changelog.rst

Changelog

Changes in v2.3.0

• All functions, classes and methods now have 484 type hints. Contributed by Chris Davis-Foster in 4
• All modules now implement __all__ to limit the objects imported when using * imports.

• Removed the following deprecated functions:

  Removed object	Suggested replacement
  pyms.Experiment.Experiment.get_expr_code	pyms.Experiment.Experiment.expr_code
  pyms.Experiment.Experiment.get_peak_list	pyms.Experiment.Experiment.peak_list
  pyms.Experiment.Experiment.store	pyms.Experiment.Experiment.dump
  pyms.Experiment.store_expr	pyms.Experiment.Experiment.dump
  pyms.GCMS.Class.GCMS_data.get_scan_list	pyms.GCMS.Class.GCMS_data.scan_list
  pyms.GCMS.Class.GCMS_data.get_tic	pyms.GCMS.Class.GCMS_data.tic
  pyms.Gapfill.Class.MissingPeak.get_common_ion	pyms.Gapfill.Class.MissingPeak.common_ion
  pyms.Gapfill.Class.MissingPeak.get_common_ion_area	pyms.Gapfill.Class.MissingPeak.common_ion_area
  pyms.Gapfill.Class.MissingPeak.get_exact_rt	pyms.Gapfill.Class.MissingPeak.exact_rt
  pyms.Gapfill.Class.MissingPeak.get_qual_ion1	pyms.Gapfill.Class.MissingPeak.qual_ion1
  pyms.Gapfill.Class.MissingPeak.get_qual_ion2	pyms.Gapfill.Class.MissingPeak.qual_ion2
  pyms.Gapfill.Class.MissingPeak.get_rt	pyms.Gapfill.Class.MissingPeak.rt
  pyms.Gapfill.Class.MissingPeak.set_common_ion_area	pyms.Gapfill.Class.MissingPeak.common_ion_area
  pyms.Gapfill.Class.MissingPeak.set_exact_rt	pyms.Gapfill.Class.MissingPeak.exact_rt
  pyms.Gapfill.Class.Sample.get_missing_peaks	pyms.Gapfill.Class.Sample.missing_peaks
  pyms.Gapfill.Class.Sample.get_mp_rt_area_dict	pyms.Gapfill.Class.Sample.rt_areas
  pyms.Gapfill.Class.Sample.get_name	pyms.Gapfill.Class.Sample.name
  pyms.Gapfill.Function.transposed
  pyms.IonChromatogram.IonChromatogram.get_mass	pyms.IonChromatogram.IonChromatogram.mass
  pyms.IonChromatogram.IonChromatogram.get_time_step	pyms.IonChromatogram.IonChromatogram.time_step
  pyms.IonChromatogram.IonChromatogram.set_intensity_array	pyms.IonChromatogram.IonChromatogram.intensity_array
  pyms.Mixins.MaxMinMassMixin.get_max_mass	pyms.Mixins.MaxMinMassMixin.max_mass
  pyms.Mixins.MaxMinMassMixin.get_min_mass	pyms.Mixins.MaxMinMassMixin.min_mass
  pyms.Mixins.MassListMixin.get_mass_list	pyms.Mixins.MassListMixin.mass_list
  pyms.Mixins.TimeListMixin.get_time_list	pyms.Mixins.TimeListMixin.time_list
  pyms.Mixins.IntensityArrayMixin.get_intensity_array	pyms.Mixins.IntensityArrayMixin.intensity_array
  pyms.Mixins.IntensityArrayMixin.get_matrix_list	pyms.Mixins.IntensityArrayMixin.intensity_array_list
  pyms.Peak.Class.Peak.get_area	pyms.Peak.Class.Peak.area
  pyms.Peak.Class.Peak.get_ic_mass	pyms.Peak.Class.ICPeak.ic_mass
  pyms.Peak.Class.Peak.get_ion_areas	pyms.Peak.Class.Peak.ion_areas
  pyms.Peak.Class.Peak.get_mass_spectrum	pyms.Peak.Class.Peak.mass_spectrum
  pyms.Peak.Class.Peak.get_pt_bounds	pyms.Peak.Class.Peak.bounds
  pyms.Peak.Class.Peak.get_rt	pyms.Peak.Class.Peak.rt
  pyms.Peak.Class.Peak.get_UID	pyms.Peak.Class.Peak.UID
  pyms.Peak.Class.Peak.set_area	pyms.Peak.Class.Peak.area
  pyms.Peak.Class.Peak.set_ic_mass	pyms.Peak.Class.ICPeak.ic_mass
  pyms.Peak.Class.Peak.set_ion_areas	pyms.Peak.Class.Peak.ion_areas
  pyms.Peak.Class.Peak.set_mass_spectrum	pyms.Peak.Class.Peak.mass_spectrum
  pyms.Peak.Class.Peak.set_pt_bounds	pyms.Peak.Class.Peak.pt_bounds
  pyms.Utils.Utils.is_positive_int
  pyms.Utils.Utils.is_list_of_dec_nums

