pyproject.toml

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# pyproject.toml -- MEvoLib project configuration

## Generic configuration
[project]
name = "MEvoLib"
dynamic = [
    "version",
]
requires-python = ">= 3.8"
description = "Molecular Evolution Library for Python"
readme = "README.md"
authors = [
    {name = "Jorge Alvarez-Jarreta", email = "jalvarez@ebi.ac.uk"}
]
license = {text = "Apache License 2.0"}
keywords = [
    "bioinformatics",
    "phylogenetics",
    "molecular evolution",
    "comparative genomics",
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Environment :: Console",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: Apache Software License",
    "Natural Language :: English",
    "Programming Language :: Python :: 3 :: Only",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Software Development :: Libraries :: Python Modules",
]
dependencies = [
    "biopython >= 1.79",
    "dendropy >= 4.5.2",
    "numpy >= 1.23.2",
]

[project.optional-dependencies]
cicd = [
    "black",
    "coverage",
    "ete3",
    "mypy",
    "pylint",
    "pytest",
    "six",
    "types-requests",
]
dev = [
    "ipython",
]
doc = [
    "mkdocs",
    "mkdocs-autorefs",
    "mkdocs-gen-files",
    "mkdocs-literate-nav",
    "mkdocs-material",
    "mkdocs-material-extensions",
    "mkdocs-section-index",
    "mkdocstrings",
    "mkdocstrings-python",
]

[project.urls]
repository = "https://github.com/JAlvarezJarreta/mevolib"
paper = "https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1303-3"

[project.scripts]
fetch_genbank_seqs = "mevolib.fetch.BioSeqs:main"
get_genes = "mevolib.cluster:main"
get_align = "mevolib.align:main"
get_inference = "mevolib.inference:main"

[tool.setuptools]
package-dir = {"" = "."}

[tool.setuptools.dynamic]
version = {attr = "mevolib.__version__"}

[tool.setuptools.package-data]
"mevolib.data" = ["rCRS.gb"]

[build-system]
requires = [
    "setuptools >= 60",
    "setuptools-scm >= 8.0",
    "wheel",
]
build-backend = "setuptools.build_meta"

[tool.black]
line-length = 110

[tool.pylint.messages_control]
max-line-length = 110
disable = [
    "invalid-name",
    "similarities",
    "too-few-public-methods",
    "too-many-arguments",
    "too-many-locals",
    "too-many-statements",
    "unspecified-encoding",
    "wildcard-import"
]

[tool.mypy]
ignore_missing_imports = true
warn_unused_configs = true

[tool.pytest.ini_options]
addopts = "-v --tb=native"
testpaths = ["tests"]
norecursedirs = ["data", "docs", "*.egg_info"]

[tool.coverage.run]
branch = true
source = [
    "mevolib",
]

[tool.coverage.report]
exclude_lines = [
    # Do not complain about missing debug-only code
    "def __repr__",
    "if self\\.debug",
    # Do not complain if tests do not hit defensive assertion code
    "raise AssertionError",
    "raise NotImplementedError",
    # Do not complain if non-runnable code is not run
    "if __name__ == .__main__.:",
    "def main",
    # Do not complain about abstract methods, they are not run
    "@(abc\\.)?abstractmethod",
]