| 9a7ef50 | Alex Nitz | 20 March 2024, 15:51:52 UTC | don't keep file open within injectionset (#4667) * don't keep file open within injectionset * update docstring | 20 March 2024, 15:51:52 UTC |
| 62a4921 | Jacob Buchanan | 20 March 2024, 13:29:53 UTC | PyGRB injection finder/combiner fixes (#4661) * Fix inj_finder cutting all datasets * inj_combiner raises error if no valid files * Cosmetic fixes * Update bin/pygrb/pycbc_grb_inj_combiner Co-authored-by: Francesco Pannarale <francesco.pannarale@ligo.org> --------- Co-authored-by: Francesco Pannarale <francesco.pannarale@ligo.org> | 20 March 2024, 13:29:53 UTC |
| 6040a0c | Lalit Pathak | 14 March 2024, 17:04:35 UTC | added support for mode-by-mode decomposition of NRHybSur3dq8 waveform… (#4520) * added support for mode-by-mode decomposition of NRHybSur3dq8 waveform model | 14 March 2024, 17:04:35 UTC |
| 5a9e76c | Gareth S Cabourn Davies | 14 March 2024, 09:35:22 UTC | Update how live fitting deals with invalid values (#4653) * Update how live fitting deals with invalid values * TDC comments * Tito's fixes * Add check for nan trigger fit values in the singles IFAR calculation | 14 March 2024, 09:35:22 UTC |
| 7bc9d62 | Gareth S Cabourn Davies | 13 March 2024, 20:45:37 UTC | Standardize logging - many places (#4654) * update minifollowup exes to use standard logging function * Update bin/live to use common options function * add named loggers to pycbc/workflow modules * common options/logging for bin/population * named loggers in pycbc/catalog * named loggers in pycbc/coordinates * named loggers in pycbc/frame * standard logging/options in bin/hwinj * named loggers in pycbc/distributions * CC * many typos / thinkos * this warning has been annoying me a while - silence it * replace logging.warn() with logging.warning() * typo | 13 March 2024, 20:45:37 UTC |
| f35d04b | Tito Dal Canton | 08 March 2024, 16:58:39 UTC | Fix import broken by change in lscsoft-glue (#4662) * Drop lscsoft-glue dependency * Glue still needed, do not drop it! | 08 March 2024, 16:58:39 UTC |
| f3c887e | Han Wang | 03 March 2024, 23:06:33 UTC | avoid using for loop in space psds; fix typo (#4657) * avoid using for loop in space psds; fix typo * change back to astropy constants | 03 March 2024, 23:06:33 UTC |
| 56b544f | Shichao Wu | 28 February 2024, 21:44:24 UTC | add support for multi-returning-value functions in transform (#4301) * add support for multi-value functions in transform * fix cc issue * Update transforms.py * fix cc issue * fix * Update transforms.py * Update transforms.py * fix cc issue * Update transforms.py * add 7 classes * fix cc issues * move LISA stuff to another PR * Update transforms.py | 28 February 2024, 21:44:24 UTC |
| fd26817 | Ian Harry | 27 February 2024, 22:30:31 UTC | Need to use atol for isclose here (#4655) | 27 February 2024, 22:30:31 UTC |
| a3f5e92 | kkacanja | 27 February 2024, 15:44:16 UTC | Allow option for workflow to end at inspiral jobs (#4612) * Updates to stopping after data inspiral jobs and statmap * Updates to stopping after data inspiral jobs and statmap * Changed typing of stop-after * Allow pycbc_make_offline_search_workflow to stop after inspiral jobs. * Fixed comment | 27 February 2024, 15:44:16 UTC |
| 7f9cb87 | Gareth S Cabourn Davies | 27 February 2024, 15:43:17 UTC | Add a template for pull requests (#4585) * Create standard_template.md * Update .github/PULL_REQUEST_TEMPLATE/standard_template.md * Update .github/PULL_REQUEST_TEMPLATE/standard_template.md * Update standard_template.md * Update standard_template.md Use some 'delete as appropriate' lists to make using the template a little less daunting | 27 February 2024, 15:43:17 UTC |
| 98007f4 | Gareth S Cabourn Davies | 27 February 2024, 12:41:28 UTC | Standardize logging: bin, bin/bank and pycbc/tmpltbank (#4631) * Standardize bank logging setup * use loggers in tmpltbank * cc * change the verbose short option to lowercase, to avoid a clash with vary-fupper * add executables in bin * import properly in pycbc_multi_inspiral * mised import * CC * more missed imports * typo | 27 February 2024, 12:41:28 UTC |
| 6b17078 | Rajiv Mayani | 27 February 2024, 08:11:07 UTC | Fix Pegasus selector profile key (#4652) Change the selector profile to `execution.site` from `execution_site`. See: https://pegasus.isi.edu/documentation/reference-guide/configuration.html | 27 February 2024, 08:11:07 UTC |
| b4784f9 | Ian Harry | 24 February 2024, 20:54:25 UTC | Avoid pegasus 5.0.7 (#4651) * Avoid pegasus 5.0.7 * Needs to be here, not in API requirements * Revert "Avoid pegasus 5.0.7" This reverts commit c9c915f45c22b5de28118edbbca29665f2afd8cf. | 24 February 2024, 20:54:25 UTC |
| b4c1a95 | Alex Nitz | 23 February 2024, 20:08:19 UTC | Add pycbc support for the snowline sampler (#4587) * add support for snowline sampler * add to examples * add snowline to some docs, fixes * cc * fix * Update snowline.py * Update snowline.py * Update snowline.py * Update pool.py * Update snowline.py | 23 February 2024, 20:08:19 UTC |
| 6b5fe83 | Thomas Dent | 23 February 2024, 18:16:16 UTC | SNR optimizer option types (#4650) * SNR optimizer option types Fix issue in non-default settings for some options that Max complained about * Use standard verbosity argument --------- Co-authored-by: maxtrevor <65971534+maxtrevor@users.noreply.github.com> | 23 February 2024, 18:16:16 UTC |
| 232a4ce | Tito Dal Canton | 20 February 2024, 17:33:57 UTC | Various fixes to `EventManager`s (#4639) * Rename "snr_<detector>" datasets to just "snr" * Do not store template duration in trigger files * Cleanup and better document `write_events()` method * Fix how gating info is written * Fix imports * Detriplicate code * Codeclimate | 20 February 2024, 17:33:57 UTC |
