Update python Docker tag to v3.11

Dockerfile-base

@@ -1,7 +1,7 @@
 #############
 ### base ###
 #############
-FROM python:3.9-slim-buster
+FROM python:3.11-slim-buster
 
 LABEL \
     org.opencontainers.image.title="BioSimulators-base" \
@@ -16,14 +16,14 @@
 
 ###################################
 # update apt package database
 RUN apt-get update -y
 
 ###################################
 # AMICI
 RUN apt-get install --no-install-recommends -y \
         g++ \
         libatlas-base-dev \
         swig
 
 ###################################
 # BioNetGen
@@ -34,9 +34,9 @@
         wget \
     \
     && cd /tmp \
     && wget https://github.com/RuleWorld/bionetgen/releases/download/BioNetGen-${BIONETGEN_VERSION}/BioNetGen-${BIONETGEN_VERSION}-linux.tgz \
     && tar xvvf BioNetGen-${BIONETGEN_VERSION}-linux.tgz \
     && mv BioNetGen-${BIONETGEN_VERSION}/ /opt/ \
     \
     && rm BioNetGen-${BIONETGEN_VERSION}-linux.tgz
 ENV PATH=${PATH}:/opt/BioNetGen-${BIONETGEN_VERSION}/
@@ -44,18 +44,18 @@
 ###################################
 # BoolNet
 ARG BOOLNET_VERSION=2.1.5
 RUN apt-get install -y --no-install-recommends \
         r-base \
         build-essential \
         gcc \
         gfortran \
         libblas-dev \
         libcurl4-openssl-dev \
         libgit2-dev \
         liblapack-dev \
         libssl-dev \
         libxml2 \
         libxml2-dev \
     \
     && Rscript \
         -e "install.packages('devtools')" \
@@ -65,22 +65,22 @@
 
 ###################################
 # CBMPy
 RUN apt-get install -y --no-install-recommends \
         gcc \
         libglpk-dev
 
 ###################################
 # COBRAPY
 RUN mkdir -p /.cache/cobrapy \
     && chmod ugo+rw /.cache/cobrapy
 
 ###################################
 # COPASI
 
 ###################################
 # GillesPy2
 RUN apt-get install -y --no-install-recommends \
         build-essential
 
 ###################################
 # GINsim
@@ -90,8 +90,8 @@
         wget \
     \
     && cd /tmp \
     && pip install ginsim \
     && wget https://raw.githubusercontent.com/GINsim/GINsim-python/master/ginsim_setup.py \
     && python ginsim_setup.py \
     \
     && rm ginsim_setup.py
@@ -102,30 +102,30 @@
 ARG LIBSBML_VERSION=5.19.0
 
 # libSBML
 RUN apt-get install --no-install-recommends -y \
         wget \
         libxml2 \
     \
     && wget https://master.dl.sourceforge.net/project/sbml/libsbml/${LIBSBML_VERSION}/stable/Linux/64-bit/libSBML-${LIBSBML_VERSION}-Linux-x64.deb \
     && dpkg -i libSBML-${LIBSBML_VERSION}-Linux-x64.deb \
     \
     && rm libSBML-${LIBSBML_VERSION}-Linux-x64.deb
 ENV LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH
 
