Initial commit before Ralph loop

2026-02-04 13:04:29 +00:00
commit fdd33a67af
89 changed files with 20660 additions and 0 deletions
@@ -0,0 +1,69 @@
+[tool.setuptools]
+py-modules = []
+packages = []
+[project]
+name = "patient-pathway-analysis"
+version = "0.1.0"
+description = "Add your description here"
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+    "darkdetect==0.8.0",
+    "decorator==5.1.1",
+    "et-xmlfile==1.1.0",
+    "executing==1.2.0",
+    "fastparquet>=2024.11.0",
+    "idna==3.4",
+    "itsdangerous==2.1.2",
+    "jedi==0.18.2",
+    "jinja2==3.1.2",
+    "jupyter-core==5.3.1",
+    "numpy==1.25.0",
+    "packaging==23.1",
+    "pandas==2.0.3",
+    "pillow==10.0.0",
+    "plotly==5.15.0",
+    "pyarrow>=20.0.0",
+    "python-dateutil==2.8.2",
+    "reflex>=0.6.0",
+    "tenacity==8.2.2",
+]
+
+[project.optional-dependencies]
+test = [
+    "pytest>=8.0.0",
+    "pytest-cov>=4.0.0",
+]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+addopts = [
+    "-v",
+    "--tb=short",
+    "--strict-markers",
+]
+markers = [
+    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
+    "integration: marks tests as integration tests (require external resources)",
+    "largedata: marks tests that require large datasets (deselect with '-m \"not largedata\"')",
+]
+
+[tool.coverage.run]
+source = ["core", "data_processing", "analysis", "visualization", "tools"]
+branch = true
+omit = [
+    "*/tests/*",
+    "*/__pycache__/*",
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "def __repr__",
+    "raise NotImplementedError",
+    "if TYPE_CHECKING:",
+]
+show_missing = true