| aa05af6 | Ian Harry | 20 February 2024, 16:21:05 UTC | Ensure approximant field is correct format (#4646) | 20 February 2024, 16:21:05 UTC |
| e7e9666 | Tito Dal Canton | 20 February 2024, 16:01:37 UTC | Fix comment bugs in #4635 (#4645) | 20 February 2024, 16:01:37 UTC |
| 42cd525 | Gareth S Cabourn Davies | 20 February 2024, 13:08:53 UTC | Bugfix: upload prep read psds function (#4644) | 20 February 2024, 13:08:53 UTC |
| e8d671a | Thomas Dent | 19 February 2024, 16:19:59 UTC | Clean up options and help for fit over multiparam (#4640) * Clean up options and help for fit over multiparam Older code that this is copied from had the option of reading fit smoothing parameter values from an input fit file, rather than from the template bank (or calculating on the fly). This is no longer done so remove the (useless) option and references to it in help for other options * Update pycbc_fit_sngls_over_multiparam Few more fixes to options, in particular 'required' & defaults | 19 February 2024, 16:19:59 UTC |
| 320ac7f | Tito Dal Canton | 19 February 2024, 16:18:02 UTC | Improve how pycbc_live handles localization-only detectors (#4635) * Improve how pycbc_live handles localization-only detectors LOD = localization-only detectors * Do not initialize single-detector FAR estimators for LOD * Only use triggering detectors for PSD var statistic * Correct the GraceDB annotation to explain which detectors contributed to the FAR and list the LOD * Only list triggering detectors in background dump filename * Code reformatting * Fixes * Fixes * Use attributes of event manager instead * Improve GraceDB annotation * Fix * Ignore loc-only detectors for rank > 0 * Further clarify which detectors are used only for localization * Main loop should go through the loc-only detectors only in rank 0 | 19 February 2024, 16:18:02 UTC |
| 9d965fa | Gareth S Cabourn Davies | 16 February 2024, 11:38:35 UTC | Bug: Live combine fits, different bin edge sizes causes an error (#4636) * Update pycbc_live_combine_single_fits * logging warn -> warning deprecation | 16 February 2024, 11:38:35 UTC |
| 08bb91c | Jacob Buchanan | 15 February 2024, 20:46:37 UTC | Update PyGRB efficiency script for HDF files (#4562) * efficiency changes * Delete old comment to retrigger checks * Update bin/pygrb/pycbc_pygrb_efficiency Co-authored-by: Francesco Pannarale <pannarale@users.noreply.github.com> * Update bin/pygrb/pycbc_pygrb_efficiency * Don't extract file contents (part 1) * Don't extract file contents (part 2) * Don't extract file contents (part 3) * Don't extract file contents (end?) * Remove missed_inj * Add FIXME * Pull template masses from template bank * Use trigger masses instead of injection masses for trigger mchirp * Avoid h5py error * dataset name correction * Avoid numpy error * Try fixing loudest onsource bestnr finding * Fix issues * Precalculate template chirp masses * Clean up --------- Co-authored-by: Francesco Pannarale <pannarale@users.noreply.github.com> | 15 February 2024, 20:46:37 UTC |
| 3fc2ad2 | Alex Nitz | 15 February 2024, 12:20:43 UTC | Revert "MNT: upgrade upload/download-artifact GitHub actions (#4595)" (#4629) This reverts commit 02f77b6d2b0b8fd2a62903f02356954d81412252. | 15 February 2024, 12:20:43 UTC |
| df3ba44 | Jacob Buchanan | 15 February 2024, 10:11:47 UTC | PyGRB: Update postprocessing functions (#4550) * Add mapping function * Implement mapping in trig combiner * Fix "template_id" dataset being written too early * Force template_id to be integer * Try adding bank files to workflow * Remove fixme * Only use one bank_file * Add template mapping to inj finder * Small change * mapping function works with trig file object * Small change * Remove typo * Add bank file opt to inj_finder * Add template masses to multi_inspiral output * sort_trigs updates * Extract trig properties * Add old imports back for CodeClimate * Remove unused bestnr opts * Update pycbc/results/pygrb_postprocessing_utils.py Co-authored-by: Francesco Pannarale <pannarale@users.noreply.github.com> * Codeclimate * Remove masses from multi inspiral output * Correct segment loading names * Add NoneType handling to _slide_vetoes function * Indentation fix * Add 's' back in * Fix docstring(?) * Codeclimate * Codeclimate * Update pycbc/results/pygrb_postprocessing_utils.py Co-authored-by: Tito Dal Canton <tito@dalcanton.it> * Uses event_ids in sort_trigs to avoid confusion * Add possibility of multiple banks (and NotImplementedError) * Remove enumerate and fix indexing issue * Check for single bank earlier * Simplify column name check * Use zip() * Update pycbc/results/pygrb_postprocessing_utils.py Co-authored-by: Tito Dal Canton <tito@dalcanton.it> * Update pycbc/results/pygrb_postprocessing_utils.py Co-authored-by: Tito Dal Canton <tito@dalcanton.it> --------- Co-authored-by: Francesco Pannarale <pannarale@users.noreply.github.com> Co-authored-by: Tito Dal Canton <tito@dalcanton.it> | 15 February 2024, 10:11:47 UTC |
| 0b11dfc | maxtrevor | 15 February 2024, 03:23:49 UTC | Added tables to dq results pages (#4633) * Added tables to dq results pages * Address Tom's comments and fix bin_trigger_rates_dq * Fix decimal formatting * Final change to formatting | 15 February 2024, 03:23:49 UTC |
