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.
In the PCCAPlus class from
lumping.pcca_plus, theoptimize_Amethod uses Scipy'soptimize.annealmethod. This is deprecated in SciPy v0.14.0 version, and it usesoptimize.basinhoppinginstead. 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!