Remove conda

[mogres]

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, setup.cfg, tox.ini and consolidate all configurations into pyproject.toml
• Add pdm.lock to pin exact versions of dependencies
• Update and simplify installation instructions
• Update and simplify 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!

[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]

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.

[mogres]

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!

[rugeli]

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]

We are ready to merge and release cellPACK 1.1.1!! Just re-requested review for some minor changes. Let me know if we're good to go ahead :)

[rugeli]

Thank you for all the hard work! I imagine you ran into plenty of unexpected issues during the transition to the new environment. Just curious: why did we add pdm run to each command? I tested without it and seemed to work fine.

[mogres]

Thank you for all the hard work! I imagine you ran into plenty of unexpected issues during the transition to the new environment. Just curious: why did we add pdm run to each command? I tested without it and seemed to work fine.

pdm run command ensures that the command runs using the python version specified in the (untracked) .pdm-python file. This ensures that the command uses the correct virtual environment even if one isn't activated (using source ./.venv/bin/activate). It's just a matter of convention and not necessary if you activate the environment beforehand!

[meganrm]

Sorry for the slow response, I was also able to set it up locally and run!