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ME-ICA / aroma

ICA-AROMA, as a Python package. A work in progress.
Apache License 2.0
7 stars 11 forks source link

Add docker with FSL for integration tests #41

Closed eurunuela closed 3 years ago

eurunuela commented 3 years ago

Closes #40 .

Changes proposed in this pull request:

vinferrer commented 3 years ago

Try sudo?

eurunuela commented 3 years ago

Apparently, the issue is that once the job is finished, the conda environment is removed. Locally, when I exit the docker image and get back in, the conda environment is no longer there. The same thing is happening with CircleCI.

I have no idea why this is happening with Aroma but it doesn't happen with other repos. I actually use nipype/nipype in a repo of mine and have no issues with it.

Any ideas @tsalo @vinferrer ?

tsalo commented 3 years ago

Maybe something's wrong with the caching? That should be the step that makes the environment persist within the Docker image, right?

eurunuela commented 3 years ago

Maybe something's wrong with the caching? That should be the step that makes the environment persist within the Docker image, right?

Right. But I honestly do not know how to check what's going wrong with the caching.

notZaki commented 3 years ago

I think the environment is still there, but conda is not recognizing it for whatever reason. Maybe it's because the environments are in /opt/conda instead of /opt/miniconda-latest, but the cache is using the latter path? Not really sure what's going on there.

Try using the complete path to the environment when activating it, like in this commit.

eurunuela commented 3 years ago

Wow, thank you @notZaki ! I'm surprised that made the trick. When I tested locally I could see the environment under miniconda-latest. I don't know why saving the environment in miniconda-latest and reading it from conda works. This is pretty weird but it works now. Thank you!

eurunuela commented 3 years ago

Well, that was a crazy ride with the conda environments and the environment variables, but it works now!

I would like to know what you think @vinferrer @notZaki @tsalo

eurunuela commented 3 years ago

I think the environment is still there, but conda is not recognizing it for whatever reason. Maybe it's because the environments are in /opt/conda instead of /opt/miniconda-latest, but the cache is using the latter path? Not really sure what's going on there.

It looks like this is not the case in the main branch. I will open a PR with a quick fix for it. This is really weird anyway.