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add reader for Cobaya's MCMC chains (requires GetDist) #167
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… run CobayaMCMCReader without GetDist
…that loadMCSamples is not defined
Codecov Report
@@ Coverage Diff @@
## master #167 +/- ##
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Coverage 95.09% 95.10%
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Files 16 17 +1
Lines 1672 1715 +43
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+ Hits 1590 1631 +41
- Misses 82 84 +2
Continue to review full report at Codecov.
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…lumn as `logP` (cobayas second column is the log-posterior) instead of `chi2`
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This looks like a very nice addition. I assume that since you're a Cobaya aficionado you've tested this 'in the wild' in addition to the tests you've put in here?
Once @Stefan-Heimersheim has finished #158 for dynesty, I think the only one we're missing is cosmosis. @Pablo-Lemos does cosmosis have it's own chain formatting, or does it just rely on polychord/multinest?
I believe CosmoSIS has its own formatting, and in fact annoyingly does not generate a paramnames file |
…his actually should not happen in Cobaya
… cobaya MCMC samples requires getdist
This introduces a chain reader for Cobaya's MCMC chains. Cobaya (different from CosmoMC) no longer provides
.paramnames
files for its MCMC chains, but instead works with.yaml
files which are simultaneously Cobaya's input files. These contain all information on the sampling parameters and derived parameters, including the tex string. TheCobayaMCMCReader
that is implemented here uses GetDist to infer the parameter labels used for the pandas dataframe as well as the tex strings for the.tex
dictionary. Since GetDist is a requirement for Cobaya anyhow, having it as a requirement for anesthetic'sCobayaMCMCReader
shouldn't be too bad.Fixes #129
Checklist:
flake8 anesthetic tests
)pydocstyle --convention=numpy anesthetic
)python -m pytest
)