General code tidy-up

[joewandy]

General code tidy-up for issue #47. This is done as a preliminary work before trying to speed up the pipeline (issue #45).

Main changes:

• Changed the import to use loguru instead of the standard logging. This needs less configuring and looks prettier with line number etc.
• Set the default log level to INFO in the initialisedb script. This means we don't see the debug messages by default. We were printing a lot of stuff to the screen, which slows things down.
• Removed import * statements everywhere I saw it, and only imported what we need.
• Added tqdm progress bar to Pipfile. Please do a pipenv install.
• Replaced printing a lot of stuff with showing progress bars instead. I also changed many previously info messages to debug instead (we can change them back if needed).
• Added 1301_peak_cmpd_export.json, 1301_peak_int_export.json and tissues_life_stages_combine_whole_flymet3.csv to the test data folder.
• Added a script reset_data.py to quickly delete existing database and pickled files.