update pre-commit and use ruff for linting/formating (#105)

* update pre-commit and use ruff for linting/formating

* use python 3.11 for lint

* try pydantic 1.

---------

Co-authored-by: Jonathan Healy <[email protected]>

.github/workflows/cicd.yaml

@@ -27,7 +27,7 @@ jobs:
  cache-dependency-path: setup.py
 
  - name: Lint code
- if: ${{ matrix.python-version == 3.8 }}
+ if: ${{ matrix.python-version == 3.11 }}
  run: |
  python -m pip install pre-commit
  pre-commit run --all-files

.pre-commit-config.yaml

@@ -1,57 +1,24 @@
 repos:
  - repo: https://github.com/PyCQA/isort
- rev: 5.12.0
+ rev: 5.13.2
  hooks:
  - id: isort
  language_version: python
 
- - repo: https://github.com/psf/black
- rev: 22.12.0
+ - repo: https://github.com/astral-sh/ruff-pre-commit
+ rev: v0.3.5
  hooks:
- - id: black
- args: ["--safe"]
- language_version: python
-
- - repo: https://github.com/pycqa/flake8
- rev: 6.0.0
- hooks:
- - id: flake8
- language_version: python
- args: [
- # E501 let black handle all line length decisions
- # W503 black conflicts with "line break before operator" rule
- # E203 black conflicts with "whitespace before ':'" rule
- "--ignore=E501,W503,E203,C901",
- ]
- - repo: https://github.com/chewse/pre-commit-mirrors-pydocstyle
- # 2.1.1
- rev: v2.1.1
- hooks:
- - id: pydocstyle
- language_version: python
- exclude: ".*(test|scripts).*"
- args:
- [
- # Check for docstring presence only
- "--select=D1",
- ]
- # Don't require docstrings for tests
- # '--match=(?!test).*\.py']
- # -
- # repo: https://github.com/pre-commit/mirrors-mypy
- # rev: v0.770
- # hooks:
- # - id: mypy
- # language_version: python3.8
- # args: [--no-strict-optional, --ignore-missing-imports]
+ - id: ruff
+ args: ["--fix"]
+ - id: ruff-format
 
- - repo: https://github.com/PyCQA/pydocstyle
- rev: 6.3.0
+ - repo: https://github.com/pre-commit/mirrors-mypy
+ rev: v1.9.0
  hooks:
- - id: pydocstyle
+ - id: mypy
  language_version: python
- exclude: ".*(test|scripts).*"
- #args: [
- # Don't require docstrings for tests
- #'--match=(?!test|scripts).*\.py',
- #]
+ exclude: tests/.*
+ additional_dependencies:
+ - types-requests
+ - types-attrs
+ - pydantic~=1.10

pyproject.toml

@@ -1,11 +1,28 @@
-[flake8]
-ignore = "D203"
-exclude = [".git", "__pycache__", "docs/source/conf.py", "build", "dist"]
-max-complexity = 12
-max-line-length = 90
-
 [tool.isort]
 profile = "black"
 known_first_party = "stac_fastapi.pgstac"
 known_third_party = ["rasterio", "stac-pydantic", "sqlalchemy", "geoalchemy2", "fastapi", "stac_fastapi"]
 sections = ["FUTURE", "STDLIB", "THIRDPARTY", "FIRSTPARTY", "LOCALFOLDER"]
+
+[tool.mypy]
+ignore_missing_imports = true
+namespace_packages = true
+explicit_package_bases = true
+exclude = ["tests", ".venv"]
+
+[tool.ruff]
+line-length = 90
+
+[tool.ruff.lint]
+select = [
+ "C",
+ "E",
+ "F",
+ "W",
+ "B",
+]
+ignore = [
+ "E203", # line too long, handled by black
+ "E501", # do not perform function calls in argument defaults
+ "B028", # No explicit `stacklevel` keyword argument found
+]

scripts/ingest_joplin.py

@@ -1,4 +1,5 @@
 """Ingest sample data during docker-compose"""
+
 import json
 import sys
 from pathlib import Path

setup.py

@@ -64,7 +64,5 @@
  install_requires=install_requires,
  tests_require=extra_reqs["dev"],
  extras_require=extra_reqs,
- entry_points={
- "console_scripts": ["stac-fastapi-pgstac=stac_fastapi.pgstac.app:run"]
- },
+ entry_points={"console_scripts": ["stac-fastapi-pgstac=stac_fastapi.pgstac.app:run"]},
 )

