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PCCA contains deprecated method

Open Zsailer opened this issue 9 years ago • 0 comments

In the PCCAPlus class from lumping.pcca_plus, the optimize_A method uses Scipy's optimize.anneal method. This is deprecated in SciPy v0.14.0 version, and it uses optimize.basinhopping instead. Scipy returns a couple warnings about this.

I have not yet investigated these methods enough to see how much of a difference this makes. I'd be happy to look into this more and submit a PR with the new method. I'm sure it's pretty trivial.

Thanks for all the great work here, too!

Zsailer avatar Sep 24 '14 16:09 Zsailer