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fraenkel-lab / OmicsIntegrator

This repository is the working directory for the Garnet-Forest bundle of python scripts for analyzing diverse forms of 'omic' data in a network context.
http://fraenkel.mit.edu/omicsintegrator
BSD 2-Clause "Simplified" License
31 stars 21 forks source link

Set max networkx, numpy, and scipy versions #29

Closed agitter closed 6 years ago

agitter commented 6 years ago

Impose a maximum supported networkx version in requirements.txt.

Closes #28.

agitter commented 6 years ago

The Travis build failed. I'm checking our last build that passed to see what else has changed. SciPy version 0.19.1 was used in the successful build and 1.0.0 was used in the build that failed.

agitter commented 6 years ago

This still failed with a max SciPy version. I believe the error comes from https://github.com/fraenkel-lab/OmicsIntegrator/blob/10089ee2850a95f808fca7e530e8baea7a947dc9/scripts/motif_regression.py#L101

We're getting divide by 0 errors in SciPy's linregress [here].(https://github.com/scipy/scipy/blob/v0.19.1/scipy/stats/_stats_mstats_common.py#L106-L118)

That's a separate problem, so I'll create a new issue. Setting a max NumPy version solved the build errors.

agitter commented 6 years ago

@AmandaKedaigle @zfrenchee we don't a formal code review policy for this repository, so I plan to merge this in a few days. Let me know if you have any comments.

AmandaKedaigle commented 6 years ago

This looks good to me! Will comment on the other thread about divide by zero errors.