| c272f83 | Arthur Tolley | 14 February 2024, 18:14:34 UTC | [pycbc_live] Simplify and fix how CLI options are passed to the SNR optimizer (#4628) * adding non-optimizer specific options to args_to_string * correct formatting * simplifying if snr opt seed * Adding extra-opts arg * updating options in live example run.sh * restoring deleted space * removing redundant default * moving all snr optimizer options to snr_opt_extra_opts * updating argument help descriptions * removing snr_opt options from pycbc live * removing seed option from example * removing args_to_string * Actually, even simpler --------- Co-authored-by: Tito Dal Canton <tito.dalcanton@ijclab.in2p3.fr> | 14 February 2024, 18:14:34 UTC |
| 0f43c7b | Tito Dal Canton | 13 February 2024, 11:48:09 UTC | Fix broken --version option (#4630) * Fix broken --version option, add CI test, cleanup and simplify related code * Fix bug preventing .so files from being found * Fix missing import, typo, more codeclimate * pycbc_coinc_time needs dqsegdb; deduplicate --help commands | 13 February 2024, 11:48:09 UTC |
| e2c35ef | Jacob Buchanan | 10 February 2024, 18:46:53 UTC | Sky error fix (#4502) | 10 February 2024, 18:46:53 UTC |
| ddaa94d | Michael J. Williams | 09 February 2024, 16:51:26 UTC | Standardize logging in bin/inference (#4621) * inference: standardize verbose argument Only change scripts that already had a verbose argument * revert logging change in pycbc_inference_plot_gelman_rubin Partially reverts 9b7fa3d68e45a65a544f55d8a221ac44949ad6a5 | 09 February 2024, 16:51:26 UTC |
| 02f77b6 | Clément Robert | 09 February 2024, 16:49:33 UTC | MNT: upgrade upload/download-artifact GitHub actions (#4595) | 09 February 2024, 16:49:33 UTC |
| e1984b6 | Gareth S Cabourn Davies | 09 February 2024, 16:37:18 UTC | Slightly incomplete example in frame documentation (#4624) | 09 February 2024, 16:37:18 UTC |
| e24180e | Yifan Wang | 07 February 2024, 15:37:33 UTC | fix for injection file created from pycbc_create_injections (#4623) * fix for injection file created from pycbc_create_injections * Update bin/pycbc_convertinjfiletohdf Co-authored-by: Gareth S Cabourn Davies <gareth.cabourndavies@ligo.org> --------- Co-authored-by: Gareth S Cabourn Davies <gareth.cabourndavies@ligo.org> | 07 February 2024, 15:37:33 UTC |
| 479a3ff | Yifan Wang | 05 February 2024, 13:48:03 UTC | Fix a bug in pycbc_coinc_findtrigs (#4618) * fix the numpy ndarray bug * typo | 05 February 2024, 13:48:03 UTC |
| d010ec5 | Ian Harry | 05 February 2024, 12:59:32 UTC | Need to create .cvmfscatalog file (#4619) | 05 February 2024, 12:59:32 UTC |
| 806750c | Gareth S Cabourn Davies | 05 February 2024, 09:28:15 UTC | Workflow changes needed to manage offline gracedb upload prep (#4535) * Workflow changes needed to manage preparation of offline gracedb upload files * fix change removed after rebase * Allow waveforms to not be given * IH comments | 05 February 2024, 09:28:15 UTC |
| ec8bd5d | Gareth S Cabourn Davies | 05 February 2024, 09:20:04 UTC | Some changes to HFile.select() and SingleDetTriggers (#4545) * Some changes to HFile.select() and mask_to_n_loudest_clustered * missed comma * Some CC problemas * Update * revert changes which meant kwargs couldnt be passed to mask_to_n_loudest_clustered_events * CC / fixes * Use list rather than numpy array for mask * remove messing about with the mask dtyping * initialise a transparent mask if it is not given * Fix problem when the filter value may not be available to the HFile * thinko in pycbc_bin_trigger_rates_dq * Don't make a huge boolean mask of all True values and then run nonzero on it = BAD IDEA * CC * re-enable option to have no mask * efficiency saving in pycbc_plot_hist * no mask option in trig_dict * typo * allow None maks in mask_size * thought i could apply another mask but I cant * get filter_func back, use new interface for recent changes * Some minor fixes * cc * allow option to do a logical and on masks * various minor bugfixes * max z problem * fixes to pycbc_page_snglinfo * use alternative dict for beter clarity * IWH comments * add check for required datasets (mostly to remind people to add the required dataset list if they add a new ranking\!) * fix bad check, remove min_snr option * remove option from CI * Fix bug with applying premask and using filter_rank threshold at the same time * stop checking for required datasets - this is difficult when so may different types use the same function * CC prefers np.flatnonzero(arr) to arr.nonzero()[0] * Fix a couple of rarely-used scripts, remove unused imports, whitespace | 05 February 2024, 09:20:04 UTC |
| c2c356e | Tito Dal Canton | 02 February 2024, 15:53:55 UTC | Improvements to single fit plots (#4509) * Improvements to single fit plots * Apply suggestions from Gareth Co-authored-by: Gareth S Cabourn Davies <gareth.cabourndavies@ligo.org> --------- Co-authored-by: Gareth S Cabourn Davies <gareth.cabourndavies@ligo.org> | 02 February 2024, 15:53:55 UTC |
| 7774496 | Thomas Dent | 02 February 2024, 09:50:52 UTC | fix thinko in option parsing for defaults (#4615) * fix thinko in option parsing for defaults When an option is not given at all getattr on the args object gives None, but we don't want to translate that into "--option-name None" on the command line. * bugfix obviously we needed to define 'key_name' first .. | 02 February 2024, 09:50:52 UTC |
| 91d5a17 | Tito Dal Canton | 01 February 2024, 17:58:36 UTC | Revert #4213, a temporary numpy version pin (#4614) * Revert "Update requirements.txt (#4213)" This reverts commit da8a66816618749e187d3cbe6b7c17ccc007f33b. * Ian's suggestion * Try to fix codeclimate | 01 February 2024, 17:58:36 UTC |
| 09a4bb1 | Facundo Tuesca | 01 February 2024, 10:59:33 UTC | Remove M2Crypto dependency (#4613) | 01 February 2024, 10:59:33 UTC |
