Notebook fixes

[MichaelClerx]

Three(!) notebooks were failing.

The nuts one failed because rhat_all_params had been removed from the API (not deprecated), so fixed that as well

[codecov]

Codecov Report

Merging #1201 into master will not change coverage.
The diff coverage is n/a.

@@            Coverage Diff            @@
##            master     #1201   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           82        82           
  Lines         8254      8254           
=========================================
  Hits          8254      8254           

Impacted Files	Coverage Δ
pints/__init__.py	100.00% <ø> (ø)

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[rccreswell]

In residuals-autocorrelation.ipynb, the Lotka-Volterra example was randomly failing on some runs due to a bad initial condition far away from the true parameter values (it would still have worked eventually, but with more MCMC iterations than we were doing in the notebooks). I moved the initial condition slightly closer to the true values, which seems to give a consistent correct result with the same number of iterations.

[DavAug]

Sorry my bad for removing the rhat_all_params function instead of deprecating it.

Looks good to me, I have difficulties to figure out what has changed in the constant_and_multiplicative notebook though :D

[MichaelClerx]

Sorry my bad for removing the rhat_all_params function instead of deprecating it.

No worries!

Looks good to me, I have difficulties to figure out what has changed in the constant_and_multiplicative notebook though :D

Yeah github doens't like notebooks much (they contain embedded images, which makes github think there's a massive change).
You can check it out with a local client (I use meld) by doing git difftool master. You need to tell it which tool though, which is something I always google :D

Changes to the notebook are small: just moved the imports around and made sure pints.plot was imported. It's important to always restart and re-run the notebook before submitting the final one: sometimes you've deleted a crucial import or variable from the notebook but it still works because it's remembered in the state

[martinjrobins]

thanks @MichaelClerx for catching this