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pyproject.toml
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[tool.poetry]
name = "capfinder"
version = "0.4.3"
description = "A package for decoding RNA cap types"
authors = ["Adnan M. Niazi <[email protected]>"]
license = "MIT"
readme = "README.md"
documentation = "https://adnaniazi.github.io/capfinder"
homepage = "https://adnaniazi.github.io/capfinder"
repository = "https://github.com/adnaniazi/capfinder"
classifiers = [
"Development Status :: 4 - Beta",
"Intended Audience :: Developers",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Topic :: Software Development :: Libraries :: Python Modules",
"Typing :: Typed",
]
packages = [{ include = "capfinder", from = "src" }]
[tool.poetry.dependencies]
python = ">=3.10, <3.13"
parasail = "^1.3.4"
mpire = "^2.8.0"
tqdm = "^4.66.1"
pytest-mock = "^3.11.1"
matplotlib = "^3.8.0"
loguru = "^0.7.2"
bokeh = "^3.3.0"
toml = "^0.10.2"
types-toml = "^0.10.8.7"
types-tqdm = "^4.66.0.20240106"
pod5 = "^0.3.10"
comet-ml = "^3.39.3"
polars = "^0.20.21"
hpack = "^4.0.0"
httpx = "^0.27.0"
biopython = "^1.83"
pre-commit = "^3.7.0"
keras = "^3.3.2"
tensorflow = "^2.16.1"
keras-tuner = "^1.4.7"
prefect = "^2.18.3"
prefect-dask = "^0.2.8"
scikit-learn = "^1.4.2"
pysam = "^0.22.1"
typer = "^0.12.3"
imbalanced-learn = "^0.12.3"
# JAX dependencies
jax = { version = "*", optional = true }
[tool.poetry.extras]
cpu = ["jax"]
gpu = ["jax"]
tpu = ["jax"]
[[tool.poetry.source]]
name = "pypi"
priority = "primary"
[tool.poetry.group.dev.dependencies]
autoflake = "*"
black = "*"
flake8 = "*"
flake8-bugbear = "*"
flake8-builtins = "*"
flake8-comprehensions = "*"
flake8-debugger = "*"
flake8-eradicate = "*"
flake8-logging-format = "*"
isort = "*"
mkdocstrings = { version = ">=0.18", extras = ["python"] }
mkdocs-material = "*"
mypy = "*"
pep8-naming = "*"
pre-commit = "*"
pymdown-extensions = "*"
pytest = "*"
pytest-github-actions-annotate-failures = "*"
pytest-cov = "*"
python-kacl = "*"
pyupgrade = "*"
tryceratops = "*"
ruff = "^0.5.1"
types-setuptools = "*"
[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"
[tool.isort]
profile = "black"
src_paths = ["src", "tests"]
[tool.black]
target-version = ["py310", "py311", "py312"]
include = '\.pyi?$'
[tool.pytest.ini_options]
addopts = """\
--cov capfinder \
--cov tests \
--cov-report term-missing \
--no-cov-on-fail \
"""
[tool.coverage.report]
fail_under = 0
exclude_lines = ['if TYPE_CHECKING:', 'pragma: no cover']
[tool.mypy]
disallow_any_unimported = false
disallow_untyped_defs = true
no_implicit_optional = true
strict_equality = true
warn_unused_ignores = true
warn_redundant_casts = true
warn_return_any = true
check_untyped_defs = true
show_error_codes = true
ignore_missing_imports = true
[tool.poetry.scripts]
capfinder = "capfinder.cli:app"
[tool.setuptools_scm]
[tool.setuptools.packages.find]
where = ["src"]
[tool.setuptools.package-data]
"capfinder.model" = ["*.keras"]