 # LibSBMLSim
 RUN apt-get install --no-install-recommends -y \
         wget \
         build-essential \
         cmake \
         swig \
         libbz2-dev \
     \
     && PY_EXEC_PATH=$(which python) \
     && PY_PREFIX=$(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 \
     && tar xvvf v${LSBMLSIM_VERSION}.tar.gz \
     && cd libsbmlsim-${LSBMLSIM_VERSION} \
     && mkdir build \
     && cd build \
     && PYTHON_MAJOR_MINOR_VERSION=$(echo $PYTHON_VERSION | cut -d . -f 1-2) \
@@ -134,8 +134,8 @@
         -D LIBSBML_LIBRARY=/usr/lib64/libsbml.so \
         -D WITH_PYTHON=ON \
         -D PYTHON_PREFIX=${PY_PREFIX} \
         -D PYTHON_EXECUTABLE:FILEPATH=${PY_EXEC_PATH} \
         -D PYTHON_INCLUDE_DIR:PATH=/usr/local/include/python${PYTHON_MAJOR_MINOR_VERSION} \
         -D PYTHON_LIBRARY:FILEPATH=/usr/local/lib/libpython${PYTHON_MAJOR_MINOR_VERSION}.so \
         .. \
     \
@@ -143,39 +143,39 @@
     && make install \
     \
     && cd /tmp \
     && rm v${LSBMLSIM_VERSION}.tar.gz \
     && rm -r libsbmlsim-${LSBMLSIM_VERSION}
 
 ###################################
 # MASSpy
 RUN apt-get install -y --no-install-recommends \
         git \
         gcc \
         build-essential \
         libfreetype6-dev \
         libfreetype6 \
         pkg-config \
     \
     && mkdir -p /.cache/cobrapy
 
 ###################################
 # NetPyNe
 RUN apt-get install -y --no-install-recommends \
     gcc \
     g++ \
     make \
     libmpich-dev \
     mpi \
     mpi-default-bin \
     mpich
 
 ###################################
 # NEURON
 RUN apt-get install -y --no-install-recommends \
     gcc \
     g++ \
     make
 RUN pip install neuron
 ENV NEURON_HOME=/usr/local
 
 ###################################
@@ -190,16 +190,16 @@
 # SUNDIALS
 # 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-${SUNDIALS_VERSION} \
     && mkdir build \
     && cd build \
     && cmake .. \
@@ -207,24 +207,24 @@
     && make install \
     \
     && cd /tmp \
     && rm sundials-${SUNDIALS_VERSION}.tar.gz \
     && rm -r sundials-${SUNDIALS_VERSION}
 ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
 
 # Assimulo
 RUN apt-get install -y --no-install-recommends \
         g++ \
         gfortran \
         libblas-dev \
         liblapack-dev \
         git
 
 # PySCeS
 RUN apt-get install -y --no-install-recommends \
         git \
         gcc \
         gfortran \
         libgfortran5
 
 # Configure PySCeS
 COPY .pys_usercfg.ini /Pysces/.pys_usercfg.ini
@@ -237,9 +237,9 @@
 
 ###################################
 # RBApy
 RUN apt-get install -y --no-install-recommends \
         gcc \
         libglpk-dev
 
 ###################################
 # Smoldyn
@@ -254,17 +254,17 @@
 
 ###################################
 # XPP
 RUN apt-get install -y --no-install-recommends \
         wget \
         make \
         gcc \
         libx11-dev \
         libc6-dev \
         libx11-6 \
         libc6 \
     \
     && cd /tmp \
     && wget http://www.math.pitt.edu/~bard/bardware/xppaut_latest.tar.gz \
     && mkdir xpp \
     && tar zxvf xppaut_latest.tar.gz --directory xpp \
     && cd xpp \
@@ -282,7 +282,7 @@
     && apt-get install --no-install-recommends -y \
         xvfb \
     && mkdir /tmp/.X11-unix \
     && chmod 1777 /tmp/.X11-unix \
     \
     && rm -rf /var/lib/apt/lists/*
 COPY xvfb-startup.sh /xvfb-startup.sh
@@ -298,8 +298,8 @@
 # configure matplotlib cache and config to avoid warnings
 RUN mkdir -p /.cache/matplotlib \
     && mkdir -p /.config/matplotlib \
     && chmod ugo+rw /.config/matplotlib \
     && chmod ugo+rw /.cache/matplotlib
 
 # Configure default simulator options
 ENV ALGORITHM_SUBSTITUTION_POLICY=SIMILAR_VARIABLES \