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pyproject.toml
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[tool.poetry]
name = "colrev"
version = "0.12.3"
description = "CoLRev: An open-source environment for collaborative reviews"
authors = ["Gerit Wagner <[email protected]>", "Julian Prester <[email protected]>"]
license = "MIT"
readme = "README.md"
homepage="https://colrev.readthedocs.io/en/latest/"
repository = "https://github.com/CoLRev-Environment/colrev"
documentation = "https://colrev.readthedocs.io/en/latest/"
keywords = ["research", "reproducible research", "open science", "literature", "literature review", "systematic review", "systematic literature review"]
classifiers = [
"Development Status :: 4 - Beta",
"License :: OSI Approved :: MIT License",
"Natural Language :: English",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Topic :: Scientific/Engineering",
"Operating System :: OS Independent",
"Typing :: Typed",
]
include = ["CONTRIBUTING.md", "CHANGELOG.md", "LICENSE", "README.md", "colrev/py.typed"]
[tool.poetry.scripts]
colrev = "colrev.ui_cli.cli:main"
colrev-sync = "colrev.packages.sync.src.sync:main"
colrev-hooks-check = "colrev.hooks.check:main"
colrev-hooks-format = "colrev.hooks.format:main"
colrev-hooks-report = "colrev.hooks.report:main"
colrev-hooks-share = "colrev.hooks.share:main"
colrev-hooks-update = "colrev.hooks.update:main"
[tool.poetry.dependencies]
python = ">=3.9, <4"
click = "^8.1.6"
click_completion = "^0.5.2"
click-repl = "^0.3.0"
inquirer = "^3.1.3"
glom = "^22.1.0"
Jinja2 = "^3.1.2"
tqdm = "^4.64.1"
GitPython= "^3.1.29"
pre-commit = "^2.20.0"
"zope.interface" = "^5.5.0"
dacite = "^1.6.0"
dataclasses-jsonschema = "^2.15.3"
dictdiffer = "^0.9.0"
imagehash = "^4.3.1"
rapidfuzz = "^3.5.2"
bib-dedupe = "^0.7.6"
docker = "6.0.0"
lxml = "^4.9.1"
pandas = "^1.5.0"
openpyxl = "^3.1.2" # required by pandas for Excel
pandasql = "^0.7.3"
PyYAML = "^6.0.0"
feedparser = "^6.0.10" # internally?
pybtex = "^0.24.0" # internally?
toml = "^0.10.2"
requests = "<2.32.0"
urllib3 = "<2.0" # https://github.com/google-deepmind/alphafold/issues/867
requests-cache = "^0.9.6"
beautifulsoup4 = "^4.11.1"
lingua-language-detector = "^2.0.2"
alphabet-detector = "^0.0.7"
pycountry = "^22.3.5"
nameparser = "^1.1.2"
number-parser = "^0.3.2"
pymupdf = "^1.24.3"
pyalex = "^0.10"
crossrefapi = "^1.5.0"
semanticscholar = "^0.6.0"
pygithub = "^2.3.0"
m2r = "^0.3.1"
dash = {version = "^2.11.1", optional = true }
Sphinx = {version = "^5.2.3", optional = true }
sphinx-autodoc-typehints = {version = "^1.19.4", optional = true }
sphinx-click = {version = "^4.3.0", optional = true }
sphinx-rtd-theme = {version = "^1.1.1", optional = true }
sphinx-copybutton = {version = "^0.5.2", optional = true}
"sphinxcontrib.datatemplates" = {version = "^0.9.2", optional = true }
sphinx-design = {version = "^0.5.0", optional = true }
sphinx_collapse = {version = "^0.1.2", optional = true }
repoze-sphinx-autointerface = {version = "^1.0.0", optional = true }
pylint = {version = "3.0.1", optional = true }
pytest = {version = "^7.2.1", optional = true }
pytest-mock = {version = "^3.10.0", optional = true }
pytest-skip-slow = {version = "^0.0.5", optional = true }
requests-mock = {version = "^1.10.0", optional = true }
coverage = {extras = ["toml"], version = "^7.3.2", optional = true }
types-click = {version = "^7.1.8", optional = true }
# Can't do 0.21 with poetry because of https://github.com/python-poetry/poetry/issues/9293
docutils = {version = "!=0.21.post1", optional = true }
[tool.poetry.extras]
web_ui = ["dash"]
docs = ["Sphinx", "sphinx-autodoc-typehints", "sphinx-click", "sphinx-rtd-theme", "sphinxcontrib.datatemplates", "sphinx_collapse", "repoze-sphinx-autointerface", "sphinx-design", "sphinx-copybutton", "docutils"]
dev = ["pylint", "pytest", "coverage", "types-click", "pytest-mock", "requests-mock", "pytest-skip-slow"]
[tool.mypy]
python_version = 3.8
warn_unused_configs = true
ignore_missing_imports = true
[[tool.mypy.overrides]]
module = [
"requests.*",
"yaml.*",
"pkg_resources.*",
]
ignore_missing_imports = true
[tool.pylint.MAIN]
extension-pkg-whitelist = "lxml.etree"
load-plugins = ["colrev.linter.colrev_direct_status_assign", "colrev.linter.colrev_missed_constant_usage", "colrev.linter.colrev_records_variable_naming_convention"]
[tool.pylint.'MESSAGES CONTROL']
disable = ["R0801"]
[tool.coverage.report]
omit = [
"colrev/packages/*", # omit reference implementation
"/usr/*", # omit everything in /usr
"*crossrefapi/crossref/*",
"colrev/env/grobid_service.py",
"/tmp/*",
"tests/*",
"*/bib-dedupe/bib_dedupe/*",
]
[tool.coverage.run]
omit = [
"colrev/packages/*", # omit reference implementation
"/usr/*", # omit everything in /usr
"*crossrefapi/crossref/*",
"colrev/env/grobid_service.py",
"colrev/ops/upgrade.py",
"/tmp/*",
"tests/*",
"*/bib-dedupe/bib_dedupe/*",
]
[tool.ruff]
line-length = 160
[tool.ruff.lint]
per-file-ignores = { "**/{tests,docs}/*" = ["E501"] }
[build-system]
# requires = ["poetry>=1.2.0b1"]
requires = ["poetry-core>=1.0.0", "cython<3.0"]
build-backend = "poetry.core.masonry.api"