VERSION" >> $GITHUB_ENV
@@ -30,11 +30,6 @@ jobs:
         env:
           BIOSIMULATIONS_GCLOUD_CONFIG: ${{ secrets.BIO_JSON_CONTENT }}
 
-      - name: Get new base tag
-        run: |
-          BASE_IMG=ghcr.io/biosimulators/bio-check-base
-          echo "BASE_IMG=$BASE_IMG" >> $GITHUB_ENV
-
       - name: Test build base image
         run: |
           docker build --no-cache -f ./Dockerfile-base -t ${{ env.BASE_IMG }}:${{ env.BASE_VERSION }} .
diff --git a/Dockerfile-base b/Dockerfile-base
@@ -70,52 +70,10 @@ COPY ./model-examples/sbml-core/Elowitz-Nature-2000-Repressilator /app/data/Elow
 # create readme for poetry
 RUN echo "BioCompose Server" > /app/README.md
 
-# install poetry and deps
+# install poetry deps
 RUN python3.10 -m pip install --upgrade pip \
     && python3.10 -m pip install poetry \
     && poetry config virtualenvs.in-project true \
     && poetry env use 3.10 \
     && poetry install --without=api,worker
 
-
-# install smoldyn
-# RUN . /app/.venv/bin/activate \
-#     && wget https://www.smoldyn.org/smoldyn-2.73.tgz \
-#     && tar -xzf smoldyn-2.73.tgz \
-#     && cd smoldyn-2.73 \
-#     && cd build \
-#     && cmake .. -DENABLE_PYTHON=ON -DPYTHON_EXECUTABLE=$(which python3.10) \
-#     && make \
-#     && make install
-# && rm -rf /var/lib/apt/lists/* \
-# && apt-get clean \
-# && apt-get autoclean
-
-# RUN . /app/.venv/bin/activate \
-#     && curl -O https://download.opensuse.org/repositories/home:/dilawar/xUbuntu_22.04/amd64/smoldyn_2.64.4-1+2.1_amd64.deb \
-#     && dpkg -i smoldyn_2.64.4-1+2.1_amd64.deb
-
-# RUN . /app/.venv/bin/activate \
-#     && echo 'deb http://download.opensuse.org/repositories/home:/dilawar/xUbuntu_22.04/ /' | tee /etc/apt/sources.list.d/home:dilawar.list \
-#     && curl -fsSL https://download.opensuse.org/repositories/home:dilawar/xUbuntu_22.04/Release.key | gpg --dearmor | tee /etc/apt/trusted.gpg.d/home_dilawar.gpg > /dev/null \
-#     && apt update \
-#     && apt install smoldyn
-
-# fix python version constraint, lock env, and check compatible
-# RUN sed -i 's/python = ">=3.10"/python = "^3.10"/' /app/pyproject.toml \
-#     && poetry lock \
-#     && poetry check
-
-# TODO: fix this eventually, but for now (10/2024) biosimulators-processes is not used
-# RUN rm -r biosimulator_processes
-
-# remove existing cobra installation TODO: clean this up
-# RUN poetry remove cobra && poetry remove zarr
-
-# install project deps (shared)
-# RUN chmod +x /app/assets/install_deps.sh \
-#     && /app/assets/install_deps.sh /app/assets/requirements.base.txt
-
-
-# TODO: create shared tooling module which is a set of the sum of api and worker data_model.py & shared.py
-# COPY ./assets/shared.py /app/shared.py
diff --git a/assets/configs/requirements.github.txt b/assets/configs/requirements.github.txt
@@ -1,8 +1,3 @@
-requests-toolbelt~=1.0.0
-seaborn~=0.13.2
-pydantic~=2.8.2
-numpy
-pandas 
-pytest
-tellurium
-python-dotenv
+python-dotenv
+fastapi
+yaml