PySAM problems with Python 3.8 + OS X

[bede]

pip install alignparse fails for me inside a clean MacOS 10.14 + Python 3.8 environment created with conda due to a PySAM build issue. Using Python 3.7 or else installing pysam with conda in 3.8 works just fine.

Quite likely to be a Mac only issue that will be resolved in a future pysam update, but you could consider creating an evironment.yml to allow conda to users to install prebuilt dependencies via
conda env create -f environment.yml

Edit: conda would also allow managed installation of minimap2

[khdcrawford]

We have an environment.yml file in the main repo that I think should work for this. It specifies using Python 3.6 to avoid the issues with pysam. I just tested creating the environment locally on my machine and it seemed to work, but let me know if you run into issues! Thanks for your quick review, @bede!

[jbloom]

@khdusenbury: Maybe we should also update the docs on installation to say that alignparse requires Python 3.6 or higher, and is currently tested on Python 3.6 and 3.7. It should work on 3.8 (except for the pysam issues which are outside our purview), but right now the Travis tests only run for 3.6 and 3.7.

[khdcrawford]

Implemented in PR #59.

[afrubin]

@khdusenbury: Maybe we should also update the docs on installation to say that alignparse requires Python 3.6 or higher, and is currently tested on Python 3.6 and 3.7. It should work on 3.8 (except for the pysam issues which are outside our purview), but right now the Travis tests only run for 3.6 and 3.7.

Just wanted to point out that the README still has the old language ("requires Python 3.6 or 3.7").

[jbloom]

@afrubin: Good point. I've created a pull request for @khdusenbury to review that should address this issue (pull request #60).