feat: simplified Python environment

Dockerfile

@@ -20,15 +20,15 @@ COPY Pipfile /app/Pipfile
 COPY Pipfile.lock /app/Pipfile.lock
 
 # install environment
-RUN pipenv sync
+RUN pipenv install --system --deploy
 
 # force reinstall of matplotlib due to inconsistent version
-RUN pipenv run pip uninstall -y matplotlib \
-    && pipenv run pip install "matplotlib==3.2.0" \
-    && pipenv run python -c "import matplotlib.font_manager"
+RUN pip uninstall -y matplotlib \
+    && pip install "matplotlib==3.2.0" \
+    && python -c "import matplotlib.font_manager"
 
 # install assimulo because pipenv fails to install it
 ARG ASSIMULO_VERSION=3.2.5
-RUN pipenv run pip install git+https://github.com/modelon-community/Assimulo.git@Assimulo-${ASSIMULO_VERSION}
+RUN pip install git+https://github.com/modelon-community/Assimulo.git@Assimulo-${ASSIMULO_VERSION}
 
-CMD /bin/bash /xvfb-startup.sh pipenv run ipython
+CMD /bin/bash /xvfb-startup.sh ipython

Dockerfile-base

@@ -124,7 +124,7 @@ RUN apt-get install --no-install-recommends -y \
         swig \
         libbz2-dev \
     \
-    && PY_EXEC_PATH=$(pipenv run which python) \
+    && PY_EXEC_PATH=$(python) \
     && PY_PREFIX=$(echo ${PY_EXEC_PATH} | rev | cut -d "/" -f 3- | rev) \
     && cd /tmp \
     && wget https://github.com/libsbmlsim/libsbmlsim/archive/refs/tags/v${LSBMLSIM_VERSION}.tar.gz \

README.md

@@ -26,7 +26,7 @@ We recommend that users use the hosted versions of runBioSimulations at https://
 
 Each validated simulation tool is available as Docker image. Most of the validated simulation tools are also available as Python APIs. See https://biosimulators.org for information about the interfaces available for each tool and where they can be obtained.
 
-A Docker image with a Pipenv environment with Python APIs for most of the validated simulation tools is available at https://github.com/orgs/biosimulators/packages/container/package/biosimulators. An iPython shell for this environment can be launched by installing Docker and running the commands below. Information about using the Python APIs in the image is available at https://biosimulators.org/help.:
+A Docker image with a Python environment with APIs for most of the validated simulation tools is available at https://github.com/orgs/biosimulators/packages/container/package/biosimulators. An iPython shell for this environment can be launched by installing Docker and running the commands below. Information about using the Python APIs in the image is available at https://biosimulators.org/help.:
 ```
 docker pull ghcr.io/biosimulators/biosimulators
 docker run -it --rm ghcr.io/biosimulators/biosimulators