https://github.com/gwastro/pycbc

sort by:
Revision Author Date Message Commit Date
5d35c81 Prepping for release (#2535) 01 March 2019, 17:17:05 UTC
47c5ed4 add dummy phase time file 01 March 2019, 16:30:07 UTC
3d6a737 remove cvmfs setup for now 01 March 2019, 16:28:53 UTC
9b2c441 verbose mount 01 March 2019, 16:24:48 UTC
49ae8b1 use cvmfs setup command 01 March 2019, 16:19:17 UTC
932fb0e dump cvmfs config file 01 March 2019, 15:44:55 UTC
fc2bb40 manual cvmfs configuration 01 March 2019, 15:39:22 UTC
0182109 Set the CVMFS user 01 March 2019, 15:34:30 UTC
96a614a typo 01 March 2019, 15:28:44 UTC
77797a5 fix path for debian 01 March 2019, 15:25:09 UTC
588fab3 debugging cvmfs 01 March 2019, 15:20:58 UTC
be9bde1 add additional osg cvmfs config files 01 March 2019, 15:13:04 UTC
3105e84 config.d file for OSG CVMFS 01 March 2019, 15:06:16 UTC
17da8d5 config file for OSG CVMFS 01 March 2019, 15:05:24 UTC
2c0dd89 OSG CVMFS public key 01 March 2019, 15:04:54 UTC
1a018f2 more cvmfs debugging 01 March 2019, 14:57:59 UTC
8753c14 cvmfs debugging 01 March 2019, 14:47:04 UTC
be030d5 strace failing command 01 March 2019, 14:38:33 UTC
0d382ce explicitly mount and ls all needed directories 01 March 2019, 14:34:58 UTC
5a053e7 explicitly list repositories 01 March 2019, 14:32:54 UTC
b42cf4c leave cvmfs management to autofs 01 March 2019, 14:28:46 UTC
47bc15c fixed typo 01 March 2019, 14:21:34 UTC
36ed4ee fixed cvmfs config path 01 March 2019, 14:18:32 UTC
58cb02e put the sudo on mv not curl 01 March 2019, 14:15:14 UTC
c2ca731 debugging cvmfs 01 March 2019, 14:01:17 UTC
3d69530 set up cvmfs before install 01 March 2019, 13:55:32 UTC
d51e0b8 create cvmfs config file 01 March 2019, 13:49:45 UTC
390b20f Quick fix for SNR in plot_posterior (#2513) * Quick fix for SNR in plot_posterior * Add samples attributes to read_samples * Codeclimate indentation issue * Codeclimate indentation 01 March 2019, 13:37:22 UTC
3250ab9 Priors on 1D marginal posterior plots (#2527) * add ability to plot prior on 1d marginal plots * check for 1D marginal plotting * add doc to option utils function * have plot_prior use the new function * fix doc string in plot prior * have function return prior rather than samples * fix typos * add doc for new arguments * fix code climate issues * fix typo * make quoted range depend on the veritcal lines * only reduce to default if no percentiles specified * take the half way point of the max/min percentile for the quoted value * fix typo in doc string 01 March 2019, 09:58:40 UTC
335fd3e Use automatically determined number of sig. figs in posterior titles (#2534) * don't force number of decimal places to be 2 * round to 2 sig fix in uncertainty * use automatic sig fig estimation in marginal titles * fix example formatting 01 March 2019, 09:57:57 UTC
4f91165 Fix storage format of coinc segments in coinc code (#2517) * Fix storage format of coinc segments in coinc code * remove segments/coinc * comment change to restart travis * switch to detectorcombination/segments everywhere * hdf.py fix * more hdf.py fixes * more hdf fix * more fix * more fix * Revert "more fix" This reverts commit d2595d50fa1da6c689c105c7405276fb7a0c7ee4. * Revert "more fix" This reverts commit 5c4271df350c2b6cce76f2ccb293697f80d4eee0. * Revert "more hdf fix" This reverts commit be2c0e39d2141a6f3f0263dcfe001ef0b557ddb9. * Revert "more hdf.py fixes" This reverts commit 0ba5f2dd525d68c1c7d4fc35fba1c64334cbdcfe. * Revert "hdf.py fix" This reverts commit 54dec81f02d2f23c2a736204f5d774d9f15a4f84. * Revert "switch to detectorcombination/segments everywhere" This reverts commit dd09facb1f7348d56d9f0bdab7ca5a56bd25d5b3. * pep8 too long line fix * switch to segments/{} use fully in combine_statmap * change to segment/{} format in hdfinjfind * add missing change * fix attribute key * fix attribute key in coinc_hdfinjfind * Update pycbc_multiifo_combine_statmap Correct coping of segments and attributes * requested changes 28 February 2019, 15:27:19 UTC
b42e697 Update README.md 28 February 2019, 09:57:55 UTC