| 6915369 | Gareth S Cabourn Davies | 30 January 2024, 09:50:32 UTC | Live: produce empty trigger fit plot for detectors with no triggers (#4600) * Live: produce empty trigger fit plot for detectors with no triggers * allow for below-threshold triggers | 30 January 2024, 09:50:32 UTC |
| fbfd8b9 | maxtrevor | 26 January 2024, 21:39:37 UTC | O4b idq offline update (#4603) * Start offline dq workflow rework * Modified stat * Rewrote dq workflow * Added note for future suggested changes to dq workflow * Finished first draft of offline workflow * Fixed a comment * Removed unneeded argument to make dq workflow * Made bin templates executable * WOrking version of offline dq workflow * Reverting non-functional changes in stat.py * linting * Reverted more non-functional changes * Reverted low-latency related features * Rearrange imports * Addressed Ian's comments * Simplified masking in dq workflow * Modify dq workflow to avoid using numpy arrays * Use vetoed times followup in example (#4597) * Use vetoed times followup in example * Fix statistic files double-definition * Addressed more comments from Tom * Addressed Gareth's comments on parser arguments * Don't allow dq stat to uprank candidates * Modify dq trigger rate plots to not use dq trigger rates below 1 * Address Tom's most recent comment * Readded [Min 1] to dq plot's y-axis label * Pass bank plotting tags to dq template bin plots * Update bin/plotting/pycbc_plot_dq_flag_likelihood Co-authored-by: Thomas Dent <thomas.dent@usc.es> * Update bin/workflows/pycbc_make_offline_search_workflow Co-authored-by: Thomas Dent <thomas.dent@usc.es> * Use abs() correctly * Break up 2 try/ecept cases --------- Co-authored-by: Gareth S Cabourn Davies <gareth.cabourndavies@ligo.org> Co-authored-by: Thomas Dent <thomas.dent@usc.es> | 26 January 2024, 21:39:37 UTC |
| 1906013 | Gareth S Cabourn Davies | 26 January 2024, 16:55:49 UTC | Standardise logging: bin/all_sky_search and pycbc/events (#4576) * add level to default logging * Decrease logging level for debug information in coinc_findtrigs * decrease logging level for some information in sngls_findtrigs * add named logger in pycbc/events/cuts.py * add named logger in pycbc/events/significance.py * REVERT ME: an example of usage * CC fix * Revert "REVERT ME: an example of usage" This reverts commit eb647e0b164c56091b4ad41a5c92df3e04ecc307. * Use init_logging throughout all_sky_search * give pycbc/events modules named loggers * missed the fact that the level was set to warn, not info, as default before * CC * missed an import * start moving verbose argparse into common facility * add common_options to all_sky_search executables * set --verbose default value to zero * pycbc not imported in some codes * CC * rename function to be more decriptive | 26 January 2024, 16:55:49 UTC |
| 2fd3852 | Shichao Wu | 25 January 2024, 20:25:03 UTC | Fix psd len issue (#4611) * Update __init__.py * Update estimate.py * fix typo * fix cc issue | 25 January 2024, 20:25:03 UTC |
| da72a89 | hoangstephanie | 25 January 2024, 13:42:58 UTC | Add the code to generate the sky grid that will be used by pycbc_multi_inspiral (#4485) * Add the code to generate the sky grid that will be used by pycbc_multi_inspiral * Minor changes on formatting and CLI * Change comments * Replace the explicit calculation of the norm with a numpy function and let the output file extension be given * Modify help messages * Remove non-used imports and write input values in the output file * Calculate the time delay corresponding to each sky point * Change the calculation of the angular spacing | 25 January 2024, 13:42:58 UTC |
| 4246b2c | Tito Dal Canton | 18 January 2024, 16:53:28 UTC | Fix docs/.gitignore (#4605) | 18 January 2024, 16:53:28 UTC |
| fe19555 | Tito Dal Canton | 17 January 2024, 16:08:51 UTC | Add the ability to choose how to sort injections in minifollowups (#4602) * Add the ability to choose how to sort injections in minifollowups * Minor cleanup * Minor refactor * Tom's comments * Update example search workflow * Further thoughts and suggestions * Tom's suggestion * Fix bug and Tom's suggestion | 17 January 2024, 16:08:51 UTC |
| 4784e77 | Gareth S Cabourn Davies | 17 January 2024, 14:43:02 UTC | Scripts for dealing with preparation of offline gracedb upload files (#4534) * Scripts for dealing with preparation of offline gracedb upload files * Update bin/all_sky_search/pycbc_make_bayestar_skymap Co-authored-by: Tito Dal Canton <tito@dalcanton.it> * reinstate SNR timeseries being saved into HDF * TDC comments * TDC comments 2 * Remove unneeded import --------- Co-authored-by: Tito Dal Canton <tito@dalcanton.it> Co-authored-by: Tito Dal Canton <tito.dalcanton@ijclab.in2p3.fr> | 17 January 2024, 14:43:02 UTC |
| 438680d | Tito Dal Canton | 17 January 2024, 12:15:59 UTC | Fix error querying Virgo frame type (#4523) * Fix error querying Virgo frame type * Typo * Typo * Implement Ian's suggestion * Make it work * Use an actual DeprecationWarning | 17 January 2024, 12:15:59 UTC |
| fb8991d | Gareth S Cabourn Davies | 11 January 2024, 15:26:32 UTC | Use vetoed times followup in example (#4597) * Use vetoed times followup in example * Fix statistic files double-definition | 11 January 2024, 15:26:32 UTC |
| feb8dfa | Gareth S Cabourn Davies | 22 December 2023, 12:43:59 UTC | bug in choosing the far calculation method (#4593) * bug in which IFO combo is used for calculating the FAR in each combination during HR * Safety catch | 22 December 2023, 12:43:59 UTC |
