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biosimulations / biosimulations-physiome

Command-line application for publishing the Physiome model repository of physiological models to the BioSimulations repository for simulation projects
https://docs.biosimulations.org/repositories/physiome
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Skip plots that require marker style or encode OpenCOR's custom style annotations into L1V4 #32

Open jonrkarr opened 2 years ago

jonrkarr commented 2 years ago

Because SED-ML L1V3 doesn't capture plot style, OpenCOR uses custom style annotations in conjunction with L1V3. BioSimulations ignores these custom style annotations. Because style can be critical (e.g., plots can look very different with markers vs lines), we should either:

  1. Use OpenCOR to import these L1V3 files and re-export them to L1V4 with style encoded into SED-ML (if OpenCOR can do this).
  2. For now, skip plots that are annotated with marker styles (because the plot might look very different without lines).
  3. Use lxml or similar to read this information from OpenCOR SED-ML files, encode the style into SED-ML L1V4, and export the file to SED-ML L1V4.

@agarny, could we use OpenCOR for option 1? or will this be possible soon?