Unipressed

Added

* The `taxon_id` argument to `IdMapper.submit` [[36]](https://github.com/multimeric/Unipressed/pull/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](https://github.com/multimeric/Unipressed/pull/37)]. This pulls upstream changes from Uniprot. For a full list of changes [view this commit diff](https://github.com/multimeric/Unipressed/pull/31/commits/7e620c46175b6ec03e073fc78444a43e96821c31).
* Uniref's `created` `query` parameter has been replaced by `last_modified`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`

Changed

* Auto-generated type definitions for the datasets have been regenerated [[31](https://github.com/multimeric/Unipressed/pull/31)]. This pulls upstream changes from Uniprot. For a full list of changes [view this commit diff](https://github.com/multimeric/Unipressed/pull/31/commits/3dcf6f9b405807c44c9252eb6a603e915827021f).
* Auto-generated type definitions for the ID mapper have been regenerated [[30](https://github.com/multimeric/Unipressed/pull/30), [hlfernandez](https://github.com/hlfernandez)]
* Remove Python 3.7 support and support 3.12

Added
* `DatasetClient.search()` now has an `include_isoform` parameter, which specifies if you want isoforms to be returned [[27](https://github.com/multimeric/Unipressed/pull/27), [godotgildor](https://github.com/godotgildor)]
* Python 3.11 is now officially supported

Changed
* Auto-generated type definitions have been regenerated [[28](https://github.com/multimeric/Unipressed/pull/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

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](https://github.com/ebi-uniprot/uniprot-rest-api/issues/293)), ensuring that it will return a valid job status even when the API itself does not. [[#21](https://github.com/multimeric/Unipressed/issues/21)]

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`

**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:
python
{
"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