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CHANGELOG.md

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Changelog

1.3.0

Changed

  • Auto-generated type definitions for the datasets have been regenerated [#31]. This pulls upstream changes from Uniprot. For a full list of changes view this commit diff.
  • Auto-generated type definitions for the ID mapper have been regenerated [#30, @hlfernandez]
  • Remove Python 3.7 support and support 3.12

1.2.0

Added

  • DatasetClient.search() now has an include_isoform parameter, which specifies if you want isoforms to be returned [#27, @godotgildor]
  • Python 3.11 is now officially supported

Changed

  • Auto-generated type definitions have been regenerated [#28]. This pulls upstream changes from Uniprot which are description-only:
    • All the cc_ query fields for Arba and Unirule such as cc_cofactor and cc_domain hav updated descriptions
    • Uniparc's list of databases has increased in the database query field

1.1.0

Changed

  • unipressed.IdMappingClient.get_status() now returns a Literal, which gives your type checker/IDE access to the possible return values.

Fixed

  • unipressed.IdMappingClient.get_status() now wraps a bug in the UniProt API (#293), ensuring that it will return a valid job status even when the API itself does not. [#21]

1.0.0

Changed

  • Breaking: Reworked the search API. Broadly this means that rather than using unipressed.UniprotkbSearch, you should now use the unipressed.UniprotkbClient class, which encapsulates the dataset's APIs. You can then perform a search query using Uniprotkb.search().
  • Breaking: Restructured the Python package. Most imports have changed.

Added

  • The new client objects support .fetch_one() and .fetch_many() which can be used to look up one or more database entries using their IDs
  • An ID mapping client. This can be accessed as unipressed.IdMappingClient

0.2.0

Note, if you are using Visual Studio Code, please update Pylance to at least version 2022.8.20. A bug in earlier versions will give you false errors with this new release of unipressed.

Added

  • Also allow strings within the query dictionary, so that e.g. this is now allowed:

    {
    "and_": [
        "foo*",
        "*bar"
    ]
}

    This will search for all proteins that have any field that starts with foo and any field that ends with bar.

  • Auto generated docstrings for all fields

  • Examples to the documentation of each field

  • Certain missing query fields for the arba dataset:

    • cc_scl_term

  • Certain missing query fields for the proteomes dataset:

    • organism_id
    • taxonomy_id

  • Certain missing query fields for the unirule dataset:

    • cc_scl_term

  • Certain missing query fields for the uniparc dataset:

    • taxonomy_id

  • Certain missing query fields for the uniprotkb dataset:

    • organism_id
    • taxonomy_id
    • virus_host_id

Removed

  • Uniprot seem to have removed certain uniprokb query fields, so these are now not part of the accepted query type:
    • ft_metal
    • ftlen_metal
    • ft_ca_bind
    • ftlen_ca_bind
    • ft_np_bind
    • ftlen_np_bind
  • Likewise, some uniprotkb return fields have been removed:
    • ft_ca_bind
    • ft_metal
    • ft_np_bind

Internal

  • Move from pyhumps to inflection for code generation
  • Add a test for the date field
  • Added tests for all datasets
  • Add types for code generation API