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[WIP] Tpt2.8: same commits as before but ontop of the newest master.#429

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schwancr wants to merge 12 commits intomsmbuilder:masterfrom schwancr:tpt2.8

+3,313-69

Commits on Jul 8, 2014

initial addition for finding paths differently...
schwancr
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added new code to do path finding in tpt.py This algorithm is what @brycecr used in msmexplorer as suggested in Frank Noe's paper on TPT. Additionally I re-wrote the dijkstra code so that it's a bi…
schwancr
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updated print statements when finding paths.
schwancr
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started adding a new tpt test
schwancr
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moved stuff in tpt.py around and added citations
schwancr
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added a new test for the new path finding code, but commented out the FindPaths test since it was written for the old code. I don't think it's necessary to have a test other than knowing if it actu…
schwancr
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regenerated FindPaths reference with the new code. I think this is ok since the other test is an example where I know the answer. It would be nice, however to have a transition matrix with a known …
schwancr
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forgot to add the new tpt reference folder for the FindPaths.py test
schwancr
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started adding scipy tpt
schwancr
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small changes FindPaths.py and indentation fixes in tpt.py
schwancr
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got stuff running. fixed print statements
schwancr
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Commits on Oct 17, 2014

stuff from quite a while ago...
schwancr
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