CHANGELOG.md

All notable changes will be documented in this file

[1.0.0] 2020-07-06

Version 1.0 release of bilby

Changes

• Minor bug fixes and typo changes only from 0.6.9, see git.ligo.org/lscsoft/bilby/-/merge_requests?scope=all&utf8=%E2%9C%93&state=merged&milestone_title=1.0.0 for details

[0.6.9] 2020-05-21

Changes

• Improvement to the proposal step in dynesty (!774)
• Fix a bug in checking and making directories (!792)
• Clean up of the default prior files (!789)

[0.6.8] 2020-05-13

Added

• Option to sample in the sky frame (!786)
• Multiprocessing to reconstruction of marginalized parameters (!782)
• Generic reweighting method for likelihood / priors (!776)
• Parameterized EOS sampling (!543)
• Implementation of the UltraNest sampler (!766)
• Implementation of arVix result files (!772)
• Added basic pre-commit behaviour (!763)

Changes

• Updated the default PSD to O4 (!757)
• Make multinest allow long file names, optional and work with MPI (!764 !785)
• Add min/max to aligned spin prior (!787)
• Reduce redudant code (!703)
• Added testing for python 3.8 (!762)
• Improvements to the waveform plot (!769)

[0.6.7] 2020-04-15

Changes

• Allow dynesty to run with multiprocessing (!754)
• Rewrite ptemcee implementation (!750)
• Change 'source frame' to 'detector frame' in L34-35 of compare_samplers tutorial (!745)
• Allow lal dictionary to be passed through to '_base_lal_cbc_fd_waveform' (!752)

[0.6.6] 2020-03-06

Changes

• Fix bug where injected values are not present for corner plot (!749)
• Significant backwards-incompatible improvements to dynesty checkpointing (!746)
• Improve checkpoint interval calculation with dynesty (!741)
• Fix reading of PriorDict class from result file (!739)
• Fix definition of time for time-domain lalsimulation waveforms (!736)
• LaTeX text formatting for plots by default (!702)

Added

• Normalisation dynamically computed when using prior constraints (!704)

[0.6.5] 2020-02-14

Changes

• Fix for time reconstruction bug (!714)
• Resolved errors Waveform longer than the frequency array (!710)
• Prior reading clean-up (!715)
• More efficient dynesty restarting (!713)
• PP tests show 123 sigma bounds by default (!726)

Added

• HealPixPrior (!651)
• GW prior documentation (!720)
• Multiple contours to PP tests plots (!721)
• Distance marginalization for non-luminosity-distance parameters (!719)

Removed

• Pipenv (!724)

[0.6.4] 2020-01-30

Changes

• Discontinue python2.7 support (!697)
• Minor adjustments to the act calculation method (!679, !707)
• Restructure of the prior module (!688)
• Improvements to the documentation (!708, !700)
• Bug fix when maximum < minimum (!696)

Added

• Improved waveform error handling (!653)
• Waveform check to the CI (!698)

[0.6.3] 2020-01-03

Changed

• Fixed an issue with the ROQ segment scaling (!690)

[0.6.2] 2019-12-20

Added

• Introduced conditional prior sets (!332)(!673)(!674)
• Introduced joint priors (!668)
• Added a check to make sure sampling time exists before trying to update (!672)

Changed

• Fixed a caching issue with the waveform generators (!630)
• Fixed an issue that made the dynamic dynesty sampler not work (!667)
• Changed the backend docker files (!669)
• Fixed an error when plotting time domain data when using filtfilt=True
• Interped priors now dynamically update when new yy values are set (!675)
• Fixed the ROQ scaling checks (!678)

[0.6.1] 2019-12-02

HotFix release following 0.6.0 fixing a minor bug in the generation of derived parameters.

