Switch from Python setuptools to Pixi

[plandes]

This modernizes the build to pixi and currently provides the following:

• Run the unit tests in controlled lock (file) environments
• Build a distribution wheel

[Copilot]

Pull Request Overview

This PR modernizes the build system by migrating from Python setuptools to Pixi, a modern cross-platform package manager. It removes legacy setuptools configuration files and introduces comprehensive Pixi configuration for environment management, task execution, and package building.

• Removes setuptools-based configuration files (setup.py, setup.cfg, requirements-nlp.txt)
• Introduces comprehensive Pixi configuration with multi-environment support and task definitions
• Updates test files to use proper unittest structure instead of standalone script execution
• Modernizes dependency management and CI/CD workflows to use Pixi

Reviewed Changes

Copilot reviewed 16 out of 27 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
pyproject.toml	New comprehensive project configuration with Pixi environments and build settings
setup.py, setup.cfg, requirements-nlp.txt	Removed legacy setuptools configuration files
tests/todo/test_mortality_prediction.py	Converted from script to proper unittest structure
tests/todo/test_mimic_code.py	Converted to unittest with commented TODOs for missing functions
tests/core/test_*.py	Cleaned up path manipulation imports
pyhealth/tasks/*.py	Removed deprecated pkg_resources imports
makefile	Updated build system to use Pixi commands
.github/workflows/test.yml	Updated CI to use Pixi instead of pip
LICENSE.md	Added new BSD-3-Clause license file

Comments suppressed due to low confidence (10)

pyproject.toml:23

• Python 3.13 does not exist yet. The latest stable Python version is 3.12. Consider changing to ">=3.10,<3.13" or similar.

requires-python = ">=3.13,<3.14"

pyproject.toml:25

• PyTorch 2.7.1 does not exist. The latest PyTorch version is around 2.1.x. Consider using "torch~=2.1.0" or remove the specific patch version.

  "torch~=2.7.1",

pyproject.toml:28

• RDKit 2025.3.3 is a future version that does not exist. Consider using a current stable version like "rdkit~=2023.9.0".

  "rdkit==2025.3.3",

pyproject.toml:98

• Python 3.13 does not exist yet. This should match the requires-python field and use an existing Python version.

python = "~=3.13"

pyproject.toml:126

• Python 3.13 does not exist yet. This should use an existing Python version that matches the project requirements.

python = "~=3.13"

.github/workflows/test.yml:24

• Python 3.13 does not exist yet. Use an existing Python version like '3.12' or '3.11'.

          python-version: '3.13'

tests/todo/test_mimic_code.py:104

• The class name 'Test' is too generic. Consider a more descriptive name like 'TestMimicCode' or 'MimicCodeTests'.

class Test(unittest.TestCase):

tests/todo/test_mortality_prediction.py:418

• The class name 'Test' is too generic. Consider a more descriptive name like 'TestMortalityPrediction' or 'MortalityPredictionTests'.

class Test(unittest.TestCase):

tests/todo/test_mortality_prediction.py:419

• The method name 'test' is too generic. Consider more descriptive names like 'test_mimic3_mortality_prediction' and 'test_multimodal_mortality_prediction'.

    def test(self):

tests/todo/test_mimic_code.py:105

• The method name 'test' is too generic. Consider a more descriptive name like 'test_mimic_code_functionality'.

    def test(self):

[Copilot]

The variable dependencies is a list but version() expects a string package name. This should be version(dependencies[0]) or loop through the dependencies list.

Suggested change

	version(dependencies)
	version(dependencies[0])

[Copilot]

Copilot encountered an error and was unable to review this pull request. You can try again by re-requesting a review.

[jhnwu3]

Works! Will need to update the metadata to PyHealth 2.0a, but let's keep this rolling!