pyproject.toml

[tool.poetry]
name = "oktoberfest"
version = "0.8.3"  # <<COOKIETEMPLE_FORCE_BUMP>>
description = "Public repo oktoberfest"
authors = ["Wilhelmlab at Technical University of Munich"]
license = "MIT"
readme = "README.rst"
homepage = "https://github.com/wilhelm-lab/oktoberfest"
repository = "https://github.com/wilhelm-lab/oktoberfest"
documentation = "https://oktoberfest.readthedocs.io"
packages = [
    { include = "oktoberfest" },
]
classifiers = [
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
]


[tool.poetry.dependencies]
python = ">=3.9.0,<3.11.0"
click = ">=8.0.0"
rich = ">=10.3.0"
PyYAML = ">=5.4.1"

anndata = "^0.10.5post1"
array-api-compat = "1.7.1"
matplotlib = "^3.6.3"
mokapot = ">=0.9.1,<0.11.0"
numpy = ">=1.20,<1.25"
seaborn = ">=0.12.2,<0.14.0"
spectrum-fundamentals = ">=0.7.8,<0.8.0"
spectrum-io = ">=0.6.4,<0.7.0"
picked_group_fdr = ">=0.7.1"

#dlomix = {extras = ["rltl-report", "wandb"], url="https://github.com/wilhelm-lab/dlomix/tarball/feature/bmpc", optional = true}
#tensorflow = {version = ">=2.13,<2.16", extras = ["and-cuda"], optional = true}
#wandb = {version = "^0.17.5", optional = true}
koinapy = "^0.0.7"

[tool.poetry.dev-dependencies]
pytest = ">=6.2.3"
coverage = {extras = ["toml"], version = ">=5.3"}
safety = ">=1.9.0"
typeguard = ">=2.12.0"
xdoctest = {extras = ["colors"], version = ">=0.15.0"}
sphinx = ">=4.0.2"
sphinx-autobuild = ">=2021.3.14"
pre-commit = ">=2.11.1"
flake8 = ">=3.8.4"
black = ">=20.8b1"
flake8-bandit = ">=2.1.2"
flake8-bugbear = ">=21.4.3"
flake8-docstrings = ">=1.5.0"
flake8-rst-docstrings = ">=0.2.3"
pep8-naming = ">=0.11.1"
darglint = ">=1.5.8"
pre-commit-hooks = ">=4.0.1"
sphinx-rtd-theme = ">=1.0.0"
sphinx-click = ">=3.0.0"
Pygments = ">=2.8.1"
pyteomics = ">=4.7.3"
types-requests = ">=2.25.2"
types-attrs = ">=19.1.0"
Jinja2 = ">=3.0.1"
mypy = ">=0.910"
pyupgrade = ">=2.31.0"
openpyxl = ">=3.0.10"

[tool.poetry.scripts]
oktoberfest = "oktoberfest.__main__:main"

[tool.poetry.group.dev.dependencies]
sphinx-autodoc-typehints = ">=1.24,<3.0"

#[tool.poetry.extras]
#dlomix = ["dlomix", "tensorflow"]

[tool.black]
line-length = 120

[tool.mypy]
strict = false
pretty = true
show_column_numbers = true
show_error_codes = true
show_error_context = true
ignore_missing_imports = true

[tool.isort]
multi_line_output=3
include_trailing_comma=true
balanced_wrapping=true
line_length=120
profile = "black"

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

[tool.coverage.run]
branch = true
source = ["oktoberfest"]

[tool.coverage.report]
show_missing = true
exclude_also = [
    "if TYPE_CHECKING:"
]

[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"

[tool.setuptools_scm]