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dwhswenson / contact_map

Contact map analysis for biomolecules; based on MDTraj
GNU Lesser General Public License v2.1
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Future proof ParameterFixer #95

Closed sroet closed 4 years ago

sroet commented 4 years ago

While working on #94 I discovered that ParameterFixer might be a bit to strict in the way we handle query and haystack

The new implementation allows a developer to choose the type of mixing they want for a mismatched query or haystack. For ContactDifference it makes sense to do a intersection as we also do that with the map so we do that as the default.

I think this should future-proof the class just incase we ever want a way of fixing these attributes by for example making a union (some iteratively building of the map), or maybe a difference (making a ContactFrequency that does not include a certain other ContactMap) etc

sroet commented 4 years ago

After this, any immediate changes coming in? I'm thinking of releasing 0.7 after merging (was planning to do that PR before bed, but this seems like it should be included). 0.7 is weird because it is the version of Contact Map Explorer without a ContactMap, so I feel like it should be short-lived. Current WIP stuff from both of us can go toward 0.8, in my opinion.

If you want 0.7 to be short lived you should cut it after merging this one in (I am looking forward to see if #93 builds correctly on the tag ).

94 is at the moment feature complete, and I should be able to update/check the examples (which might conflict with your work on splitting the examples?) and add tests in the coming days, but not today.

sroet commented 4 years ago

If there are no further comments, feel free to merge on green