pyproject.toml

# Build system configuration
[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"

# Project metadata
[project]
name = "flexidot"
description = "Flexible dotplotting of genomic sequences."
readme = "README.md"
requires-python = ">=3.8"
license = { text = "GNU Lesser General Public License v3 (LGPLv3)" }
authors = [
    { name = "Kathrin M. Seibt" },
    { name = "Thomas Schmidt" },
    { name = "Tony Heitkam" },
]

# Classifiers for project categorization
classifiers = [
    "Programming Language :: Python :: 3",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
]

# Project dependencies
dependencies = [
    "biopython",
    "colormap>=1.3.0",
    "colour",
    "easydev",
    "matplotlib",
    "numpy",
    "regex",
    "rich",
]

# Dynamic versioning
dynamic = ["version"]

# Project URLs
[project.urls]
homepage = "https://github.com/flexidot-bio/flexidot"
documentation = "https://github.com/flexidot-bio/flexidot"
repository = "https://github.com/flexidot-bio/flexidot"

# Command-line script entry point
[project.scripts]
flexidot = "flexidot.app:main"

# Hatch build configuration
[tool.hatch.build]
source = "src"

# Exclude files and directories from the build
exclude = ["environment.yml", ".github", ".vscode"]

# Hatch versioning configuration
[tool.hatch.version]
source = "vcs"

# Version control system (VCS) versioning
[tool.hatch.version.vcs]
tag-pattern = "v*"         # Git tags starting with 'v' will be used for versioning
fallback-version = "0.0.0"

# Version file location for VCS
[tool.hatch.build.hooks.vcs]
version-file = "src/flexidot/_version.py"

# Optional dependencies for testing and development
[project.optional-dependencies]
tests = ["pytest", "pytest-cov", "hatch"]
dev = [
    "hatch",
    "isort",
    "mkdocs-jupyter",
    "mkdocs-material",
    "mkdocs",
    "mkdocstrings-python",
    "mkdocstrings",
    "notebook",
    "numpydoc-validation",
    "pre-commit",
    "pymdown-extensions",
    "pytest-cov",
    "pytest",
    "ruff",
    "seaborn",
]

[tool.pytest.ini_options]
addopts = "-v --cov=flexidot --cov-branch --cov-report=xml --cov-report=term"
testpaths = ["tests"]
python_files = ["test_*.py"]

[tool.ruff]
target-version = "py310"
line-length = 88
fix = true

[tool.ruff.lint]
select = [
    "C", # mccabe rules
    "F", # pyflakes rules
    "E", # pycodestyle error rules
    "W", # pycodestyle warning rules
    "B", # flake8-bugbear rules
    "I", # isort rules
    #"D", # pydocstyle rules
]
ignore = [
    "C901", # max-complexity-10
    "E501", # line-too-long
    "I001", # isort-imports
    "B905", # `zip()` without an explicit `strict=` parameter
]

# Don't auto-fix docstring issues - they're too fragile
unfixable = ["D"]

[tool.ruff.lint.per-file-ignores]
"tests/*" = ["D"] # Ignore all pydocstyle rules in tests

[tool.ruff.lint.pydocstyle]
convention = "numpy"

[tool.ruff.format]
indent-style = "space"
quote-style = "single"

[tool.ruff.lint.isort]
known-third-party = [
    "Bio",
    "colormap",
    "colour",
    "easydev",
    "matplotlib",
    "numpy",
    "regex",
]
known-first-party = ["flexidot"]
force-sort-within-sections = true


[tool.isort]
profile = "black"
known_third_party = [
    "Bio",
    "colormap",
    "colour",
    "easydev",
    "matplotlib",
    "numpy",
    "regex",
]
known_first_party = ["flexidot"]
default_section = "THIRDPARTY"
force_sort_within_sections = true

[tool.numpydoc_validation]
checks = [
    "all",  # report on all checks
    "ES01", # but don't require an extended summary
    "EX01", # or examples
    "SA01", # or a see also section
    "SS06", # and don't require the summary to fit on one line
]
exclude = [ # don't report on checks for these
    '\.__init__$',
    '\.__repr__$',
    '\.__str__$',
]
override_SS05 = [ # allow docstrings to start with these words
    '^Process ',
    '^Assess ',
    '^Access ',
]

# Don't process filepaths that match these regex patterns
exclude_files = [
    '^_version\\.py$',
]

[tool.mypy]
# Type hint strictness settings
python_version = "3.10"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = true

# Disable specific error codes for false positives and external library type issues
# arg-type: Path vs str conversions for functions expecting str in other modules
# attr-defined: Attribute access on objects from external libraries (pandas, pyhmmer)
# union-attr: Pandas DataFrame operations that mypy can't fully type check
# index: Indexing operations on Union types from pandas
disable_error_code = ["arg-type", "attr-defined", "union-attr", "index"]

[tool.pydocstyle]
convention = "numpy"
match-dir = "[^\\.].*"     # matches all dirs that don't start with a dot
match = "(?!test_).*\\.py" # matches files that don't start with 'test_' but end with '.py'