• Renamed pyms.Gapfill.Function.file2matrix to pyms.Gapfill.Function.file2dataframe. The function now returns a Pandas DataFrame.
• Split pyms.IntensityMatrix.IntensityMatrix into two classes: pyms.IntensityMatrix.BaseIntensityMatrix and pyms.IntensityMatrix.IntensityMatrix. This makes subclassing easier.
• Split pyms.Peak.Class.Peak into three classes: pyms.Peak.Class.AbstractPeak, pyms.Peak.Class.Peak, pyms.Peak.Class.ICPeak. ~pyms.Peak.Class.ICPeak is returned when a mass is passed to the ~pyms.Peak.Class.Peak constructor instead of a mass spectrum.

• Added the following functions and classes:

  pyms.Gapfill.Function.MissingPeakFiletype pyms.IntensityMatrix.AsciiFiletypes pyms.IntensityMatrix.IntensityMatrix.bpc pyms.IonChromatogram.IonChromatogram.is_eic pyms.IonChromatogram.IonChromatogram.is_bpc pyms.IonChromatogram.ExtractedIonChromatogram pyms.IonChromatogram.BasePeakChromatogram pyms.Spectrum.array_as_numeric pyms.Utils.Utils.is_path pyms.Utils.Utils.is_sequence pyms.Utils.Utils.is_sequence_of pyms.Utils.Utils.is_number pyms.eic

• The ia parameter of pyms.IonChromatogram.IonChromatogram was renamed to intensity_list`.

Changes in v2.2.22-beta2

• pyms.Spectrum.Scan and pyms.Spectrum.MassSpectrum can now accept any values for mass and intensity that that can be converted to a float or int. This includes strings representing numbers. Previously only int and float values were permitted.

• If the mass and intensity values supplied to a pyms.Spectrum.Scan or a pyms.Spectrum.MassSpectrum are float, int, or a data type derived from numpy.number, the data is stored in that type. For other data types, such as strings, decimal.Decimal etc., the data is stored as float.

  If the data contains values in mixed types then, in most cases, all values will be converted to float. If you wish to control this behaviour you should construct a numpy.ndarray with the desired type. See https://numpy.org/devdocs/user/basics.types.html for a list of types.

• A TypeError is no longer raised when creating a pyms.Spectrum.Scan or a pyms.Spectrum.MassSpectrum with a float, int etc. rather than a sequence. Instead, value is treated as being the sole element in a list.
• Passing a non-numeric string or a list of non-numeric strings to pyms.Spectrum.Scan or pyms.Spectrum.MassSpectrum now raises a ValueError and not a TypeError as in previous versions.
• pyms.Peak.Class.Peak.ion_areas now accepts dictionary keys as float as well as int.

Changes in v2.2.22-beta1

• ~pyms.GCMS.IO.ANDI.ANDI_reader and pyms.Spectrum.Scan were modified to allow ANDI-MS files to be read if the data either:

  • had the m/z data stored from highest m/z to lowest; or
  • contained 0-length scans.