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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.

v0.0.55 - 2024-07-01

Changed

  1. Support NumPy 2.0

v0.0.54 - 2024-05-23

Added

  1. Added SimpleInterval to the pure Python implementation. This should allow the base library to work when the C extensions are not installed.

Fixed

  1. Guarded qsize invocations on platforms that don't support it.
  2. Error message logging in ms-deisotope were invoking using incorrect syntax.

v0.0.53 - 2023-10-01

Changed

  1. Return to requiring a minimum pyteomics version, starting at 4.6.2 now to avoid the pandas dependency from 4.6.1
  2. Allow overriding the read_schema parameter for MzMLLoader objects, to be used when handling mzML files which have invalid XSD URIs. This defaults to using a pre- compiled schema in pyteomics.

v0.0.52 - 2023-09-04

Changed

  1. Pinned pyteomics to 4.6.0 pending pandas dependency change

v0.0.51 - 2023-08-28

Fixed

  1. Multiprocessing logging uses the logger system better
  2. More corrected type annotations

v0.0.50 - 2023-07-20

Fixed

  1. UnitInt extension converted to pure Python type to cooperate with Cython 3.

v0.0.49 - 2023-06-14

Changed

  1. The default compressor for MzMLbSerializer has been changed to default to the default compressor from psims (currently blosc).

v0.0.48 - 2023-05-22

Added

  1. More type annotations and documentation.

Fixed

  1. Avoid excessive hysterical reloading of spectra from mzML files when trying to find precursor scan IDs.
  2. Fix an outdated placeholder filter in PeakDependencyNetwork that caused the first peak in any spectrum to be ignored.

v0.0.47 - 2023-05-08

Added

  1. More type annotations

Changed

  1. Arrays used to reconstruct deconvoluted peak sets are not guaranteed to be copied.

Removed

Fixed

  1. WrappedScan objects now properly propagate overridden attributes when copied.
  2. More docstring formatting was fixed and missing arguments were described

Security

v0.0.46 - 2023-01-22

Added

  1. Documentation for the ms_deisotope.peak_set module.
  2. Added FunctionScorer to ms_deisotope.scoring to allow user-defined scoring functions to be used without sub-classing. This incurs some extra overhead on every call, so performance may be worse than a built-in sub-class.

Changed

  1. ms_deisotope.deconvolution.prepare_peaklist now coerces a tuple of parallel sequences or numpy arrays of m/z and intensities properly, so the caller does not need to zip them into a list of (mz, intensity) pairs.

Fixed

  1. ms_deisotope.deconvolute_peaks was incorrectly calling ms_deisotope.deconvolution.prepare_peaklist too late, so no useful coercion was done for the user. prepare_peaklist is now correctly called before passing the provided peak list to the deconvolution machinery, removing the need for users to call it explicitly.

v0.0.45 - 2023-01-14

Added

  • More type annotations for ProcessedScan-yielding readers.
  • C accelerators for pyteomics's unit-scalars and CV-params to speed up parsing and reduce memory usage.
  • Created a low level C API for stripped-down peak lists that does not use the GIL, limited use-cases currently.
  • Loads of type annotations.
  • Added a -X option to pass raw key-value pairs to the mzML converter in ms-index mzml to make experimental configuration easier.

v0.0.44 - 2022-10-09

Added

Changed

  1. The minimum NumPy version on Python 3.10 was increased to 1.23.2

Deprecated

Removed

Fixed

  1. Fix software ID in mzML writing.

Security

v0.0.43 - 2022-09-29

Added

  1. Add support for os.PathLike objects to ms_deisotope.MSFileLoader.

Changed

  1. mzML and mzXML now properly capture the relationship between instrument configuration and software.

Deprecated

Removed

Fixed

  1. Fixed division in _binsearch used for precursor-clustering.

Security

v0.0.42 - 22-06-15

Added

  1. Added close parameter to MzMLSerializer and MzMLbSerializer to reflect the change made upstream in psims. These govern the automatic closing behavior of the buffer after completing the data document. If you need the buffer to remain open after completing file writing, pass close=False to the writer.

Changed

Deprecated

Removed

Fixed

Security

v0.0.40 - 22-06-14

Added

  • Make CVPrimitiveWrapperMeta hashable.

