vanheeringen-lab/genomepy: Release 0.8.1

[0.8.1] - 2020-05-11 Added Now using the UCSC rest API genomepy search now accepts taxonomy IDs genomepy search will now return taxonomy IDs and Accession numbers The README.txt will now store taxonomy IDs and Accession numbers Gene annotations: Downloading of annotation file (BED/GTF/GFF3) from URL Automatic search for annotation file (GTF/GFF3) in genome directory when downloading from URL Option for URL provider to link to annotation file (to process is similarly to other providers) Automatic annotation sanitizing (and skip sanitizing flag -s for genomepy install) Option to only download annotation with genomepy install -o Plugins: Blacklists are automatically unzipped. Multithreading support for plugins, thanks to alienzj! STAR now uses the annotation file for a (one-pass) splice-aware index Changed sizes no longer a plugin, but always gets executed genomepy FUNCTION --help texts expanded all genomepy classes exported when imported into Python all providers now let you know when they are downloading assembly information. more descriptive feedback to installing & many errors Removed Sizes plugin Old tests Removed outdated dependency xmltodict Fixed genomepy config options made more robust README.txt will no longer: update 3x for each command drop regex info have duplicate lines Refactoring Genome class moved to genome.py Many functions moved to utils.py Many other functions made static methods of a class Genome.track2fasta and Genome.get_random_sequence optimized All Provider classes now store their genomes as a dict-in-dict, with the assembly name as key. Many Provider class functions now standardized. Many functions moved to from the daughter classes to the ProviderBase class. README.txt file generation and updating standardized Unit tests! all functions now have an individual test. Almost all test use functions already tested prior to them. Old tests incorporated in several extra tests (e01, e02, e03). Raise statements now use more fitting errors All instances of os.remove exchanged for os.unlink Almost all warnings fixed Extensive, COVID19-enabled, and somewhat pointless alphabetizing, optimizing and/or organizing changes to imports everywhere .gitignore .travis.yml release_checklist.md cli.py strings (many strings with .format() replaced with f-strings