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pyproject.toml
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pyproject.toml
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[tool.poetry]
name = "pygenomeviz"
version = "1.1.0"
description = "A genome visualization python package for comparative genomics"
authors = ["moshi4"]
license = "MIT"
homepage = "https://moshi4.github.io/pyGenomeViz/"
repository = "https://github.com/moshi4/pyGenomeViz/"
readme = "README.md"
keywords = [
"bioinformatics",
"genomics",
"matplotlib",
"visualization",
"comparative-genomics",
]
classifiers = [
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Framework :: Matplotlib",
]
[tool.pytest.ini_options]
minversion = "6.0"
addopts = "--cov=src --tb=long -vv --cov-report=xml --cov-report=term"
testpaths = ["tests"]
[tool.ruff]
src = ["src", "tests"]
line-length = 88
# Lint Rules: https://docs.astral.sh/ruff/rules/
[tool.ruff.lint]
select = [
"F", # pyflakes
"E", # pycodestyle (Error)
"W", # pycodestyle (Warning)
"I", # isort
"D", # pydocstyle
]
ignore = [
"D100", # Missing docstring in public module
"D101", # Missing docstring in public class
"D104", # Missing docstring in public package
"D105", # Missing docstring in magic method
"D205", # 1 blank line required between summary line and description
"D400", # First line should end with a period
"D401", # First line should be in imperative mood
"D403", # First word of the first line should be properly capitalized
"D415", # First line should end with a period, question mark, or exclamation point
]
[tool.ruff.lint.pydocstyle]
convention = "numpy"
[tool.poetry.scripts]
pgv-blast = "pygenomeviz.scripts.blast:main"
pgv-mummer = "pygenomeviz.scripts.mummer:main"
pgv-mmseqs = "pygenomeviz.scripts.mmseqs:main"
pgv-pmauve = "pygenomeviz.scripts.pmauve:main"
pgv-download = "pygenomeviz.scripts.download:main"
pgv-gui = "pygenomeviz.scripts.gui:main"
[tool.poetry.dependencies]
python = "^3.8"
matplotlib = ">=3.6.3"
biopython = ">=1.80"
numpy = ">=1.21"
streamlit = { version = ">=1.32.0", optional = true, python = ">=3.8,<3.9.7 || >3.9.7,<4.0" }
[tool.poetry.group.dev.dependencies]
ruff = ">=0.4.0"
pre-commit = ">=3.5.0"
pytest = ">=8.0.0"
pytest-cov = ">=4.0.0"
ipykernel = ">=6.13.0"
[tool.poetry.group.docs.dependencies]
mkdocs = ">=1.2"
mkdocstrings = { extras = ["python"], version = ">=0.19.0" }
mkdocs-jupyter = ">=0.21.0"
mkdocs-material = ">=8.2"
black = ">=22.3.0"
[tool.poetry.extras]
gui = ["streamlit"]
[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"