| 8ab13ba | Tito Dal Canton | 22 December 2023, 12:14:38 UTC | Do not set matplotlib's backend in internal modules (#4592) | 22 December 2023, 12:14:38 UTC |
| dcdc896 | segomezlo | 21 December 2023, 23:55:11 UTC | Dev comments for the pycbc_multi_inspiral executable (#4513) * Dev comments for the pycbc_multi_inspiral executable * minor changes to dev comments pycbc_multi_inspiral * minor change in dev comments pycbc_multi_inspiral * Update dev comments pycbc_multi_inspiral * Update pycbc_multi_inspiral * Update pycbc_multi_inspiral * Update dev comments for pycbc_multi_inspiral * Update on dev comments for pycbc_multi_inspiral Simplified the comments in the argparse section of the code. And moved some of the important details to https://github.com/gwastro/pycbc/pull/4513#discussion_r1370128384 . This has been done in order to keep track of them and migrate them to issues and PRs in the near future * Update to dev comments pycbc_multi_inspiral * Update dev comments pycbc_multi_inspiral * Update dev comments pycbc_multi_inspiral * Update dev comments pycbc_multi_inspiral * Update dev comments pycbc_multi_inspiral | 21 December 2023, 23:55:11 UTC |
| dab3943 | Alex Nitz | 14 December 2023, 19:18:21 UTC | fixes to mkl for large sizes (#4583) * prototype fixes * Update mkl.py * ws * also update class interface * typo | 14 December 2023, 19:18:21 UTC |
| af4154b | Michael J. Williams | 14 December 2023, 15:52:41 UTC | Add support for nessai sampler in pycbc inference (#4567) * add basic support for nessai sampler * enable all options and resuming in nessai * fix prior bounds in nessai model * tweak resuming and samples in nessai interface * change outdir to avoid namespace conflicts * tweaks to nessai sampler class * fix nessai checkpointing and other minor tweaks * fix for reading in nessai result files * use callback for checkpointing in nessai * start addressing codeclimate issues * add nessai to auxiliary samplers * add additional comments for nessai * make simple sampler example 2d nessai does not support 1d likelihoods, so this change is neede to test nessai in the CI * fix call to rng.random * add nessai to samplers example and update plot * set minimum version for nessai * force cpu-only version of torch * add missing epsie jump proposal * add plot-marginal to samplers plot * fix whitespace * use lazy formatting in logging functions * move functions to common nested class * update for change common nested class * address more code climate issues | 14 December 2023, 15:52:41 UTC |
| 9d5ae66 | Connor Weaving | 14 December 2023, 09:43:16 UTC | Adding likelihood to multi_signal model for inference of LISA signals. (#4582) * Changes to likelihood for multiple modes * Added multi mode likelihood for wfs that don't need detector response computed. * Experimenting with multi signal likelihood and bbhx * Futher likelihood testing for multiple modes * Test * Still testing likelihood * Almost fixed the cross term likelihood * Testing * Final tests * Multi signal likelihood for lisa bbhx cleanup * Tidy before pr * Added check for f_lower to set to -1 (pycbc default value) if f_lower not set in params. * Update docs examples with delta_f value * Undo hard coded delta_f * Add error when f_lower not supplied * Undo previous change from sequence. Added Exception when f_lower not provided in get_fd_det_waveform. * Removed exception * Correct indents * Removed TODO from relbin. Removed delta_f as a required parameter when using the get_fd_det_waveform_sequence method | 14 December 2023, 09:43:16 UTC |
| f3f6ffe | Arthur Tolley | 13 December 2023, 16:28:07 UTC | Enforcing consistent int types for both objects (#4586) | 13 December 2023, 16:28:07 UTC |
| 74fe248 | Gareth S Cabourn Davies | 13 December 2023, 12:14:09 UTC | CI changes to use split_binned hist (#4578) * CI changes to use split_binned hist * change back to mtotal now that is fixed by #4577 * revert related but unnecessary change | 13 December 2023, 12:14:09 UTC |
| fc3c0e2 | kkacanja | 13 December 2023, 05:52:50 UTC | Added parameter try-index to allow for more iterations for placing points (#4581) * Update pycbc_brute_bank to include option to cut wavelength and save the lower frequency * Removed Logging * Update pycbc_brute_bank Still need to fix the completion percentage * Add index to get bank to try more * Renamed the variable * Fixed Syntax | 13 December 2023, 05:52:50 UTC |
| 5e9004f | Gareth S Cabourn Davies | 07 December 2023, 16:45:15 UTC | split/bin parameters in pycbc_fit_sngls_split_binned (#4577) * allow pycbc_fit_sngls_split_binned to use generic parameters for splits ans bin parameters * testing printing * lazy formattign in logging * TD comments * Update bin/all_sky_search/pycbc_fit_sngls_split_binned Co-authored-by: Thomas Dent <thomas.dent@usc.es> * code efficiency * parameter rename * give choices to options --------- Co-authored-by: Thomas Dent <thomas.dent@usc.es> | 07 December 2023, 16:45:15 UTC |
| d340bc6 | Jacob Buchanan | 07 December 2023, 12:45:52 UTC | PyGRB postprocessing: segment writing/loading (#4542) * Try fixing load_segment_dict * Use segments/GPS time API more correctly * Use h5py correctly * Codeclimate * Add comment * condense segment list creation Co-authored-by: Francesco Pannarale <pannarale@users.noreply.github.com> * Plural start/end time in file output * Codeclimate --------- Co-authored-by: Francesco Pannarale <pannarale@users.noreply.github.com> | 07 December 2023, 12:45:52 UTC |
