CHANGELOG.md

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.

0.35.0 - 2024-11-01

Added

• Add ParamBuilder to make building Param easier
• Add unit_mut to ByteArrayViewMut
• Add error handling logic to nativeID format parsing logic
• Add MZReaderBuilder type to the public API
• Add more metadata types to the public API
• Add spectrum_reference to ScanEvent
• Add source-manipulation functions to Generic3DIonMobilityFrameSource
• Added method to retrieve the raw spectrum from any USI (#15)
  • Added USI::download_spectrum_blocking and USI::download_spectrum_async to retrieve the designated spectrum from a PROXI server

Changed

• Change the hashing function for mzdata::spectrum::Collator to IdentityHasher

Fixed

• Fix multiple errors in BinaryArrayMap3D

0.35.0 - 2024-11-01

Added

• Add ParamBuilder to make building Param easier
• Add unit_mut to ByteArrayViewMut
• Add error handling logic to nativeID format parsing logic
• Add MZReaderBuilder type to the public API
• Add more metadata types to the public API
• Add spectrum_reference to ScanEvent
• Add source-manipulation functions to Generic3DIonMobilityFrameSource
• Added method to retrieve the raw spectrum from any USI (#15)
  • Added USI::download_spectrum_blocking and USI::download_spectrum_async to retrieve the designated spectrum from a PROXI server

Changed

• Change the hashing function for mzdata::spectrum::Collator to IdentityHasher

Fixed

• Fix multiple errors in BinaryArrayMap3D

0.34.0 - 2024-10-31

Fixed

• Fix parsing precursor charge in MGF files (#13)

• fix parsing precursor charge in MGF files

  This fixes two issues:

  • the charge value in the PEPMASS header can have the same suffixed format as the CHARGE header
  • the order of the headers isn't determined, so the charge value should still be saved correctly if the CHARGE header is before the PEPMASS header

0.33.0 - 2024-10-17

Fixed

• Fixed crash while mgf parsing (#12)

• Fixed rare crash while mgf parsing
• Fixed silent error that returns an unfinished spectrum
• Handle charge when the sign is at the tail

0.32.0 - 2024-10-14

Added

• Add some Thermo scan trailer values to ThermoRawReaderType
• Add NativeSpectrumIdentifierFormatTerm::format

Changed

• Upgraded mzpeaks and mzsignal dependencies

0.31.0 - 2024-10-03

Changed

• Upgrade to thermorawfilereader v0.3.0

Fixed

• Test on thermo feature instead of dependency (#10)
• Fix mass_charge_ratio order of operations error

0.30.0 - 2024-09-23

Added

• Add MZReaderBuilder to make configuring MZReaders easier
• Add CV-derived dissociation methods and energies, update vendored PSI-MS CV
• Add more descriptive failure messages when parsing MGF files
• Add more descriptive errors and failure messages when encountering errors while parsing mzML files

Fixed

• Publicly re-export mzpeaks dependency to guarantee mz_read works (#9) Prevent downstream users needing to declare a dependency on mzpeaks when using mz_read macro. This also prevents potential version mismatches.

0.29.0 - 2024-09-07

Added

• Add PROXI format parser/serializer in mzdata:io:proxi, no network request feature.

Changed

• Upgrade thermorawfilereader to v0.2.9, theoretically making an absent .NET framework to be non-fatal
• Upgrade mzsignal and enable new AVX feature

Fixed

• Change average_spectra to take an iterator over SpectrumLike (#6)

• Allowed average from an iterator and added more documentation

---

0.28.1 - 2024-09-01

Fixed

• Revert mzsignal change to fix downstream crashes while averaging

0.28.0 - 2024-08-30

Added

• Add PeakDataIterDispatch to the public API
• Add more descriptive documentation for meta-metadata types.

Changed

• Upgraded mzpeaks v0.20.0, mzsignal v0.21.0, thermorawfilereader v0.2.7

0.27.0 - 2024-08-25

Added

• Add dispatching implementation to PeakDataIter and RefPeakDataIter
• Add basic USI parsing

Fixed

• Do not panic when requested MGF ID not in the index (#5)
• Port #5 to all other reader types

0.26.0 - 2024-08-10

Added

• Added Unit::VoltSecondPerSquareCentimeter
• Added BinaryArrayMap3D::ion_mobility_unit
• Add get and iter methods for PeakDataLevel and RefPeakDataLevel
• Add tutorial for spectrum types
• Add Sample to the MSDataFileMetadata
• Add basic usi parsing.

