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CHANGELOG.md

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1.11.2 [11/02/2021]

  • pinned numpy dependency to <1.20 to fix incompatibility with lalsuite 6.81
  • updated ephemerides instructions and citation requests in README
  • fixed setup of FrequencyModulatedArtifactWriter class

1.11.1 [26/01/2021]

  • matplotlib will no longer be automatically forced to agg, but only if env["DISPLAY"] is not set
  • improved default scaling of MCMC corner plots
  • fixed missing unit for tp binary parameter in MCMC default plot labels

1.11.0 [20/01/2021]

  • LALSuite >= 6.80 now required
  • simplified calls to F-stat prediction
  • Writer:
    • internal cleanup of sftfilenames vs sftfilepath
    • SFTs are validated at end of run_makefakedata()
  • core and search classes: improved and fixed non-standard detection statistics
    • fixed basic twoFX and BSGL computation logic for transient and semicoherent cases, generalized to Ndet>2
    • reorganised methods for these computations
    • additional results are stored as class attributes
    • for transients, the detection statistic is now called explicitly maxTwoF
  • grid classes now initiate their .search object at instantiation instead of at first run() call

1.10.1 [20/01/2021]

  • bugfix for MCMCSearch.plot_prior_posterior()

1.10.0 [08/01/2021]

  • documentation now available from https://pyfstat.readthedocs.io
  • added gridcorner module for plotting GridSearch results
  • removed the specialist grid-based classes which were deprecated in 1.9.0
  • internal changes to search classes
    • should ideally not change anything for standard CW use cases
    • but fix some corner cases and make for more robustness
    • made tstart,tend optional in get_fullycoherent_twoF()
    • adapted most high-level search classes to this change
    • grid searches now internally use named-column ndarrays
    • some cleanup to keys storage in MCMC classes
    • changed helper_functions.get_doppler_params_output_format() to return dict
    • fixed sorting of output fmt specifiers for both MCMC and grid classes
    • changed GridSearch.inititate_search_object() to internal method _initiate_search_object()
  • line-robust statistics are now always stored and returned as log10BSGL (for consistency with LALSuite)
  • made various class methods private that had no obvious end-user use case
  • MCMCSearch.run(): initiate search object before checking for old data
  • MCMCGlitchSearch.plot_cumulative_max(): add savefig option (defaults to false)
  • GridSearch.plot_2D(): renamend save option to savefig for consistency with other plotting functions
  • removed unused ComputeFstat.get_full_CFSv2_output()
  • removed unused helper functions:
    • compute_P_twoFstarcheck()
    • compute_pstar()
    • twoFDMoffThreshold()
  • new example other_examples/PyFstat_example_spectrogram.py
  • some improvements to tests and examples
  • KNOWN ISSUES: implementation of line-robust statistic BSGL will need to be overhauled

1.9.0 [30/10/2020]

  • new class InjectionParametersGenerator
    • draws dicts of parameters from arbitrary priors
    • can then be directly passed e.g. to Writer as **params
    • and derived AllSkyInjectionParametersGenerator
  • deprecate various grid-based specialist classes:
    • these were all more or less unmaintained since a long time
      • SliceGridSearch
      • GridUniformPriorSearch
      • SlidingWindow
      • FrequencySlidingWindow
      • EarthTest
      • DMoff_NO_SPIN
    • will be removed in next version unless users speak up

1.8.0 [13/10/2020]

  • big overhaul of cumulative twoF calculations and plotting
  • Writer: fix expected sftfilepattern in multi-IFO and custom-TSFT cases
  • fixed internal consistency of parameter names:
    • Freq->F0 and phi0->phi for all PyFstat classes/functions
    • consistent conversion to lalappas arguments
  • fixed parsing of injectSqrtSX and assumeSqrtSX arguments
  • helper_functions.predict_fstat() no longer takes **kwargs
  • new instructions and helpful scripts for setting up developer environments (venv or conda)
  • various improvements to test suite

1.7.3 [21/09/2020]

  • GridSearch: will now always include the end point in each 1D parameter points array
  • restored MCMCSearch.plot_chainconsumer() to a workable state
    • optional dependency checked and documented more cleanly
    • the injections parameter option for this is actually called "truth" not "truths
  • fixed checks of injection parameter keys for other MCMC plotting functions

1.7.2 [18/09/2020]

  • improved GridSearch.check_old_data_is_okay_to_use()
  • minor logging improvements for Writer, GridSearch, TransientGridSearch
  • new binary_mcmc_vs_grid example
  • minor improvements to tests and other examples

1.7.1 [16/09/2020]

  • LALSuite 6.76 now required
  • predict_fstat() helper function made more flexible
  • Writer: fixed check_cached_data_okay_to_use() for multiple IFOs
  • MCMCSearch and derived classes now store sampler as an attribute
  • fixes to MCMC plotting
    • proper scaling of injection parameters in walker plots
    • proper display of prior (not logprior) in prior_posterior comparisons
  • consistently close figure objects after saving
  • all classes now announce their creation to the logger
  • flake8 compliance
  • code style now complying to stricter black 20.8b standards
  • improvements to examples

