PyTorch wheel in requirements_data.txt requires Python 3.12 but environment.yml specifies Python 3.10

[dkoh0207]

Hi all — thank you for open-sourcing this excellent work.

I’ve been trying to run the notebooks from the plinder training workshop. Unfortunately, the instructions for setting up the development environment in the documentation are not working for me:

https://plinder-org.github.io/plinder/contribution/development.html#creating-the-conda-environment

Steps to reproduce

conda env create -f environment.yml
conda activate plinder
pip install -r requirements_data.txt

Output

ERROR: torch-2.5.1+cpu-cp312-cp312-linux_x86_64.whl is not a supported wheel on this platform.

It appears that the last PyTorch wheel listed in requirements_data.txt targets a Python 3.12 environment (cp312), while the environment.yml file specifies Python 3.10:

dependencies:
  - python=3.10.*

Is this due to an outdated environment.yml file, or am I missing a step in the setup process?

For reference, here is the current environment.yml:

#
# Conda environment definition with dependencies
#
name: plinder
channels:
  - conda-forge
  - defaults
  - bioconda
dependencies:
  - python=3.10.*
  - reduce
  - openstructure
  - mmseqs2
  - foldseek
  - plip=2.3.0
  - pip:
    - keyrings.google-artifactregistry-auth==1.1.2

Any guidance would be greatly appreciated. Thanks!

[OleinikovasV]

Thank you so much for the kind words and for flagging it up. This should be addressed in the PR #105 .