pyproject.toml

[build-system]
requires = ["setuptools>=45", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "get_model"
version = "0.1.0"
description = "GET: a foundation model of transcription across human cell types"
readme = "README.md"
authors = [
    { name = "Xi Fu", email = "fuxialexander@gmail.com" }
]
license = { text = "CC BY-NC 4.0" }
requires-python = ">=3.10"
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "License :: Other/Proprietary License",
    "Programming Language :: Python :: 3",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]

dependencies = [
    "einops",
    "gcell @ git+https://github.com/GET-Foundation/gcell.git@main",
    "genomespy",
    "hydra-core",
    "lightning",
    "matplotlib",
    "minlora @ git+https://github.com/cccntu/minLoRA.git@main",
    "numpy",
    "omegaconf",
    "pandas",
    "pyranges @ git+https://github.com/pyranges/pyranges@master",
    "scipy",
    "seaborn",
    "timm",
    "torch",
    "torchmetrics",
    "tqdm",
    "wandb",
    "zarr<3",
]

[project.optional-dependencies]
dev = [
    "pytest>=7.0.0",
    "pytest-cov>=4.0.0", 
    "pytest-mock>=3.10.0",
    "pytest-asyncio>=0.21.0",
    "sphinx>=7.0.0",
    "sphinx-rtd-theme>=1.3.0",
    "myst-parser>=2.0.0",
    "sphinx-autodoc-typehints>=1.25.0",
    "mypy>=1.0.0",
    "pre-commit>=3.0.0",
    "setuptools_scm",
    "towncrier",
    "ipykernel",
    "jupyter",
    "nbsphinx",
    "nbformat",
    "snapatac2",
    "scanpy",
    "scikit-misc",
]
tutorial = [
    "ipykernel",
    "jupyter",
    "nbsphinx",
    "nbformat",
    "snapatac2",
    "scanpy",
    "scikit-misc",
]

[project.urls]
Documentation = "https://fuxialexander.github.io/get_model/"
Repository = "https://github.com/fuxialexander/get_model"

[tool.setuptools]
include-package-data = true

[tool.setuptools.packages.find]
where = ["./"]  # Start looking for packages inside the get_model folder
exclude = ["test*"]  # Exclude test packages
include = ["get_model*"]  # Only include packages starting with "get_model"

[tool.setuptools.package-data]
"get_model" = ["config/**/*.yaml", "**/*.yaml", "**/*.json", "config/*.yaml"]

[tool.hatch.build.targets.wheel]
packages = ["get_model"]

[tool.hatch.envs.default.scripts]
test = "pytest {args:tests}"
test-cov = "pytest --cov {args:tests}"
docs = "sphinx-build -b html docs/source docs/build/html"

[tool.hatch.build.hooks.vcs]
version-file = "get_model/_version.py"  # Update this path if the version file is inside get_model

[tool.hatch.metadata]
allow-direct-references = true

[tool.pytest.ini_options]
addopts = [
    "--import-mode=importlib",
    "--strict-markers",
    "--doctest-modules",
]
testpaths = ["./tests"]
xfail_strict = true
filterwarnings = [
    "error:The specified parameters:FutureWarning",
    "ignore:FigureCanvasAgg is non-interactive:UserWarning",
]

[tool.coverage.run]
data_file = "test-data/coverage"
source_pkgs = ["gcell"]
omit = ["tests/*"]

[tool.coverage.xml]
output = "test-data/coverage.xml"

[tool.coverage.paths]
source = [".", "**/site-packages"]

[tool.coverage.report]
exclude_also = [
    "if __name__ == .__main__.:",
    "if TYPE_CHECKING:",
    '@(numba\.|nb\.)njit.*',
]

[tool.ruff]
src = ["./"]

[tool.ruff.format]
docstring-code-format = true

[tool.ruff.lint]
select = [
    "E",       # Error detected by Pycodestyle
    "F",       # Errors detected by Pyflakes
    "W",       # Warning detected by Pycodestyle
    "UP",      # pyupgrade
    "I",       # isort
    "TCH",     # manage type checking blocks
    "TID251",  # Banned imports
    "ICN",     # Follow import conventions
    "PTH",     # Pathlib instead of os.path
    "PYI",     # Typing
    "PLR0917", # Ban APIs with too many positional parameters
    "PT",      # Pytest style
    "SIM",     # Simplify control flow
]
ignore = [
    "E501",  # line too long
    "E402",  # module level import not at top of file
    "F841",  # Unused variable
]

[tool.ruff.lint.isort]
known-first-party = ["get_model"]

[tool.towncrier]
package = "get_model"
directory = "docs/release-notes"
filename = "docs/release-notes/{version}.md"
single_file = false
package_dir = "./"
issue_format = "{{pr}}`{issue}`"
title_format = "(v{version})=\n### {version} {{small}}`{project_date}`"

[tool.towncrier.fragment.bugfix]
name = "Bug fixes"

[tool.towncrier.fragment.doc]
name = "Documentation"

[tool.towncrier.fragment.feature]
name = "Features"

[tool.towncrier.fragment.misc]
name = "Miscellaneous improvements"

[tool.towncrier.fragment.performance]
name = "Performance"

[tool.towncrier.fragment.breaking]
name = "Breaking changes"

[tool.towncrier.fragment.dev]
name = "Development Process"