fix precommit (#75)

* add tox, update pre-commit config, lint

* add precommit check

* fix syntax

* remove python-version

* switch pre-commit to 3.8

.github/workflows/cicd.yaml

@@ -40,6 +40,9 @@ jobs:
         with:
           python-version: "3.8"
 
+      - name: Lint code
+        uses: pre-commit/[email protected]
+
       - name: Install pipenv
         run: |
           python -m pip install --upgrade pipenv wheel

.pre-commit-config.yaml

@@ -1,35 +1,34 @@
 repos:
-    -
-        repo: https://github.com/pre-commit/mirrors-isort
-        rev: v4.3.21
-        hooks:
-            - id: isort
-              language_version: python3.7
+    - repo: https://github.com/PyCQA/isort
+      rev: 5.4.2
+      hooks:
+        - id: isort
+          language_version: python3.8
     -
         repo: https://github.com/psf/black
         rev: stable
         hooks:
             - id: black
               args: ['--safe']
-              language_version: python3.7
+              language_version: python3.8
     -
         repo: https://github.com/pre-commit/pre-commit-hooks
         rev: v2.4.0
         hooks:
             - id: flake8
-              language_version: python3.7
+              language_version: python3.8
               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']
+                  '--ignore=E501,W503,E203,C901']
     -
         repo: https://github.com/chewse/pre-commit-mirrors-pydocstyle
         # 2.1.1
         rev: 22d3ccf6cf91ffce3b16caa946c155778f0cb20f
         hooks:
             - id: pydocstyle
-              language_version: python3.7
+              language_version: python3.8
               args: [
                  # Check for docstring presence only
                  '--select=D1',
@@ -40,5 +39,5 @@ repos:
         rev: v0.770
         hooks:
             -   id: mypy
-                language_version: python3.7
+                language_version: python3.8
                 args: [--no-strict-optional, --ignore-missing-imports]

alembic/env.py

@@ -72,7 +72,9 @@ def run_migrations_online():
     configuration = config.get_section(config.config_ini_section)
     configuration["sqlalchemy.url"] = get_connection_url()
     connectable = engine_from_config(
-        configuration, prefix="sqlalchemy.", poolclass=pool.NullPool,
+        configuration,
+        prefix="sqlalchemy.",
+        poolclass=pool.NullPool,
     )
 
     with connectable.connect() as connection:

alembic/versions/131aab4d9e49_create_tables.py

@@ -6,10 +6,10 @@
 
 """  # noqa
 import sqlalchemy as sa
+from geoalchemy2.types import Geometry
 from sqlalchemy.dialects.postgresql import JSONB
 
 from alembic import op
-from geoalchemy2.types import Geometry
 
 # revision identifiers, used by Alembic.
 revision = "131aab4d9e49"

stac_api/__init__.py

@@ -0,0 +1 @@
+"""stac_api"""

stac_api/api/__init__.py

@@ -1,2 +1,4 @@
 """api module"""
 from .routes import create_endpoint_from_model, create_endpoint_with_depends
+
+__all__ = ("create_endpoint_from_model", "create_endpoint_with_depends")

stac_api/api/extensions/__init__.py

@@ -1,9 +1,16 @@
 """stac_api.api.extensions"""
-from .context import ContextExtension  # noqa
+from .context import ContextExtension
+from .fields import FieldsExtension
+from .query import QueryExtension
+from .sort import SortExtension
+from .tiles import TilesExtension
+from .transaction import TransactionExtension
 
-# from .extension import ApiExtension  # noqa
-from .fields import FieldsExtension  # noqa
-from .query import QueryExtension  # noqa
-from .sort import SortExtension  # noqa
-from .tiles import TilesExtension  # noqa
-from .transaction import TransactionExtension  # noqa
+__all__ = (
+    "ContextExtension",
+    "FieldsExtension",
+    "QueryExtension",
+    "SortExtension",
+    "TilesExtension",
+    "TransactionExtension",
+)

stac_api/api/routes.py

@@ -2,9 +2,9 @@
 from typing import Callable, Type
 
 from fastapi import Depends
+from pydantic import BaseModel
 from starlette.requests import Request
 