stac_fastapi/pgstac/app.py

@@ -46,8 +46,7 @@
 
 if enabled_extensions := os.getenv("ENABLED_EXTENSIONS"):
  extensions = [
- extensions_map[extension_name]
- for extension_name in enabled_extensions.split(",")
+ extensions_map[extension_name] for extension_name in enabled_extensions.split(",")
  ]
 else:
  extensions = list(extensions_map.values())
@@ -57,7 +56,7 @@
 api = StacApi(
  settings=settings,
  extensions=extensions,
- client=CoreCrudClient(post_request_model=post_request_model),
+ client=CoreCrudClient(post_request_model=post_request_model), # type: ignore
  response_class=ORJSONResponse,
  search_get_request_model=create_get_request_model(extensions),
  search_post_request_model=post_request_model,
@@ -90,8 +89,8 @@ def run():
  reload=settings.reload,
  root_path=os.getenv("UVICORN_ROOT_PATH", ""),
  )
- except ImportError:
- raise RuntimeError("Uvicorn must be installed in order to use command")
+ except ImportError as e:
+ raise RuntimeError("Uvicorn must be installed in order to use command") from e
 
 
 if __name__ == "__main__":

stac_fastapi/pgstac/core.py

@@ -1,4 +1,5 @@
 """Item crud client."""
+
 import re
 from typing import Any, Dict, List, Optional, Union
 from urllib.parse import unquote_plus, urljoin
@@ -136,7 +137,7 @@ async def _get_base_item(
 
  return item
 
- async def _search_base(
+ async def _search_base( # noqa: C901
  self,
  search_request: PgstacSearch,
  request: Request,
@@ -172,10 +173,10 @@ async def _search_base(
  req=search_request_json,
  )
  items = await conn.fetchval(q, *p)
- except InvalidDatetimeFormatError:
+ except InvalidDatetimeFormatError as e:
  raise InvalidQueryParameter(
  f"Datetime parameter {search_request.datetime} is invalid."
- )
+ ) from e
 
  next: Optional[str] = items.pop("next", None)
  prev: Optional[str] = items.pop("prev", None)
@@ -207,8 +208,8 @@ async def _add_item_links(
  and all([collection_id, item_id])
  ):
  feature["links"] = await ItemLinks(
- collection_id=collection_id,
- item_id=item_id,
+ collection_id=collection_id, # type: ignore
+ item_id=item_id, # type: ignore
  request=request,
  ).get_links(extra_links=feature.get("links"))
 
@@ -255,7 +256,7 @@ async def item_collection(
  bbox: Optional[BBox] = None,
  datetime: Optional[DateTimeType] = None,
  limit: Optional[int] = None,
- token: str = None,
+ token: Optional[str] = None,
  **kwargs,
  ) -> ItemCollection:
  """Get all items from a specific collection.
@@ -340,7 +341,7 @@ async def post_search(
  item_collection = await self._search_base(search_request, request=request)
  return ItemCollection(**item_collection)
 
- async def get_search(
+ async def get_search( # noqa: C901
  self,
  request: Request,
  collections: Optional[List[str]] = None,
@@ -432,5 +433,6 @@ async def get_search(
  except ValidationError as e:
  raise HTTPException(
  status_code=400, detail=f"Invalid parameters provided {e}"
- )
+ ) from e
+
  return await self.post_search(search_request, request=request)

stac_fastapi/pgstac/db.py

@@ -2,7 +2,16 @@
 
 import json
 from contextlib import asynccontextmanager, contextmanager
-from typing import AsyncIterator, Callable, Dict, Generator, Literal, Union
+from typing import (
+ AsyncIterator,
+ Callable,
+ Dict,
+ Generator,
+ List,
+ Literal,
+ Optional,
+ Union,
+)
 
 import attr
 import orjson
@@ -36,14 +45,17 @@ async def con_init(conn):
 ConnectionGetter = Callable[[Request, Literal["r", "w"]], AsyncIterator[Connection]]
 
 
-async def connect_to_db(app: FastAPI, get_conn: ConnectionGetter = None) -> None:
+async def connect_to_db(
+ app: FastAPI, get_conn: Optional[ConnectionGetter] = None
+) -> None:
  """Create connection pools & connection retriever on application."""
  settings = app.state.settings
  if app.state.settings.testing:
  readpool = writepool = settings.testing_connection_string
  else:
  readpool = settings.reader_connection_string
  writepool = settings.writer_connection_string
+
  db = DB()
  app.state.readpool = await db.create_pool(readpool, settings)
  app.state.writepool = await db.create_pool(writepool, settings)
@@ -62,15 +74,13 @@ async def get_connection(
  readwrite: Literal["r", "w"] = "r",
 ) -> AsyncIterator[Connection]:
  """Retrieve connection from database conection pool."""
- pool = (
- request.app.state.writepool if readwrite == "w" else request.app.state.readpool
- )
+ pool = request.app.state.writepool if readwrite == "w" else request.app.state.readpool
  with translate_pgstac_errors():
  async with pool.acquire() as conn:
  yield conn
 
 
-async def dbfunc(conn: Connection, func: str, arg: Union[str, Dict]):
+async def dbfunc(conn: Connection, func: str, arg: Union[str, Dict, List]):
  """Wrap PLPGSQL Functions.
 
  Keyword arguments:

stac_fastapi/pgstac/extensions/filter.py

@@ -1,4 +1,5 @@
 """Get Queryables."""
+
 from typing import Any, Optional
 
 from buildpg import render