verilylifesciences / site-selection-tool Goto Github PK

Expected Behavior

All tests pass.

Actual Behavior

Notebook execution fails with AssertionError: Predictions must extend farther into the future than ground truth data.
See the full results in https://github.com/verilylifesciences/site-selection-tool/runs/2686564795?check_suite_focus=true

Steps to Reproduce the Problem

Run GitHub Action https://github.com/verilylifesciences/site-selection-tool/actions/workflows/python-package.yml

Expected Behavior

Run GitHub action Test Metis Python package and notebooks on unchanged code, action succeeds.

Actual Behavior

https://github.com/verilylifesciences/site-selection-tool/runs/2017133803?check_suite_focus=true

Please note that a PR was just merged, which triggered the GitHub Action, but the code is unchanged since the prior run of the GitHub Action which was successful for the PR.
https://github.com/verilylifesciences/site-selection-tool/actions/runs/579750192

Steps to Reproduce the Problem

1. Navigate to https://github.com/verilylifesciences/site-selection-tool/actions?query=workflow%3A%22Test+Metis+Python+package+and+notebooks%22
2. Click on "Run Workflow"
3. Choose branch "main"

The code lint check is in the continuous integration workflow, but currently disabled.

The next step is to specify the desired configuration for what is/is not lint. Here's a good example from the Tensorflow project:

• https://github.com/tensorflow/tensorflow/blob/master/CONTRIBUTING.md#python-coding-style
• https://github.com/tensorflow/tensorflow/blob/master/tensorflow/tools/ci_build/pylintrc
• see also https://www.pylint.org/

One of our subpackages requires 3.7. Check to see if we can remove this depencency.

Expected Behavior

Run GitHub action Test Metis Python package and notebooks on unchanged code, action succeeds.

Actual Behavior

Action fails on assembling a forecast from open covid data https://github.com/verilylifesciences/metis/runs/1737103620?check_suite_focus=true

Steps to Reproduce the Problem

1. Navigate to https://github.com/verilylifesciences/metis/actions?query=workflow%3A%22Test+Metis+Python+package+and+notebooks%22
2. Click on "Run Workflow"
3. Choose branch "main"

We're getting the error ImportError: cannot import name 'optim' from 'flax' link. I believe it's now preferred to use optax in place of flax.optim. deflaux has temporarily fixed this issue by pinning the flax version in #40.