Loqusdb

Fixed
- Update to setuptools >= v.70 to address a security issue in the `package_index` module

Fixed
- Updated issue templates

Changed
- When using QUAL values, treat . as 0 quality

Added
- Basic cli tests touching fixed deprecated code
Changed
- Unfreezed PyMongo in requirements.txt
- Replaced deprecated pymongo `.count()` function with `count_documents()` in code.

Fixed
- `Deprecated config in setup.cfg` error when installing the package

Added
- Script to correct contig name
- Expanded instructions on how to set up an instance and load data into database
Changed
- GitHub actions run tests using MongoDB versions 3.2, 4.4 and 5.0
Fixed
- Restore command accepts custom database name
- Restore command uses either database URI or host:port params