CHANGELOG.md

Changelog

1.4.0

Added

• The taxon_id argument to IdMapper.submit [#36]
• Detailed type annotations for IdMapper.submit, that enforce only certain pairs of source/dest databases

Changed

• Auto-generated type definitions for the datasets have been regenerated [#37]. This pulls upstream changes from Uniprot. For a full list of changes view this commit diff.
  • Uniref's created query parameter has been replaced by last_modified
  • UniprotKB has lost various fields: xref_genevisible, xref_dosac-cobs-2dpage", xref_swiss-2dpage, xref_ucd-2dpage, xref_world-2dpage, xref_epd, xref_maxqb, xref_ko and xref_genevisible

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