Changed

  • Updated automatic release workflow
  • Allow ProcessingMethod to repeat terms

Deprecated

Removed

Fixed

Security

v0.0.39 - 22-05-29

Added

Changed

  • When using ms_deisotope.test.common.datafile, if the file isn't found in the package data directory, it will be downloaded from GitHub. Downloaded files will be stored in the test_data/ directory under the path returned by ms_deisotope.config.get_config_dir.
  • Use internal C extensions to speed up unit primitives.
  • When isal is installed, use isal.isal_zlib in place of the stock zlib.

Deprecated

Removed

Fixed

Security

v0.0.38 - 22-04-28

Added

  • Added IonMobilityAware3DMzMLbSerializer to ms_deisotope.output.mzmlb.
  • Added IBT10 reporter ions to TMTReporterExtractor
  • Added extract-reporter-ions to ms-index to extract reporter ions to CSV.

Changed

  • Raised minimum ms_peak_picker version to v0.1.38
  • Changed the default dx of Scan.average and Scan.average_with from 0.01 to 0.002 to reduce distortion when centroiding averaged spectra.
  • Change logging to be consistent across modules.

Deprecated

Removed

  • Removed deprecated ScanProcessor.get_precursor_peak_for_product_scans

Fixed

Security

v0.0.36 - 2022-01-15

Added

  1. Added get_writer to ms_deisotope.output which will guess which writer (and compression) to use from a file path or name of a file-like object.
  2. Added an option to skip envelope decoding during deserialize_deconvoluted_peak_set as a theoretical optimization.

Changed

Deprecated

Removed

Fixed

  1. Restore unpickling of ThermoRawLoaders

Security

v0.0.35 - 2021-12-29

Added

  1. Added toggle_peak_loading to PeakSetDeserializingMixin to toggle loading and parsing of deconvoluted peak sets.
  2. Refactored MSFileLoader into a callable class, ms_deisotope.data_source.infer_type.FormatGuesser. There is now a ms_deisotope.output.ProcessedMSFileLoader callable that can be used to determine the correct opener for processed mzML, MGF, and mzMLb files.

Changed

Deprecated

Removed

Fixed

  1. Added a missing parameter use_index to ProcessedMGFLoader that made positional argument passing fail when unpickling instances of this subclass.
  2. Repaired peak_collection fused functions to optimize DeconvolutedPeakSetIndexed too.
  3. Fixed TheoreticalIsotopicPattern.total using an uninitialized accumulator.

Security

v0.0.33 - 2021-12-05

Added

  1. Added an example script for splitting a FAIMS file into separate mzML files.
  2. Added an example script for ion mobility and charge state deconvolving Waters HDMSe data.
  3. Added Waters MassLynx SDK bindings for reading Waters .RAW folders directly on Windows when the SDK C library is present.
  4. Added a new command ms-index maintenance register-waters-masslynx to register the location of the Waters MassLynx SDK if it is not installed in the expected location.
  5. Improved documentation of mzMLb reading and writing.

Changed

Deprecated

Removed

Fixed

Security

v0.0.32

Added

Changed

  1. Added an extra ms_level index to Thermo readers.
  2. PROXI server now uses appropriate JSON types in its USI response.
  3. ProcessedMGFLoader's iterator behavior will bind generated ProcessedScan objects, keeping parity with ProcessedMzMLLoader.
  4. The mzml, mzmlb and mgf commands for ms-index can now handle reading mzML files from STDIN.

Deprecated

Removed

Fixed

Security

v0.0.31

Added

Changed

Deprecated

Removed

Fixed

  1. PeakSetMethods facet __call__ properly detects peak modes.

Security

v0.0.30 - 2021-9-2

Added

  1. Added ms_deisotope.clustering.alignment to provide a home for SpectrumAlignment and SpectrumAlignmentGraph.

Changed

Deprecated

Removed

Fixed

  1. MzMLSerializer correctly interprets centroid-only but not peak-picked Scan objects.
  2. Using _InterleavedGroupedScanIteratorImpl on Py2 no longer uses a deque as it is missing insert.
  3. LCMSFeatureSetFit now has n_points in the pure Python version.
  4. SpectrumAlignment now works properly.
  5. Fix error in MzMLSerializer when trying to serialize a spectrum that has been peak-picked but where the peak set was empty.

Security

v0.0.29 - 2021-7-8

Fixed

  1. Fix specifying the precursor m/z, charge and polarity of a spectrum from CSV or via data_source.memory.make_scan.

v0.0.28 - 2021-7-7

Added

  1. Added string parsing and formatting to IDFormat for those terms which define a nativeID format.
  2. Added an id_format property to FileInformation and ScanFileMetadataBase which retrieves the nativeID format or formats for a given file.

