CHANGES IN VERSION 2.48.0
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

  o Switched to using the `httr2` package for making HTTP requests
  o Reorganized and renamed documentation for the `UniProt.ws` class and its
  methods
  o Converted unit testing framework from `testthat` to `tinytest`
  o Added the `README.md` file from the vignette
  o Improved handling of API responses: empty results with code 200 are
  now caught and handled properly
  o The `collapse` argument in `queryUniProt` now shows both `OR` and `AND`
  options

BUG FIXES AND MINOR IMPROVEMENTS

  o Added an example to `queryUniProt()`
  o Fixed formatting issues in unit tests and corrected indentation in code
  o Adjusted internal logic to support queries returning larger result sets
  o Re-added `Sys.sleep()` call to respect rate limits
  o Set `n` argument in internal use of `head()`

CHANGES IN VERSION 2.46.0
-------------------------

BUG FIXES AND MINOR IMPROVEMENTS

    o No significant changes.

CHANGES IN VERSION 2.44.0
-------------------------

BUG FIXES AND MINOR IMPROVEMENTS

    o No significant changes.

CHANGES IN VERSION 2.42.0
-------------------------

NEW FEATURES

    o `pageSize` and `n` arguments added to `queryUniProt` to expose
    underlying API request defaults. It is recommended to set the pageSize
    to a large value e.g. 500 for large queries.

BUG FIXES AND MINOR IMPROVEMENTS

    o Support for directly mapping to 'Ensembl' IDs with `select`.
    o Fixed issue with pagination with large queries (over 25 results) in
    `queryUniProt` (@jdreyf, #23)

CHANGES IN VERSION 2.40.0
-------------------------

USER VISIBLE CHANGES

    o Convert vignette from RSweave to web-based RMarkdown

BUG FIXES AND MINOR IMPROVEMENTS

    o Increase fault tolerance of unit tests
    o Add examples to `mapUniProt` documentation

CHANGES IN VERSION 2.38.0
-------------------------

USER VISIBLE CHANGES

    o `UniProt.ws` uses the https://rest.uniprot.org/ API interface for queries.
    o `mapUniprot` is an exported function to directly map identifiers via
    UniProt and is used by the `select` method.
    o `allToKeys` and `allFromKeys` provide all the available `to` and `from`
    keys for mapping identifiers
    o `returnFields` provides all the possible inputs to the `columns` argument
    in the `select` and `mapUniProt` functions (ids in the `name` column)

CHANGES IN VERSION 2.27.0
-------------------------

BUG FIXES AND MINOR IMPROVEMENTS

    o (2.27.1) Fix bug when selecting column GENEID. The mapping mapped both
    GENEID and ENTREZ_GENE to P_ENTREZGENE. When returning columsn used match to
    identify but would only pick up first match which was ENTREZ_GENE entry.


CHANGES IN VERSION 1.2.0
-------------------------

NEW FEATURES

    o UniProt.ws creates an object that talks directly to the web
    services at UniProt.  As such, it provides access to a tremendous
    library of IDs etc. directly from UniProt.

    o When the package loads there will be acces to a Uniprot.ws
    object, this object has select, keys, cols and keytypes methods
    that behave the way these methods normally do for the other
    annotation packages.

    o One important difference from other packages is that the user
    must use the species method to set the species to their organism
    of choice (by default it is set for humans).  This is because the
    web resource is too big to return values for all these species at
    the same time.  Uniprot currently has support for over 21,000
    different species.

    o Please see the manual pages and associated vignette for more
    detailed information about how to use this resource.