DeleteMolecules as default behavior and DeleteComplex as keyword

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There has been some discussion in the past of making DeleteMolecules the 
default behavior for degradation rules and implementing a DeleteSpecies (or 
DeleteComplex) keyword for deleting entire complexes. Currently, the opposite 
is the convention. The advantage of doing this would be that a degradation rule 
would then do exactly as the rule specifies, i.e., A() -> Null() would delete 
the molecule A() rather than the entire complex connected to A(). The major 
disadvantage would be the loss of backward compatibility.

Original issue reported on code.google.com by lh64@cornell.edu on 24 Sep 2012 at 10:31

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Original comment by lh64@cornell.edu on 24 Sep 2012 at 10:32

• Changed title: DeleteMolecules as default behavior and DeleteComplex as keyword

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Since this change would affect nearly every existing model with deletion, we 
should stay with the old convention until there's a major new version (i.e. 
version 3.0) along with a new manual.

I feel that version 2.2.x should be the "long term stable" distribution . Users 
should be confident that the core interface remains constant. We should 
restrict ourselves to bug-fixes, minor features, and improved support for 
analysis (e.g. better parameter scanning/estimation). Changes that improve BNG 
and NFsim compatibility would be the primary exception to the "stability" 
principle.

Original comment by justinshogg on 24 Sep 2012 at 3:06

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I agree that the backward incompatibility issue looms very large here.  I think 
we should not make this change in the current version, if ever.

Original comment by jrfae...@gmail.com on 24 Sep 2012 at 8:59

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I agree that it's a low priority issue at this point and will cause a lot of 
headaches to change. It should be pushed off to a later development cycle. 
However, I also think that deleting an entire complex is pretty non-intuitive 
as default behavior and that a change is in order at some point. There has been 
a case recently, in fact, of a new user getting confused by this and not 
realizing that the DeleteMolecules keyword exists. Will leave the issue in the 
queue with a "Low" priority tag.

Original comment by lh64@cornell.edu on 26 Sep 2012 at 12:50

• Added labels: Priority-Low
• Removed labels: Priority-Medium