init public release

2026-09-08 10:59:05 +02:00
commit 9cdf012717
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+
+[project]
+name = "medax-pipeline"
+version = "1.0.1"
+description = "An ETL pipeline to transfer FHIR data into a graph database"
+authors = [
+    "Ilya Mazien",
+    "Tom Gebhardt",
+    "Lea Michaelis",
+    "Ron Henkel",
+    "Benjamin Winter",
+    "Dagmar Waltemath",
+    "Judith Wodke"
+]
+
+license = "MIT"
+readme = "README.md"
+requires-python = ">=3.10"
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Natural Language :: English",
+    "Topic :: Scientific/Engineering :: Medical-Informatics",
+]
+dependencies = [
+    "pyyaml>=5.0",
+    "biocypher>=0.16.0,<1.0.0",
+    "more-itertools",
+    "appdirs",
+    "treelib==1.6.4",
+    "rdflib>=6.2.0,<7.0.0",
+    "networkx>=3.0,<4.0",
+    "stringcase>=1.2.0,<2.0.0",
+    "neo4j-utils==0.0.7",
+    "pandas>=2.0.1,<3.0.0",
+    "pooch>=1.7.0,<2.0.0",
+    "tqdm>=4.65.0,<5.0.0",
+    "requests>=2.31.0,<3.0.0",
+    "python-dotenv>=1.0.0,<2.0.0",
+    "beautifulsoup4>=4.12.3,<5.0.0",
+    "lxml>=5.1.0,<6.0.0",
+]
+
+[project.urls]
+Homepage = "https://www.medizin.uni-greifswald.de/medizininformatik/research/current-projects/medax/"
+Repository = "https://git.uni-greifswald.de/MILA_public/medax_pipeline"
+
+# biocypher is pulled from a feature branch via uv's source override
+[tool.uv.sources]
+#biocypher = { git = "https://github.com/biocypher/biocypher.git", branch = "feat/dynamic-node-property-headers" } #enable this to test the feature branch again
+
+
+[tool.uv]
+package = false
+
+# Dev dependencies (PEP 735 dependency groups, natively understood by uv)
+[dependency-groups]
+dev = [
+    "sphinx>=5.0.0",
+    "sphinx-design>=0.3.0,<0.4.0",
+    "sphinx-rtd-theme>=1.0.0",
+    "sphinx-last-updated-by-git>=0.3",
+    "sphinx-autodoc-typehints>=1.18.0",
+    "myst-parser>=0.18.0,<0.19.0",
+    "yapf>=0.32.0,<0.33.0",
+    "pytest>=6.0",
+    "tox>=3.20.1",
+    "pre-commit>=2.17.0",
+    "bump2version",
+    "coverage>=6.0",
+    "pytest-cov>=3.0.0,<4.0.0",
+    "hypothesis>=6.50.1,<7.0.0",
+    "isort>=5.10.1,<6.0.0",
+    "ipython>=8.7.0,<9.0.0",
+    "ipykernel>=6.23.1,<7.0.0",
+    "sphinxext-opengraph>=0.8.2,<0.9.0",
+    "coverage-badge>=1.1.0,<2.0.0",
+    "nbsphinx>=0.9.2,<0.10.0",
+    "black>=23.9.1,<24.0.0",
+    "flake8>=6.1.0,<7.0.0",
+]
+
+# --- Tool configs below are build-tool-agnostic and carried over unchanged ---
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "--ignore=mdm2neo4j"
+log_cli = true
+log_level = "INFO"
+markers = [
+    "requires_neo4j: Requires connection to a Neo4j server",
+    "requires_postgresql: Requires connection to a PostgreSQL server",
+    "inject_driver_args(driver_args): Arguments for the Driver",
+]
+
+[tool.black]
+line-length = 80
+target-version = ['py310']
+include = '\.pyi?$'
+exclude = '''
+(
+  /(
+      \.eggs
+    | \.git
+    | \.hg
+    | \.mypy_cache
+    | \.tox
+    | \.venv
+    | _build
+    | buck-out
+    | build
+    | dist
+  )/
+)
+'''
+
+[tool.isort]
+from_first = true
+line_length = 80
+multi_line_output = 3
+include_trailing_comma = true
+use_parentheses = true
+known_num = "numpy,pandas"
+sections = "FUTURE,STDLIB,THIRDPARTY,NUM,FIRSTPARTY,LOCALFOLDER"
+no_lines_before = "LOCALFOLDER"
+balanced_wrapping = true
+force_grid_wrap = 0
+length_sort = "1"
+indent = "    "
+profile = "black"
+
+[tool.flake8]
+ignore = ["E203", "D200", "D202", "D401", "D105", "W504"]
+per-file-ignores = [
+    "docs/source/conf.py:D100",
+    "tests/*:D100,D101,D102",
+    "*/__init__.py:F401",
+]
+max-line-length = 80
+count = true