import plink-ng as a git dependency

[aryarm]

Compared to VCFs, PLINK files are a much more efficient format for storing and working with GWAS datasets. Reading from PLINK files takes seconds, while I've estimated that reading from VCFs can take half an hour for even the small datasets we want to work with. We'll eventually want to list the Python API for plink-ng (aka pgenlib) as a dependency of this tool, so that we can properly support reading and writing PLINK files. Currently our code just assumes this dependency is installed instead of installing it automatically via poetry.

Unfortunately, pgenlib has not yet been published to PyPi, so we'll have to install it directly from the Github repo in the subdirectory that it lives in. poetry-core added support for installing git packages from subdirectories in v1.1.0a7 (yesterday, on 3/5/22). So this PR adds pgenlib to the pyproject.toml file using the new syntax and updates poetry and poetry-core to support installing it.

[aryarm]

Looks like the readthedocs build failed because python-poetry/poetry-core#288 hasn't been merged in yet. And we will eventually want python-poetry/poetry-core#300 and python-poetry/poetry#5172 .

The git url gets resolved to this

git+https://github.com/chrchang/[email protected]#subdirectory2.0/Python

instead of this

git+https://github.com/chrchang/[email protected]#subdirectory=2.0/Python

(notice the equal sign after #subdirectory?)

Update
It seems python-poetry/poetry-core#288 has been merged now. At this point, we just need to wait for the release of poetry-core v1.1.0b1 and its appearance on conda-forge.

[aryarm]

ok, I just rebased and updated the pyproject file to require 1.1.0b1

But the readthedocs build still failed

it looks like we'll still need python-poetry/poetry-core#300 in order to get this to work :(
for more details see python-poetry/poetry-core#300 (comment)

[aryarm]

closing in favor of #68