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pyproject.toml
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pyproject.toml
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[project]
name = "mibi-bioasq"
authors = [
{name = "Jan Heinrich Merker", email = "[email protected]"},
{name = "Alexander Bondarenko", email = "[email protected]"},
{name = "Adrian Viehweger", email = "[email protected]"},
{name = "Matthias Hagen", email = "[email protected]"},
]
description = "MiBi at BioASQ 2024"
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 = [
"annotated-types~=0.7.0",
"beautifulsoup4~=4.12",
"click~=8.1",
"dspy-ai~=2.4.5",
"elasticsearch7~=7.17",
"elasticsearch7-dsl~=7.3",
"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",
"importlib-metadata~=8.0",
"instructor~=0.6.2",
"joblib~=1.3",
"jupyter~=1.0",
"llama-index-llms-ollama~=0.1.2",
"llama-index-llms-openai~=0.1.9",
"llama-index-postprocessor-rankgpt-rerank~=0.1.3",
"loguru~=0.7.2",
"lxml~=5.1",
"nltk~=3.8",
"openai~=1.3",
"pandas~=2.0",
"pubmed-parser~=0.3.1",
"pydantic~=2.5",
"pyrate-limiter~=3.2",
"pyterrier-caching @ git+https://github.com/seanmacavaney/pyterrier-caching.git@464c983b2785bdf14da0078cb5b6c8fa41336b73",
"pyterrier-dr @ git+https://github.com/terrierteam/pyterrier_dr.git@c620231ebc5dba55486302aaee92aa9033a3c69e",
"pyterrier-t5 @ git+https://github.com/terrierteam/pyterrier_t5.git@63756ebc2968ab03f46a61f0b391e27873226d75",
"python-dotenv~=1.0",
"python-terrier~=0.10.0",
"rank_bm25~=0.2.2",
"rouge-score~=0.1.2",
"requests~=2.31",
"sentence_transformers~=3.1.1",
"scispacy~=0.5.4",
"tqdm~=4.64",
"toml~=0.10.2",
"torch~=2.0",
"transformers~=4.31",
"unpywall~=0.2.3",
]
dynamic = ["version"]
[project.optional-dependencies]
tests = [
"bandit[toml]~=1.7",
"lxml-stubs~=0.5.1",
"mypy~=1.5",
"pandas-stubs~=2.0",
"pytest~=8.0",
"pytest-cov~=6.0",
"ruff~=0.4.1",
"types-tqdm~=4.66",
]
[project.urls]
"Homepage" = "https://github.com/alebondarenko/mibi-bioasq"
"Bug Tracker" = "https://github.com/alebondarenko/mibi-bioasq/issues"
[project.scripts]
mibi = "mibi.cli:cli"
[build-system]
requires = [
"setuptools~=69.0",
"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',
]