| 6b5a377 | Alex Nitz | 06 December 2023, 19:33:47 UTC | quickstart example for making a simple pycbc workflow (#4570) * add start to quickstart workflow example * updates * fixes * update * make folder name default with better name * demonstrate another part * ws | 06 December 2023, 19:33:47 UTC |
| d6f588c | Gareth S Cabourn Davies | 06 December 2023, 13:10:34 UTC | update lalsimulation cvmfs path (#4580) * update lalsimulation cvmfs path * missed that the mount location needs to be changed as well * more references to previsou CVMFS location | 06 December 2023, 13:10:34 UTC |
| bc6e864 | Gareth S Cabourn Davies | 06 December 2023, 09:13:12 UTC | remove removal of downranked triggers (#4579) * remove removal of downranked triggers * add brief explanation into the caption | 06 December 2023, 09:13:12 UTC |
| 0d8ae9e | Gareth S Cabourn Davies | 04 December 2023, 13:14:35 UTC | Fix cases where ifar limit was not being applied (#4574) * Fix cases where ifar limit was not being applied * some more missed cases / long lines * redoing a couple more long lines * missed one more place * unrelated bug where the IFOs were not in the right order for use with the significance_dict | 04 December 2023, 13:14:35 UTC |
| 992940c | Arthur Tolley | 28 November 2023, 12:07:40 UTC | correcting numpy call based on import (#4571) | 28 November 2023, 12:07:40 UTC |
| 694d04a | Gareth S Cabourn Davies | 24 November 2023, 13:23:00 UTC | Fix over-verbose offline workflow generator after init_logging change (#4569) | 24 November 2023, 13:23:00 UTC |
| a203541 | Gareth S Cabourn Davies | 23 November 2023, 13:33:00 UTC | Use gating windows in sngl_minifollowup and allow 'triggers within vetoes' option (#4549) * Use gating windows in sngl_minifollowup - also allow 'triggers within vetoes' option * Minor fixes * add infor if fewer triggers than requested * Allow pycbc_sngls_minifollowup to use single ranking statistic * Fix bug in rank_stat_single for quadsum/phasetd statistics * mask may be boolean now * fix broken pycbc_page_snglinfo due to bugfix * page_snglinfo to use the ranking statistic used * missed change | 23 November 2023, 13:33:00 UTC |
| b45658d | Alex Nitz | 20 November 2023, 22:03:51 UTC | Update __init__.py (#4564) * Update __init__.py This would modify init_logging in pycbc to work with a 'count' argument. This means if you give --verbose, the logging level is 'INFO', iv you give it twice (or -vv), it will use 'DEBUG'. If you keep giving (verbose) the logging level will decrease in increments in 10, but those don't have canonical names, and would be up to the user to use at their volition. * Update pycbc/__init__.py Co-authored-by: Thomas Dent <thomas.dent@usc.es> * Update __init__.py * Update __init__.py * Update pycbc/__init__.py Co-authored-by: Thomas Dent <thomas.dent@usc.es> --------- Co-authored-by: Thomas Dent <thomas.dent@usc.es> | 20 November 2023, 22:03:51 UTC |
| 9b8ecb0 | Ian Harry | 15 November 2023, 11:44:55 UTC | Fix plot_singles and optimize memory (#4566) * Fix plot_singles and optimize memory * Tom's comment * Use np.max * Remove redundant lines | 15 November 2023, 11:44:55 UTC |
| f4f7bf1 | Praveen Kumar | 13 November 2023, 19:22:09 UTC | added scaling of initial pop in snr_optimizer (#4561) * added scaling of initial pop * init popn in optimize_di & pso func * added changes in optimize_pso * usig logging.debug for snr | 13 November 2023, 19:22:09 UTC |
| 93b5f98 | Arthur Tolley | 10 November 2023, 16:38:30 UTC | [pycbc live] Allowing the use of psd variation in the ranking statistic for pycbc live (#4533) * Modifying files to include psd variation in single detector statistic calculation * ending variation.py with a blank line * Changing to an increment agnostic solution * removing change already fixed * Updating function names and docstrings * removing ToDos and adding more helpful comments * Removing unused import * Codeclimate fixes * Removing excess logging and whitespace mistakes * Removing unused objects + codeclimate fixes * Updating comments and docstrings, removing matchedfilter changes * Revert "Updating comments and docstrings, removing matchedfilter changes" This reverts commit 0e6473a12874b2dbb02952260b81c908540afff7. * Removing matchedfilter changes, updating comments and docstrings * Move --verbose to the end of the commands * more comment updates * Repositioning filter recreation * Changes to comments and removing whitespace Co-authored-by: Thomas Dent <thomas.dent@usc.es> * removing refchecks * Adding option veification for psd variation * Apply suggestions from code review Co-authored-by: Thomas Dent <thomas.dent@usc.es> * fixing EOL error * Refactoring the filter creation function * codeclimate fixes * undo * full_filt func * removing indentation * code climate * code climate * try to quiet codeclimate * codeclimate doesn't know PEP8 * brackets obviate line continuation --------- Co-authored-by: Thomas Dent <thomas.dent@usc.es> | 10 November 2023, 16:38:30 UTC |
| 3249806 | Ian Harry | 06 November 2023, 17:37:10 UTC | Update singularity image if release (#4563) | 06 November 2023, 17:37:10 UTC |
| 642b08f | Gareth S Cabourn Davies | 03 November 2023, 17:02:27 UTC | Add warning re failed builds on releases (#4557) I made this mistake: bad idea Here I add an explicit warning on the release instruction page so that I am more careful about this in future | 03 November 2023, 17:02:27 UTC |
| dec5c19 | ETVincent | 02 November 2023, 13:16:24 UTC | Update pycbc_pygrb_plot_stats_distribution (#4538) Updated to match old stats_dist branch. Co-authored-by: Francesco Pannarale <pannarale@users.noreply.github.com> | 02 November 2023, 13:16:24 UTC |
