update internal base version and poetry deps and container builds

Dockerfile-base

@@ -75,7 +75,7 @@ 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
+    && poetry install --without=api,worker,pysces,masspy
 
 
 # install smoldyn

assets/.BASE_VERSION

@@ -1 +1 @@
-0.1.4
+0.1.5

compose_worker/Dockerfile-compose_worker

@@ -23,27 +23,27 @@ RUN apt-get update && apt-get install -y libatlas-base-dev \
 
 # SUNDIALS --> installation path is default cmake (/usr/local) with LD_LIBRARY_PATH as runtime location
 # ignore certificate checking because certificate was expired as of 2021-11-10
-ARG SUNDIALS_VERSION=2.6.2
-RUN apt-get install -y --no-install-recommends \
-        wget \
-        cmake \
-        make \
-        g++ \
-    \
-    && cd /tmp \
-    && wget --no-check-certificate https://computing.llnl.gov/sites/default/files/inline-files/sundials-${SUNDIALS_VERSION}.tar.gz \
-    && tar xvvf sundials-${SUNDIALS_VERSION}.tar.gz \
-    && cd sundials-${SUNDIALS_VERSION} \
-    && mkdir build \
-    && cd build \
-    && CFLAGS="-fPIC" cmake .. \
-    && make \
-    && make install \
-    \
-    && cd /tmp \
-    && rm sundials-${SUNDIALS_VERSION}.tar.gz \
-    && rm -r sundials-${SUNDIALS_VERSION}
-ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
+# ARG SUNDIALS_VERSION=2.6.2
+# RUN apt-get install -y --no-install-recommends \
+#         wget \
+#         cmake \
+#         make \
+#         g++ \
+#     \
+#     && cd /tmp \
+#     && wget --no-check-certificate https://computing.llnl.gov/sites/default/files/inline-files/sundials-${SUNDIALS_VERSION}.tar.gz \
+#     && tar xvvf sundials-${SUNDIALS_VERSION}.tar.gz \
+#     && cd sundials-${SUNDIALS_VERSION} \
+#     && mkdir build \
+#     && cd build \
+#     && CFLAGS="-fPIC" cmake .. \
+#     && make \
+#     && make install \
+#     \
+#     && cd /tmp \
+#     && rm sundials-${SUNDIALS_VERSION}.tar.gz \
+#     && rm -r sundials-${SUNDIALS_VERSION}
+# ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
 
 ############################################
 # App content
@@ -56,37 +56,29 @@ ENV PATH="/root/.local/bin:$PATH"
 RUN poetry install --only=worker --no-cache
 
 # Install Assimulo from source for Pysces
-RUN apt-get update \
-    && apt-get install -y libblas-dev \
-    liblapack-dev \
-    libatlas-base-dev \
-    python3-distutils \
-    python3-dev \
-    && git clone https://github.com/modelon-community/Assimulo.git \
-    && cd Assimulo \
-    && poetry run pip install --upgrade setuptools pip wheel Cython numpy \
-    && poetry run python3 setup.py install --sundials-home=/usr/local --blas-home=/usr/lib/x86_64-linux-gnu
-
-# && cd Assimulo \
-# && rm -rf build \
-# && poetry run python3 setup.py install --sundials-home=/usr/local --blas-home=/usr/lib/x86_64-linux-gnu
-
-# 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
+# RUN apt-get update \
+#     && apt-get install -y libblas-dev \
+#     liblapack-dev \
+#     libatlas-base-dev \
+#     python3-distutils \
+#     python3-dev \
+#     && git clone https://github.com/modelon-community/Assimulo.git \
+#     && cd Assimulo \
+#     && poetry run pip install --upgrade setuptools pip wheel Cython numpy \
+#     && poetry run python3 setup.py install --sundials-home=/usr/local --blas-home=/usr/lib/x86_64-linux-gnu
 
 # install masspy TODO: implement this
-RUN git clone https://github.com/biosimulators/Biosimulators_MASSpy.git \
-    && cd Biosimulators_MASSpy \
-    && rm pyproject.toml
+# 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]"
 
 ENTRYPOINT ["poetry", "run", "python3", "main.py"]
 
+
 #############################
 # Fenics