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

Remove conda #294

Open
wants to merge 22 commits into
base: main
Choose a base branch
from
Open

Remove conda #294

wants to merge 22 commits into from

Conversation

mogres
Copy link
Collaborator

@mogres mogres commented Oct 17, 2024

Problem

Closes #293

Solution

Changed the dependency management platform from conda to pyenv + pdm

with @rugeli

Type of change

  • Breaking change (fix or feature that would cause existing functionality to not work as expected)
  • This change requires a documentation update

Change summary:

  • Remove setup.py
  • Add pyproject.toml and pdm.lock
  • Update installation instructions
  • Update github workflows to use pdm for setup with cache
  • Add github workflow to automatically create requirements files

Steps to Verify:

  1. Follow installation instructions in docs/INSTALL.md to install cellPACK using pyenv + pdm.
  2. Run tests using pdm run pytest
  3. Pack a test recipe using pack -r cellpack/tests/recipes/v2/test_spheres.json

Many thanks to Philip Garrison for laying the groundwork for this transition!

Copy link

github-actions bot commented Oct 17, 2024

Packing analysis report

Analysis for packing results located at cellpack/tests/outputs/test_spheres/spheresSST

Ingredient name Encapsulating radius Average number packed
ext_A 25 236.0

Packing image

Packing image

Distance analysis

Expected minimum distance: 50.00
Actual minimum distance: 50.01

Ingredient key Pairwise distance distribution
ext_A Distance distribution ext_A

1. Download the installer

```bash
curl -sSLO https://pdm.fming.dev/install-pdm.py
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

In my case, this command didn't trigger the installation, I used the one from the instruction (curl -sSL https://pdm-project.org/install-pdm.py | python3 -) instead, and it worked smoothly.

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This command just downloads the installer. Step 3 in the instructions (python install-pdm.py) runs the downloaded installer and installs pdm. Thanks for checking this!

Copy link
Collaborator

@rugeli rugeli left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I was able to follow the instructions to install pyenv and pdm, successfully create a virtual environment, and run a packing. Thank you for making these updates, they'll be a great help for our future development!

@mogres mogres requested a review from meganrm October 31, 2024 18:37
* Update makefile to move cleanup
* Specify base python in tox.ini
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

Migrate from setup.py to pyproject.toml using PDM
3 participants