diff --git a/.github/workflows/code_checks.yml b/.github/workflows/code_checks.yml index c8aae34..0de132b 100644 --- a/.github/workflows/code_checks.yml +++ b/.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' diff --git a/backend/__init__.py b/backend/__init__.py index e69de29..02a9009 100644 --- a/backend/__init__.py +++ b/backend/__init__.py @@ -0,0 +1 @@ +"""Backend package.""" diff --git a/backend/api/__init__.py b/backend/api/__init__.py index e69de29..747ed4e 100644 --- a/backend/api/__init__.py +++ b/backend/api/__init__.py @@ -0,0 +1 @@ +"""Backend API package.""" diff --git a/backend/api/delirium.py b/backend/api/delirium.py index ec20690..1595e64 100644 --- a/backend/api/delirium.py +++ b/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 diff --git a/backend/api/routes.py b/backend/api/routes.py index fd4afde..306333b 100644 --- a/backend/api/routes.py +++ b/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, ) diff --git a/poetry.lock b/poetry.lock index 9fe8138..22bf4ed 100644 --- a/poetry.lock +++ b/poetry.lock @@ -33,6 +33,38 @@ doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphin test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] trio = ["trio (>=0.23)"] +[[package]] +name = "boolean-py" +version = "4.0" +description = "Define boolean algebras, create and parse boolean expressions and create custom boolean DSL." +optional = false +python-versions = "*" +files = [ + {file = "boolean.py-4.0-py3-none-any.whl", hash = "sha256:2876f2051d7d6394a531d82dc6eb407faa0b01a0a0b3083817ccd7323b8d96bd"}, + {file = "boolean.py-4.0.tar.gz", hash = "sha256:17b9a181630e43dde1851d42bef546d616d5d9b4480357514597e78b203d06e4"}, +] + +[[package]] +name = "cachecontrol" +version = "0.14.0" +description = "httplib2 caching for requests" +optional = false +python-versions = ">=3.7" +files = [ + {file = "cachecontrol-0.14.0-py3-none-any.whl", hash = "sha256:f5bf3f0620c38db2e5122c0726bdebb0d16869de966ea6a2befe92470b740ea0"}, + {file = "cachecontrol-0.14.0.tar.gz", hash = "sha256:7db1195b41c81f8274a7bbd97c956f44e8348265a1bc7641c37dfebc39f0c938"}, +] + +[package.dependencies] +filelock = {version = ">=3.8.0", optional = true, markers = "extra == \"filecache\""} +msgpack = ">=0.5.2,<2.0.0" +requests = ">=2.16.0" + +[package.extras] +dev = ["CacheControl[filecache,redis]", "black", "build", "cherrypy", "furo", "mypy", "pytest", "pytest-cov", "sphinx", "sphinx-copybutton", "tox", "types-redis", "types-requests"] +filecache = ["filelock (>=3.8.0)"] +redis = ["redis (>=2.10.5)"] + [[package]] name = "certifi" version = "2024.6.2" @@ -44,6 +76,116 @@ files = [ {file = "certifi-2024.6.2.tar.gz", hash = "sha256:3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516"}, ] +[[package]] +name = "cfgv" +version = "3.4.0" +description = "Validate configuration and produce human readable error messages." +optional = false +python-versions = ">=3.8" +files = [ + {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"}, + {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"}, +] + +[[package]] +name = "charset-normalizer" +version = "3.3.2" +description = "The Real First Universal Charset Detector. 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+python-versions = "*" +files = [ + {file = "webencodings-0.5.1-py2.py3-none-any.whl", hash = "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78"}, + {file = "webencodings-0.5.1.tar.gz", hash = "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923"}, +] + [[package]] name = "websockets" version = "12.0" @@ -1079,4 +1917,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "6ae398a4abf9657126951c7064964d8cdec00e6dcc40b87ebf245218cd93aa1e" +content-hash = "a283fdc7a3bbe26098c4b1b2b990cfe5468efa87fbac28954d010dce20435741" diff --git a/pyproject.toml b/pyproject.toml index 594f80a..d4d7d4d 100644 --- a/pyproject.toml +++ b/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 = 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# 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"