🐛 Bug: Notebook conversion in workflow

[miquelduranfrigola]

Describe the bug.

Automated workflows are failing due to an issue in the Colab Notebook workflow: https://github.com/ersilia-os/ersilia/actions/runs/7048990424/job/19186425834

@megamanics : Do you know what may be happening here? Thanks!

Describe the steps to reproduce the behavior

No response

Expected behavior.

No response

Screenshots.

No response

Operating environment

GitHub Actions Ubuntu

Additional context

No response

[megamanics]

it looks like it started with this commit: https://github.com/ersilia-os/ersilia/commit/2f3c038fb2ebab81a4da5c97929287d009071e64

Try reverting this version to narrow down the source of the problem?

[miquelduranfrigola]

This is useful, thanks! @GemmaTuron do we still need levenshtein? Perhaps we have it as optional?

[miquelduranfrigola]

I have removed the levenshtein dependency (it was not really necessary) but unfortunately this did not solve the issue. I have decided to remove the workflow step related to the notebook working with Python API. It is somewhat redundant with the CLI step. I am unsure what was going on, in my opinion, it is related to the notebook conversion command.

[GemmaTuron]

Hi @miquelduranfrigola

I don't understand, the point of this action was to test the Python API command, the CLI was just an addition, so if anything the CLI is what should be removed.

[GemmaTuron]

I don't think the issue is with the conversion command, since this works fine for the notebook run with the CLI commands. The issue is quite simple: we need to install pandas so that the output can be parsed

try:
    import pandas as pd
except ModuleNotFoundError:
    pd = None

File ~/miniconda3/envs/ersilia/lib/python3.10/site-packages/ersilia/core/model.py:212, in ErsiliaModel._api_runner_return(self, api, input, output, batch_size)
    210 def _api_runner_return(self, api, input, output, batch_size):
    211     if output == "pandas" and pd is None:
--> 212         raise Exception
    213     if output == "json":
    214         R = []

[GemmaTuron]

I've tried simply by adding pandas to the installs, it works in my local but for some reason it does not in the workflow file? https://github.com/ersilia-os/ersilia/actions/runs/7260232462/workflow

[miquelduranfrigola]

Yes, I do not manage to solve this issue either, @GemmaTuron . For now, I have commented out the API

[miquelduranfrigola]

Hi @GemmaTuron - I am apparently unable to solve this issue. Should we seek help?

[GemmaTuron]

@miquelduranfrigola please see my comments regarding pandas in #928 If we make it a requirement of Ersilia I think the problem will be solved.

[miquelduranfrigola]

I am ok with having pandas as a dependency.