Update branch #8
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* add plugin handling for waveforms * cc * cc * add debugging, don't require m1/m2 for all waveforms * add waveform plugin docs * ws * forgot to commit this * Collin's comments * test
…#3311) * 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
* try fixing numpy to 1.18.5 for py37 * add more numpy settings; make it <1.19 rather than pinning to 18.5
* add generic spherical <-> cartesian transforms; deprecation warnings for spin12 transforms * fix typo, use sphericaltocartesian in common cbc transforms * fix typos, register transform * update example ini file * initialize cartesian to spherical with right arguments in test * fix bug in inverse transform * pep8
* register some new parameter labels * fix seconds in delta tc
added a class of LISA to detector.py
issues by code climate
Removal of plotting method Addition of transformation method from Ground Based Detectors (GBD) to LISA
Changes in coordinate transfromation
Issue for line 336, 337, 274, 374
Addition of docstrings
Changes for code climate issues
* add standard prior for BBH with uniform comoving volume * add marginalized phase example config file * add standard data settings for o1 and o2 * add standard dynesty and emcee_pt configs * add config file and bash script to create dynesty workflow * add files for emcee pt
* Add time dependent frame-type option in datafind.py * Allow time-variable frame type * Resolving whitespace concerns * Changes on the PR in response to feedback
* Implement the idea of time-dependent options * Support TDOs in inspiral jobs * Support TDOs in minifollowups * Pull off into dedicated function * Calculate_psd can use dedicated function directly * Typo fix * Fixing up CC, one bug, and a few issues * Missed this
* Sieve only points in time range * Is INT4 not LIGOTimeGPS * math.ceil * Need to catch 0 or -ve duration earlier
* add duration support for phenom hm waveforms * estimate by scaling frequency
* initial version * updates and fixes * cc Co-authored-by: Sumit Kumar <sumit.kumar@atlas2>
* To store only n-loudest while writing live background. This can reduc… e storage requirement * Actually get N after partitioning * Fixing parsing arg name Co-authored-by: Bhooshan Gadre <bhooshan.gadre@ligo.org>
* Change hashing function in offline bank creation to be safe when used with python3 * some other python3 compatibility fixes
* We should be consistent about units * update docs * fix cyclic bound for uniform angle * update unittest * ws
* hook up boundary types to dynesty * nc * ws * ws
* add ability to append data in base_hdf write_data * add write start time method to base sampler io * add update_checkpoint_history function to base sampler file * add update sampler history to base mcmc file * write run start time when starting up run * call update checkpoint history in base mcmc's checkpoint * fix various bugs * add run end time attribute * handle no act or burn in having been calculated
* cyclic support for ultranest, output logl * ws
Co-authored-by: Bhooshan Gadre <bhooshan.gadre@ligo.org>
* add gate and paint function * add option to copy * Update gate.py Co-authored-by: Alex Nitz <alex.nitz@gmail.com>
* try to speed up rvs * speed up rvs by doing batch draws * fix typos
* fix typo * simplify mpi launch process * simplify pool calls * fixes * fixes * Update dynesty.py * cc * detected case where not launched
* fix typo * simplify mpi launch process * simplify pool calls * fixes * fixes * Update dynesty.py * cc * detected case where not launched * enable multicore support for ultranest * cc
* update gate method to include selectable type * ws * comments * cc * com
* Implement a resolve_url_to_file function * Update to add local CVMFS registry * Typo fix * Typo fix and allow localhost * Attrs is needed so rethinking needed * Typoe fix * Another typo * Always need local PFN * All CVMFS URLs * Numerous codeclimate issues
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