Bilby

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
-

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

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.

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

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

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.