MAINT: adjust regex for genome data semantic types

[Sann5]

Regexes defining the file collections of semantic types GenomeData[Loci], GenomeData[Genes], GenomeData[Proteins] had the following structure:

class <name>DirectoryFormat(model.DirectoryFormat):
    <name> = model.FileCollection(r'(.*\_)?<name>[0-9]*\.<extension>$',
                                format=<format>)

• where <name> is either loci, genes or proteins
• <format> is the format of the files like FASTA of gff and <extension> is the associated file extension

We propose changing the regex to something like

(.*\/)?(.*)\.<extension>$

basically matching any random file name with an optional parent directory. The keyword <name> (loci, genes or proteins) is redundant as the specific formats are anyways linked to their respective semantic types. Ergo there is no need to indicate that in file names.

Additional Info

This PR blocks bokulich-lab/q2-moshpit#154

[misialq]

Hey @Sann5,
I think you should simplify those regexes even more - there isn't really any need to have that part which recognizes slashes (since it may or may not be there, we may as well jsut get rid of it altogether). Also, you should simplify all the tests: there is no need for all those test cases with pre- and suffixes anymore - one case should be enough.

[Sann5]

@misialq done :)

[Sann5]

@misialq I also changed some paths in the transformer tests :)

[misialq]

LGTM ✅ @lizgehret over to you!

[lizgehret]

changes all look reasonable on my end 👍