add formats that make sample (or other) ids explicit

[bokulich-lab]

add formats that make sample (or other) ids explicit

[colinvwood]

Changes in q2-assembly are (at least partially) blocked by bokulich-lab/q2-assembly#66

[gregcaporaso]

@ebolyen pointed out that we can add a method on the format that gives us tuples or a dict mapping sample ids to relative filepaths in the Archive, so that will achieve the same goal without having to create new manifest formats. So we should do that for the next release (2023.11), and take a pass to use these throughout in places where we're parsing filenames to access the sample ids.

[misialq]

Sounds good - thanks @gregcaporaso and @ebolyen! 🙏

[gregcaporaso]

Since this issue was opened in the context of the ContigSequencesDirFmt, let's update all code that is using that format (e.g., here) as needed to use the lookup that @colinvwood added in #57, and then close this one out.

@colinvwood, could you put this on your list? It's a nice-to-have for the 2023.11 release, but not essential.

[colinvwood]

@gregcaporaso what about other formats that could use this approach, e.g. the PR @misialq linked above--should we open separate issues? that is in fact its own issue not a PR, whoops

[colinvwood]

After looking at the places in q2-assembly where we could use this new approach, I think that things will be much more refactorable once we have corresponding functionality for the mag directory format(s).

[gregcaporaso]

Ok, makes sense. Do we have an issue for updating the MAG directory format(s)? Could you create one if not?