refactor new base and api version

.github/workflows/deploy-microservices.yml

@@ -67,31 +67,25 @@ jobs:
           sudo chmod +x /usr/local/bin/docker-compose
           docker-compose --version  # Check if Docker Compose is installed correctly
 
-      - name: Build API microservice image
-        run: docker-compose build api
-
-      - name: Build worker microservice image
-        run: docker-compose build worker
-
       - name: Authorize push script
         run: chmod +x ./docker/scripts/push_image.sh
 
+      - name: Build API microservice image
+        run: docker-compose build api
+
       - name: Deploy API microservice container to GHCR
         run: |
           rm api/spec/openapi_3_1_0_generated.yaml
           python3 api/openapi_spec.py
           sudo rm -r api/__pycache__
           ./assets/docker/scripts/push_image.sh api ${{ env.API_VERSION }}
-        # STABLE CONTENT:
-        # - run: |
-        #   rm compose_api/spec/openapi_3_1_0_generated.yaml
-        #   python3 compose_api/openapi_spec.py
-        #   sudo rm -r compose_api/__pycache__
-        #   ./docker/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: Build worker microservice image
+        run: docker-compose build worker
+
       - name: Deploy worker microservice container to GHCR
         run: |
           sudo rm -r compose_api/__pycache__

Dockerfile-base

@@ -1,14 +1,13 @@
 # FROM ubuntu:22.04
 FROM continuumio/miniconda3:latest
 
-LABEL org.opencontainers.image.title="bio-check-base" \
+LABEL org.opencontainers.image.title="bio-compose-server-base" \
     org.opencontainers.image.description="Base Docker image for BioCompose REST API management, job processing, and datastorage with MongoDB, ensuring scalable and robust performance." \
     org.opencontainers.image.url="https://biosimulators.org/" \
     org.opencontainers.image.source="https://github.com/biosimulators/bio-check" \
     org.opencontainers.image.authors="Alexander Patrie <[email protected]>, BioSimulators Team <[email protected]>" \
     org.opencontainers.image.vendor="BioSimulators Team"
 
-# SHELL ["/bin/bash", "-c"]
 SHELL ["/usr/bin/env", "bash", "-c"]
 
 # shared env
@@ -32,7 +31,10 @@ RUN mkdir -p /Pysces \
     && mkdir -p /root/Pysces \
     && mkdir -p /root/Pysces/psc \
     && conda env create -n server -f environment.base.yml -y \
-    && echo "conda activate server" >> ~/.bashrc
+    && echo "conda activate server" >> ~/.bashrc \
+    && source ~/.bashrc \
+    && conda env export --no-builds > config/environment.base.lock.yml \
+    && rm -f environment.base.yml
 
 
 # # create conda env from yml and ensure env activation

api/Dockerfile-api

@@ -11,8 +11,10 @@ EXPOSE 3001
 
 RUN source ~/.bashrc \
     && conda env update -n server -f config/environment.api.yml \
-    && conda run pip install -e . \
-    && conda clean --all --json -y
+    && conda run pip install -e . --root-user-action=ignore \
+    && conda env export --no-builds > config/environment.api.lock.yml \
+    && conda clean --all --json -y \
+    && rm -f config/environment.api.yml
 
 # RUN source ~/.bashrc \
 #     && poetry install --without=composition,dev,worker --no-cache

assets/docker/.BASE_VERSION

@@ -1 +1 @@
-0.0.4-test
+0.0.5-test

worker/Dockerfile-worker

@@ -6,7 +6,6 @@ FROM ghcr.io/biosimulators/bio-compose-server-base:latest
 SHELL ["/usr/bin/env", "bash", "-c"]
 
 COPY ./ .
-# COPY ../assets/docker/config/environment.base.yml ../assets/docker/config/environment.worker.yml .
 
 ENV TEST_SBML_FP="test_fixtures/Elowitz-Nature-2000-Repressilator/BIOMD0000000012_url.xml" \
     TEST_PSC_FP="/Pysces/psc/BIOMD0000000012_url.xml.psc" \
@@ -46,20 +45,17 @@ RUN source ~/.bashrc \
     libboost-math-dev \
     libboost-serialization-dev \
     && conda env update -n server -f config/environment.worker.yml \
-    && conda run pip install -e . \
+    && conda run pip install -e . --root-user-action=ignore \
+    && conda env export --no-builds > config/environment.worker.lock.yml \
+    && conda clean --all --json -y \
+    && rm -f config/environment.worker.yml \
     && rm -rf /var/lib/apt/lists/* \
     && apt-get autoremove -y \
-    && apt-get clean \
-    && conda clean --all --json -y
+    && apt-get clean
 
-# && conda install -c conda-forge -c pysces pysces \
-# && conda env update -n server -f config/environment.worker.yml \
-# && conda install "numpy<1.22.0" \
-# && conda run pip install amici biosimulators-amici --root-user-action=ignore \
-# && rm -rf config \
 ENTRYPOINT ["bash", "-c", "source ~/.bashrc && conda run python3 main.py"]
 
-# --root-user-action=ignore
+
 #############################
 # Fenics installation