| 1fcb16c | Thomas Dent | 02 November 2023, 09:23:04 UTC | Non-coinc ifos in minifollowup trig plots (#4548) | 02 November 2023, 09:23:04 UTC |
| 7fb6d91 | Ian Harry | 01 November 2023, 09:17:05 UTC | Optimize memory usage of pycbc_fit_sngls_split_binned (#4543) * Optimize memory usage of pycbc_fit_sngls_split_binned * Need add option here * Comments on PR * Example doesn't use code being edited! * Update bin/all_sky_search/pycbc_fit_sngls_split_binned Co-authored-by: Thomas Dent <thomas.dent@usc.es> --------- Co-authored-by: Thomas Dent <thomas.dent@usc.es> | 01 November 2023, 09:17:05 UTC |
| 7d24aa0 | Shichao Wu | 31 October 2023, 15:34:01 UTC | add coordinates_space.py (#4289) * add coordinates_space.py * add LISA/SSB frame params * add LISA_to_GEO and GEO_to_LISA * add coordinates_space into FieldArray * add doc and Astropy support * update comments on sympy * use fsolve from scipy instead * fix cc issues * fix cc issues * minor fix * update * not use iteration * decouple LISA orbit and more accurate Earth * rename * remove jplephem * add the angular displacement of the Earth * use radians * make func readable in .ini * reverse back to master * correct psi range * reverse to master * fix unit issue in earth_position_SSB * put LISA to the "right" position * add LISA specific transform classes here * change names * update * make a package for coordinates * remove coordinates_space import * move __all__ into __init__.py * remove all coordinates_space * change TIME_OFFSET to seconds * fix SOBHB issue * rename * add SSB or LISA params into fid_params * rename * fix cc issues * fix cc issue * fix cc issue * update * update * fix * add default names * overwrite params with same names * remove pre-fixed names * remove all pre-fixed names * not pop * fix inverse transform * update tc * not overwrite * add SNR support for multi-model * Update waveform.py * t0 issue * t0 issue * Update space.py * add obstime * np.mod(psi_newframe, 2*np.pi) * fix obstime * add support for array inputs * Update hierarchical.py * just use Alex's implementation * CustomTransformMultiOutputs is in another PR, so remove it * add LDC and LAL convention correction * use pycbc standard names * more meaningful name * use pycbc standard names * Update relbin.py * Update parameters.py * remove unnecessary changes * fix cc issue * fix cc issue * fix cc issue * fix cc issue * compactify * compactify * add __all__ back * Update transforms.py * Update transforms.py * Update test_transforms.py * Update transforms.py * update doc * fix time warning * Update space.py * Update test_transforms.py * Create test_coordinates_space.py * fix cc issues * fix cc issues * fix cc issue * Update tox.ini * Update tox.ini * Update tox.ini * Update tox.ini * Update tox.ini * Update tox.ini * Update tox.ini * Update test_coordinates_space.py * add inline doc * Update tox.ini * add check of bbhx * Update test_coordinates_space.py * Update tox.ini * Update test_coordinates_space.py * add MultibandRelativeTimeDom into hierarchical.py * Update __init__.py * Update hierarchical.py * Update hierarchical.py * Update relbin.py * Update hierarchical.py * Update hierarchical.py * Update relbin.py * Update hierarchical.py * Update hierarchical.py * Update hierarchical.py * Update hierarchical.py * Update hierarchical.py * Update relbin.py * Update hierarchical.py * Update hierarchical.py * Update relbin.py * Update __init__.py * Update space.py * Update space.py * Update space.py * fix psi issue * Update test_coordinates_space.py * Update test_coordinates_space.py | 31 October 2023, 15:34:01 UTC |
| 9332804 | Tito Dal Canton | 31 October 2023, 11:13:28 UTC | Fix error in aligned_stoch_bank (#4546) | 31 October 2023, 11:13:28 UTC |
| 03a58ae | maxtrevor | 31 October 2023, 00:37:07 UTC | Read DQ flags with finer time resolution (#4547) * Read DQ flags with finer time resolution * No default sample rate for dq flags * No default sample rate for dq * Add type for frequency command line option | 31 October 2023, 00:37:07 UTC |
| 54fbcfb | Praveen Kumar | 30 October 2023, 20:33:23 UTC | Plotting order for KDE scatter (#4544) * unexpected events * added temp-volume in cl * unexpected events * added temp-volume in cl * adding sort-type to commandline * size of labelpad changed * added decreasing option in sort-type * added a comment for sorting arrays * minor change to dictionary * clarify sort option --------- Co-authored-by: Thomas Dent <thomas.dent@usc.es> | 30 October 2023, 20:33:23 UTC |
| f85f8bf | Bhooshan Uday Varsha Gadre | 30 October 2023, 15:48:02 UTC | allow psd var sample rate to change as needed (#4541) * Use same sample rate as strain for PSD variation instead of hardcoded 2048 Hz * make srate int * strain is already preprocessed (resampled to requested sample rate via opts) so it is not even needed. Does PSD var really need fixed sample rate of 2048? * Removing unused resample to make codeclimate happy in variation.py --------- Co-authored-by: Bhooshan Gadre <bhooshan.gadre@ligo.org> | 30 October 2023, 15:48:02 UTC |
| 0f279ba | kkacanja | 25 October 2023, 19:44:05 UTC | Update pycbc_brute_bank to include option to cut wavelength and save … (#4506) * Update pycbc_brute_bank to include option to cut wavelength and save the lower frequency * Removed Logging * Update pycbc_brute_bank Still need to fix the completion percentage * Update pycbc_brute_bank * Update pycbc_brute_bank * Update pycbc_brute_bank Debugged test example * Update pycbc_brute_bank * Update pycbc_brute_bank * Testing Condor Condor installation is not working properly for the checks after I changed two lines. * Testing Testing with file used before swapping two lines caused errors * Update pycbc_brute_bank Swapped two lines to be within the if statment | 25 October 2023, 19:44:05 UTC |