[0.6.0] 2019-12-02

Added

• A bilby-implemenatation of the dynesty rwalk proposal method (!640)
• An ACT estimate to the rwalk option (!643)
• HTML waveform plots and general improvements to the waveform plot (!641, !659)
• Add a function to resample bilby generated with a uniform in mass ratio and chirp_mass prior to uniform in component mass (!642)
• Adds checking to the ROQ usage: warning messages generated when out of bounds (!549)
• A safety check to the time reconstrucion (!633)
• Added the kombine sampler (!637)
• Added in-plane spins (!646)

Changes

• Changed the PriorDict base class to from OrderedDict to just dict. This fixes an issue with pickling priors (!652)
• Improvements to the behaviour of the conversion functions (!647)
• Prevent chirp mass railing for the GW150914 examples (!635)

[0.5.9] 2019-10-25

Added

• Default reflective boundaries for calibration parameters !623
• Support for inferring method arguments !608

Changes

• Speed up the prior evaluations by implementing directly with checks to scipy !627
• Soft initalisation option for the Sampler class !620
• Improvements to JSON reading and writing for functions !621
• Fixed bug in prior reading !618 !617
• Fixes to the examples !619 !614 !626 !616
• Update to the test mode storing extra information !613
• Minor improvements to the ptemcee sampler
• Improved contributing guidelines !610

Removed

• Default printing of bilby version at import !608

[0.5.8] 2019-09-26

Added

• Progress bar in post-processing step

Changed

• Fixed implementation of calibration !607
• Fixed interaction with dynesty for reflective bounds !604
• Fixed behaviour of n_effective with check pointing !603
• Fixed testing of constants !605
• Fixed bug in bilby_result with python2.7

[0.5.7] 2019-09-19

Added

• bilby_convert_resume file CL tool for converting dynesty resume files into preresults !599

Changes

• Change the constants (Msun, REarth etc) to match the values in LAL !597
• Change the Greenwhich Mean Sidereal Time conversion to match the method in LAL !597
• Update dynesty requirement to 1.0.0
• Improve integration of bounds with dynesty !589
• Fixed issue with mutable default argument !596
• Allow the use of n_effective in dynesty !592
• Allow the use of n_periodic in cpnest !591
• Fix bug in dt calc

[0.5.6] 2019-09-04

Changes

• Deprecation of the old helper functions (e.g., fetch open data)
• Improvements to the documentation
• Fix a bug in the dt calculations of the GW likelihood
• Various small bug fixes

Added

• LAL version information in the meta data

[0.5.5] 2019-08-22

Added

• Reading/writing of the prior in a JSON format
• Checks for marginalization flags

Changes

• Improvements to the examples: reorganisation and fixing bugs
• Fixed bug with scipy>=1.3.0 and spline
• Removed the sqrt(2) normalisation from the scalar longitudinal mode
• Improve PSD filename reading (no longer required "/" to read local files)
• Fix bug in emcee chains
• Added a try/except cluase for building the lookup table

[0.5.4] 2019-07-30

Added

• Analytic CDFs
• Reading/writing of grid results objects

Changed

• Dynesty default settings changed: by default, now uses 30xndim walks. This was shown (!564) to provide better convergence for the long-duration high-spin tests.
• Fix bug in combined runs log evidence calculations
• Fixed bugs in the nightly tests

[0.5.3] 2019-07-23

Added

• Jitter time marginalization. For the time-marginalized likelihood, a jitter is used to ensure proper sampling without artifacts (!534)
• Zero likelihood mode for testing and zero-likelihood test to the nightly C.I ((!542)
• 15D analytic Gaussian test example (!547)

Changes

• Dynesty version minimum set to 0.9.7. Changes to this sampler vastly improve performance (!537)
• Improvements to waveform plotting (!534)
• Fixed bugs in the prior loading and added tests (!531 !539 !553 !515)
• Fixed issue in 1D CDF prior plots (!538)
• ROQ weights stored as npz rather than json (memory-performance improvement) (!536)
• Distance marginalisation now uses cubic rather than linear interpolation. Improves distance/inclination posteriors for high SNR systems. (!552)
• Inputs to hyperpe modified to allow for more flexible sampling prior specification and improve efficiency. (!545)
• Fix definition of some spin phase parameters (!556).

