Stingray

-------------------

Docs
^^^^

- Add newly-accepted JOSS paper to docs, update citation information, and fresh new badges (`829 <https://github.com/StingraySoftware/stingray/pull/829>`__)

-------------------

Bug Fixes
^^^^^^^^^

- Fix issue with FITS headers, especially for RXTE data (`853 <https://github.com/StingraySoftware/stingray/pull/853>`__)

-----------------

New Features
^^^^^^^^^^^^

- Add a compute_rms function to LombScarglePowerspectrum (`828 <https://github.com/StingraySoftware/stingray/pull/828>`__)
- Introduced FITSReader class for lazy-loading of event lists (`834 <https://github.com/StingraySoftware/stingray/pull/834>`__)
- implementation of the shift-and-add technique for QPOs and other varying power spectral features (`849 <https://github.com/StingraySoftware/stingray/pull/849>`__)


Bug Fixes
^^^^^^^^^

- The ``fold_events`` function now checks if the keyword arguments (`kwargs`) are in the list of optional parameters.
If any unidentified keys are present, it raises a `ValueError`.
This fix ensures that the function only accepts valid optional parameters and provides a clear error message for unsupported keys. (`837 <https://github.com/StingraySoftware/stingray/pull/837>`__)


Internal Changes
^^^^^^^^^^^^^^^^

- Eliminated runtime dependency on setuptools (`852 <https://github.com/StingraySoftware/stingray/pull/852>`__)
- Moved configuration to pyproject.toml as recommended by PEP 621 (`842 <https://github.com/StingraySoftware/stingray/pull/842>`__)
- Added pre-commit hooks in ``pre-commit-config.yaml`` (`847 <https://github.com/StingraySoftware/stingray/pull/847>`__)
- Improved main page of the documentation (`748 <https://github.com/StingraySoftware/stingray/pull/748>`__)

-----------------

New Features
^^^^^^^^^^^^

- Add function to calibrate event lists based on RMF file (`804 <https://github.com/StingraySoftware/stingray/pull/804>`__)
- Speed up computation of pds for large arrays (`808 <https://github.com/StingraySoftware/stingray/pull/808>`__)
- Add support for XTE science event data (`816 <https://github.com/StingraySoftware/stingray/pull/816>`__)
- A friendlier API for the non-paralyzable dead time model model (`800 <https://github.com/StingraySoftware/stingray/pull/800>`__)

Bug Fixes
^^^^^^^^^

- Fix issue when setting a property from a FITS file read (`814 <https://github.com/StingraySoftware/stingray/pull/814>`__)
- Fix case when analyze_segments has an invalid segment (`822 <https://github.com/StingraySoftware/stingray/pull/822>`__)
- Substitute np.asarray with np.asanyarray everywhere, to avoid copying memory maps into memory if possible (`824 <https://github.com/StingraySoftware/stingray/pull/824>`__)


Internal Changes
^^^^^^^^^^^^^^^^

- Dead time model fixes: more stable computations, better plotting of check_A and check_B (`800 <https://github.com/StingraySoftware/stingray/pull/800>`__)
- Bumped jinja version to 3.1.4 (`825 <https://github.com/StingraySoftware/stingray/pull/825>`__)

-----------------

New Features
^^^^^^^^^^^^
- Power colors à la Heil et al. 2015 (`780 <https://github.com/StingraySoftware/stingray/pull/780>`__)
- Calculate colors and intensities on a segment-by-segment basis in event lists (`781 <https://github.com/StingraySoftware/stingray/pull/781>`__)
- A function to randomize data in small bad time intervals (`782 <https://github.com/StingraySoftware/stingray/pull/782>`__)
- The Lomb Scargle Fourier Transform (fast and slow versions) and the corresponding :class:`LombScargleCrossspectrum` and :class:`LombScarglePowerspectrum` (`737 <https://github.com/StingraySoftware/stingray/pull/737>`__)
- A JAX implementation of the Gaussian Process tool by `Hubener et al <https://arxiv.org/abs/2205.12716>`_
for QPO detection and parameter analysis. (`739 <https://github.com/StingraySoftware/stingray/pull/739>`__)
- Extend join operation for events to arbitrary array attributes, not just pi and energy (`742 <https://github.com/StingraySoftware/stingray/pull/742>`__)
- Allow the creation of empty light curves. (`745 <https://github.com/StingraySoftware/stingray/pull/745>`__)
- Make StingrayTimeseries into a generalized light curve, with a less strict naming but implementing much of the underlying computing useful for Lightcurve as well. (`754 <https://github.com/StingraySoftware/stingray/pull/754>`__)
- Our fast implementation of histograms is now safer (failing safely to the equivalent numpy histogram functions), more consistent (ranges moved to range, for consistency with numpy), and accept complex weights as well! (`764 <https://github.com/StingraySoftware/stingray/pull/764>`__)