| 68e527b | Thomas Dent | 19 October 2023, 22:18:03 UTC | Rationalize some calls to waveform properties (#4540) * rationalize some calls to waveform properties * Only allow explictly listed names * don't try to change function name * g g | 19 October 2023, 22:18:03 UTC |
| f1e16ea | Jacob Buchanan | 19 October 2023, 17:14:01 UTC | PyGRB bugfixes/corrections (#4443) * Fix array indexing * Move polarization calculations to avoid NameError * naming correction * Correct naming correction * Fix coh_ifosnr sky location variables * Fix inj results plots (maybe not completely) * Make skygrid plot work (units questionable) * Fix double numpy import * Clarify units * Codeclimate * Use proper degree naming convention * Revert sky error change * Miniscule change to retrigger test | 19 October 2023, 17:14:01 UTC |
| e8f0b82 | Shichao Wu | 19 October 2023, 15:02:36 UTC | update parameters.py (#4397) * update parameters.py * fix cc issue * Update parameters.py * Update parameters.py * fix cc issues * Update parameters.py | 19 October 2023, 15:02:36 UTC |
| 8ab4471 | Jacob Buchanan | 19 October 2023, 11:51:02 UTC | PyGRB writing/loading timeslides (#4427) * Timeslides written and loaded * More commented stuff * Make event manager write slide offset * Slide offset is actually slide offset now * Write full timeslide information * Try writing full slide info another way * Load timeslides using new file output * Load fix + keep sanity checks * Correct number of ids * "slide shift" sounds better than "slide offset" * Bring back slide id * Codeclimate fix * Move time slides column to search group * Load time slides from search group * Avoid layers in output files * Try different placement in eventmgr * Try ifo/search group * Add search group copying to trig cluster * Get number of sets right for bar updating * Add more search group copying to work with bins | 19 October 2023, 11:51:02 UTC |
| 3259ec5 | Gareth S Cabourn Davies | 17 October 2023, 16:00:59 UTC | Set back to development (#4536) | 17 October 2023, 16:00:59 UTC |
| 30b3be8 | Gareth S Cabourn Davies | 17 October 2023, 12:13:26 UTC | Prepare for release v2.4.0 (#4531) | 17 October 2023, 12:13:26 UTC |
| 03f64a2 | Shichao Wu | 13 October 2023, 17:14:48 UTC | Update get.sh (#4532) | 13 October 2023, 17:14:48 UTC |
| 2b157f6 | Gareth S Cabourn Davies | 13 October 2023, 09:47:32 UTC | Set back to development (#4529) | 13 October 2023, 09:47:32 UTC |
| 9418384 | Ian Harry | 12 October 2023, 13:09:30 UTC | Prepare for release (#4526) | 12 October 2023, 13:09:30 UTC |
| cee6437 | Collin Capano | 11 October 2023, 20:39:41 UTC | Don't overwrite default numpy bindings from liglow in record.io (#4525) * Don't overwrite default numpy bindings from liglow in record.io * Change to not include any bindings that numpy already defines | 11 October 2023, 20:39:41 UTC |
| d7325c3 | Gareth S Cabourn Davies | 11 October 2023, 14:54:39 UTC | Apply some needed efficiency savings to pycbc_bin_trigger_rates_dq (#4519) * Apply a few efficiency savings to pycbc_bin_trigger_rates_dq * Us more logging. stat-threshold now has a default * Some improvements to logging * Move background_bins after trigger loading, allow indices_only return in HFile.select * Use sngl-ranking straight away in the select function * Descope PR * cleanup reversion to descope * cleanup reversion to descope * Explicit numpy types * gt --> ge * IH bugfix * apply some logic around psd var reweighting * wrap trigger selection to allow for missing psd_var_val case * remove checks around the psd_var_val | 11 October 2023, 14:54:39 UTC |
| d1bc127 | Arthur Tolley | 11 October 2023, 12:27:26 UTC | [pycbc live] Don't add snr options to command if they don't exist (#4518) * Don't run snr optimizer setup if not optimizing snr * moving the check to a more appropraite place * setting snr_opt_options to None if not optimizing | 11 October 2023, 12:27:26 UTC |
| ec9221a | Gareth S Cabourn Davies | 10 October 2023, 08:16:55 UTC | Make logging better for pycbc_make_offline_workflow (#4517) * Make logging better for pycbc_make_offline_workflow * comment * Fix bug * CC complaint - there are some other, but these havent been changed by this PR * CC * Update pycbc/workflow/core.py Co-authored-by: Tito Dal Canton <tito@dalcanton.it> * IH/TDC comments * use warnings module --------- Co-authored-by: Tito Dal Canton <tito@dalcanton.it> | 10 October 2023, 08:16:55 UTC |
| fa89889 | Gareth S Cabourn Davies | 09 October 2023, 17:13:03 UTC | Add details of closest triggers to the injection minifollowup (#4503) * Add details of closest triggers (not just event) to the injection minifollowup * Dont know how this was deleted * Wrap titles with quotes Co-authored-by: Ian Harry <iwharry@googlemail.com> * Use existing functions to reduce the number of trigger times being stored * Let the max window be set as a command line argument, deal with case where closest trigger is far away from the injection * remove import I thought I would use but didnt * Use the loudest SNR event in a tiny window instead of simply closest time * missed re-setting the ifo in this loop * Apply suggestions from code review * TD comment --------- Co-authored-by: Ian Harry <iwharry@googlemail.com> | 09 October 2023, 17:13:03 UTC |
| 5a14871 | Alex Nitz | 06 October 2023, 17:42:04 UTC | Update mac-test.yml (#4522) | 06 October 2023, 17:42:04 UTC |
