CHANGES IN VERSION 1.37.3
+ Update within the tests only (not within the R code base): library database path for lvl spectral matching testing (required after removal of the local SQLite database from msPurityData).

CHANGES IN VERSION 1.37.2
+ Bug fix for subsetting the grouped data frame in the `average_xcms_grouped_msms_indiv` function

CHANGES IN VERSION 1.37.1
+ Removed library_spectra.db direct reference from msPurityData package (too large for Bioconductor)
+ spectralMatching() now downloads default library database from Zenodo (https://zenodo.org/records/18700802) and uses BiocFileCache with MD5 verification
+ spectral_matching() (deprecated function) now requires explicit library_db_pth parameter; default library no longer available
+ Added BiocFileCache to Imports for automatic caching of remote databases

CHANGES IN VERSION 1.30.1 / 1.31.1
+ Update example for purityX causing build error

CHANGES IN VERSION 1.27.1
+ createMSP fix - now uses the median precursor MZ and precursor RT in the MSP file

CHANGES IN VERSION 1.21.2
+ Fixes due to mz and intensity being named in columns for mzR and XCMS
+ Fixes for connection{base} file() opening changes (no longer accept w+a in function in R v4.2)
+ Update tests for the above
+ Update a reference of grpid in averageXFragSpectra functions more explicit (no change in functionality)
+ Typo fix in vignette

CHANGES IN VERSION 1.21.1
+ Bugfix for frag4feature for XCMS 3 compatability https://github.com/computational-metabolomics/msPurity/pull/93
+ Remove imports that are no longer used

CHANGES IN VERSION 1.19.2
+ XCMS 3 compatability update (M-R-JONES) https://github.com/computational-metabolomics/msPurity/pull/91

CHANGES IN VERSION 1.19.1
+ Bug fix for flagRemove (full width was not calculated as expected)

CHANGES IN VERSION 1.17.2
+ Update dev to match bug fixes in master

CHANGES IN VERSION 1.16.2
+ Author list updated

CHANGES IN VERSION 1.17.1
+ Update dev to match bug fixes in master

CHANGES IN VERSION 1.16.1
+ Update of createDatabase to record all intra average spectra in database
+ Add license and copyright info to code
+ Add github workflow CI (and subsequent formatting updates to pass tests)

CHANGES IN VERSION 1.15.1
+ Update dev to match bug fixes in master

CHANGES IN VERSION 1.14.1
+ Update of rdpc algorithm (see https://github.com/computational-metabolomics/msPurity/issues/78)
+ Update of align algorithm (see https://github.com/computational-metabolomics/msPurity/issues/79)
+ Fix for spectralMatching of type 'scan' previously incorrectly outputing no matches

CHANGES IN VERSION 1.13.2
+ Update dev to match bug fixes in master

CHANGES IN VERSION 1.12.2
+ Fix to allow large files to be processed with combineAnnotation (in some cases the summary report should be excluded)

CHANGES IN VERSION 1.13.1
+ Update dev to match bug fixes in master

CHANGES IN VERSION 1.12.1
+ Bug fix for combineAnnotations - MS1 lookup not handling CAMERA adducts correctly
+ Fillpeaks bug fix see github #68
+ Documentation fixes

CHANGES IN VERSION 1.13.0
+ Bioconductor dev (automatic version bump)

CHANGES IN VERSION 1.12.0
+ Bioconductor release (automatic version bump)

CHANGES IN VERSION 1.11.5
+ frag4feature fileid fix for conversion from factor to character
+ Add missing plyr:: reference (thanks jsaintvanne)

CHANGES IN VERSION 1.11.3/4
+ Overhaul of combineAnnotation function. Uses local database now as previously
  API calls would take too much time to finish and was not usable
+ Various updates of createMSP to make compatible with Galaxy workflows
+ Parameter added to purityA to allow user to change the PPM tolerance for MZ
  values between scans when calculated the interpolated precursor ion purity
+ Update of spectralMatching results columns to include additional details
  (e.g. retention time)
+ Update of spectralMatching so that either PostgreSQL or MySQL database can be
  used as input to either query or library

CHANGES IN VERSION 1.11.2
+ Bug fix for EIC with MSMS data

CHANGES IN VERSION 1.11.1
+ Bug fix for duplicate MSP spectra when not using metadata table
+ Added xcms3 to xcmsSet conversion for "create database" code
+ Fix for sirius combine annotations (incorrect column format)

