Upgrade to python 3.11

[mogres]

Problem

Updates the python version to 3.11, since python 3.9 will be deprecated in October 2025

Solution

Added support for python 3.11 and changed the build backend to use uv for faster installs.

Type of change

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

Change summary:

• Update pyproject.toml to use python 3.11
• Use uv as build backend
• Update README.md to provide installation instructions
• Updated the pull request and issue templates
• Update the github actions to use uv

Steps to Verify:

1. Install uv

curl -LsSf https://astral.sh/uv/install.sh | sh

2. Install cellPACK with python 3.11

uv sync

3. Activate environment

source .venv/bin/activate

4. Pack a test recipe

pack -r cellpack/tests/recipes/v2/test_spheres.json -c cellpack/tests/packing-configs/test_config.json

You can also run commands using uv run COMMAND without activating the environment.

[github-actions]

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

Distance analysis

Expected minimum distance: 50.00
Actual minimum distance: 50.01

Ingredient key	Pairwise distance distribution
ext_A

[rugeli]

Worked fine on my end, uv is pretty handy indeed!

[mogres]

Worked fine on my end, uv is pretty handy indeed!

Thanks @rugeli! Do we need to do any testing for the cellPACK client? Or would this work regardless.

[rugeli]

Worked fine on my end, uv is pretty handy indeed!

Thanks @rugeli! Do we need to do any testing for the cellPACK client? Or would this work regardless.

@mogres feel free to merge it! Alli and I can deal with any client issues that come up and update docker files.