577b56d allow dpi to be set on command line (#2528) 28 February 2019, 09:32:06 UTC
674f2a5 Allow psd group to be specified in plot_psd (#2531) * allow psd group to be provided in plot_psd * figure out whether to plot reference psd from the given args * give more helpful error message 27 February 2019, 16:52:25 UTC
d80e19b fit_sngls_by_template analysis time output (#2509) * alter fit_sngls_by_template to also output time analysed as a file attribute * some testing and unused imports removed * add in count of triggers in each template (not thresholded or pruned) * adding smoothing of total number of counts per template to fit_over_param * adding count_total to multiparam fitting * update to use numpy diff * commenting, slight change to order of calculation without affecting numerical values * rewrite hash/template_id reordering in order to make it clearer * allow count_in_template input data not to exist, add missing sort * allow count in template not to exist, fix naming * Add comments to number in template calc, formatting 27 February 2019, 16:51:33 UTC
6108456 multi-ifo changes to pycbc_page_segtable (#2519) * multi-ifo changes to pycbc_page_segtable * Updated to use itertools module, and deal with default ifos value more pythonically * kick Travis * fix typo to sort comp segs issue * removing commented-out lines, formatting fixes * PEP8 again 27 February 2019, 16:50:08 UTC
27e95bd Set back to development 27 February 2019, 16:48:57 UTC
c259699 Prepping for release 27 February 2019, 12:02:08 UTC
c86b3c5 Turnoff recalculating Jacobian in emcee pt (#2526) * turn off computing jacobian * add a warning message to the docs 27 February 2019, 10:17:38 UTC
b067b89 only allow master process to print to screen when using mpi (#2525) 27 February 2019, 10:17:27 UTC
f36f081 Fix marginal phase (#2524) * add back the marginalized phase gaussian noise class * update models init * pep8 27 February 2019, 10:17:10 UTC
8fe2b5e only use acl from nacl test if it is the only test being done (#2521) 26 February 2019, 15:09:17 UTC
8ce1fcc add logging for coinc / single buffer size (#2520) 25 February 2019, 21:42:34 UTC
4221580 adding multi-ifo functionality to foundmissed plotting script (#2516) * adding multi-ifo functionality to foundmissed plotting script * fix some TypeError issues * adding multi-ifo functionality to foundmissed plotting script * fix some TypeError issues * slightly compress snr calculation, only do if needed * add warning about decisive distance to options 25 February 2019, 11:44:58 UTC
cbb2719 add multi ifo support to pycbc live (#2386) * enable background for all combination of ifos * remvove some notimplemented stubs * output file produced again * add method to get number of buffer elements * background accumulates in each detector * fixes in coinc picker * re-enable coincs and singles * allow for bank to be called with get_template method * minor readability * make sure overwhitened strain returnes stilde with epoch set * preliminary pvalue followup calculator * allow multiple stat files to be provided, one for each detector pair * add pvalue combining * bug fixes * add stuff * fixes from tito / tom * remove redundant comment * climate stuff * more climate * doc fixes * one typo * adjust background time used if shorter than strain buffer * use round in returning sample rate * make integer * another bug 23 February 2019, 23:32:33 UTC
11ae334 Thin inference samples on the fly (#2492) * add setters for thin start/interval/end * add methods for thinning samples on disk to base_mcmc io * remove prethin_interval attribute in io in favor of just using thinned_by * get rid of start iteration, max iterations options in SingleTempMCMCIO.write_samples * thin samples before writing in SingleTemp write_samples * always create samples and sampler_group when new files are created * make last_iteration optional in write_samples * add prethinning functions to base_mcmc * add set prethin options from config * add prethinning support to emcee * typo * prethin -> thin; remove prethin