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[WIP] Change from conda to uv #141

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[WIP] Change from conda to uv #141

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9951313
remove versioneer
mbackenkoehler Aug 14, 2025
072f30e
disable long_description in setup.py
mbackenkoehler Aug 14, 2025
2aa9174
an environment that resolves all deps
mbackenkoehler Aug 14, 2025
18a703e
towards a working env (...albeit ancient)
mbackenkoehler Sep 4, 2025
26dbd43
pin github deps by version tag
mbackenkoehler Sep 4, 2025
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59 changes: 59 additions & 0 deletions pyproject.toml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,59 @@
[project]
name = "kinoml"
version = "0.1.0"
description = "Structure-informed machine learning for kinase modeling"
requires-python = ">=3.8,<3.12"
dependencies = [
"pandas",
"numpy < 2.0",
"requests",
"pint==0.19.2",
"appdirs",
"tqdm",
"openff-toolkit @ git+https://github.com/openforcefield/openff-toolkit.git@0.14.5",
"openff-units @ git+https://github.com/openforcefield/openff-units.git@0.2.0",
"openff-utilities @ git+https://github.com/openforcefield/openff-utilities.git@v0.1.13",
"xgboost",
"openeye-toolkits>=2020.2.0",
"bravado",
"biopandas",
"awkward",
"pyarrow>=6.0.1",
"mdanalysis>=2.0.0",
"matplotlib",
"ruamel.yaml",
"dask",
"dask-jobqueue",
"papermill==2.2.*",
"watermark",
"torch>=1.8.0",
"torch-geometric",
"pytorch-lightning",
"jupyterlab",
"nglview",
"pytest",
"pytest-cov",
"pytest-xdist",
"codecov",
"nbval",
"Sklearn_PyTorch",
"opencadd @ git+https://github.com/volkamerlab/opencadd.git@v1.0.1",
"openmm>=8.3.1",
"cachetools>=5.5.2",
"rdkit==2022.3.3",
]

[[tool.uv.sources.openeye-toolkits]]
index = "openeye-toolkits-conda"

[[tool.uv.sources.Sklearn_PyTorch]]
url = "https://github.com/ValentinFigue/Sklearn_PyTorch/archive/1b56a43e41de331ecdf73d08418f75bb34c9fa06.tar.gz"

[[tool.uv.index]]
name = "openeye-toolkits-conda"
url = "https://pypi.anaconda.org/OpenEye/simple"

[build-system]
requires = [ "setuptools>=42", "wheel"]
build-backend = "setuptools.build_meta"

8 changes: 3 additions & 5 deletions setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@
"""
import sys
from setuptools import setup, find_packages
import versioneer

short_description = __doc__.split("\n")

Expand All @@ -25,10 +24,9 @@
author='OpenKinome',
author_email='jaime.rodriguez-guerra@choderalab.org',
description=short_description[0],
long_description=long_description,
long_description_content_type="text/markdown",
version=versioneer.get_version(),
cmdclass=versioneer.get_cmdclass(),
# long_description=long_description,
# long_description_content_type="text/markdown",
version="0.1",
license='MIT',

# Which Python importable modules should be included when your package is installed
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