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.

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

MNT: Pin environment #2863

Closed
wants to merge 12 commits into from
Closed

Conversation

effigies
Copy link
Member

Trying to apply #2853's environment pin approach.

Here, I took the conda= line from 21.0.3's environment, and added lines from nipreps-containers here. I then removed pretty much everything non-numeric that can be installed through pip, ending with:

name: base
channels:
  - conda-forge
  - defaults
dependencies:
  - conda=4.11.0=py38h578d9bd_0
  - python=3.8
  - mkl=2021.3
  - mkl-service=2.4
  - nodejs=16
  - numpy=1.20
  - pandas
  - scikit-image=0.19
  - scikit-learn=0.24
  - scipy=1.6
  - seaborn=0.11
  - traits=6.2
prefix: /opt/conda

Then I created a new environment, installed fmriprep and re-exported:

$ conda env create -n tmp-fmriprep-21-0 -f docker/files/environment.yml
$ conda activate tmp-fmriprep-21-0
$ pip install .
$ conda env export

Then I dropped nipreps tools, since they're very likely to get re-updated between releases and they're all pure Python.

@mgxd
Copy link
Collaborator

mgxd commented Sep 27, 2022

will need to update circle's docker orb

@effigies
Copy link
Member Author

effigies commented Sep 27, 2022

It needs fixing on 20.2.x as well. Would you mind fixing it there, and I can merge forward into this PR? (Or point me to a commit where you did it on master?)

@mgxd
Copy link
Collaborator

mgxd commented Sep 27, 2022

4feb341

Start with environment defined in nipreps/miniconda/py38_1.4.2
Remove most non-numeric libraries
Build environment
Install fMRIPrep (no extras)
Re-export
Remove nipreps
@effigies effigies added this to the 21.0.x (Maintenance) milestone Dec 3, 2022
@effigies
Copy link
Member Author

effigies commented Dec 7, 2022

21.0.x will not have further releases. Closing.

@effigies effigies closed this Dec 7, 2022
@effigies effigies deleted the mnt/pin_environment branch August 24, 2023 03:41
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
Archived in project
Development

Successfully merging this pull request may close these issues.

2 participants