boolean * fix doc string * make last_iteration parameter dependent * only do integrity check if parameters have been written * only update burn in, calculate acl if new samples have been written * remove redundant logging message * fix bug in resizing * use max samples per chain instead of thin_factor * remove max_iterations, start_iteration options from multi tempered write_samples * make thin samples a stand alone function * add support to base_multitemper * add support to emcee_pt * have burn in module handle the difference between iteration and index * define autocorrelation time * fix off by one error in thin start point * add attribute info to BaseMCMC doc string * minor typo * add to docs * fix code climate issues * remove left over "max_iterations" * load thinning from config for emcee_pt * add some verbosity about thinning * fix issues with figuring out thin interval, file thinning * move thinned_by to top level attrs * thin start should be burn in index, not iteration * wrong thin interval in act * reducing verbosity * docs * update example config files * more docs * pep8 23 February 2019, 23:31:37 UTC
426cae0 Merge branch 'pr/2499' 23 February 2019, 16:53:09 UTC
0f5874f minor changes to kickstart Travis also replace import of segments from glue -> from ligo 22 February 2019, 23:51:21 UTC
3acd4dd AAAARRRRGGGHHHH!!!! 22 February 2019, 20:39:07 UTC
20acc26 Sigh 22 February 2019, 20:39:07 UTC
7a078e1 segmentsUtils problem 22 February 2019, 20:39:07 UTC
7b2fef9 Fixing bug 22 February 2019, 20:39:07 UTC
078ecdf Missed a place 22 February 2019, 20:39:07 UTC
026b673 Add to requirements 22 February 2019, 20:39:07 UTC
1e45332 glue.segments -> ligo.segments 22 February 2019, 20:39:07 UTC
826acb6 slight clarification in comments 21 February 2019, 22:57:56 UTC
0b35c05 Inference: do not ignore option "fields" in posterior (#2514) 20 February 2019, 15:54:10 UTC
723f3b7 estimate.py: a few more Python 3 int division fixes (#2510) 19 February 2019, 19:25:21 UTC
8de7c31 Bump matplotlib version to 2.0.0 (#2512) 19 February 2019, 19:23:26 UTC
14750e5 add time estimates for NRTidal (#2511) Allows PhenomD_NRTidal and PhenomPv2_NRTidal to be used with get_td_wavefrom and get_td_wavefrom_from_fd 19 February 2019, 18:32:49 UTC
4ee581f changes to logic order, removal of repetition and superfluous code 19 February 2019, 16:37:37 UTC
286ec27 remove changes to fit by template code (moving to separate PR) 19 February 2019, 15:11:33 UTC
e4265c0 remove requirement to have --ifos on command line for multiifo - use input file structure instead 19 February 2019, 15:11:33 UTC
117a5e8 remove check that wasnt particularly helpful, but made unwanted changes to the format 19 February 2019, 15:11:33 UTC
c5c78a9 some changes to fit_sngls_by_template and hdf_injfind for multi-ifo operation 19 February 2019, 15:11:33 UTC
f59e1d2 Some Python 3 compatibility fixes (#2508) * gaussian.py: minor division fix for Python 3 compatability * utils.py: move division fixes for Python 3 compatibility 19 February 2019, 14:58:29 UTC
de7f01e pycbc.psd: minor mods to estimate.py for python3 (#2507) 19 February 2019, 14:37:37 UTC
a2914cd Add constraint section to inference doc. (#2506) 15 February 2019, 14:04:19 UTC
d1f4eb5 codeclimate / PEP8 14 February 2019, 13:19:44 UTC
aa71697 remove some debug-level comments and unnecessary lines 14 February 2019, 13:19:44 UTC
95eeca2 Add bank params option 14 February 2019, 13:19:44 UTC
a05b05b Trying to make exp_fit sngl stats work 14 February 2019, 13:19:44 UTC
75e20ba spacing 14 February 2019, 13:19:44 UTC
19e66a0 Adding pycbc_process_sngls A script to apply cuts, rerank and cluster single trigger hdf files 14 February 2019, 13:19:44 UTC
9f2bf58 Some additional plumbing in feeding sngls to stat module 14 February 2019, 13:19:44 UTC
0c67403 stat.py: added extension of exp fit statistic 14 February 2019, 13:19:44 UTC
a065653 split off generalized cluster algorithm in events/coinc.py 14 February 2019, 13:19:44 UTC
