Mob-suite

- Fixed impact of contig ordering impacting the final results reproducibility (issue 160)
- Fixed biopython issue with gc_fraction available from version 1.80 onwards (issue 163)

This release includes small but important convenience fixes such as fix to 152 issue where in cases when there are absolutely no plasmid biomarkers (i.e. empty biomarkers report) `mob_typer` would fail. Additionally, this release improves marker reporting consistency between biomarkers and the main plasmid typing reports generated by mob_recon and mob_typer. The biomarkers report introduced since v3.1.7 lists the main plasmid biomarkers and their coordinates. Finally, plasmid databases were cleaned, synced and redundant files removed. A new databases archive url was updated and now points to https://zenodo.org/records/10304948/files/data.tar.gz?download=1

- Fixed permanently issue 152 and added a unit test `test_mob_recon_no_plasmid_biomarkers()`
- Updated the core database archive `data.tar.gz`: a) removed redundant `host_range_ncbirefseq_plasmidDB.txt` and `host_range_ncbirefseq_plasmidDB.csv`; b) updated `clusters.txt` with new `mob_typer` biomarker results for consistency (the cluster codes and number of records did not change)
- Improved biomarkers report consistency with other reports by making sure that all markers listed in the `mob_typer` report are present in the biomarkers report. Implemented a new unit tests listed in `test_databases_consistency.py`

This release includes a fix to 150 where uninitialized databases to mob_typer would result in confusing error messages. Additionally, this release includes the addition of a new biomarkers blast report file which will be automatically generated by mob_recon and optionally by mob_typer if the --biomarker_report_file parameter is included. This file contains the filtered biomarker blast results for oriT, replicon, relaxase, and mate-pair-formation as a single tab-delimited file of blast results with an included column labelling which biomarker type the sequence belongs to.

This update includes fixes to issues 149 with thanks to rpetit3 additionally, addresses the generation of mge reports with empty results when called through mob-typer

Largely resolving issues with MOB-cluster not running due to changes in ETE3 DB parameters

Fixed an issue with ETE3 database not being set with default database