pyproject.toml

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

[project]
name = "alphadia"
requires-python = ">=3.10.0"
dynamic = ["version", "dependencies", "optional-dependencies"]

authors = [
    {name = "Mann Labs", email = "wallmann@biochem.mpg.de"}
]
description = "A novel proteomics search engine for DIA data based on end-to-end transfer learning."
readme = "README.md"
keywords = [
    "mass spectrometry",
    "proteomics",
    "search engine",
    "DIA",
    "data-independent acquisition",
    "bioinformatics",
    "AlphaPept",
    "AlphaPept ecosystem",
]
license = {file = "LICENSE.txt"}
classifiers = [
    "Development Status :: 4 - Beta",
    # "Development Status :: 5 - Production/Stable",
    # "Development Status :: 6 - Mature",
    # "Development Status :: 7 - Inactive"
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: Apache Software License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]

[project.urls]

"Paper preprint" = "https://www.biochem.mpg.de/mann"
Repository = "https://github.com/MannLabs/alphadia"
#Documentation = "https://readthedocs.org"
#Changelog = "https://github.com/me/spam/blob/master/CHANGELOG.md"
Issues = "https://github.com/MannLabs/alphadia/issues"
"Mann Labs Homepage" = "https://www.biochem.mpg.de/mann"

[tool.setuptools.packages]
find = {}

[tool.setuptools.dynamic]
# https://stackoverflow.com/a/73600610
dependencies = {file = ["requirements/requirements_loose.txt"]}
optional-dependencies = { stable = { file = ["requirements/requirements.txt",
] }, test = { file = [ "requirements/requirements_test.txt",
] }, development = { file = ["requirements/requirements_development.txt", "requirements/requirements_test.txt", "requirements/requirements_docs.txt"
] }}
version = {attr = "alphadia.__version__"}

[project.scripts]
alphadia = "alphadia.cli:run"

[tool.ruff]
extend-exclude = ["misc/.bumpversion.cfg", "tests"]

[tool.ruff.lint]
select =  [
    # pycodestyle
    "E",
    # Pyflakes
    "F",
    # pyupgrade
    "UP",
    # flake8-bugbear
    "B",
    # flake8-simplify
    "SIM",
    # isort
    "I",
    #"ALL"
]

ignore = [
    "D",
    "ANN",
    "SLF001", # Private member accessed TODO this needs to be fixed in alphabase

    "E501",  # Line too long  (ruff wraps code, but not docstrings)
    "B028",  #  No explicit `stacklevel` keyword argument found (for warnings)
    "B905",  # This causes problems in numba code: `zip()` without an explicit `strict=` parameter
    "COM812", #may cause conflicts when used with the formatter
    "ISC001", #may cause conflicts when used with the formatter
    "D211", # no-blank-line-before-class
    "D213", # multi-line-summary-second-line
    "S101", # Use of `assert` detected
    "INP001", # implicit namespace package.
    "ERA001", # Found commented-out code
    "D203", # 1 blank line required before class docstring
    "TD002", "TD003", "FIX002",  # things around TO-DO
    "PT011", #pytest.raises(ValueError) is too broad
    "G004", "EM102", # Logging statement uses f-string
    "TRY003", # Avoid specifying long messages outside the exception class
    "ANN101", # Missing type annotation for `self` in method
    "ANN102", # Missing type annotation for `cls` in classmethod
    "ANN002", # Missing type annotation for `*args`
    "ANN003", # Missing type annotation for `**kwargs
    "FA102", # Missing `from __future__ import annotations
    "EM101", # Exception must not use a string literal, assign to variable first
    "D104", # Missing docstring in public package
    "ANN204", # Missing return type annotation for special method `__init__`
    "D401", # First line of docstring should be in imperative mood
    "B023", # Function definition does not bind loop variable
    "PD901", # Avoid using the generic variable name `df` for DataFrames"
    "TCH003", # Move standard library import into a type-checking block
]