[0.5.2] 2019-06-18

Added

• Method to read data in using gwpy get (and associated example)
• Adds a catch for broken resume files with improves reporting

Changed

• Updated and fixed bugs in examples
• Resolve sampling time persistence for runs which are interupted
• Improvements to the PP plot
• Speed up of the distance calculation
• Fixed a bug in the inteference of bilby command line arguments with user specified command lines
• Generalised the consistency checks for ResultLists
• Fixes to some tests
• Makes the parameter conversion a static method rather than a lambda expression

[0.5.1] 2019-06-05

Added

• Option for the GraceDB service URL
• Precessing BNS
• Functionality to make a waveform plot

Changed

• Changes to ROQ weight generation: finer time-steps and fixed a bug in the time definition
• Fixed typo "CompactBinaryCoalesnce" -> "CompactBinaryCoalescence" (old class now has deprecation warning)
• Fixed a minor bug in the frequency mask caching
• Minor refractoring of the GWT likelihood and detector tests
• Initial samples in dynesty now generated from the constrained prior

[0.5.0] 2019-05-08

Added

• A plot_skymap method to the CBCResult object based on ligo.skymap
• A plot_calibration_posterior method to the CBCResult object
• Method to merge results

Changed

• Significant refactoring of detector module: this should be backward conmpatible. This work was done to break the large detector.py file into smaller, more manageable chunks.
• The periodic_boundary option to the prior classes has been changed to boundary. This breaks backward compatibility. The options to boundary are {'periodic', 'reflective', None}. Periodic boundaries are supported as before. Reflective boundaries are supported in dynesty and cpnest.
• Minor speed improvements by caching intermediate steps
• Added state plotting for dynesty. Use check_point_plot=True in the run_sampler function to create trace plots during the dynesty checkpoints
• Dynesty now prints the progress to STDOUT rather than STDERR
• detector module refactored into subpackage. Maintains backward compatibility.
• Specifying alternative frequency bounds for the ROQ now possible if the appropriate params.dat file is passed.

Removed

• Obsolete (and potentially incorrect) plot_skymap methods from gw.utils

[0.4.5] 2019-04-03

Added

• Calibration method and plotting
• Multivariate Gaussian prior
• Bayesian model diminsionality calculator
• Dynamic dynesty (note: this is in an alpha stage)
• Waveform caching

Changes

• Fixed bugs in the ROQ time resolution
• Fixed bugs in the gracedb wrapper-method
• Improvements to the pp-plot method
• Improved checkpointing for emcee/ptemcee
• Various perforance-related improvements

[0.4.4] 2019-04-03

Added

• Infrastucture for custom jump proposals (cpnest-only)
• Evidence uncertainty estimate to cpnest

Changed

• Bug fix to close figures after creation
• Improved the frequency-mask to entirely remove values outside the mask rather than simply set them to zero
• Fix problem with Prior prob and ln_prob if passing multiple samples
• Improved cpnest prior sampling

Removed

[0.4.3] 2019-03-21

Added

• Constraint prior: in prior files you can now add option of a constraint based on other parameters. Currently implements mass-constraints only.
• Grid likelihood: module to evaluate the likelihood on a grid

Changed

• The GWTransientLikelihood no longer returns -inf for m2 > m1. It will evaluate the likelihood as-is. To implement the constraint, use the Constraint priors.

[0.4.2] 2019-03-21

Added

• Fermi-Dirac and SymmetricLogUniform prior distributions
• Multivariate Gaussian example and BNS example
• Added standard GWOSC channel names
• Initial work on a fake sampler for testing
• Option for aligned spins
• Results file command line interface
• Full reconstruction of marginalized parameters

Changed

• Fixed scheduled tests and simplify testing environment
• JSON result files can now be gzipped
• Reduced ROQ memory usage
• Default checkpointing in cpnest

[0.4.1] 2019-03-04

Added

• Support for JSON result files
• Before sampling a test is performed for redundant priors

Changed

• Fixed the definition of iota to theta_jn. WARNING: this breaks backward compatibility. Previously, the CBC parameter iota was used in prior files, but was ill-defined. This fixes that, requiring all scripts to use theta_jn in place of iota
• Changed the default result file store to JSON rather than hdf5. Reading/writing of hdf5 files is still intact. The read_in_result function will still read in hdf5 files for backward compatibility
• Minor fixes to the way PSDs are calculated
• Fixed a bug in the CBC result where the frequency_domain model was pickled
• Use pickling to store the dynesty resume file and add a write-to-resume on SIGINT/SIGKILL
• Bug fix in ROQ likelihood
• Distance and phase marginalisation work with ROQ likelihood
• Cpnest now creates checkpoints (resume files) by default

Removed

[0.4.0] 2019-02-15

Changed

• Changed the logic around redundancy tests in the PriorDict classes
• Fixed an accidental addition of astropy as a first-class dependency and added a check for missing dependencies to the C.I.
• Fixed a bug in the "create-your-own-time-domain-model" example
• Added citation guide to the readme

[0.3.6] 2019-02-10

Added

• Added the PolyChord sampler, which can be accessed by using sampler='pypolychord' in run_sampler
• emcee now writes all progress to disk and can resume from a previous run.

