- Modify SQLite3 code around lines 355-370 in taxonomic_composition.py to something UPSERT-like, to remove the need for including ALL taxids in the 'cumulative' table. This is one of the slowest parts of the entire code now because it isn't indexed.
- Flesh out the CONTRIBUTING document with more details.
- Fix the logging handling in all programs. They should all issue getLogger to instantiate their own logger and not rely on the module functions (i.e. logging.DEBUG etc).