Changed

• Change MzMLWriterType methods to be generic to peaks. All the writing methods are generic over peak types so long as they satisfy the BuildArrayMapFrom constraint. The type still needs type parameters for default behavior. This may cause parameter inference issues for RawSpectrum in which case use SpectrumWriter::write.

Documentation

• More docs

Fixed

• Fix mzpeaks API breakage

0.25.0 - 2024-07-26

Added

• Add NativeSpectrumIdentifierFormatTerm and MassSpectrometerFileFormatTerm enums for CV subsets
  • NativeSpectrumIdentifierFormatTerm corresponds to "native spectrum identifier format" and includes a regular expression from the controlled vocabulary for parsing ids.
  • MassSpectrometerFileFormatTerm corresponds to "mass spectrometer file format". No extra behavior.
• Add IonMobilityFrameGroup plus associated iterators and traits.
• Add BuildArrayMap3DFrom and BuildFromArrayMap3D traits
• Add IonMobilityFrameWriter trait
• Add read_checksum to MzMLReaderType
• Add BuildArrayMap3DFrom and BuildFromArrayMap3D to the public API
• Add IonMobilityFrameWriter implementation for mzML and mzMLb
  • FeatureDataLevel and RefFeatureDataLevel to mirror the peak set equivalents for IonMobilityFrameLike
  • Implement From<MultiLayerIonMobilityFrame> for RawSpectrum to let IonMobilityFrameWriter re-use most of SpectrumWriter.

Changed

• Change RawSpectrum to be SpectrumLike over all peak types.
• Upgrade controlled vocabulary
• Rename methods of IonMobilityFrameWriter to not clash with SpectrumWriter

Fixed

• Fixed error in setting highest observed m/z in SpectrumLike::update_summaries

0.24.0 - 2024-07-18

Changed

• Upgrade mzsignal to v0.18.0

0.23.0 - 2024-07-17

Changed

• Upgraded serde, rayon

Fixed

• Don't write duplicate CV params about MS level
• Write the correct size of the chromatogram list in mzML
• Fix up type names in the spectrum documentation

0.22.0 - 2024-07-16

Added

• Add owning variants for write_all SpectrumWriter
• Add ChromatogramSource trait for producing Chromatograms
• Add name and unit to ByteArrayView

Changed

• Change OffsetIndex key to Box<str> This reduces memory consumption.
• Upgraded mzsignal minimum version

Fixed

• Fix error in search-by-time methods

0.21.0 - 2024-07-01

Added

• Add Dimensionless to Unit for arrays without units
• Add ion mobility stacked spectra support, initial build out of trait system.
• Add Boolean variant to ParamValue types

Fixed

• Fixed #3 empty spectrum from trailing newlines in MGF

0.20.0 - 2024-05-30

Fixed

• Handle unknown mass analyzers slightly more gracefully.
• Actually use the fast path when pre-encoding arrays

0.19.0 - 2024-05-26

Added

• Add more convenience methods for populating InstrumentConfiguration and ParamDescribed types
• Support writing to STDOUT properly in mzconvert example

Fixed

• Fixed the creation of InstrumentConfiguration from Thermo RAW files

0.18.0 - 2024-05-25

Changed

• Upgraded mzpeaks minimum version to 0.12.0, mzsignal minimum version to 0.13.0
• Change how spectrum summary descriptions are calculated
  • Do not pre-emptively re-calculate summaries when writing to avoid decoding overhead.
  • Added update_summaries to SpectrumLike and fetch_summaries to RefPeakDataLevel to do this work.
• Upgrade mzsignal minimum version to 0.14.0

Fixed

• Fix changelog

0.17.0 - 2024-05-18

Changed

• Upgraded mzpeaks minimum version to 0.12.0, mzsignal minimum version to 0.13.0
• Change how spectrum summary descriptions are calculated
  • Do not pre-emptively re-calculate summaries when writing to avoid decoding overhead.
  • Added update_summaries to SpectrumLike and fetch_summaries to RefPeakDataLevel to do this work.

