fix: re-implemented dockerfile contents and added future deps

scripts/Dockerfile-BioSimulators

@@ -27,46 +27,6 @@ LABEL \
     extra.identifiers.biotools="smoldyn" \
     maintainer="Steven Andrews <[email protected]>"
 
-# Set up headless environment
-# RUN apt-get -y update \
-#     && apt-get install --no-install-recommends -y \
-#         xvfb \
-#     && rm -rf /var/lib/apt/lists/* \
-#     && mkdir /tmp/.X11-unix \
-#     && chmod 1777 /tmp/.X11-unix
-# COPY xvfb-startup.sh .
-# RUN chmod +x xvfb-startup.sh
-# ARG RESOLUTION="1920x1080x24"
-# ARG XARGS=""
-# ENV XVFB_RES="${RESOLUTION}" \
-#     XVFB_ARGS="${XARGS}"
-#
-# # install Smoldyn and its dependencies
-# COPY smoldyn*.whl /tmp/
-# RUN cd /tmp \
-#     && WHEEL_PATH=$(ls smoldyn*.whl) \
-#     && pip install "${WHEEL_PATH}[biosimulators]" \
-#     && rm smoldyn*.whl
-#
-# # fonts for matplotlib
-# RUN apt-get update -y \
-#     && apt-get install -y --no-install-recommends libfreetype6 \
-#     && rm -rf /var/lib/apt/lists/*
-#
-# # configure matplotlib
-# RUN mkdir -p /.cache/matplotlib \
-#     && mkdir -p /.config/matplotlib \
-#     && chmod ugo+rw /.config/matplotlib \
-#     && chmod ugo+rw /.cache/matplotlib
-#
-# ENV VERBOSE=0 \
-#     MPLBACKEND=PDF
-#
-# # setup entry point
-# ENTRYPOINT ["/bin/bash", "/xvfb-startup.sh", "python", "-m", "smoldyn.biosimulators"]
-# CMD []
-
-# Set up headless environment and install necessary packages
 RUN apt-get -y update \
     && apt-get install --no-install-recommends -y \
         xvfb \
@@ -90,7 +50,12 @@ RUN cd /tmp \
     && pip install "${WHEEL_PATH}[biosimulators]" \
     && rm smoldyn*.whl
 
-# configure matplotlib cache and config directories
+# fonts for matplotlib
+RUN apt-get update -y \
+    && apt-get install -y --no-install-recommends libfreetype6 \
+    && rm -rf /var/lib/apt/lists/*
+
+# configure matplotlib
 RUN mkdir -p /.cache/matplotlib \
     && mkdir -p /.config/matplotlib \
     && chmod ugo+rw /.config/matplotlib \