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sys-bio / tellurium

Python Environment for Modeling and Simulating Biological Systems
http://tellurium.analogmachine.org/
Apache License 2.0
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Is experiment class deprecated? #222

Closed matthiaskoenig closed 7 years ago

matthiaskoenig commented 7 years ago

Is the content of tephrasedml.py deprecated? or is this still used? Mainly the experiment class. With the latest tellurium changes I am not sure if this has been replaced.

If this is replaced, what is the new way to run phrasedml with sbml?

0u812 commented 7 years ago

I think all of the use-cases for the experiment class are covered by inline OMEX strings. I updated the examples in the docs to use inline OMEX. I would be in favor of deprecating the experiment class (it was originally hacked together for a demo and seems rather limited IMO).

matthiaskoenig commented 7 years ago

Yes, I strongly agree and would remove it. Than I can rewrite the tests for the new inline omex.

Same question for tellurium.tecombine.py. Looks also completely deprecated. It would help a lot to remove this also if it is not used anymore.

0u812 commented 7 years ago

Sounds good to me. Anyone else using these?

matthiaskoenig commented 7 years ago

I think with major release 2.0.0 we can remove all the deprecated things. Especially because replacement functions exist.

matthiaskoenig commented 7 years ago

tellurium.phrasedml.py and tellurium.tecombine.py will be removed. If functionality is required this will be ported.