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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File | Mode | Size |
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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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