Fixed

• Fix changelog

0.16.0 - 2024-05-07

Added

• Added Thermo instrument methods to Thermo instrumentConfiguration
• Add Hash implementation for Param, Value, and associated ref types
• Add referenceParamGroup inference for instrumentConfiguration when writing mzML, and escape newlines in Param values

Fixed

• Properly set compression in store_compressed
• Empty buffer coercion failure on Linux (#2)
• Prevent slice coercion from failing in coerce_mut
• Prevent potential unwrap failures in PeakData.base_peak when dealing with unorderable floats

0.15.0 - 2024-05-02

Added

• Added store_compressed to DataArray to support compression at-will
• Added encode_array to specify compression state of a DataArray in BinaryArrayMap

Changed

• Export the utils module for convenience

Documentation

• Add documentation for more of the param module
• Simplify and document peak type blanket traits
• Document new compression methods

Fixed

• MGF spectra are properly classified as MS2 and centroid
• PeakDataLevel is now exported as was originally intended

Maintenance

• Use git-cliff

0.14.0 - 2024-04-25

Added

• Added dependency on chrono to parse the startTimeStamp in mzML(b), and the equivalent Thermo property.
• Added more conversion convenience methods for parameter-like enums:
  • MassSpectrometryFormat
  • FormatConversion
• Added mzdata::meta::custom_software_name convenience for creating a CV parameter describing an unreleased tool. Helpers to deal with published tools will be worked on soon.
• Added MassSpectrometryRun to ThermoRawReaderType.
• Added Value and ValueRef types which are used to hold cvParam/userParam values with eager parsing. While not an actual space savings, this removes the need to repeatedly parse values if they are accessed more than once. They support coercion via the ParamValue trait in the prelude. Param and ParamCow also implement this trait and delegate it to their value field.
• Added ion_mobility, filter_string, and mass_resolution methods to ScanEvent that perform cvParam look ups.
• Added MGFStyle traits and marker types that control how MGF spectrum headers are populated. The default behavior is now encapsulated in the default style, MZDataMGFStyle.
• Added SoftwareTerm enumeration generated from the psi-ms.obo.

Changed

• The MassSpectrometryRun.start_time field is now a chrono::DateTime instead of String.
• Param and ParamCow now store their values as Value/ValueRef, which eagerly parse their values to elide the parsing cost on repeated access.
• CURIE can now be constructed with the mzdata::curie macro
• MGFWriterType now takes a fourth template parameter, a type implementing the MGFStyle trait. This is parameterized by default.
• The MGFWriterType's public API has been expanded and the internal responsibilities refactored so that the write_header and write_peaks methods are more succinct.

0.13.0 - 2024-03-28

Added

• MGFReaderType and MGFWriterType implement MSDataFileMetadata
• ThermoRawFileReader has been added to read Thermo RAW files when the .NET 8 runtime is available, using thermorawfilereader
• Source and Sink algebraic types to represent things that spectra can be read from or written to.
• mz_read and mz_write are macros to open files for reading and writing in unboxed context, but which only live within a scoped closure.
• MassSpectrometryReadWriteProcess trait for orchestrating reading from a Source, writing to a Sink, and transforming the data through an arbitrary function specified as part of the trait implementation. Like mz_read/mz_write, the scope enclosed by the trait method.

Changed

• MGFWriterType now generates a spectrum title when one is absent, rather than defaulting to the spectrum's native ID.
• CURIE can now be compared to Param
• Renamed ScanWriter to SpectrumWriter and ScanSource to SpectrumSource for consistency with other trait naming conventions.
• MZFileReader::open_file now returns an io::Result in keeping with the idea that reading a File might fail as well, even if it is already open, because it is the wrong type of file. This also allows file formats that cannot be read from arbitrary io::Read objects to signal failure without crashing the whole system.
• Collator, std::sync::mpsc::{Sender, SyncSender} now implement SpectrumWriter when properly parameterized.
• PeakDataLevel has been refactored into two types, PeakDataLevel is an owning type and RefPeakDataLevel is a borrowing type.

Deprecated

Removed

Fixed

Security

0.12.0 - 2024-01-29

Changed

• Require a newer version of mzsignal, fixing the rather embarrassing error of swapping FWHM and SNR during peak picking.
• Thicken the use of internal abstraction around PrecursorSelection for the future of allowing more than one SelectedIon per Precursor.

