release commit

pyproject.toml

@@ -0,0 +1,132 @@
+[tool.poetry]
+name = "MeDaX pipeline"
+version = "1.0.0"
+description = "A unifying framework for biomedical research knowledge graphs"
+authors = [
+    "Ilya Mazien",
+    "Tom Gebhardt",
+    "Lea Michaelis",
+    "Ron Henkel",
+    "Benjamin Winter",
+    "Dagmar Waltemath",
+    "Judith Wodke"
+]
+license = "MIT"
+packages = [
+    { include = "biocypher" }
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Natural Language :: English",
+    "Topic :: Scientific/Engineering :: Bio-Informatics"
+]
+repository = "https://github.com/biocypher/biocypher"
+readme = "README.md"
+
+[project.urls]
+Homepage = "https://www.medizin.uni-greifswald.de/medizininformatik/research/current-projects/medax/"
+
+[tool.poetry.dependencies]
+python = "^3.9"
+PyYAML = ">=5.0"
+more_itertools = "*"
+appdirs = "*"
+treelib = "1.6.4"
+rdflib = "^6.2.0"
+networkx = "^3.0"
+stringcase = "^1.2.0"
+neo4j-utils = "0.0.7"
+pandas = "^2.0.1"
+pooch = "^1.7.0"
+tqdm = "^4.65.0"
+
+[tool.poetry.group.dev.dependencies]
+sphinx = ">=5.0.0"
+sphinx-design = "^0.3.0"
+sphinx-rtd-theme = ">=1.0.0"
+sphinx-last-updated-by-git = ">=0.3"
+sphinx-autodoc-typehints = ">=1.18.0"
+myst-parser = "^0.18.0"
+yapf = "^0.32.0"
+pytest = ">=6.0"
+tox = ">=3.20.1"
+pre-commit = ">=2.17.0"
+bump2version = "*"
+coverage = ">=6.0"
+pytest-cov = "^3.0.0"
+hypothesis = "^6.50.1"
+isort = "^5.10.1"
+ipython = "^8.7.0"
+ipykernel = "^6.23.1"
+sphinxext-opengraph = "^0.8.2"
+coverage-badge = "^1.1.0"
+nbsphinx = "^0.9.2"
+black = "^23.9.1"
+flake8 = "^6.1.0"
+
+[build-system]
+requires = ["poetry-core<2.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry.urls]
+"Bug Tracker" = "https://github.com/biocypher/biocypher/issues"
+
+[tool.pytest.ini_options]
+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