133 lines
2.9 KiB
TOML
133 lines
2.9 KiB
TOML
[tool.poetry]
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name = "MeDaX pipeline"
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version = "1.0.0"
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description = "A unifying framework for biomedical research knowledge graphs"
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authors = [
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"Ilya Mazien",
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"Tom Gebhardt",
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"Lea Michaelis",
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"Ron Henkel",
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"Benjamin Winter",
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"Dagmar Waltemath",
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"Judith Wodke"
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]
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license = "MIT"
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packages = [
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{ include = "biocypher" }
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]
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classifiers = [
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"Development Status :: 3 - Alpha",
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"Intended Audience :: Developers",
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: MIT License",
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"Operating System :: OS Independent",
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"Programming Language :: Python",
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"Natural Language :: English",
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"Topic :: Scientific/Engineering :: Bio-Informatics"
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]
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repository = "https://github.com/biocypher/biocypher"
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readme = "README.md"
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[project.urls]
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Homepage = "https://www.medizin.uni-greifswald.de/medizininformatik/research/current-projects/medax/"
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[tool.poetry.dependencies]
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python = "^3.9"
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PyYAML = ">=5.0"
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more_itertools = "*"
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appdirs = "*"
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treelib = "1.6.4"
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rdflib = "^6.2.0"
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networkx = "^3.0"
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stringcase = "^1.2.0"
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neo4j-utils = "0.0.7"
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pandas = "^2.0.1"
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pooch = "^1.7.0"
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tqdm = "^4.65.0"
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[tool.poetry.group.dev.dependencies]
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sphinx = ">=5.0.0"
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sphinx-design = "^0.3.0"
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sphinx-rtd-theme = ">=1.0.0"
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sphinx-last-updated-by-git = ">=0.3"
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sphinx-autodoc-typehints = ">=1.18.0"
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myst-parser = "^0.18.0"
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yapf = "^0.32.0"
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pytest = ">=6.0"
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tox = ">=3.20.1"
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pre-commit = ">=2.17.0"
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bump2version = "*"
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coverage = ">=6.0"
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pytest-cov = "^3.0.0"
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hypothesis = "^6.50.1"
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isort = "^5.10.1"
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ipython = "^8.7.0"
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ipykernel = "^6.23.1"
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sphinxext-opengraph = "^0.8.2"
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coverage-badge = "^1.1.0"
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nbsphinx = "^0.9.2"
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black = "^23.9.1"
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flake8 = "^6.1.0"
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[build-system]
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requires = ["poetry-core<2.0.0"]
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build-backend = "poetry.core.masonry.api"
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[tool.poetry.urls]
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"Bug Tracker" = "https://github.com/biocypher/biocypher/issues"
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[tool.pytest.ini_options]
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log_cli = true
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log_level = "INFO"
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markers = [
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"requires_neo4j: Requires connection to a Neo4j server",
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"requires_postgresql: Requires connection to a PostgreSQL server",
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"inject_driver_args(driver_args): Arguments for the Driver",
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]
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[tool.black]
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line-length = 80
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target-version = ['py310']
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include = '\.pyi?$'
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exclude = '''
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(
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/(
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\.eggs
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| \.git
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| \.hg
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| \.mypy_cache
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| \.tox
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| \.venv
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| _build
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| buck-out
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| build
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| dist
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)/
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)
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'''
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[tool.isort]
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from_first = true
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line_length = 80
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multi_line_output = 3
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include_trailing_comma = true
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use_parentheses = true
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known_num="numpy,pandas"
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sections = "FUTURE,STDLIB,THIRDPARTY,NUM,FIRSTPARTY,LOCALFOLDER"
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no_lines_before="LOCALFOLDER"
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balanced_wrapping = true
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force_grid_wrap = 0
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length_sort = "1"
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indent = " "
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profile = "black"
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[tool.flake8]
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ignore = ["E203", "D200", "D202", "D401", "D105", "W504"]
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per-file-ignores = [
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"docs/source/conf.py:D100",
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"tests/*:D100,D101,D102",
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"*/__init__.py:F401"
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]
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max-line-length = 80
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count = true
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