e766263 Made hardware injections accept flexible list of detectors (#2505) * Made hardware injections accept flexible list of detectors * Restrict detector choices to available detectors 13 February 2019, 19:21:24 UTC
f93915e Fixed a bug in the roll function for time series. (#2500) 13 February 2019, 12:29:20 UTC
8617d96 Removed the key word return_found, as it is no longer used (#2503) 13 February 2019, 12:21:23 UTC
e0d4103 Multiifo inj statmap (#2474) * Adding multiifo_statmap_inj to the workflow * typo * Add missing line * fix setup_multiifo_statmap_inj argument * Add pycbc_multiifo_coinc_statmap_inj executable * fix background file input * correct error * typo * fix * more fixes * fix errors * fixing sorting * refactoring * fix indent * switch coinc job nameing to include the ordered ifo list * fix typo and remove whitespace * fix typo * fix wrong files given into inj_coinc * fix arguments of get_ordered_ifo_list * typo * needed precedence combination to take the correct full inspiral files * fix error * switch to conv.sec_to_year in pycbc_coinc_statmap_inj * simplify average time calculation * simplify get_ordered_ifo_list function and create select_files_by_ifo_combination method * add docstrings * codeclimate * fix ifos error * fix average time calculation, correct comment and simplify creating the combination_prec dictionary * PEP8 / codeclimate issues 12 February 2019, 23:53:49 UTC
9af8285 Add zero likelihood analytic model (#2501) * add zero likelihood analytic model * codeclimate * rename distribution and fix loglikelihood to return 0 * change docstring and fix class initialization to use correct name 12 February 2019, 21:41:05 UTC
7c813d1 add from future division (#2497) 08 February 2019, 16:17:00 UTC
f892fcf Remove unnecessary and impossible automatic transforms (#2435) * Remove unnecessary and harmful transforms from the automatically applied transforms. Add only one line in get_common_cbc_transforms: Before adding a transform from the base parameters to the requested parameters to the list of transforms which will be executed (from_base_c), check if the intersection between requested parameters and output of the transform is already in the sampled parameters. If so, do NOT add the transform. Applying these transforms here is not useful, since they only add parameters that are already known. Also, adding this would lead to errors for example in the case of Mass1Mass2ToMchirpQ: If sampling is done in q and m_total and q is requested, then mass1 and mass2 are asked for by the transform and not known, so an error will occur. * Fix style for code climate Is `if not intersect` better than `if len(intersect) < 1` ? To me the first formulation suggested by code climate seems less clear, and also continues to run if nonsense is saved in intersect (ie if it is not a list). 07 February 2019, 16:21:21 UTC
11f7714 adding multiifo combine statmap script (#2473) * adding multi-ifo combine statmap script * add in multi-ifo cluster_coinc function and initial approximation to trials factor * clean up some mis-deleted points and try to please codeclimate * including trials factor of number of ifo combinations available at that time, some minor edits and refactoring * fixing typos, naming of variables/functions and whitespace issues, refactoring of common function * Some more tidying of code, small efficiency improvement * fix typo, codeclimate * codeclimate * this should shut up codeclimate * rearrange so that clustering is done before application of trials factor * moving name_all_datasets function into io/hdf.py, adding some logging * addressing some of Tom's comments, rewriting name_all_datasets to use the inbuilt h5py iteration * changes to name_all_datasets to remove some local calls to global variables * re-organising segments data and attributes, codeclimate fix * reverting to not use h5py 'visit' methods for naming all datasets * cleaning up things * change to name_all_datasets to simplify and reduce block nesting to please codebeat * Formatting and minor refactoring in multiifo combine statmap * some simplification of get_all_subkeys, spacing 07 February 2019, 15:02:32 UTC
