pyproject.toml

[build-system]
requires = ["setuptools>=77", "wheel"]
build-backend = "setuptools.build_meta"


[project]
name = "felis"
version = "0.2.0"
description = "FELIS - Free Energy of Ligand-protein InteractionS"
readme = "README.md"
requires-python = ">=3.11,<3.13"
authors = [{ name = "FELIS developers" }]
license = "CC-BY-NC-4.0"
license-files = ["LICENSE", "THIRD_PARTY_NOTICES"]
dependencies = [
    "numpy~=1.26",
    "pandas~=2.0",
    "scipy>=1.12",
    "numexpr",
    "mdanalysis~=2.10",
    "openmm>=8.5,<8.6",
    "rdkit~=2024.9",
    "ase~=3.25",
    "gemmi",
    "networkx",
    "tqdm",
    "multiprocess",
    "matplotlib>=3.5",
    "Pillow",
    "pyyaml>=6.0",
    "packaging>=24.0",
    "parmed~=4.3",
]

[project.optional-dependencies]
test = [
    "pytest~=8.0",
    "pytest-cov~=4.1",
    "pytest-xdist~=3.3",
    "pytest-random-order~=1.2",
]

[project.urls]
Homepage = "https://github.com/ByteDance-Seed/felis"
Repository = "https://github.com/ByteDance-Seed/felis"

[tool.setuptools.packages.find]
where = ["."]
include = ["felis*", "bytemol*"]

[tool.setuptools.package-data]
"bytemol.toolkit.protein.residue_reference" = ["*.xml"]


[tool.isort]
py_version = 311
line_length = 120
known_local_folder = ["felis", "bytemol", "prolif"]
skip_gitignore = true
profile = "google"
multi_line_output = 3
include_trailing_comma = true
use_parentheses = true
force_grid_wrap = 0
combine_as_imports = true


[tool.yapf]
based_on_style = "google"
column_limit = 120


[tool.pytest.ini_options]
# Complete FELIS unit tests are run from the repository root with:
#   make test
# This executes both artifact-gated tests with FELIS_TEST_ARTIFACTS=1 and the
# standard FELIS tests under felis/tests, excluding felis/tests/testkit helpers.
log_format = "%(asctime)s %(levelname)s %(message)s"
log_date_format = "%Y-%m-%d %H:%M:%Si"
log_cli = true
log_level = "INFO"
filterwarnings = ["always"]
markers = [
    "serial",
    "artifact: tests that require the FELIS_TEST_ARTIFACTS=1 environment and produce/verify on-disk artifacts",
    "slow: tests that take a long time to run",
    "reference: tests that compare against packaged reference data",
    "external: tests that depend on external tools or services (e.g. GROMACS, OpenMM CLI, network)",
]
testpaths = ["felis"]
norecursedirs = ["submodule", ".git"]


[tool.coverage.run]
omit = ["felis/tests/*"]


[tool.pylint.MASTER]
ignore-paths = ".*deprecated.*.py, .*scripts.*.py"
init-hook = "import sys; sys.path.append('./')"

[tool.pylint.TYPECHECK]
ignored-modules = ["openmm.unit"]


[tool.pylint.FORMAT]
max-line-length = 120
ignore-long-lines = "^\\s*# .*https?://\\S+.*\\S$"


[tool.pylint."MESSAGES CONTROL"]
disable = [
    "missing-docstring",
    "broad-exception-caught",
    "no-member",
    "no-name-in-module",
    "no-self-argument",
    "invalid-name",
    "c-extension-no-member",
    "consider-using-f-string",
    "fixme",
    "use-dict-literal",
    "use-list-literal",
    "consider-using-set-comprehension",
    "consider-using-in",
    "consider-using-from-import",
    "useless-return",
    "too-many-branches",
    "unspecified-encoding",
    "useless-object-inheritance",
    "consider-iterating-dictionary",
    "consider-using-dict-items",
    "no-else-continue",
    "protected-access",
    "too-many-public-methods",
    "consider-using-enumerate",
    "superfluous-parens",
    "no-else-return",
    "arguments-differ",
    "unused-argument",
    "import-outside-toplevel",
    "consider-using-generator",
    "too-many-statements",
    "duplicate-code",
    "logging-fstring-interpolation",
    "unnecessary-lambda",
]


[tool.pylint.DESIGN]
max-args = 12
max-locals = 50
min-public-methods = 1
max-attributes = 25