pyproject.toml

[project]
name = "project-template"
version = "0.1.0"
description = "Add your description here"
readme = "README.md"
requires-python = ">=3.12"
dependencies = [
  "cloudpathlib>=0.19.0",
  "hydra-colorlog>=1.2.0",
  "hydra-core>=1.3.2",
  "kaggle>=1.6.17",
  "lightning>=2.4.0",
  "neptune>=1.12.0",
  "polars>=1.9.0",
  "rich>=13.9.2",
  "wandb>=0.18.3",
  "pandas>=2.2.3",
  "litserve>=0.2.3",
]

[dependency-groups]
docs = [
  "mkdocs-autorefs==1.2.0",
  "mkdocs-gen-files==0.5.0",
  "mkdocs-get-deps==0.2.0",
  "mkdocs-material-extensions==1.3.1",
  "mkdocs-material==9.5.41",
  "mkdocs-mermaid2-plugin==1.1.1",
  "mkdocs==1.6.1",
  "mkdocstrings-python==1.12.1",
  "mkdocstrings==0.26.2",
  "pymdown-extensions==10.11.2",
]
lint = ["pre-commit"]
torch = ["torch>=2.5.0", "torchtyping>=0.1.5"]
jax = ["jax>=0.2.21", "torchtyping>=0.1.5"]

[tool.mypy]
disable_error_code = [
  "name-defined",
] # ignore name-defined for torchtyping named shapes

[tool.uv]
dev-dependencies = ["pytest>=8.3.3"]

prerelease = "allow"
find-links = [
  "https://storage.googleapis.com/jax-releases/jax_releases.html",
  "https://storage.googleapis.com/jax-releases/libtpu_releases.html",
  "https://storage.googleapis.com/jax-releases/jax_cuda_releases.html",
  "https://storage.googleapis.com/libtpu-releases/index.html",
]

conflicts = [ # so uv will resolve the groups independently
  [
    { group = "gpu" },
    { group = "cpu" },
    { group = "tpu" },
    { group = "tpu_torch" },
  ],
]

package = true # This makes uv automatically add deepchain_mrna to PYTHONPATH

[[tool.uv.index]]
name = "pytorch-cuda11"
url = "https://download.pytorch.org/whl/cu118"
explicit = true

[tool.uv.sources]
torch = [{ index = "pytorch-cuda11", marker = "platform_system != 'Darwin'" }]
torchvision = [
  { index = "pytorch-cuda11", marker = "platform_system != 'Darwin'" },
]


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