Add option to generate SEDML file from LEMS and use this as master in exported OMEX archive

[pgleeson]

For upload to https://biosimulations.org/runs/new

Example of valid manifest file using SEDML:

<?xml version="1.0" encoding="UTF-8"?>
<omexManifest xmlns="http://identifiers.org/combine.specifications/omex-manifest">
  <content location="model.xml" format="http://purl.org/NET/mediatypes/application/lems+xml" master="false"/>
  <content location="simulation.sedml" format="http://identifiers.org/combine.specifications/sed-ml" master="true"/>
  <content location="NaConductance.channel.nml" format="http://identifiers.org/combine.specifications/neuroml" master="false"/>
  <content location="KConductance.channel.nml" format="http://identifiers.org/combine.specifications/neuroml" master="false"/>
  <content location="LeakConductance.channel.nml" format="http://identifiers.org/combine.specifications/neuroml" master="false"/>
  <content location="NML2_SingleCompHHCell.nml" format="http://identifiers.org/combine.specifications/neuroml" master="false"/>
  <content location="metadata.rdf" format="http://identifiers.org/combine.specifications/omex-metadata" master="false"/>
  <content location="expected-results.json" format="http://purl.org/NET/mediatypes/application/json" master="false"/>
  <content location="reports.h5" format="http://purl.org/NET/mediatypes/application/x-hdf" master="false"/>
</omexManifest>

What needs to be done here:

• the SEDML file needs to be generated from LEMS by running jneuroml with -sedml: see pynml.py and search for the -sedml arg there
• we already have functionality to create the OMEX archive by pointing at LEMS/NeuroML files, so that can be extended to also use a SEDML file. (Note that to get the file pointed to by the SEDML file, one will have to parse the SEDML file, or one can get it from the LEMS file that is being used to generate the SEDML file)