Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

python dependencies simplification #88

Open
Remi-Gau opened this issue Sep 18, 2023 · 2 comments · May be fixed by #89
Open

python dependencies simplification #88

Remi-Gau opened this issue Sep 18, 2023 · 2 comments · May be fixed by #89

Comments

@Remi-Gau
Copy link
Contributor

Remi-Gau commented Sep 18, 2023 •
edited
Loading

Currently the python dependencies to install are declared in those place:

  • in the setup.py
  • in the environment.yml
  • in the dockerfile

As far I can tell they do not match.

I would suggest relying only on the python packaging option to have a single source of truth for these otherwise you may run into some reproducibility issue and that would be kind of ironic...
@bclenet
Copy link
Collaborator

bclenet commented Sep 19, 2023

Hi @Remi-Gau,

Thanks ! Indeed this is very much needed. I agree on using the python packaging only.

By the way, there are other reproducibility issues with the Dockerfile that we could discuss in another thread.

@Remi-Gau Remi-Gau mentioned this issue Sep 19, 2023
Closed
@Remi-Gau
Copy link
Contributor Author

here are other reproducibility issues with the Dockerfile that we could discuss in another thread.

actually Elodie and I talked about that and I have been trying to improve things on a branch.

See the diff of this PR: https://github.com/Remi-Gau/narps_open_pipelines/pull/3/files

I can open an issue and work on this repo if you want.

@Remi-Gau Remi-Gau linked a pull request Sep 20, 2023 that will close this issue
Open
8 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

[MAINT] Update packaging Remi-Gau/narps_open_pipelines
2 participants
@Remi-Gau @bclenet