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Remove conda #294

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Remove conda #294

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mogres
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@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!

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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

@mogres mogres force-pushed the feature/remove-conda branch from 110ea0e to 5c690d3 Compare October 18, 2024 18:34
1. Download the installer

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

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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!

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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
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Migrate from setup.py to pyproject.toml using PDM
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