doc: Update steady state notebook (#2891)

Update the outdated steady state computation notebook to match the current implementation.

Various clean up and prettification.

Switch from SBML to antimony model.

Co-authored-by: Polina Lakrisenko <p.lakrisenko@gmail.com>

Author: dweindl

binder/Dockerfile

@@ -29,7 +29,7 @@ RUN adduser --disabled-password \
     ${NB_USER}
 USER ${NB_USER}
 RUN python3 -m pip install --upgrade build wheel setuptools pip && \
-    python3 -m pip install --no-cache-dir notebook jupyterlab jupyterhub jax[cpu]
+    python3 -m pip install --no-cache-dir notebook jupyterlab jupyterhub jax[cpu] antimony
 # END BINDER
 
 # BEGIN BINDER

doc/conf.py

@@ -228,6 +228,11 @@ def install_doxygen():
 )
 
 nbsphinx_execute = "never" if os.environ.get("AMICI_NO_NB_EXEC") else "auto"
+nbsphinx_execute_arguments = [
+    "--InlineBackend.figure_formats={'svg', 'pdf'}",
+    "--InlineBackend.rc={'figure.dpi': 96}",
+]
+
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]