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StingraySoftware/stingray: v1.0-beta

Matteo Bachetti; Daniela Huppenkothen; Usman Khan; Himanshu Mishra; Swapnil Sharma; John Swinbank; Amogh Desai; Haroon Rashid; Evandro Martinez Ribeiro; Abbie Stevens; Brigitta Sipőcz; Dhruv Vats; tappina; omargamal8; Meg Davis; Achilles Rasquinha; Paul Balm; Stuart Mumford; Riccardo Campana; Nitish Garg; Akash Tandon; Anurag Hota; Nick; Rashmi Raj; Sashank Mishra; Arfon Smith; Max Mahlke; Saurav Sachidanand; Sandeep Kumar; Ricardo Vallés Blanco

What's Changed

TL,DR: these things will break your code with v1.0beta:

  • Python version < 3.8
  • The gtis keyword in pulse/pulsar.py (it is now gti, without the 's')
New
  • Dropped support to Python < 3.8
  • Multi-taper periodogram, including a Lomb-Scargle implementation for non-uniformly sampled data
  • Create Count rate spectrum when calculating spectral-timing products
  • Make modulation upper limit in (Averaged)Powerspectrum work with any normalization (internally converts to Leahy for the calculation)
  • Implement Gardner-Done normalization (1 for perfect correlation, -1 for perfect anticorrelation) for Auto/Crosscorrelation
  • New infrastructure for converting EventList and LightCurve objects into Astropy TimeSeries
  • New infrastructure for converting most Stingray classes into Astropy Table objects
  • Save and load of most Stingray classes to/from many different file formats (pickle, ECSV, HDF5, FITS, and all formats compatible with Astropy Table)
  • Accept input EventList in DynamicalPowerSpectrum
  • New stingray.fourier module containing the basic timing products, usable on numpy arrays, and centralizes fft import
  • New methods in Crossspectrum and Powerspectrum to load data from specific inputs: from_events, from_lightcurve, from_time_array, from_lc_list (from_time_array was also tested using memory-mapped event lists as inputs: useful in very large datasets)
  • New and improved spectral timing methods: ComplexCovarianceSpectrum, CovarianceSpectrum, LagSpectrum, RmsSpectrum
  • Some depreciated features are now removed
  • PSDLogLikelihood now also works with a log-rebinned PDS
Improvements
  • Performance on large data sets is VASTLY improved
  • Lots of performance improvements in the AveragedCrossspectrum and AveragedPowerspectrum classes
  • Standardized use of new fast psd/cs algorithm, with legacy still available as an alternative option to specify
  • Reading calibrated photon energy from event files by default
  • In pulse/pulsar.py, methods use the keyword gti instead of gtis (for consistency with the rest of Stingray)
  • Moved CovarianceSpectrum` toVarEnergySpectrum`` and reuse part of the machinery
  • Improved error bars on cross-spectral and spectral timing methods
  • Measure absolute rms in RmsEnergySpectrum
  • Friendlier pyfftw warnings
  • Streamline PDS/CrossSp production, adding from_events, from_lc, from_lc_iterable, and from_time_array (to input a numpy array) methods
  • PDS/CrossSp initially store the unnormalized power, and convert it on the fly when requested, to any normalization
  • Adjust codecov settings with new yaml file
Bug fixes
  • Fixed error bars and err_dist for sliced (iterated) light curves and power spectra
  • Fixed a bug in how the start time when applying GTIs (now using the minimum value of the GTI array, instead of half a time bin below the minimum value)
  • All simulator errors are zero
  • Fixed coherence uncertainty
  • Documented a Windows-specific issue when large count rate light curves are defined as integer arrays (Windows users should use float or specify int-64)
  • If the variance of the lightcurve is zero, the code will fail to implement Leahy normalization
  • The value of the PLEPHEM header keyword is forced to be a string, in the rare cases that it's a number
  • and more!
New Contributors

Full Changelog: https://github.com/StingraySoftware/stingray/compare/v0.3...v1.0-beta

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