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pyproject.toml
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pyproject.toml
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[project]
name = "trec-biogen"
authors = [
{name = "Jan Heinrich Merker", email = "[email protected]"},
]
description = "Webis at TREC 2024 BioGen."
readme = "README.md"
requires-python = ">=3.10"
classifiers = [
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Operating System :: OS Independent",
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering",
]
dependencies = [
"aiohttp~=3.9",
"annotated-types~=0.7.0",
"certifi~=2024.7",
"cyclopts~=3.0",
"dspy-ai~=2.5.0",
"elasticsearch7~=7.17",
"elasticsearch7-dsl~=7.3",
"en_core_web_sm @ https://github.com/explosion/spacy-models/releases/download/en_core_web_sm-3.7.1/en_core_web_sm-3.7.1-py3-none-any.whl",
"en_core_sci_sm @ https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.4/en_core_sci_sm-0.5.4.tar.gz",
"ir-measures~=0.3.3",
"joblib~=1.4",
"jupyter~=1.0",
"more-itertools~=10.3",
"optuna~=4.0",
"optuna-integration~=4.0",
"pandas~=2.0",
"pyarrow~=18.0",
"pydantic[email]~=2.5",
"pypdf~=5.0",
"pyterrier-dr @ git+https://github.com/terrierteam/pyterrier_dr.git@123a5d0e76824b275bad910f76547b811baebebb",
"pyterrier-t5 @ git+https://github.com/terrierteam/pyterrier_t5.git@679e3320b0f7c997de108bc44f66ef15fba72f08",
"python-dotenv~=1.0",
"python-terrier~=0.12.0",
"ragas~=0.1.15",
"ray[default,data]~=2.40.0",
"ray-elasticsearch~=1.0.0",
"rouge-score~=0.1.2",
"scikit-learn~=1.5",
"spacy~=3.7",
"tqdm~=4.64",
"wandb~=0.18.1",
]
dynamic = ["version"]
[project.optional-dependencies]
tests = [
"bandit[toml]~=1.7",
"mypy~=1.5",
"pandas-stubs~=2.0",
"pyarrow-stubs~=10.0",
"pytest~=8.0",
"pytest-cov~=6.0",
"ruff~=0.8.1",
"types-tqdm~=4.66",
]
[project.urls]
"Homepage" = "https://github.com/webis-de/trec24-biogen"
"Bug Tracker" = "https://github.com/webis-de/trec24-biogen/issues"
[project.scripts]
trec-biogen = "trec_biogen.cli:app"
[build-system]
requires = [
"setuptools~=75.4",
"setuptools-scm~=8.0",
]
build-backend = "setuptools.build_meta"
[tool.setuptools.packages.find]
exclude = [
"build",
"venv",
"notebooks",
"data",
]
[tool.setuptools_scm]
[tool.ruff]
exclude = [
"build",
"venv",
"notebooks",
"data",
"scripts", # FIXME: Include again, after fixing the issues.
]
[tool.mypy]
exclude = [
"build",
"venv",
"notebooks",
"data",
"scripts", # FIXME: Include again, after fixing the issues.
]
ignore_missing_imports = true
[tool.bandit]
exclude_dirs = [
"build",
"venv",
"notebooks",
"data",
]
[tool.bandit.assert_used]
skips = ["**/test_*.py"]
[tool.pytest.ini_options]
log_cli = "True"
filterwarnings = [
'ignore:FUNCTIONS is deprecated and will be removed in future versions:DeprecationWarning',
]