Merge pull request #1 from VectorInstitute/fix_code_check_workflow

Fix code check workflow, add poetry test deps

.github/workflows/code_checks.yml

@@ -40,6 +40,7 @@ jobs:
         with:
           node-version: 18
           cache: 'npm'
+          cache-dependency-path: 'frontend/package-lock.json'
       - name: Install dependencies and check code
         run: |
           poetry env use '3.10'

backend/__init__.py

@@ -0,0 +1 @@
+"""Backend package."""

backend/api/__init__.py

@@ -0,0 +1 @@
+"""Backend API package."""

backend/api/delirium.py

@@ -1,6 +1,7 @@
 """Delirium rates API endpoints."""
 
-from typing import List, Dict
+from typing import Dict, List
+
 from fastapi import FastAPI
 from pydantic import BaseModel
 

backend/api/routes.py

@@ -6,8 +6,8 @@
 
 from backend.api.delirium import (
     get_delirium_rates,
-    get_time_trends,
     get_patient_demographics,
+    get_time_trends,
 )
 
 

pyproject.toml

@@ -12,6 +12,96 @@ fastapi = "^0.111.0"
 uvicorn = "^0.30.1"
 pydantic = "^2.7.4"
 
+[tool.poetry.group.test]
+optional = true
+
+[tool.poetry.group.test.dependencies]
+pytest = "^7.1.1"
+pre-commit = "^2.17.0"
+pytest-cov = "^3.0.0"
+codecov = "^2.1.13"
+mypy = "^1.7.0"
+ruff = "^0.2.0"
+pip-audit = "^2.7.1"
+
+[tool.mypy]
+ignore_missing_imports = true
+install_types = true
+pretty = true
+namespace_packages = true
+explicit_package_bases = true
+non_interactive = true
+warn_unused_configs = true
+allow_any_generics = false
+allow_subclassing_any = false
+allow_untyped_calls = false
+allow_untyped_defs = false
+allow_incomplete_defs = false
+check_untyped_defs = true
+allow_untyped_decorators = false
+warn_redundant_casts = true
+warn_unused_ignores = true
+warn_return_any = true
+implicit_reexport = false
+strict_equality = true
+extra_checks = true
+
+[tool.ruff]
+include = ["*.py", "pyproject.toml", "*.ipynb"]
+line-length = 88
+
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
+docstring-code-format = true
+
+[tool.ruff.lint]
+select = [
+    "A", # flake8-builtins
+    "B", # flake8-bugbear
+    "COM", # flake8-commas
+    "C4", # flake8-comprehensions
+    "RET", # flake8-return
+    "SIM", # flake8-simplify
+    "ICN", # flake8-import-conventions
+    "Q", # flake8-quotes
+    "RSE", # flake8-raise
+    "D", # pydocstyle
+    "E", # pycodestyle
+    "F", # pyflakes
+    "I", # isort
+    "W", # pycodestyle
+    "N", # pep8-naming
+    "ERA", # eradicate
+    "PL", # pylint
+]
+fixable = ["A", "B", "COM", "C4", "RET", "SIM", "ICN", "Q", "RSE", "D", "E", "F", "I", "W", "N", "ERA", "PL"]
+ignore = [
+    "B905", # `zip()` without an explicit `strict=` parameter
+    "E501", # line too long
+    "D203", # 1 blank line required before class docstring
+    "D213", # Multi-line docstring summary should start at the second line
+    "PLR2004", # Replace magic number with named constant
+    "PLR0913", # Too many arguments
+    "COM812", # Missing trailing comma
+]
+
+# Ignore import violations in all `__init__.py` files.
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["E402", "F401", "F403", "F811"]
+
+[tool.ruff.lint.pep8-naming]
+ignore-names = ["X*", "setUp"]
+
+[tool.ruff.lint.isort]
+lines-after-imports = 2
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
+[tool.ruff.lint.pycodestyle]
+max-doc-length = 88
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"