PyHealth/pyproject.toml at master · Rohit-R-Rao/PyHealth · GitHub

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#@meta {desc: "PyHealth build configuration", date: "2025-07-16"}


### Project
#
[project]
name = "pyhealth"
# must be kept in sync with git tags; is not updated by any automation tools
version = "2.0a8"
authors = [
  {name = "John Wu", email = "johnwu3@illinois.edu"},
  {name = "Chaoqi Yang"},
  {name = "Zhenbang Wu"},
  {name = "Patrick Jiang"},
  {name = "Zhen Lin"},
  {name = "Benjamin Danek"},
  {name = "Junyi Gao"},
  {name = "Paul Landes", email = "landes@mailc.net"},
  {name = "Jimeng Sun"},
]
description = "A Python library for healthcare AI"
readme = "README.rst"
requires-python = ">=3.10,<3.14"
dependencies = [
  "torch~=2.7.1",
  "torchvision",
  "transformers~=4.53.2",
  "peft",
  "accelerate",
  "rdkit",
  "ogb>=1.3.5",
  "scikit-learn~=1.7.0",
  "networkx",
  "mne~=1.10.0",
  "urllib3~=2.5.0",
  "numpy~=1.26.4",
  "tqdm",
  "polars~=1.31.0",
  "pandas~=2.3.1",
  "pandarallel~=1.6.5",
  "pydantic~=2.11.7",
]
license = "BSD-3-Clause"
license-files = ["LICENSE.md"]
keywords = [
  "heathcare AI",
  "healthcare",
  "electronic health records",
  "EHRs",
  "machine learning",
  "data mining",
  "neural networks",
  "deep learning",
]

[project.urls]
Homepage = "https://github.com/sunlabuiuc/PyHealth"
Documentation = "https://pyhealth.readthedocs.io/en/latest/about.html"
Repository = "https://github.com/sunlabuiuc/PyHealth.git"
Issues = "https://github.com/sunlabuiuc/PyHealth/issues"
Changelog = "https://github.com/sunlabuiuc/PyHealth/blob/master/CHANGELOG.md"

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"


### Hatchling
#
[tool.hatch.build.targets.wheel]
packages = ["pyhealth"]


### Pixi
#
# specifies properties for the whole workspace
[tool.pixi.project]
channels = ["conda-forge"]
platforms = ["osx-arm64", "linux-64", "linux-aarch64", "win-64"]
preview = ["pixi-build"]

# virtual environments (each under '.pixi/envs') for specific tasks
[tool.pixi.environments]
default = { features = ["pyverbase"], solve-group = "default" }
test = { features = ["pyverbase", "test"] }
base = { features = ["pyverbase", "base"] }
nlp = { features = ["pyverbase", "nlp"] }
build-pypi = { features = ["pyverbase", "build-pypi"], solve-group = "default" }
build-env = { features = ["pyverbase", "build-env"], solve-group = "default" }

# specify where to download the build backend that builds conda files
[tool.pixi.package.build]
backend = { name = "pixi-build-python", version = "0.1.*" }
channels = [
  "https://prefix.dev/pixi-build-backends",
  "https://prefix.dev/conda-forge",
]

# set the Python requirement for its environment
[tool.pixi.feature.pyverbase.dependencies]
python = "~=3.13"

# pixi directly supports depending on PyPI packages, the PyPA calls a
# distributed package a 'distribution'
[tool.pixi.feature.base.pypi-dependencies]
pyhealth = { path = ".", editable = true }

[tool.pixi.feature.test.pypi-dependencies]
pyhealth = { path = ".", editable = true }

[tool.pixi.feature.nlp.pypi-dependencies]
pyhealth = { path = ".", editable = true }

[tool.pixi.feature.nlp.dependencies]
pip = "*"

# dependencies for building the wheel
[tool.pixi.feature.build-pypi.dependencies]
hatchling = "==1.26.3"
twine = "*"  # Add this

[tool.pixi.feature.build-env.dependencies]
# pip for environment extract
pip = "*"

# dependencies needed during build/link time that are specific to the host
# machine
[tool.pixi.package.host-dependencies]
hatchling = "==1.26.3"
python = "~=3.13"


## Tasks
#
# task to use hatchling to build the wheel
[tool.pixi.feature.build-pypi.tasks]
build-wheel = "python -m hatchling build -t wheel --dir $PX_DIST_DIR"
upload-test = "twine upload --repository testpypi $PX_DIST_DIR/*"
upload = "twine upload $PX_DIST_DIR/*"


# use Python built-in unittest library for tests
[tool.pixi.feature.test.tasks.test]
cmd = "python -m unittest discover -t tests -s tests/core -p 'test_*.py' -v"
[tool.pixi.feature.nlp.tasks.testnlp]
cmd = "python -m unittest discover -t tests -s tests/nlp -p 'test_*.py' -v"

# default environment tasks
[tool.pixi.tasks]
# env sanity check
defaultenv = "python -c 'import sys; print(sys.executable, sys.version)'"
# build the conda distribution file
build-conda = "pixi build --output-dir $PX_DIST_DIR"
# export environment.yml
export = "pixi workspace export conda-environment"

# command-line program invocation
[tool.pixi.tasks.invoke]
args = [{ "arg" = "args", "default" = "" }]
env = { CLASS = "zensols.relpo.cli", PYTHONPATH = "src" }
cmd = "\npython -c \"from $CLASS import main;print('_'*80);main('{{args}}'.split())\""