CHANGES IN VERSION 1.11.0
+ Bioconductor dev (automatic version bump)

CHANGES IN VERSION 1.10.0
+ Bioconductor release (automatic version bump)

CHANGES IN VERSION 1.9.12
+ Troublshoot mac "[MSData::Spectrum::getMZIntensityPairs()] Sizes do not match" error

CHANGES IN VERSION 1.9.11
+ Bug fix for createMSP - now handles metadata with duplicate grpids

CHANGES IN VERSION 1.9.10
+ Documentation updates

CHANGES IN VERSION 1.9.9
+ NEW FUNCTION: createDatabase
    o Updated version of create_database that uses an updated schema
+ NEW FUNCTION: spectralMatching
    o Updated version spectral_matching that allows for more flexibility
+ Vignettes and documentation update

CHANGES IN VERSION 1.9.8
+ NEW FUNCTION: filterFragSpectra (for purityA objects)
    o LC-MS/MS filtering of spectra (prior to averaging)
+ NEW FUNCTIONS: averageIntraFragSpectra, averageInterFragSpectra, averageAllFragSpectra (for purityA objects)
    o LC-MS/MS averaging and filtering functionality
+ NEW FUNCTION: createMSP
    o Create msp files from purityA objects where XCMS features have been linked to fragmentation spectra
+ Updated create_database and spectral matching to have the option to use averaged fragmentation spectra

CHANGES IN VERSION 1.9.2
+ Bug fix for groupPeaks and groupPeaksEx (the ppm argument was not working and there was inconsistent behaviour with larger datasets). Thanks to Elliot for spotting (https://github.com/litepalmer)
+ Updated documentation for spectral matching

CHANGES IN VERSION 1.7.6
+ create_sql bug fix for msms spectra table. Was crashing due to incorrect ordering.
+ Add peak processing (flag remove peaks) for LC-MS XCMS data
+ Add option to for frag4feature to just link to the grouped peak rtmin and rtmax (e.g. do not need to link to individual files)

CHANGES IN VERSION 1.6.1
+ Bug fix. For pos/neg switching acquisition two files are can be generated when converting from RAW to mzML (1 for pos, 1 for neg).   The resulting files retention time scans were not being tracked properly in msPurity in these cases. This is now fixed. Thanks
  to Julien (https://github.com/jsaintvanne) for spotting the bug.

CHANGES IN VERSION 1.5.1
+ Updates for database creation (can use CAMERA objects now)
+ averageSpectra parameter 'MSFileReader' deprecated MSFileReader. Should use csvFile instead, MSFileReader option will still work but a warning will be given

CHANGES IN VERSION 1.4.1/2/3
+ Updates for Galaxy for Spectral Matching
+ Spectral matching ra_thres_t bugfix
+ Separation of sqlite database creation. Now can be called on it's own or with frag4feature
  (allows the Galaxy tool to be simplified)

CHANGES IN VERSION 1.3.9
+ Added very basic SIMS stitch compatibility
+ pcalc can handle NAs
+ Update of purityX to handle obiwarp RT correction (requires recording the RT RAW at an earlier step)
+ bug fix for when library spectra is bigger than target spectra (thanks Martin)

CHANGES IN VERSION 1.3.1
+ Add spectral matching functionality for LC-MS/MS

CHANGES IN VERSION 1.1.1
+ Added pcalc functions to be used by user
+ Added option to remove isotopes from calculation

CHANGES IN VERSION 0.99.10/11/12
+ Troubleshooting windows build failure


CHANGES IN VERSION 0.99.9
+ Offset bug fixed (previous only using extracting lower offset from mzML file)
+ Updated handling of RT corrected xcmsSet objects for frag4feature function
+ Additional column added for tracking ms/ms spectra

CHANGES IN VERSION 0.99.8
+ User option to change the mzR backend library

CHANGES IN VERSION 0.99.4/5/6/7
+ Troubleshooting mac build failure

CHANGES IN VERSION 0.99.3
+ Grouping multiple peaklist into one wide dataframe
+ Peaklists can now be averaged across each class using the function groupPeaks() for the class purityD
+ A list of dataframes can also be grouped together using the function groupPeakEx()

CHANGES IN VERSION 0.99.2
+ Updated class names purityPD to purityD
+ Updated class names purityLC to purityX
+ Updated vignette to reflect slightly different terminology
+ Added normalised TIC option for purityD

msPurity v0.99.0 (Release date: 2016-04-08)
+ Initial release!
