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pyproject.toml
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[tool.poetry]
name = "teselagen"
version = "0.5.0"
description = "Teselagen Biotechnology API client"
authors = ["Your Name <[email protected]>"]
license = "MIT"
readme = "README.md"
homepage = "https://github.com/TeselaGen/api-client"
repository = "https://github.com/TeselaGen/api-client"
documentation = "https://github.com/TeselaGen/api-client"
keywords = [
"Synthetic Biology",
"Teselagen",
"DBTL",
"CRISPR",
"DNA Assembly"
]
packages = [
{ include = "teselagen" },
]
# include = []
exclude = [
"**/.credentials",
"**/.test_configuration",
]
[tool.poetry.dependencies]
# general dependencies
python = "^3.9.6"
setuptools = "58.1.0" # Pinned for avoiding deprecation warnings when using 'python setup.py develop'
# NOTE: single_version is unstable, see https://github.com/tiangolo/poetry-version-plugin/tree/0.1.3#warning
single_version = "^1.5.1"
# test dependencies
pytest = "^6.2.5"
pytest-cov = "^3.0.0"
pytest-datadir = "^1.3.1"
pytest-notebook = "^0.10.0"
pytest-timeout = "^2.0.2"
pytest-xdist = "^2.4.0"
# library dependencies
# dna_features_viewer = "^3.1.0"
dna_features_viewer = "^3.0.3"
fastaparser = "^1.1"
# openpyxl = "^3.0.9"
openpyxl = "^3.0.7"
# pandas = "^1.3.4"
pandas = "^2.2.3"
requests = "^2.26.0"
requests-mock = "^1.9.3"
SecretColors = "^1.2.4"
# tenacity = "^8.0.1"
tenacity = "^8.0.0"
tqdm = "^4.62.3"
# optionals
# being used by examples
[tool.poetry.group.extras.dependencies]
# examples = ["fastaparser", "jupyter_contrib_nbextensions", "jupyter-console", "jupyter", "pandas", "seaborn", "tqdm"]
jupyter = { version = "^1.1.1"}
jupyter-contrib-nbextensions = { version = "^0.7.0"}
jupyter-console = { version = "^6.6.3"}
[tool.poetry.group.dev.dependencies]
seaborn = "^0.13.2"
# TODO(diegovalenzuelaiturra): Check if required for testing jupyter notebooks. Check if fixing versions is is still required.
notebook = "^7.2.2"
nglview = "^3.1.2"
nbconvert = "^6.5.0"
# testing, formaters, fixers, linters, etc.
autoflake = "^1.4"
autopep8 = "^1.6.0"
bandit = "^1.7.1"
cleanpy = "^0.3.1"
cohesion = "^1.0.0"
coverage = "^6.2"
docformatter = "^1.4"
fixit = "^0.1.4"
flake8 = "^4.0.1"
flake8-bandit = "^2.1.2"
flake8-broken-line = "^0.4.0"
flake8-bugbear = "^21.11.29"
flake8-commas = "^2.1.0"
flake8-comprehensions = "^3.7.0"
flake8-copyright = "^0.2.2"
flake8-debugger = "^4.0.0"
flake8-docstrings = "^1.6.0"
flake8-eradicate = "^1.2.0"
flake8-executable = "^2.1.1"
flake8-implicit-str-concat = "^0.4.0"
flake8-logging-format = "^0.6.0"
flake8-no-pep420 = "^2.0.0"
flake8-polyfill = "^1.0.2"
flake8-print = "^4.0.0"
flake8-pytest-style = "^1.5.1"
flake8-quotes = "^3.3.1"
flake8-simplify = "^0.14.2"
flake8-type-checking = "^1.2.0"
flake8-typing-imports = "^1.12.0"
flake8-use-pathlib = "^0.2.1"
isort = "^5.10.1"
mypy = "^0.930"
mypy-extensions = "^0.4.3"
pep8 = "^1.7.1"
pep8-naming = "^0.12.1"
pluggy = "^1.0.0"
pyclean = "^2.0.0"
pycodestyle = "^2.8.0"
pydocstyle = "^6.1.1"
pylint = "^2.12.1"
pytest = "^6.2.5"
pytest-cov = "^3.0.0"
pytest-datadir = "^1.3.1"
pytest-testinfra = "^6.4.0"
pytest-timeout = "^2.0.2"
pytest-xdist = "^2.4.0"
pyupgrade = "^2.31.0"
radon = "^5.1.0"
tryceratops = "^1.0.1"
types-PyYAML = "^6.0.1"
types-requests = "^2.26.0"
types-setuptools = "^57.4.3"
unittest2pytest = "^0.4"
vulture = "^2.3"
yapf = "^0.32.0"
# others
pre-commit = "^2.16.0"
# pre-commit = {
# version = "^2.16.0",
# python = "^3.9",
# # python = "^3.9.6",
# }
[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"
[tool.vulture]
# exclude = ["file*.py", "dir/"]
# ignore_decorators = ["@app.route", "@require_*"]
# ignore_names = ["visit_*", "do_*"]
# make_whitelist = true
# min_confidence = 100
# min_confidence = 80
min_confidence = 60
sort_by_size = true
verbose = false
paths = ["conftest.py", "setup.py", "teselagen"]