Changed

• Cosmology generalised, users can now specify the cosmology used, default is astropy Planck15
• UniformComovingVolume prior requires the name to be one of "luminosity_distance", "comoving_distance", "redshift"
• Time/frequency array generation/conversion improved. We now impose duration is an integer multiple of sampling_frequency. Converting back and forth between time/frequency arrays now works for all valid arrays.
• Updates the bilby.core.utils constants to match those of Astropy v3.0.4
• Improve the load_data_from_cache_file method

Removed

• Removed deprecated PriorSet classes. Use PriorDict instead.

[0.3.5] 2019-01-25

Added

• Reduced Order Quadrature likelihood
• PTMCMCSampler
• CBC result class
• Additional tutorials on using GraceDB and experts guide on running on events in open data

Changed

• Updated repository information in Dockerfile for PyMultinest

[0.3.4] 2019-01-10

Changes

• Renamed the "basic_tutorial.py" example to "fast_tutorial.py" and created a "standard_15d_cbc_tutorial.py"
• Renamed "prior" to "priors" in bilby.gw.likelihood.GravtitationalWaveTransient for consistency with bilby.core. WARNING: This will break scripts which use marginalization.
• Added outdir kwarg for plotting methods in bilby.core.result.Result. This makes plotting into custom destinations easier.
• Fixed definition of matched_filter_snr, the interferometer method has become ifo.inner_product.

Added

• log-likelihood evaluations for pymultinest

[0.3.3] 2018-11-08

Changes currently on master, but not under a tag.

• Removed unnecessary arguments (ra, dec, geocent_time, psi) from source functions and replaced them with **kwargs where appropriate.
• Renamed PriorSet to PriorDict
• Renamed BBHPriorSet to BBHPriorDict
• Renamed BNSPriorSet to BNSPriorDict
• Renamed CalibrationPriorSet to CalibrationPriorDict
• Added method to result to get injection recovery credible levels
• Added function to generate a pp-plot from many results to core/result.py
• Fixed a bug which caused Interferometer.detector_tensor not to update when latitude, longitude, xarm_azimuth, yarm_azimuth, xarm_tilt, yarm_tilt were updated.
• Added implementation of the ROQ likelihood. The basis needs to be specified by the user.
• Extracted time and frequency series behaviour from WaveformGenerator and InterferometerStrainData and moved it to series.gw.CoupledTimeAndFrequencySeries

Changes

• Switch the ordering the key-word arguments in result.read_in_result to put filename first. This allows users to quickly read in results by filename
• Result object no longer a child of dict. Additionally, the list of attributes and saved attributes is standardised
• The above changes effect the saving of posteriors. Users can expect that opening files made in python 2(3) which where written in 3(2) may no longer work. It was felt that the overheads of maintaining cross-version compatibility were too much. Note, working in only python 2 or 3, we do not expect users to encounter issues.
• Intermediate data products of samples, nested_samples are stored in the h5
• Time marginalised GravitationalWaveTransient works with arbitrary time priors.

[0.3.1] 2018-11-06

Changes

• Make BBH/BNS parameter conversion more logical
• Source frame masses/spins included in posterior
• Make filling in posterior with fixed parameters work
• Bug fixes

