Revision 4f75faeded2cb284dedbc856a8b2ae56075ea158 authored by Collin Capano on 20 June 2020, 18:27:09 UTC, committed by GitHub on 20 June 2020, 18:27:09 UTC
* use different acl for every chain in epsie

* create base burn in class, move common functions to there; rename MCMCBurnInTests EnsembleMCMC, first stab at creating MCMC tests for independent chains

* more changes to burn in module

* simplify the attributes in the burn in classes

* add write method to burn in classes

* add write_data method to base_hdf

* remove write_burn_in method from mcmc io; use the write method in burn in module instead

* make use of new burn in functions in sampler/base_mcmc

* have emcee and emcee pt use ensemble burn in tests

* add compute_acf function to epsie

* start separating ensemble and mcmc io methods

* stop saving thin settings to file; just return on the fly

* make read/write samples stand alone functions, and update emcee

* rename write functions; update emcee

* move multi temper read/write functions to stand alone and update emcee_pt

* pass kwargs from emcee(_pt) io functions

* simplify get_slice method

* add function to base_mcmc to calculate the number of samples in a chain

* use nsamples_in_chain function to calculate effective number of samples

* add read_raw_samples function that can handle differing number of samples from different chains

* add forgotten import

* use write/read functions from base_multitemper in epsie io

* use stand alone functions for computing ensemble acf/acls

* separate out ensemble-specific attributes in sampler module; update emcee and emcee_pt

* add acl and effective_nsample methods to epsie

* simplify writing acls and burn in

* fix various bugs and typos

* use a single function for writing both acl and raw_acls

* add some more logging info to burn in

* reduce identical blocks of code in burn in module

* fix self -> fp in read_raw_samples

* reduce code duplication in base io and simplify read raw samples function

* fix missed rename

* reduce code redundacy in sampler/base_multitemper

* whitespace

* fix bugs and typos in burn_in module

* fix code climate issues

* use map in compute_acl

* more code climate fixes

* remove unused variable; try to silence pylint

* fix issues reading epsie samples

* only load samples from burned in chains by default

* add act property to mcmc files

* fix act logging message

* fix effective number of samples calculation in epsie

* remap walkers option to chains for reading samples

* fix thinning update

* fix acceptance ratio and temperature data thinning in epsie

* allow for different fields to have differing number of temperatures when loading

* don't try to figure out how many samples will be loaded ahead of time

* store acts in file instead of acls

* write burn in status to file before computing acls

* drop write_acts function

* fix issue with getting specific chains

* fix typo

* code climate issues

* fix plot_acl
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History
File Mode Size
data
bankvetotest.py -rw-r--r-- 3.6 KB
fft_base.py -rw-r--r-- 32.5 KB
test_array.py -rw-r--r-- 20.8 KB
test_array_lal.py -rw-r--r-- 5.0 KB
test_autochisq.py -rw-r--r-- 6.5 KB
test_calibration.py -rw-r--r-- 2.9 KB
test_chisq.py -rw-r--r-- 4.8 KB
test_conversions.py -rw-r--r-- 9.2 KB
test_correlate.py -rw-r--r-- 3.1 KB
test_detector.py -rw-r--r-- 4.0 KB
test_distributions.py -rw-r--r-- 10.5 KB
test_dq.py -rw-r--r-- 5.1 KB
test_fft_unthreaded.py -rw-r--r-- 2.2 KB
test_fftw_openmp.py -rw-r--r-- 2.3 KB
test_fftw_pthreads.py -rw-r--r-- 2.3 KB
test_frame.py -rw-r--r-- 6.1 KB
test_frequencyseries.py -rw-r--r-- 23.8 KB
test_injection.py -rw-r--r-- 7.0 KB
test_io_live.py -rw-r--r-- 6.2 KB
test_lalsim.py -rw-r--r-- 16.3 KB
test_matchedfilter.py -rw-r--r-- 5.8 KB
test_pnutils.py -rw-r--r-- 4.5 KB
test_psd.py -rw-r--r-- 5.8 KB
test_resample.py -rw-r--r-- 3.4 KB
test_schemes.py -rw-r--r-- 7.5 KB
test_skymax.py -rw-r--r-- 17.7 KB
test_spatmplt.py -rw-r--r-- 3.4 KB
test_threshold.py -rw-r--r-- 2.3 KB
test_timeseries.py -rw-r--r-- 24.5 KB
test_tmpltbank.py -rw-r--r-- 25.2 KB
test_transforms.py -rw-r--r-- 3.0 KB
test_waveform.py -rwxr-xr-x 7.5 KB
test_waveform_utils.py -rw-r--r-- 4.9 KB
utils.py -rw-r--r-- 37.3 KB

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