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pyproject.toml
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pyproject.toml
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[metadata]
description-file = "README.md"
[build-system]
# virtualenv 20.0.34 partly breaks pre-commit under conda
# https://github.com/ContinuumIO/anaconda-issues/issues/12094
# Poetry uses pip and setuptools (although they're not included as dependencies)
# We don't need to list wheel here, but setting a min vr can avoid generating inferior wheels
requires = ["poetry>=1.1,<2", "virtualenv==20.0.33", "wheel>=0.36,<1.0"]
build-backend = "poetry.masonry.api"
#########################################################################################
# Poetry metadata
#########################################################################################
[tool.poetry]
name = "mandos"
version = "0.2.0"
description = "Get the biological targets of compounds."
authors = ["Douglas Myers-Turnbull"]
maintainers = ["Douglas Myers-Turnbull"]
license = "Apache-2.0"
readme = "README.md"
keywords = ["cheminformatics", "chembl", "pubchem", "drug-discovery"]
homepage = "https://github.com/dmyersturnbull/mandos"
repository = "https://github.com/dmyersturnbull/mandos"
documentation = "https://mandos-chem.readthedocs.io"
classifiers = [
"Development Status :: 3 - Alpha",
"Natural Language :: English",
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.9",
"Intended Audience :: Science/Research",
"Intended Audience :: Developers",
"Operating System :: OS Independent",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Scientific/Engineering :: Chemistry",
'Typing :: Typed'
]
[tool.poetry.urls]
CI = "https://github.com/dmyersturnbull/mandos/actions"
Issues = "https://github.com/dmyersturnbull/mandos/issues"
Download = "https://pypi.org/project/mandos/"
#########################################################################################
# Poetry build & dependencies
#########################################################################################
[tool.poetry.scripts]
mandos = "mandos.cli:cli"
[tool.poetry.dependencies]
python = "^3.10"
aioquic = {version=">=0.9, <1.0", optional=true}
chembl-webresource-client = "^0.10"
click = ">=8"
decorateme = "^0.2.3"
defusedxml = ">=0.7, <1.0"
fastapi = {version=">=0.7, <1.0", optional=true}
hypercorn = {version=">=0.11, <1.0", optional=true}
itsdangerous = {version="^2", optional=true}
loguru = ">=0.5, <1.0"
numpy = "^1.21"
orjson = "^3.6"
pandas = "^1.3"
pint = ">=0.18, <1.0"
pocketutils = "^0.8.5"
pydantic = "^1.8"
regex = ">=2021.11"
requests = "^2.26"
suretime = ">=0.1.1, <1.0"
tomlkit = ">=0.7, <1.0"
typeddfs = {version=">=0.16.4, <1.0", extras=["feather", "parquet", "excel", "xml"]}
typer = ">=0.4, <1.0"
tzdata = ">=2021.5"
joblib = {version="^1.1", optional=true}
matplotlib = {version="^3.4", optional=true}
selenium = {version="^4", optional=true}
scikit-learn = {version="^1", optional=true}
seaborn = {version=">=0.11, <1.0", optional=true}
umap-learn = {version=">=0.5, <1.0", optional=true}
[tool.poetry.extras]
analysis = ["joblib", "scikit-learn", "umap-learn"]
server = ["aioquic", "fastapi", "hypercorn", "itsdangerous"]
viz = ["matplotlib", "seaborn"]
scrape = ["selenium"]
all = ["matplotlib", "scikit-learn", "seaborn", "selenium", "umap-learn"]
[tool.poetry.dev-dependencies]
pre-commit = "^2.15"
pre-commit-hooks = "^4"
bandit = "^1.7"
flake8 = "^4"
flake8-bugbear = ">=21.9.2"
flake8-docstrings = "^1.6"
nbqa = "^1.1"
pytest = "^6"
coverage = {extras = ["toml"], version = "^6"}
pytest-cov = "^3"
Sphinx = "^4.2"
sphinx-autoapi = "^1.5"
sphinx-copybutton = ">=0.4, <1.0"
sphinx-rtd-theme = "^1"
sphinxcontrib-mermaid = ">=0.7, <1.0"
#########################################################################################
# Tyrannosaurus
#########################################################################################
[tool.tyrannosaurus.options]
align = true
sort = true
[tool.tyrannosaurus.sources]
metavm = "'ubuntu-20.04'"
metavmbox = "'ubuntu/focal64'"
pymetaversion = "'3.9'"
pycompatversions = "tool.poetry.dependencies"
pytoxversions = "tool.poetry.dependencies"
status = "'Development'"
date = "'${today}'"
copyright = "'Copyright 2020–2021'"
doc_license = "'CC BY 4.0'"
doc_license_url = "'https://creativecommons.org/licenses/by/4.0'"
version = "tool.poetry.version"
release = "tool.poetry.version"
devdeps = "tool.poetry.dev-dependencies"
precommitvr = "tool.poetry.dev-dependencies"
precommitconfigvr = "tool.poetry.dev-dependencies"
linelength = "tool.black.line-length"
authors = [
"Douglas Myers-Turnbull <github:dmyersturnbull,orcid:0000-0003-3610-4808>",
]
maintainers = "tool.tyrannosaurus.sources.authors"
[tool.tyrannosuarus.paths]
recipe = "'recipes/${name}/meta.yml'"
environment = "'environment.yml'"
[tool.tyrannosaurus.targets]
pyproject = true
init = true
tox = true
docs = true
recipes = true
environment = true
license = true
authors = true
github = true
travis = true
dockerfile = true
readme = true
changelog = true
citation = true
codemeta = true
#########################################################################################
# Testing
#########################################################################################
# This will be used in a future version of pytest:
#[tool.pytest]
[tool.pytest.ini_options]
log_cli = true
log_cli_level = "WARNING"
log_cli_format = "%(asctime)s [%(levelname)7s] %(name)s: %(message)s (%(filename)s:%(lineno)s)"
log_cli_date_format = "%Y%m%d %H:%M:%S"
[tool.coverage.paths]
source = ["mandos"]
[tool.coverage.run]
source = ["mandos"]
[tool.coverage.report]
show_missing = true
#########################################################################################
# Style checking
#########################################################################################
[tool.nbqa.mutate]
black = 1
[tool.nbqa.addopts]
black = ["--extend-ignore=E203"]
[tool.black]
line-length = 100
target-version = ["py39"]
[mypy]
check_untyped_defs = true
strict_optional = true
[tool.pycodestyle]
max-line-length = 100
statistics = true
[tool.pydocstyle]
# 212 and 213 contradict; 203 and 204 contradict; D302 is not relevant in Py3
ignore = ["D203", "D212", "D302"]