Bug Fixes
^^^^^^^^^

- When rms is low, the calculation in compute_rms often gave `NaN`. We now check for this situation and give 0 with an uncertainty as a result. (`736 <https://github.com/StingraySoftware/stingray/pull/736>`__)
- Eliminates deprecated call to `enable_deprecations_as_warnings`, and contextually, changes the code to be much more robust in catching harmful warnings. (`738 <https://github.com/StingraySoftware/stingray/pull/738>`__)
- Changes Crossspectrum.plot() function to plot the actual real and imaginary parts instead of their absolute values. (`747 <https://github.com/StingraySoftware/stingray/pull/747>`__)
- Make commits marked as [docs only] skip all CI but the docs build (`749 <https://github.com/StingraySoftware/stingray/pull/749>`__)
- Update tstart and tseg when using Lightcurve.truncate() (`753 <https://github.com/StingraySoftware/stingray/pull/753>`__)
- Changed list comprehension to generator expression to reduce memory usage. (`756 <https://github.com/StingraySoftware/stingray/pull/756>`__)
- Fix a bug with segment sizes not exact multiples of dt when dealing with light curves (`760 <https://github.com/StingraySoftware/stingray/pull/760>`__)
- Fix a bug when light curve segments contain complex values (`760 <https://github.com/StingraySoftware/stingray/pull/760>`__)
- Crossspectrum had "real" as default value. This meant that, for example, lags could not be calculated. Now the default value is "all", as it should be. (`762 <https://github.com/StingraySoftware/stingray/pull/762>`__)
- Fix plotting of spectra, avoiding the plot of imaginary parts of real numbers (`763 <https://github.com/StingraySoftware/stingray/pull/763>`__)
- Various bugfixes in `gti.py`, and a new function to interpret the mix of multiple GTIs. (`774 <https://github.com/StingraySoftware/stingray/pull/774>`__)
- Fixed subcs duplication by adding a check in the for loop that copies the attributes from table's meta items. (`776 <https://github.com/StingraySoftware/stingray/pull/776>`__)
- Various bug fixes in DynamicalPowerspectrum, on event loading and time rebinning (`779 <https://github.com/StingraySoftware/stingray/pull/779>`__)
- Fix issue with the Poisson noise calculation in lag spectra, that produced NaN errors under some conditions (`789 <https://github.com/StingraySoftware/stingray/pull/789>`__)
- Fix rms computation and error bars (`792 <https://github.com/StingraySoftware/stingray/pull/792>`__)
- Fix issue with ``Powerspectrum`` of a single light curve (`663 <https://github.com/StingraySoftware/stingray/pull/663>`__)
- Fix nphots estimate in accelsearch, that lead to an underestimation of the power of candidates (`807 <https://github.com/StingraySoftware/stingray/pull/807>`__)

Breaking Changes
^^^^^^^^^^^^^^^^

- Eliminate deprecated ``format_`` keyword from read and write methods. (`729 <https://github.com/StingraySoftware/stingray/pull/729>`__)
- Remove legacy interface and obsolete large data machinery. (`755 <https://github.com/StingraySoftware/stingray/pull/755>`__)
- Eliminate deprecated ``white_noise_level`` keyword from ``compute_rms``. (`792 <https://github.com/StingraySoftware/stingray/pull/792>`__)


Internal Changes
^^^^^^^^^^^^^^^^

- Speedup creation of events in ``EventList.from_lc`` (`757 <https://github.com/StingraySoftware/stingray/pull/757>`__)
- Separate slow tests from quick ones (`758 <https://github.com/StingraySoftware/stingray/pull/758>`__)
- Use Readthedocs for documentation building (`769 <https://github.com/StingraySoftware/stingray/pull/769>`__)
- More informative GTI messages (`787 <https://github.com/StingraySoftware/stingray/pull/787>`__)
- Eliminated the usage of astropy logging (`799 <https://github.com/StingraySoftware/stingray/pull/799>`__)

-------------------

New Features
^^^^^^^^^^^^

- Phase Dispersion Minimization as a method to search for periodic signals
in data is now implemented in the ``stingray.pulse`` submodule. To use it,
you can use the ``phase_dispersion_search`` function in
``stingray.pulse.search``. The accompanying statistical tests are located
in the ``stingray.stats`` module, under ``phase_dispersion_probability``,
``phase_dispersion_logprobability`` and ``phase_dispersion_detection_level``. (`716 <https://github.com/StingraySoftware/stingray/pull/716>`__)
- Add is_sorted function, to test if an array is sorted. (`723 <https://github.com/StingraySoftware/stingray/pull/723>`__)
- Check if invalid data are inside GTIs, and warn or raise exception accordingly (`730 <https://github.com/StingraySoftware/stingray/pull/730>`__)


Bug Fixes
^^^^^^^^^

- The method apply_gtis of the class Lightcurve is applied to all the attributes of the class Lightcurve.
This works for both inplace=True and inplace=False (`712 <https://github.com/StingraySoftware/stingray/pull/712>`__)
- Avoid allocation of an unneeded square matrix to improve memory management in ``_als`` (fix Issue 724) (`725 <https://github.com/StingraySoftware/stingray/pull/725>`__)
- Fix Issue 726 -- Loading events without fmt keyword crashes (`727 <https://github.com/StingraySoftware/stingray/pull/727>`__)


Documentation
^^^^^^^^^^^^^

- Reordered information about contributions with new ``black`` and ``towncrier`` procedures (`721 <https://github.com/StingraySoftware/stingray/pull/721>`__)


Internal Changes
^^^^^^^^^^^^^^^^

- Using `towncrier <https://github.com/hawkowl/towncrier>`__ to generate the changelogs. (`#697 <https://github.com/StingraySoftware/stingray/pull/697>`__)
- Added stingray's logo in the documentation's favicon and top bar. (`707 <https://github.com/StingraySoftware/stingray/pull/707>`__)
- Improved contributing workflow by appending ``black`` codestyle configuration to ``pyproject.toml`` and ignoring PEP-8 non-compliant ``E203``, ``W503`` in ``flake8``. (`715 <https://github.com/StingraySoftware/stingray/pull/715>`__)
- Added a scrollbar to sidebarwrapper (`718 <https://github.com/StingraySoftware/stingray/pull/718>`__)
- Simplify numba mocking code, and possibly improve code coverage estimate (`731 <https://github.com/StingraySoftware/stingray/pull/731>`__)