Open jonrkarr opened 3 years ago
Actually, the above line should be deleted because neither should be recognized in conjunction with SED-ML UniformTimeCourse.
KISAO_0000656
could be recognized for variable time courses described with the new SED-ML Analysis
class.
OK, since the dictionary in question is just 'terms Tellurium recognizes', I added the new term instead of removing the old one. Eventually when we support the generic Analysis class, we'll want it in the list.
For now, there's just an inherent contradiction in providing a 'variable step size' parameter for a uniform time course; the proper thing to do would be to provide an error. I'll leave this open until that's done.
Another possible middle ground is to raise a DeprecationWarning
to discourage its use (e.g., to communicate that this would not be portable across tools) while retaining support.
Tellurium recognizes
KISA0:0000107
for the boolean argument whether to use adaptive time steps. However, this is a term for an algorithm characteristic rather than an algorithm parameter.I added an algorithm parameter term
KISAO:0000656
for this purpose.Tellurium should either replace
KISAO:0000107
withKISAO:0000656
or recognizeKISAO:0000656
as a "synonym" forKISAO:0000107
.Here's the relevant line: https://github.com/sys-bio/tellurium/blob/3e7cfb57d448ca507e5193470f7526c98f070188/tellurium/sedml/tesedml.py#L245