                 Changes in version 1.3.3 (2026-06-23)                  

Fixed

  - Fix unwanted conversion to NAs when sample names were well numbers
    like E1 or E2 (#51, thanks for spotting this @sarah-lital)
  - Fix wrong number of columns documented in read_biotyper_report()

Changed

  - Specify the peer-reviewed article as a preferred citation source

Added

  - List open-source alternatives to maldipickr

                        Changes in version 1.3.2                        

Fixed

  - Fix typo that invalidated Zenodo integration

                 Changes in version 1.3.1 (2024-09-12)                  

Added

Features / Documentation

  - Add gather_spectra_stats() to aggregate spectra quality-check
    statistics (#45)
  - Add "Get Started" vignette for a quickstart (#48)
  - Add graphical overview
  - Add example of filtering when delineating with identification (#42)

Visibility / Readability / FAIR

  - Setup integration of Github repository with Zenodo with additional
    metadata (#49)
  - Setup correct Opengraph metadata for the website
  - Setup analytics via the NFDI4Microbiota instance of matomo
  - Add maldipickr logo in vector format to edit in the future (#42)
  - Setup R-hub checks via Github Actions

Changed

  - Use directly a simpler and more compact README.md instead of
    README.Rmd

Fixed

  - Fix implicit TRUE as T in R code.
  - Bump Github Actions Node.js to v20 to fix warnings (#47)

                 Changes in version 1.3.0 (2023-12-14)                  

Fixed

  - Fix non-unique names possibility during spectra processing (#37)

Changed

  - Deprecate ability to write RDS in process_spectra() (#38)
  - Deprecate ability to read RDS in merge_processed_spectra()
  - Change warnings in check_spectra() to messages pointing to use
    remove_spectra()

Added

  - Add get_spectra_names() to extract, format spectra names and warn
    against non-uniqueness
  - Add remove_spectra() to better handle discarding raw or processed
    spectra
  - Add {lifecycle} to better handle deprecation
  - Add sections to the function reference list to improve clarity on
    website

                 Changes in version 1.2.0 (2023-10-25)                  

Changed

  - (BREAKING) Change homemade clustering to robust hierarchical
    clustering in delineate_with_similarity() (#32). The default method
    of hierarchical clustering is the complete linkage (also known as
    farthest neighbor clustering) to ensure that the within-group
    minimum similarity of each cluster respects the threshold
  - Change sapply() calls to more type-robust vapply() calls

Added

  - (BREAKING) Set a minimum R version >= 3.2.0 (#31)
  - Add hierarchical clustering linkage method as argument to
    delineate_with_similarity()
  - Add tolerance argument to check_spectra() to allow flexible spectra
    length checks
  - Add more unit tests to key functions: pick_spectra() (#26) and
    merge_processed_spectra() (#27)

Fixed

  - Fix missing spectra names when merging spectra lists with peak-less
    spectra
  - Fix coverage update issue by adding codecov token (#34)

                 Changes in version 1.1.1 (2023-09-07)                  

Fixed

  - Fix typos for CRAN re-submission: missing brackets in reference, and
    spelling errors.

                        Changes in version 1.1.0                        

Fixed

  - (URGENT) Fix delineate_with_similarity() that did not include
    friends-of-friends in clusters after removal of {igraph} in #18. Add
    a relevant similarity matrix to test it accordingly.

                        Changes in version 1.0.2                        

Changed

  - Fix the invalid file URIs in NEWS.md and README.md

                        Changes in version 1.0.1                        

Changed

  - Fix title to title case for CRAN

                        Changes in version 1.0.0                        

Changed

  - (BREAKING) read_biotyper_report() first column is now name instead
    of spot, meaning read_many_biotyper_reports() renames all the name
    columns to original_name. This was to pick_spectra() easily usable
    with taxonomy identification reports
    (38a614173fd21315a40e0823600a2082fa0935bb)
  - (BREAKING) All functions now follow the verb_concept nomenclature,
    meaning clustering functions are now renamed accordingly (#24):
      - Change similarity_to_clusters() to delineate_with_similarity()
      - Change identification_to_clusters() to
        delineate_with_identification()
  - Refactor the delineate_with_similarity() clustering function
    (formerly: similarity_to_clusters()) without using the {igraph} nor
    {tidygraph} R packages, for fewer dependencies and simpler codebase
    (#18)
  - Update the DESCRIPTION to include the Strejcek reference (#22) and
    better highlight the package added-value
  - Refactor the pkgdown website with a more accessible font and color
    schema inline with the logo color palette
  - Change the vignettes titles and outline to better structure the
    documents
  - Refactor cosine similarity computation example by highlighting the
    dedicated coop::tcosine() instead of the t() %>% coop::cosine()

Added

  - Add long or wide output format for read_biotyper_report() (#12)
  - Document how to quickstart with the {maldipickr} package for those
    in a hurry (#15)
  - Document more precisely how to install tagged release of
    {maldipickr} package
  - Add better tests for merge_processed_spectra()
    (b39c1313fd38239b4b1821a243c9debf467fd092)
  - Document authors list according to CRAN policy
  - Add CRAN comments file to track submission notes

Removed

  - Deprecate the CHANGELOG.md in favor of the R specific NEWS.md (#20)
  - Remove redundant check after symbolic links creation (#19)

Fixed

  - Fix summarise() usage in pick_spectra(), with code simplification
    (#11)
  - Remove symbolic links created for importing acqu spectra files (#21)
  - Fix CRAN warnings regarding qpdf
    (3b19dd36a6ec0f5dc277418c98977c526981b6e3)
  - Fix masked relevant to_pick column in the vignette (#17)

                        Changes in version 0.1.1                        

Added

  - Add citation file for R (CITATION) and for GitHub CITATION.cff
  - Add a CHANGELOG.md (Common Changelog)

Changed

  - Improve the package description according to CRAN recommendations

                        Changes in version 0.1.0                        

  - First stable version

                     Changes in version 0.0.0.9000                      

  - Added a NEWS.md file to track changes to the package.