0.11.0 - 2024-01-24

Added

• Added an hdf5_static flag to build the HDF5 library from source at build time.

Removed

• Removed SpectrumLike from the crate root, it is more appropriately imported with the rest of the prelude.

0.9.0 - 2024-01-20

Added

• RestartableGzDecoder added to mzdata::io to provide an io::Seek compatible GZIP decompressor, with the caveat that seeking backwards requires re-reading everything read thus far and that seeks cannot be relative to the EOF.
• Added documentation to more examples.

Fixed

• infer_from_stream handles compressed streams correctly without triggering an unexpected EOF error.
• MGFWriterType properly formats additional annotations.

0.8.0 - 2024-01-10

Added

• Added close to the SpectrumWriter trait which "closes" the formatted structure of the file. As Rust lacks a notion of a "closed" io::Write, the underlying writer isn't actually "closed" until the whole struct is dropped.
• Added Drop implementation for MzMLWriterType and MzMLbWriterType which ensures that the close method is called to make the resulting file well-formed.
• Added new peak picking methods MultiLayerSpectrum::pick_peaks_in_intervals and RawSpectrum::pick_peaks_in_intervals_into that pick peaks only in selected m/z regions.
• Added MassSpectrometryRun to record information found on or near the <run> element in mzML which includes several default values otherwise absent from the data model. It is accessible via MSDataFileMetadata::run_description trait method, included in the prelude.
• Added the MSDataFileMetadata::spectrum_count_hint which returns the total number of spectra in the file, if available.
• Added MSDataFileMetadata implementations for SpectrumIterator, StreamingSpectrumIterator, and SpectrumGroupingIterator where their sources do.
• SpectrumGroupingIterator and other such iterator support RandomAccessSpectrumGroupingIterator.

Changed

• SpectrumWriter no longer applies a lifespan requirement on individual writing operations.
• filename is no longer a required dependency, it is only needed to use MzMLbReaderType::from_file which otherwise panics. It introduces unpredictable and difficult to diagnose compilation errors.
• MGFWriterType skips MS1 spectra automatically.

Fixed

• Properly track whether the spectrumList has been finished by mzML parsers.
• Iteration over SpectrumGrouping when there are missing components has been fixed.
• Binary data arrays may panic if empty on certain platforms with certain compression schemes.

0.7.0 - 2023-12-25

Added

• Limited async mzML reader support
• mzMLb read and write support
• Reading mzML and MGF from STDIN. HDF5, and ergo mzMLb is not supported on non-seek-able I/O devices. See the from_stdin example.
• Parsing of mzML run and spectrumList metadata, although they are still not a part of the common data model
• Spectrum averaging now has eager averaging and averaging_deferred adapter implementations as iterator adapters on SpectrumGroupIterator. The deferred adapter is preferred for distributing the process with rayon. See the averaging_writer example.
• Added ordered parallel iteration collation with mzdata::spectrum::Collator to make consuming rayon iterators easier while preserving the original order. See averaging_writer example.
• The mzML and mzMLb writers now write the total ion chromatogram and base peak chromatogram

Changed

• RandomAccessScanIterator methods now return mutable references to self, making them actually useful in a chain.
• Make some window size attributes smaller as they do not require double precision.
• Clean up the internal implementation of the various internal SpectrumBuilder types.
• Factor up mzdata::spectrum::signal to be less monolithic and a complete redesign of the traits used to convert mzpeaks to and from binary arrays.
• Massive refactoring of mzdata::io::traits to make more traits depend upon SpectrumSource instead of SpectrumIterator and to make things slightly less verbose.
• Switched the default mzsignal backend to nalgebra instead of intel-mkl for simplicity.

0.5.0 - 2021-09-22

Added

• MzML writing via mzdata::io::mzml::MzMLWriter
• Added feature flags to allow the user to choose amongst more flate2 backends (zlib default, zlib-ng-compat, miniz_oxide)
• Grouped iteration mode for connecting precursor and product spectra over an iterator stream using the groups method of SpectrumSource.

Changed

• Re-structuring and renaming of the various iterator mechanisms for more consistency. ScanIterator -> SpectrumIterator, et cetera. Minor refactoring of this sort expected to come for SpectrumSource as responsibilities are worked out.

Deprecated

Removed

Fixed

• Fixed documentation in several places, particularly where it was substantially out of date.

Security