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pyproject.toml
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pyproject.toml
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[tool.poetry]
name = "prymer"
version = "2.2.0"
description = "Python primer design library"
readme = "README.md"
authors = [
"Yossi Farjoun <[email protected]>",
"Jeff Gentry <[email protected]>",
"Tim Fennell <[email protected]>",
"Nils Homer <[email protected]>",
"Erin McAuley <[email protected]>",
"Matt Stone <[email protected]>",
]
license = "MIT"
homepage = "https://github.com/fulcrumgenomics/prymer"
repository = "https://github.com/fulcrumgenomics/prymer"
documentation = "https://github.com/fulcrumgenomics/prymer"
keywords = ["bioinformatics", "genomics", "dna"]
classifiers = [
"Development Status :: 3 - Alpha",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Environment :: Console",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Software Development :: Documentation",
"Topic :: Software Development :: Libraries :: Python Modules",
]
include = ["LICENSE"]
[tool.poetry.dependencies]
python = "^3.11"
pyproject_hooks= "^1.0.0,!=1.1.0"
pybedlite = "^1.0.0"
strenum = "^0.4.15"
fgpyo = "^0.8.0"
pysam = "^0.22.1"
ordered-set = "^4.1.0"
[tool.poetry.group.dev.dependencies]
poetry = "^1.8.2"
mypy = "^1.5.1"
pytest = "^7.4.4"
pytest-cov = "^4.1.0"
pytest-mypy = "^0.10.3"
pytest-ruff = "^0.3.1"
ruff = "0.3.3"
# dependencies for building docs
mkdocs-autorefs = { version = ">=0.5.0,<1.1.0" }
mkdocs-include-markdown-plugin = { version = ">=6.0.1" }
mkdocs-material = { version = ">=9.2.8" }
mkdocs-table-reader-plugin = { version = ">=2.0.1" }
mkdocs = { version = ">=1.5.2" }
mkdocs-gen-files = { version = ">=0.5.0" }
mkdocs-literate-nav = { version = ">=0.6.1" }
mkdocs-section-index = { version = ">=0.3.9" }
mkdocstrings-python = { version = ">=1.6.2" }
mkdocstrings = { version = ">=0.23.0" }
black = "^24.4.2"
pytest-doctestplus = "^1.2.1"
[tool.poetry.urls]
"Bug Tracker" = "https://github.com/fulcrumgenomics/prymer/issues"
[build-system]
requires = ["poetry-core>=1.6"]
build-backend = "poetry.core.masonry.api"
[tool.git-cliff.changelog]
header = ""
trim = true
body = """
{% for group, commits in commits | group_by(attribute="group") %}
## {{ group | upper_first }}
{% for commit in commits %}
- {{ commit.message | upper_first }} ({{ commit.id | truncate(length=8, end="") }})\
{% endfor %}
{% endfor %}\n
"""
[tool.git-cliff.git]
conventional_commits = true
commit_parsers = [
{ message = "^.+!:*", group = "Breaking"},
{ message = "^feat*", group = "Features"},
{ message = "^fix*", group = "Bug Fixes"},
{ message = "^docs*", group = "Documentation"},
{ message = "^perf*", group = "Performance"},
{ message = "^refactor*", group = "Refactor"},
{ message = "^style*", group = "Styling"},
{ message = "^test*", group = "Testing"},
{ message = "^chore\\(release\\):*", skip = true},
{ message = "^chore*", group = "Miscellaneous Tasks"},
{ body = ".*security", group = "Security"}
]
filter_commits = false
[tool.mypy]
files = ["prymer", "tests"]
python_version = "3.11"
strict_optional = false
check_untyped_defs = true
disallow_incomplete_defs = true
disallow_untyped_calls = true
disallow_untyped_decorators = true
disallow_untyped_defs = true
no_implicit_optional = true
warn_no_return = true
warn_redundant_casts = true
warn_return_any = true
warn_unreachable = true
warn_unused_configs = true
warn_unused_ignores = true
exclude = ["site/", "docs/"]
[[tool.mypy.overrides]]
module = "defopt"
ignore_missing_imports = true
[tool.pytest.ini_options]
minversion = "7.4"
addopts = [
"--ignore=docs/scripts",
"--color=yes",
"--cov",
"--cov-report=xml",
"--cov-branch",
"--mypy",
"--ruff",
"--doctest-plus",
"--doctest-modules",
"-v"
]
doctest_optionflags = "NORMALIZE_WHITESPACE ELLIPSIS"
doctest_plus = "enabled"
testpaths = [
"prymer", "tests"
]
[tool.ruff]
include = ["prymer/**/*.py", "tests/**/*.py"]
line-length = 100
target-version = "py311"
output-format = "full"
[tool.ruff.lint]
select = ["C901", "B", "E", "F", "I", "W", "Q"]
ignore = ["E203", "E701"]
unfixable = ["B"]
[tool.ruff.lint.isort]
force-single-line = true