Esmecata

Add

* Function `get_domain_or_superkingdom_from_ncbi_tax_database` in `esmecata.utils` to check if domain is called domain or superkingdom in NCBI Taxonomy database.

Fix

* Taxonomic rank `superkingdom` has been renamed to `domain` in recent version of the NCBI Taxonomy database. Fix several related issues in different parts of EsMeCaTa.
* `esmecata_gseapy` was not working with results from `esmecata precomputed` due to missing `proteome_tax_id.tsv` in `2_annotation` folder.

Fix

* KeyError when using precomputed database from EsMeCaTa article (as there is no `KEGG_reaction` in these databases).

Modify

* Replace `datapane` by `arakawa` for HTML report creation in `esmecata_report` (issue 20). Make HTMLs standalone (they are a lot bigger but bo not require internet to display).
* Replace `ete3` by `ete4` as ete3 is no longer maintained (issue 18).

Fix

* Issue with tax synonyms on the same tax rank when filtering rank in `proteomes`.

Modify

* Use taxon ID to search for taxon presence in precomputed database.
* Use Trusted publisher to publish on PyPI.

Add

* New command `esmecata_create_db` to create database from different output folders of esmecata (`from_runs`).
* Full release of `esmecata precomputed` associated with the first version of [esmecata precomputed database](https://doi.org/10.5281/zenodo.13354073).
* Option threshold (`-t`) to precomputed.
* Add `--gseapyCutOff` option to `gseapy_enrichr`.
* A check after database creation to detect taxon with few predicted proteins compared to higher affiliated taxon.
* Check the good format of the gzip file.
* Header `KEGG_reaction` in annotation_reference from `annotation_uniprot` to avoid issues with `esmecata_create_db`.

Fix

* Issue with protein IDs from UniParc during annotation (incorrect split on '|').
* Fix issue in `get_taxon_obs_name` function.
* Issues in test.

Modify

* Add database version in log.
* Rename `test_workflow.py` into `test_workflow_uniprot.py`, to better reflect what is done.
* Update workflow figure.
* Update readme.
* Update article_data folder and the associated readme.

Fix

* Issue with proteomes from UniParc during clustering (incorrect split on '|').
* Issue in test with updated taxonomic group.