Andrew Charlwood
76838887e6
Move 6 packages (core, config, data_processing, analysis, visualization, cli) into src/ to reduce root clutter. Merge tools/data.py into data_processing/transforms.py. Move docs to docs/. Path resolution via .pth file (setup_dev.py), pytest pythonpath config, and sys.path bootstrap in rxconfig.py and CLI entry points. Clean up pyproject.toml deps (remove stale pins, add snowflake-connector-python). Fix tomllib import for Python 3.10 compatibility. All 113 tests pass.
58 lines
1.3 KiB
TOML
58 lines
1.3 KiB
TOML
[project]
|
|
name = "patient-pathway-analysis"
|
|
version = "0.1.0"
|
|
description = "Add your description here"
|
|
readme = "README.md"
|
|
requires-python = ">=3.10"
|
|
dependencies = [
|
|
"fastparquet>=2024.11.0",
|
|
"numpy>=1.25.0",
|
|
"pandas>=2.0.3",
|
|
"pillow>=10.0.0",
|
|
"plotly>=5.15.0",
|
|
"pyarrow>=20.0.0",
|
|
"reflex>=0.6.0",
|
|
"snowflake-connector-python>=3.0.0",
|
|
"tomli>=2.0.0",
|
|
]
|
|
|
|
[project.optional-dependencies]
|
|
test = [
|
|
"pytest>=8.0.0",
|
|
"pytest-cov>=4.0.0",
|
|
]
|
|
|
|
[tool.pytest.ini_options]
|
|
pythonpath = ["src"]
|
|
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 = ["src/core", "src/data_processing", "src/analysis", "src/visualization"]
|
|
branch = true
|
|
omit = [
|
|
"*/tests/*",
|
|
"*/__pycache__/*",
|
|
]
|
|
|
|
[tool.coverage.report]
|
|
exclude_lines = [
|
|
"pragma: no cover",
|
|
"def __repr__",
|
|
"raise NotImplementedError",
|
|
"if TYPE_CHECKING:",
|
|
]
|
|
show_missing = true
|