1f7e0ff Remove the gating file module (#2373) * Revert "Setup gating files at the workflow level (#1865)" This reverts commit 73c0b71e87c4b80d426dc55e520b559571636295. Conflicts: pycbc/workflow/gatefiles.py * Remove gating here too * Force resolve_url for file input options * Keep track of original PFN 07 February 2019, 12:03:55 UTC
c469790 Removing frequency lines (#2488) * Functions to measure and subtract lines from the data * Fixes and improvements * Remove argument function (=numpy.angle) * Fix Codacy/codeclimate issues * Docstrings and a few codeclimate issues 06 February 2019, 18:27:56 UTC
55f902a Make waveform visible (#2490) 06 February 2019, 14:21:06 UTC
f0a9a80 Update setup.py 04 February 2019, 14:18:12 UTC
ef06c47 set for release 04 February 2019, 13:01:48 UTC
48c7524 correlate unittest was was broken for the Correlator class (#2486) * update correlate test * update correlate test * Update test_correlate.py 04 February 2019, 12:56:28 UTC
8f406e0 p3 env in travis (#2481) 03 February 2019, 19:49:00 UTC
db06239 Update matchedfilter_cpu.pyx (#2483) 03 February 2019, 18:01:04 UTC
d11d106 Cythonize apply fd time shift (#2480) * add cython file for frequency domain time shift * have separate functions for single and double precision * add a test for single precision * increase tolerance for single precision test * move cython functions into utils_cpu 03 February 2019, 12:36:42 UTC
0536aaf Add unit test for apply_fd_time_shift (#2477) * add unit test for apply_fd_time_shift * Update test_waveform_utils.py 01 February 2019, 21:39:50 UTC
9a1a24e optimized model for only calculating the extrinsic parameters (#2419) * add stubs * more stuff * fixes * fix the hh normalization * fix sign error * use phase marginalization * ws * detector acche * simplify * bug in phase marg * update * fixes * cc * cc * update * cc * test * cc * try to use base data model * fixes * fix rebase * rename fixes 01 February 2019, 16:07:24 UTC
9597d53 Merge cuda decompress (#2453) * First pass at GPU waveform interpolation * Several bugfixes; add function API * Add scheme support for inline linear waveform decompression * Add missing numpy import to decompress_cpu * Comment out flag forcing no-copy in injfilterrejector---breaks CUDA * Remove inline code from compress.py * Update a 'syncthreads' to '__syncthreads' * Remove caching of GPU chi-squared bin layout Caching as previously implemented could lead to stale lookups returning incorrect cached bin layouts. For now, we simply remove the caching entirely. * Make scheme-dependent versions of 'apply_fseries_time_shift' * Fix typo * Add missing numpy import * Fix variable name reference * More refactoring and bugfixing in CUDA fseries_time_shift * Fix memory read in CUDA kernel * Fix types for CUDA prepared call * Fix copy in CUDA fseries_time_shift * Allow copy to move GPU array in sinegaussian * Fix copy bugs in CUDA time-shift * Fix function signature in CUDA time shift * Fix bug in CPU decompression introduced by GPU changes * Fix various Codacy issues * Codacy complaints * Remove unused import * Fix some codeclimate stuff 01 February 2019, 15:02:05 UTC
a33c4c8 Correct sampling_parameters to sampling_params in documentation (#2459) 01 February 2019, 09:27:15 UTC
2b66db7 Removed unused imports of matplotlib.pyplot (#2454) * removed unused imports of matplotlib.pyplot these were all backend-unprotected, meaning Qt or similar would start unnecessarily * removed another unused import 30 January 2019, 23:02:28 UTC
8789e5e Multiifo inj coinc (#2466) * Adding injection coincidence jobs (no statmap) * remove unused backgroundfile argument (for now) * debug * add missing return line * debug * Addressing Tom's comments * Rename everything and add leaving coincidence log * add missing line * codeclimate * shorten using zip(*...) and small formatting fixes * fix issues with no longer explicitly assigning ifos= * make codeclimate happer (?) 28 January 2019, 14:30:38 UTC
back to top