Changed

  1. The default behavior of _InterleavedGroupedScanIteratorImpl, the implementation of grouped iterators, when producing a new ScanBunch that any product scans whose precursor ID that has been in the product map for more than self.ms1_buffering productions will be added to the produced ScanBunch to prevent loss of information if iteration is interrupted.
  2. quick_index.index now tries much harder to start from an MS1 scan if it can.

Deprecated

Removed

Fixed

Security

v0.0.27 - 2021-6-21

Added

  1. Added TMT11 to ms_deisotope.qc.signature.
  2. Added ms_deisotope.output.mzml.IonMobilityAware3DMzMLSerializer to write processed 3D IMS-MS spectra from mobility frames with feature maps.
  3. Added ms_deisotope.output.mzml.ProcessedGeneric3DIonMobilityFrameSource to read processed feature maps out from 3D IMS-MS spectra.
  4. Made Generic3DIonMobilityFrameSource wrapper iterable and more sequence-like.
  5. Added ms-index ms1-spectrum-diagnostics to the CLI to collect relatively low level MS1 spectrum metadata.

Changed

  1. Made LCMSFeatureProcessor consider fewer combinations of feature sets, lowering the upper bound on the combinations. Such cases that required this should be quite rare.
  2. IonMobilityFrame is closer to being a first-class object instead of an immutable data wrapper.

Deprecated

Removed

Fixed

  1. Iterating over MS3-containing datasets in grouped mode will now properly group MS3 spectra with their MS2 spectra. Applies for higher exponentiated MSn as well.
  2. TheoreticalIsotopicPattern.incremental_truncation consistently respects its truncation threshold.

Security

v0.0.26 - 2021-5-30

Added

  1. Add ion_mobility_type property to ScanBase to allow checking ion mobility type on the scan object itself.
  2. Add a prototype FAIMSFilter and FAIMSDemultiplexingIterator to data_source.query.
  3. Add a new examples set to the repository showing other ways to use the library's features.

Changed

  1. Ensure that any lingering MSn scans are flushed with the final MS1 scan when an interleaved scan iteration strategy is wrapping up.
  2. Made LCMSFeatureProcessor substantially faster and more memory efficient during dependence graph solving by introducing a Cython implementation. The solver is still vulnerable to high density noise clusters slowing it down, but will no longer completely OOM when these are wide enough.

Deprecated

Removed

Fixed

Security

v0.0.25 - 2021-5-02

Added

  1. Added has_array method to RawDataArrays and RawDataArrays3D to semantically query whether an array collection has an array of a particular type (like a flavor of ion mobility) without iteratively probing.
  2. Added ms_deisotope.data_source.scan.mobility_frame.Generic3DIonMobilityFrameSource which can serve a ion mobility-aware data structure when there is a profile-mode m/z, intensity and ion mobility array in a single spectrum like the one produced by MSConvert's combine-ion-mobility-spectra option.

Changed

  1. Scan.plot will automatically call pick_peaks if not self.is_profile and self.peak_set is None to avoid unexpectedly ending up without a plot in this common scenario.

Deprecated

Removed

Fixed

  1. Fixed Docker container build process to use latest released versions of libraries.

Security

v0.0.24 - 2021-4-10

Added

Changed

Deprecated

Removed

Fixed

  1. Made feature_fit.map_coord helper structure properly comparable.

Security

[v0.0.23rc] - 2021-4-9

Added

Changed

  1. Re-aliased Processed*Deserializer to Processed*Loader where * is MzML, MGF, or MzMLb.

Deprecated

Removed

Fixed

  1. The Waters SDK no longer uses absolute local imports.
  2. The Waters driver registration code no longer introduces None into the list of paths and breaks on Py3.

Security

v0.0.22 - 2021-4-4

Added

  1. ms_deisotope.data_source now exports scan_from_csv and make_scan helper methods.
  2. ms_deisotope.data_source.mzmlb.MzMLbLoader is now available for reading mzMLb HDF5 files when pyteomics.mzmlb is available.
  3. ms_deisotope.output.MzMLbSerializer is now available for writing mzMLb HDF5 files when psims.mzmlb is available. This is further exposed through ms-index mzmlb for CLI conversion. Expect this feature to undergo further evolution as the extended indices used for other features may also be stored in mzMLb as extra datasets.