1.7.0 [31/08/2020]

  • Writer: fix binary tp handling and clean up injection parameter parsing
  • MCMCSearch plotting improvements:
    • add injection parameters through "truths" kwarg
    • F->2F fixes
    • fix failures for single-parameter posteriors
  • removed unused Bunch class
  • refactored some core functions into BaseSearchClass methods or moved to helper_functions
  • removed deprecated options/functions:
    • ComputeFstat option estimate_covering_band
    • Writer options minStartTime, maxStartTime
    • MCMCSearch.get_median_stds()
  • new internal class SearchForSignalWithJump which SemiCoherentGlitchSearch and GlitchWriter inherit from

1.6.0 [19/08/2020]

  • Writer classes, including several backwards-incompatbile changes:
    • removed lots of default values where there isn't really a logical "default"; e.g. detectors and signal parameters now always need to be explicitly set.
    • more flexible setup getting info from noiseSFTs (tstart, duration now optional and used as constraints)
    • can now auto-estimate SFT frequency band if not set by user (assuming a single-template search)
    • added manual ephemerides options
    • removed add_noise option, same behaviour can still be controlled through options sqrtSX or noiseSFTs
    • no .cff file generated any more if h0==0 (no signal)
    • verbose option for make_cff() and make_data() methods
    • clearer error messages in many cases
  • ComputeFstat, SemiCoherentSearch and derived classes:
    • fixed internal maxStartTime default if not set by user
    • by that, fixed the SemiCoherentSearch segments auto-setup
    • added Tsft as user option
    • clearer error and logging messages
  • improved helper_functions.get_sft_array()
  • extended, cleaned up and further modularised test suite
  • updated examples to changes in Writer and other classes

1.5.2 [06/08/2020]

  • fixed semi-coherent search bug introduced in 1.5.0:
    • last segment was always skipped due to off-by-one error in segment boundary calculation.
  • MCMC searches:
    • extended print_summary() with new get_summary_stats() helper and deprecated get_median_stds()
    • fixes to some of the more exotic prior types.
  • Extended MCMC test coverage.

1.5.1 [30/07/2020]

  • The only change in this release is an updated README to point to the new 1.5+ Zenodo record.

1.5.0 [30/07/2020]

  • new default coverage band behaviour for all search classes:
    • estimate from search ranges (GridSearch) or prior (MCMCSearch) unless minCoverFreq, maxCoverFreq set
    • negative values can be used to reproduce old default of setting from SFT width
    • explicit option estimate_covering_band deprecated
  • semicoherent searches:
    • sped up by only calling ComputeTransientFstatMap once per point
    • BSGL now computed from summed F-stats, not for each segment
    • per-segment results now stored in attribute twoF_per_segment instead of det_stat_per_segment
  • MCMC searches: save twoF for each sample to .dat file
  • Writer:
    • options minStartTime, maxStartTime deprecated
    • always use tstart, duration for actual data range
    • and use transientStartTime, transientTau for transients
  • transient-on-GPU output file writing fix
  • examples:
    • all output now goes to a directory "PyFstat_example_data"
    • added mcmc_vs_grid_simple_example

1.4.2 [14/07/2020]

  • small fixes to search classes:
    • get_max_twoF() fixed for TransientGridSearch
    • fix column header format for per-Doppler-point transient Fmn output files
    • fixed regexp deprecation warning
    • throw warning if using MCMCSearch.generate_loudest() called for transients

1.4.1 [13/07/2020]

  • Writer: fix SFT counting for non-contiguous or overlapping SFTs

1.4.0 [13/07/2020]

  • now fully python3.8 compatible
  • now using versioneer for versioning
  • require lalsuite>=6.72
  • added docker images, provided through github packages
  • Writer class:
    • new options randSeed, noiseSFTs and windowing
    • change default sqrtSX from 1 to 0
    • improved support for sources in binaries
  • search classes:
    • improved support for sources in binaries
    • additional file outputs for MCMC (including full posterior samples)
    • improved output file headers with version and options strings
    • improved MCMC walker plotting
    • implemented CFS feature injectSqrtSX
    • manual ephemerides option
    • new options estimate_covering_band and RngMedWindow
    • extended get_covering_band() to deal with fkdot bands
    • improved GridSearch logic to reuse (or not) old results
  • removed injection_helper_functions module
  • fixed placement of temporary output files
  • improved error handling for lal programs
  • added 1to1 test against CFSv2
  • reorganised and improved examples
  • various minor bug fixes and code cleanup

1.3 [21/01/2020]

  • python3 migration
  • enforce black style checker
  • smarter ephemerides finding
  • pycuda as optional dependency
  • improved test suite
  • improved logic in Writer class
  • fixes to ComputeFstat flags handling
  • various minor bug fixes

1.2 [08/05/2018]

  • reorganised examples
  • timing of transient F-stat map function

1.1.2 [23/04/2018] and before

  • see git commit history