Api first pass - Githubissues

astheeggeggs / lshmm

code to run Li and Stephens

MIT License

3 stars 3 forks source link

Api first pass #8

Closed jeromekelleher closed 2 years ago

jeromekelleher commented 2 years ago

Here's a first pass at cleaning up the public API so we can push a release to pypi @astheeggeggs

The idea is that users won't need (or shouldn't have access to, really) the internal namespace and will just use the functions lshmm.forward() etc.

All seems to be working OK, except for the viterbi sub-package. Can't get that to work, but have to go now. I'll pick this up again when I get a chance.

Did you hit issues like this?

jeromekelleher commented 2 years ago

Aha! Figured it out. The viterbi package was conflicting with the viterbi function. Took me ages to figure that one out!

That should be the main API surface picked out now, so how about we make an alpha package for pypi and push it up there?

jeromekelleher commented 2 years ago

Some updates here

I removed pydocstyle. I couldn't figure out what it wants and it seems really very overly proscriptive and unhelpful
I disabled the docs build for now as it's a bit tricky
Did a bit of a refresh on the nox config and the CI.

Hopefully this will get the build completing successfully on CI.

jeromekelleher commented 2 years ago

How's it looking @astheeggeggs? I'm assuming a lot of this stuff came from cookiecutter and you didn't hand craft these configs?

astheeggeggs commented 2 years ago

Yep, you're exactly right - lots of this stuff is from cookiecutter and I left well alone!

astheeggeggs commented 2 years ago

Aha! Figured it out. The viterbi package was conflicting with the viterbi function. Took me ages to figure that one out!

That should be the main API surface picked out now, so how about we make an alpha package for pypi and push it up there?

oh, whoa - sorry about the viterbi pain!