[0.3] 2018-11-02

Added

• Joint-likelihood added
• PyMC3 works with the GravitationalWaveTransient likelihood
• flake8 syntax checking in CI
• Binary neutron star source model
• Allow units to be included in parameter labels
• Add nested samples to dynesty output
• Add more __repr__ methods
• Add ability to plot max likelihood and draws from the posterior
• Document samplers in more detail
• Added the CPNest sampler
• Adds custom titles to corner plots
• Adds plotting of the prior on 1D marginal distributions of corner plots
• Adds a method to plot time-domain GW data
• Added pipenv as a dependency manager
• Hyperparameter estimation now enables the user to provide the single event evidences
• Add nested samples to nestle output
• Prior and child classes now implement the __eq__ magic method for comparisons
• Added default kwargs for each sampler class
• Added NestedSampler and MCSampler helper classes
• Added sampler_requirements.txt file
• Add AlignedSpin gw prior
• Add units to know prior files
• Add pipenv functionality
• Tests run in custom dockerfiles

Changes

• Fix construct_cbc_derived_parameters
• Autocorrelation calculation moved into parent class
• Fix interpretation of kwargs for dynesty
• PowerSpectralDensity structure modified
• Fixed bug in get_open_data
• Modified how sampling in non-standard parameters is done, the non_standard_sampling_parameter_keys kwarg has been removed
• .prior files are no longer created. The prior is stored in the result object.
• Removed external_sampler and external_sampler_function attribute from Sampler
• Made conversion of number of livepoint kwargs consistent and streamlined throughout the Nested sampler classes
• Fix label creation in plot_multiple, evidences and repeated plots.
• Changed the way repr works for priors. The repr can now be used to re-instantiate the Prior in most cases
• Users can now choose to overwrite existing result files, rather than creating a .old file.
• Make likelihood values stored in the posterior correct for dynesty and nestle
• pymultinest output now stored in {outdir}/pm_{label}/

Removed

• Removes the "--detectors" command line argument (not a general CLI requirement)

[0.2.2] 2018-09-04

Added

• Add functionality to sample in redshift and reconstruction of source frame masses.
• Add functionality to combine result objects.
• Enable initial values for emcee to be specified.
• Add support for eccentric BBH

Changed

• Specifying detectors by name from the default command line options has been removed.
• The prior on polarisation phase has been reduced to [0, pi].
• More prior distributions added.
• More samplers supported, pymc3
• More core likelihoods, Poisson, Student's-t
• Result print function fixed
• Add snr functions as methods of Interferometer
• The paths between imports where changed so that calls such as bilby.WaveformGenerator no longer work. Instead, we need to use bilby.gw.WaveformGenerator. This was done to keep things cleaner going forward (when, for example, there may be multiple wfg's).
• Samplers reorganised into individual files.

[0.2.1] 2018-07-18

Added

• InterferometerStrainData now handles both time-domain and frequencu-domain data
• Adds documentation on setting data (https://lscsoft.docs.ligo.org/bilby/transient-gw-data.html)
• Checkpointing for dynesty: the sampling will be checkpointed every 10 minutes (approximately) and can be resumed.
• Add functionality to plot multiple results in a corner plot, see bilby.core.result.plot_multiple().
• Likelihood evaluations are now saved along with the posteriors.

Changed

• Changed to using setuptools for installation.
• Clean up of real data handling: all data is now windowed with a 0.4s roll off (unless set otherwise) and low-pass filtered.
• Add explicit method to create a power spectral density from time-domain data
• Clean up of PowerSpectralDensity() - addds set_from methods to handle various ways to define the PSD.
• Clean up of detectors.py: adds an InterferometerStrainData to handle strain data and InterferometerSet to handle multiple interferometers. All data setting should primarily be done through the Interferometer.set_strain_data.. methods.
• Fix the comments and units of nfft and infft and general improvement to documentation of data.
• Fixed a bug in create_time_series
• Enable marginalisation over calibration uncertainty in Inteferemeter data.
• Fixed the normalisation of the marginalised GravtitationalWaveTransient likelihood.
• Fixed a bug in the detector response.

[0.2.0] 2018-06-17

First pip installable version https://pypi.org/project/BILBY/ .

Added

• Reoriganisation of the directory into bilby.core and bilby.gw.
• Reading of frame files.
• Major effort to update all docstrings and add some documentation.
• Marginalized likelihoods.
• Examples of searches for gravitational waves from a Supernova and using a sine-Gaussian.
• A PriorSet to handle sets of priors and allows reading in from a standardised prior file (see https://lscsoft.docs.ligo.org/bilby/prior.html).
• A standardised file for storing detector data.

Removed

• All chainconsumer dependency as this was causing issues.