WIP: integrate sketching utils from directsketch

[bluegenes]

In directsketch, I tried to come up with a set of sketching utils that would make reading parameters + building sketches easier and more standardized. I introduced a series of buildutils -- BuildRecord,BuildManifest, BuildCollection, etc that are similar to their sourmash counterparts, but enable building and updating.

Here, I copy the utils over from directsketch and replace the two async functions with sync counterparts that enable writing the sigs and manifest from the buildutils. Then, I use BuildCollection in manysketch to manage parameter string handling, sig template generation, and sig writing.

To do:

• benchmark as-is
• add/use par_iter across sig templates and benchmark

Future:

• allow translation

[bluegenes]

status:
zip files are getting written, but can't (yet) be read with sourmash. Running into this error again:

sourmash.exceptions.Panic: sourmash panicked: thread 'unnamed' panicked with 'called `Result::unwrap()` on an `Err` value: InvalidArchive("Extra data field contains disk number")' at src/core/src/storage/mod.rs:390

Apparently the zip that is installed in my environment is v2.2, which has the bug mentioned here, and not v2.0, which is in Cargo.toml.

...why/how?

Update: I'm not sure why/how that was happening, but I did some cleaning + updating, and now the right versions seem to be installing. Hopefully this will stay fixed.

[bluegenes]

The only remaining failing tests are the ones with "incomplete" param strings -- i.e. user doesn't provide a moltype or doesn't provide a ksize. Temporarily commented out.

The current parameter strategy = DNA default (k=31,scaled=1000,noabund), then modify any parameters that are provided. Previously, we required a moltype and ksize to be present in the parameter string.

What do we want to require? I think maybe the right solution may be to require moltype, but not necessarily scaled or ksize? If a moltype is provided, we can use the default scaled/ksize. However, we don't necessarily want to assume DNA if the moltype is not provided?

thoughts @ctb?

Update: I've changed the strategy to require moltype. I think this matches our sketch fromfile strategy.