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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[v0.1.45] - 2023-12-05

v0.1.44 - 2023-12-05

Fixed

  1. Fixed Cython code compatibility with Python 3.11. See cython/issues/5894 and cpython/issues/112768

v0.1.43 - 2023-10-12

Fixed

  1. Fixed problem with conversion of a pre-centroided list of peaks with repeated m/z values near the end of the mass range, or where the peak list is a single peak long.

v0.1.42 - 2023-08-04

Fixed

  1. Fixed Cython 3 compatibility. There is now the potential for errors that were previously undetected to error out with a traceback.

Changed

  1. The plot module will more aggressively use scientific notation offsets to simplify y tick labels.

v0.1.41 - 2023-07-14

Fixed

  1. Fixed a non-determinism problem during sorting of the m/z and intensity arrays prior to picking peaks.

v0.1.40 - 2022-10-09

Changed

  1. The required NumPy version for Python 3.10+ is now 1.23.2

v0.1.38 - 2022-03-24

Added

Changed

Deprecated

Removed

Fixed

  • Properly skip adjacent m/z points at equal intensity to the most recently fit peak.

Security

v0.1.37 - 2022-03-21

Added

Changed

Deprecated

Removed

Fixed

  • PeakSet.between properly behaves for query m/z values beyond either end of the PeakSet's m/z range

Security

v0.1.36 - 2022-03-21

Added

  • Added fast path for skipping search for m/z index coordinates when picking peaks.
  • Added method to get_occupied_intervals for GridAverager to get coordinates on the m/z axis.

Changed

Deprecated

Removed

Fixed

  • PeakSet.all_peaks_for properly behaves for query m/z values beyond either end of the PeakSet's m/z range

Security

v0.1.35 - 2022-02-15

Added

Changed

  • Registered Python versions supported changed to Py37-39

Deprecated

Removed

Fixed

Security

v0.1.34 - 2022-02-14

Added

  1. Added the peak_statistics.zero_pad function to fill sparse arrays with delimiting zero values, and a scan_filter.ZeroFiller (label: zero_fill) filter.
  2. Added ms_peak_picker.scan_averaging.GridAverager which makes averaging a fixed set of spectra more efficient

Changed

  1. ms_peak_picker.pick_peaks no longer returns None when the input arrays are empty, instead returning an empty PeakIndex.
  2. The linear_resampling filter now uses a 0.005 m/z spacing.
  3. ms_peak_picker.pick_peaks will now enforce signal_to_noise_threshold when the input data is already centroided but the definition of "signal to noise" ratio differs from profile mode spectra.
  4. average_signal now accepts a parameter num_threads to control the number of threads launched with OpenMP. Odd numbers work best.

Deprecated

Removed

Fixed

  1. ms_peak_picker.reprofile now does not segfault when the peak list(s) are empty.
  2. Fixed segfault when ms_peak_picker._c.peak_statistics.curve_reg_dv encounters a singular matrix

Security

Released