updates to all builds

Dockerfile-base

@@ -8,6 +8,9 @@ LABEL org.opencontainers.image.title="bio-check-base" \
     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
 ENV DEBIAN_FRONTEND=noninteractive \
     MONGO_URI="mongodb://mongodb/?retryWrites=true&w=majority&appName=bio-check" \
@@ -16,24 +19,26 @@ ENV DEBIAN_FRONTEND=noninteractive \
 
 # copy docker
 COPY assets/docker/config/.biosimulations.json /.google/.bio-check.json
-COPY assets/docker/config/base-config/.pys_usercfg.ini /Pysces/.pys_usercfg.ini
-COPY assets/docker/config/base-config/.pys_usercfg.ini /root/Pysces/.pys_usercfg.ini
+COPY assets/docker/config/.pys_usercfg.ini /Pysces/.pys_usercfg.ini
+COPY assets/docker/config/.pys_usercfg.ini /root/Pysces/.pys_usercfg.ini
 COPY pyproject.toml assets/docker/shared.py assets/test_fixtures /app/
-COPY assets/docker/config/base-config/ assets/docker/config/worker-config/ /app/config/
+COPY assets/docker/config/environment.api.yml assets/docker/config/environment.worker.yml /app/config/
 
 # cd /app
 WORKDIR /app
 
 RUN mkdir -p /Pysces \
     && mkdir -p /Pysces/psc \
     && mkdir -p /root/Pysces \
-    && mkdir -p /root/Pysces/psc
-# pip install . --root-user-action=ignore
+    && mkdir -p /root/Pysces/psc \
+    && echo "conda activate server" >> ~/.bashrc
+
+
 # # create conda env from yml and ensure env activation
-RUN conda env create -f config/environment.base.yml -y \
-    && rm -f config/environment.base.yml \
-    && conda env export --no-builds > config/environment.lock.yml \
-    && poetry lock
+# RUN conda env create -f config/environment.base.yml -y \
+#     && rm -f config/environment.base.yml \
+#     && conda env export --no-builds > config/environment.lock.yml \
+#     && poetry lock
 
 # create lockfile conda analogy: conda env export --no-builds > environment.lock.yml
 # && conda create -n conda-env python=3.10 -y \

api/Dockerfile-api

@@ -9,8 +9,12 @@ COPY ./ ./
 
 EXPOSE 3001
 
-RUN source ~/.bashrc \
-    && poetry install --without=composition,dev,worker --no-cache
+RUN conda env create -n server -f config/environment.api.yml -y \
+    && rm -rf config \
+    && conda clean --all --json -y
 
-ENTRYPOINT ["bash", "-c", "source ~/.bashrc && poetry run uvicorn main:app --host 0.0.0.0 --port 3001 --reload"]
+# RUN source ~/.bashrc \
+#     && poetry install --without=composition,dev,worker --no-cache
+
+ENTRYPOINT ["bash", "-c", "source ~/.bashrc && uvicorn main:app --host 0.0.0.0 --port 3001 --reload"]
 

assets/docker/.BASE_VERSION

@@ -1 +1 @@
-0.0.2-test
+0.0.2

worker/Dockerfile-worker

@@ -7,8 +7,6 @@ SHELL ["/usr/bin/env", "bash", "-c"]
 
 COPY ./ ./
 
-# WORKDIR /app/worker
-
 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"
@@ -32,8 +30,7 @@ ENV TEST_SBML_FP="test_fixtures/Elowitz-Nature-2000-Repressilator/BIOMD000000001
 #     && apt-get clean
 
 # TODO: perhaps run --no-install-recommends?
-RUN source ~/.bashrc \
-    && apt-get update  \
+RUN apt-get update  \
     && apt-get install -y \
     meson \
     g++ \
@@ -61,15 +58,14 @@ RUN source ~/.bashrc \
     libboost-chrono-dev \
     libboost-math-dev \
     libboost-serialization-dev \
-    && conda install -c conda-forge -c pysces pysces -y \
-	&& conda env update -n conda-env -f config/environment.worker.yml \
-    && poetry install --without=api,composition,dev --no-cache \
+	&& conda env create -n server -f config/environment.worker.yml -y \
+    && rm -rf config \
     && rm -rf /var/lib/apt/lists/* \
     && apt-get autoremove -y \
     && apt-get clean \
     && conda clean --all --json -y
 
-ENTRYPOINT ["bash", "-c", "source ~/.bashrc && poetry run python3 main.py"]
+ENTRYPOINT ["bash", "-c", "source ~/.bashrc && python3 main.py"]
 
 # --root-user-action=ignore
 #############################