Disk optimization

[ArnaudBelcour]

WARNING:

• change in intermediary files of clustering and annotation in order to reduce disk space used by EsMeCaTa and the number of operations performed by the methods. Instead of assigning one file per observation name, this new version assigns one file per taxon used by EsMeCaTa. This removes a lot of redundant work that slowed EsMeCaTa and could lead to issue.
• annotation with eggnog-mapper is now the default workflow methods of EsMeCaTa. The previous annotation methods with UniProt has been moved to annotation_uniprot and workflow_uniprot.

Add

• Add sub-commands annotation_uniprot and workflow_uniprot to use the old method of protein annotation.
• Add check subcommand that performs the first step of EsMeCaTa without downloading the proteomes. This is helpful when you want to have a glimpse on the available knowledge for your dataset.
• Error message if incorrect extension is given as input to esmecata.

Fix

• Missing import in proteomes.
• Github Actions.

Modify

• Modify intermediary files to associate them with taxon name selected by EsMeCaTa instead of the observation name (based on an idea of @PaulineGHG). This change replaces tsv files, that were created for each observation names. Now they will be created for each taxon instead. This means that observation names with the same taxon will be associated with the same file. This reduces the redundancy of the file and decreases the number of operations made by EsMeCaTa.
• Modify how the log json files are created so if a run failed, a new log json file is created instead of erasing the previous ones.
• Move from setup.py and setup.cfg to pyproject.toml.
• Update readme and tutorial.
• Update license year.

Remove

• Remove sub-commands annotation_eggnog and workflow_eggnog which are now the default sub-commands annotation and workflow.