pyproject.toml

[build-system]
requires = ["setuptools>=64", "setuptools_scm[toml]>=6.2", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "xchemalign"
classifiers = [
    "Development Status :: 3 - Alpha",
    "License :: OSI Approved :: Apache Software License",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
]
description = "Tools to generate data suitable for loading into Fragalysis"
dependencies = [
    'rdkit == 2023.3.2',
    'numpy == 1.26.4',
    'pandas == 1.5.3',
    'pyyaml == 6.0',
    'gemmi == 0.6.0',
    'im-standardize-molecule == 0.1.0',
    'scp == 0.14.5',
    'GitPython == 3.1.41',
    'ligand_neighbourhood_alignment@git+https://github.com/xchem/ligand_neighbourhood_alignment',
    'pytest',
    'pytest-order',
    'tqdm',
    'requests',
    'requests-toolbelt'
] # Add project dependencies here, e.g. ["click", "numpy"]
dynamic = ["version"]
license.file = "LICENSE"
readme = "README.md"
requires-python = ">=3.10,<3.12.0"

#[tool.setuptools.packages.find]
#where = ["src/xchemalign"]

[project.optional-dependencies]
dev = [
    "black",
    "mypy",
    "pipdeptree",
    "pre-commit",
    "pydata-sphinx-theme>=0.12",
    "pylint",
    "pytest-cov",
    "sphinx-autobuild",
    "sphinx-copybutton",
    "sphinx-design",
    "tox-direct",
    "types-mock",
]

#[project.scripts]
#ligand_neighbourhood_alignment = "xchem.__main__:main"

#[project.urls]
#GitHub = "https://github.com/ConorFWild/xchem-align"

#[[project.authors]] # Further authors may be added by duplicating this section
#email = "conor.wild@sky.com"
#name = "jfi22496"

[tool.setuptools_scm]
write_to = "src/xchemalign/_version.py"

[tool.mypy]
ignore_missing_imports = true
install_types = true
non_interactive = true
check_untyped_defs = true

[tool.pylint.'MESSAGES CONTROL']
disable = """
    c-extension-no-member,
    consider-using-f-string,
    import-error,
    invalid-name,
    line-too-long,
    missing-class-docstring,
    missing-function-docstring,
    missing-module-docstring,
    R,
    W,
    too-many-lines,
"""

[tool.isort]
float_to_top = true
profile = "black"

[tool.black]
line-length = 119

[tool.pytest.ini_options]
testpaths = ['tests']

#[tool.pytest.ini_options]
## Run pytest with all our checkers, and don't spam us with massive tracebacks on error
#addopts = """
#    --tb=native -vv --doctest-modules --doctest-glob="*.rst"
#    --cov=ligand_neighbourhood_alignment --cov-report term --cov-report xml:cov.xml
#    """
## https://iscinumpy.gitlab.io/post/bound-version-constraints/#watch-for-warnings
#filterwarnings = "error"
## Doctest python code in docs, python code in src docstrings, test functions in tests
#testpaths = "docs src tests"

#[tool.coverage.run]
#data_file = "/tmp/ligand_neighbourhood_alignment.coverage"

#[tool.coverage.paths]
## Tests are run from installed location, map back to the src directory
#source = ["src", "**/site-packages/"]

# tox must currently be configured via an embedded ini string
# See: https://github.com/tox-dev/tox/issues/999
#[tool.tox]
#legacy_tox_ini = """
#[tox]
#skipsdist=True

#[testenv:{pre-commit,mypy,pytest,docs}]
## Don't create a virtualenv for the command, requires tox-direct plugin
#direct = True
#passenv = *
#allowlist_externals =
#    pytest
#    pre-commit
#    mypy
#    sphinx-build
#    sphinx-autobuild
#commands =
#    pytest: pytest {posargs}
#    mypy: mypy src tests {posargs}
#    pre-commit: pre-commit run --all-files {posargs}
#    docs: sphinx-{posargs:build -EW --keep-going} -T docs build/html
#"""