Changed

  1. Scan objects explicitly are not hashable.
  2. Changed the delimiter argument of ms_deisotope.data_source.text.scan_from_csv to be a regular expression to handle arbitrary whitespace delimiters, and added an optional skiprow argument to allow you to skip headers in the all-too-common text spectrum exports that spectrum viewers provide.
  3. Removed the resampling API from RunningWeightedAverage, improving memory efficiency.

Deprecated

Removed

Fixed

  1. Made random-access gzip compressor interface idzip compatible with Py3 buffered IO streams.
  2. Added an additional flag -D to indicate to ms-index metadata-index that the input file is an a deisotoped and charge state deconvolved mzML to extract additional fields.
  3. Fixed an interface error in ms_deisotope._c.feature_map.processor.

Security

v0.0.21

Added

Changed

  1. All grouped scan iterators now use an interleaved iteration strategy to handle interleaving of MS1 scans that are not the precursor of a subsequent series of MSn scans. When using start_from_scan, product scans which follow the first MS1 but not actually produced from that first MS1 scan will be included in the product scan list for that ScanBunch.
  2. guess_type now includes the input object in the error message when it fails to locate a loader type to reduce the amount of blind guessing at the problem.

Deprecated

Removed

Fixed

  1. Retrieving the precursor scan is now safer with thermo_raw_net.ThermoRawLoader
  2. ms-index spectrum-clustering now remembers source files when scans are loaded in memory
  3. Use a more thorough precursor scan determination algorithm for ThermoRawLoader implementations
  4. Fixed ms-deisotope's sequential scan numbering when there is scan interleaving

Security

v0.0.19 - 2020-11-24

Added

Changed

  1. Make peak_set.merge able to merge more than 2 DeconvolutedPeakSet instances

Deprecated

Removed

Fixed

  1. Always infer the precursor scan relationship in ThermoRaw readers using the "Master Scan Number" header

Security

v0.0.18 - 2020-10-09

Added

  1. Added CHANGELOG.md
  2. Added the option for ProcessedMzMLLoader to detect and handle deconvoluted peak lists from other tools and to load them without crashing while looking for ms_deisotope-specific extra data. This behavior can be customized by overriding the deserialize_external_deconvoluted_peak_set method in a derived class.
  3. Added a time attribute to RandomAccessScanSource-based readers which lets you use index and slice notation with time values (floats) using the standard minute unit common across ms_deisotope.
  4. Made ms_deisotope.data_source.mgf.MGFLoader, ms_deisotope.peak_set.decharge, and ms_deisotope.processor.process part of the top-level module's API.
  5. Added RawDataArray.size property to report the length of the m/z and intensity array.
  6. Added default_precursor_ion_selection_window (-D) to the ms-deisotope command line tool.
  7. Add drift time aware variant of DeconvolutedPeak, IonMobilityDeconvolutedPeak which has a drift_time attribute.
  8. Added more documentation on the truncate_after parameter for deconvolution.

Changed

  1. The _reindex method of DeconvolutedPeakSet has been renamed reindex to reflect that it should be part of the type's public API since user code may need to call it if they apply some new transformation to the list of peaks.
  2. The composition_list argument to HybridAveragineCompositionListPeakDependenceGraphDeconvoluter is now optional.
  3. The incremental_truncation option for deconvolute_peaks and ExhaustivePeakSearchDeconvoluterBase-based strategies now apply truncation to all fits, not just those passing the initial full-width fit. This required more invasive changes to the implementations of AveragineDeconvoluterBase and MultiAveragineDeconvoluterBase but is now more consistent with the original intent behind incremental_truncation.
  4. Scan.clear now takes a full parameter which will discard the peak_set, deconvoluted_peak_set, and product_scans attributes' data. This more aggressively frees memory.
  5. Scan.average and Scan.average_with now skip scans with empty signal arrays.
  6. The ScanProcessor.deconvolute_precursor_scan method now explicitly requests product_scans be passed as an argument. It also extracts co-isolating precursor ions from the isolation window even if a deconvoluted peak is not found for the precursor ion.
  7. MzMLSerializer now propagates all PrecursorInformation.annotations as parameters.
  8. ScanProcessor now reports coisolation even when the precursor peak is not found (though it still omits it if an unacceptable solution is reported).

Fixed

  1. When using the CompositionList-based deconvoluters with a mass shift, the theoretical isotopic pattern will now have the correct monoisotopic m/z.
  2. IntervalTreeNode.overlaps is now consistent with SpanningMixin.overlaps.
  3. ms-deisotope CLI now properly handles the case when the MSn average option -an is not passed.
  4. ms-deisotope CLI now properly builds the extended scan index when processing a file with only MSn spectra