Bioinformatics:
* Commands were reworked down to `start` and `finish`. Start creates the jobs, launches them and creates database records. Finish uploads the results to the database and produces reports without the need of a browser.
* `report` command was added to re-generate reports
* Analysis on sample level now works as intended
* Runs now notify via e-mail upon completion
* Prior `concatinated` file for projects was integrated into source code
* Default stdout is now set to info level. Some messages updated to better reflect this
End-user:
* Organism names are now properly capitalized
*microSALT now arbitrarily suggests novel ST (needs review)
* Reports are now produced in both pdf and csv format
* Genome info (size, n50, contigs used etc .) was added through QUAST
* Removed reference database version from summary page
* Removed haplotype information (plus/minus strand) from microSALT
Internal:
* Pymysql will no longer complain
* All results are now restructured into subfolders better
* External sample IDs now have stronger support
* Configuration has been reduced to a single file, passed by standard path or $MICROSALT_CONFIG
* Job creator script was rewritten to handle objectification better
* Refactored report page
* Data timestamps now work independently of folder timestamps
* Installation no longer requires develop flag