Plotter for MCMC diagnostics

[zihaoxu98]

This PR adds a class called Plotter, which can generate the needed plots to diagnose MCMC result. Currently, there are four plots: burn-in, marginal posterior, corner, and auto corr plot for convergence check (see emcee doc)

To use it,

from appletree import Plotter

file_name = '/project2/lgrandi/mhliu0001/ambe_fit_backend/fit_ambe_sr0_with_outliers.h5'
plotter = Plotter(file_name)
plotter.make_all_plots()

Note that a long iteration will slow down the plotting, especially the corner plot.

[coveralls]

Pull Request Test Coverage Report for Build 8168645414

Details

• 190 of 202 (94.06%) changed or added relevant lines in 2 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage increased (+1.3%) to 85.075%

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Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
appletree/plot.py	188	200	94.0%

Totals
Change from base Build 8158759385:	1.3%
Covered Lines:	2263
Relevant Lines:	2660

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💛 - Coveralls

[dachengx]

Thanks @zihaoxu98 . This is a feature we wanted for a long time. Just a few minor points needed more revising.

[dachengx]

I added some tests of the plotting function.