som-shahlab / ehr_ml

Code for doing machine learning with various EHRs
MIT License
21 stars 3 forks source link

Add requirements.txt to install instructions #9

Closed jason-fries closed 3 years ago

jason-fries commented 3 years ago

The current instructions don't cover all the dependencies needed to run CLMBR, we're missing packages like torch, tqdm, etc. Let's add a requirements.txt (currently not include in the instructions at https://github.com/som-shahlab/ehr_ml/blob/master/doc_src/source/setup.rst) to handle full install process.

woffett commented 3 years ago

I added some extra instructions to doc_src/source/setup.rst, but the current instructions are not great. Ideally we could just run poetry install once and wouldn't have to separately install PyTorch and embedding_dot (poetry allows for adding GitHub repositories as dependencies), but there are issues with getting Poetry to play nicely with each:

There are a few existing GitHub issues / StackOverflow pages that confirm these are open issues that others are also experiencing:

EthanSteinberg commented 3 years ago

This is now fixed.