-from pydantic import BaseModel
 from stac_api.api.models import APIRequest
 
 
@@ -18,7 +18,8 @@ def create_endpoint_from_model(
     """
 
     def _endpoint(
-        request: Request, request_data: request_model,  # type:ignore
+        request: Request,
+        request_data: request_model,  # type:ignore
     ):
         """endpoint"""
         resp = func(request_data, request=request)
@@ -28,14 +29,16 @@ def _endpoint(
 
 
 def create_endpoint_with_depends(
-    func: Callable, request_model: Type[APIRequest],
+    func: Callable,
+    request_model: Type[APIRequest],
 ) -> Callable:
     """
     Create a fastapi endpoint where request model is a dataclass.  This works best for validating query/patm params.
     """
 
     def _endpoint(
-        request: Request, request_data: request_model = Depends(),  # type:ignore
+        request: Request,
+        request_data: request_model = Depends(),  # type:ignore
     ):
         """endpoint"""
         resp = func(

stac_api/clients/postgres/core.py

@@ -6,16 +6,16 @@
 from urllib.parse import urlencode, urljoin
 
 import attr
+import geoalchemy2 as ga
 import sqlalchemy as sa
+from sqlakeyset import get_page
 from sqlalchemy import func
 from sqlalchemy.orm import Session as SqlSession
 from stac_pydantic import ItemCollection
 from stac_pydantic.api import ConformanceClasses, LandingPage
 from stac_pydantic.api.extensions.paging import PaginationLink
 from stac_pydantic.shared import Link, MimeTypes, Relations
 
-import geoalchemy2 as ga
-from sqlakeyset import get_page
 from stac_api.api.extensions import ContextExtension, FieldsExtension
 from stac_api.clients.base import BaseCoreClient
 from stac_api.clients.postgres.session import Session

stac_api/clients/postgres/session.py

@@ -5,12 +5,12 @@
 from typing import Iterator
 
 import attr
+import psycopg2
 import sqlalchemy as sa
 import sqlalchemy.exc
+from fastapi_utils.session import FastAPISessionMaker as _FastAPISessionMaker
 from sqlalchemy.orm import Session as SqlSession
 
-import psycopg2
-from fastapi_utils.session import FastAPISessionMaker as _FastAPISessionMaker
 from stac_api import errors
 
 logger = logging.getLogger(__name__)
@@ -35,16 +35,20 @@ def context_session(self) -> Iterator[SqlSession]:
 
 @attr.s
 class Session:
+    """Database session management"""
+
     reader_conn_string: str = attr.ib()
     writer_conn_string: str = attr.ib()
 
     @classmethod
     def create_from_env(cls):
+        """create from environment"""
         return cls(
             reader_conn_string=os.environ["READER_CONN_STRING"],
             writer_conn_string=os.environ["WRITER_CONN_STRING"],
         )
 
     def __attrs_post_init__(self):
+        """post init"""
         self.reader: FastAPISessionMaker = FastAPISessionMaker(self.reader_conn_string)
         self.writer: FastAPISessionMaker = FastAPISessionMaker(self.writer_conn_string)

stac_api/models/__init__.py

@@ -0,0 +1 @@
+"""stac_api.models"""

stac_api/models/database.py

@@ -4,15 +4,15 @@
 from datetime import datetime
 from typing import Optional
 
+import geoalchemy2 as ga
 import sqlalchemy as sa
 from shapely.geometry import shape
 from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.ext.declarative import declarative_base
+from stac_pydantic.shared import DATETIME_RFC339
 
-import geoalchemy2 as ga
 from stac_api import config
 from stac_api.models import schemas
-from stac_pydantic.shared import DATETIME_RFC339
 
 BaseModel = declarative_base()
 

stac_api/models/decompose.py

@@ -6,10 +6,11 @@
 import geoalchemy2 as ga
 from pydantic import BaseModel
 from pydantic.utils import GetterDict
+from stac_pydantic.shared import DATETIME_RFC339
+
 from stac_api import config
 from stac_api.errors import DatabaseError
 from stac_api.models.links import CollectionLinks, ItemLinks, filter_links
-from stac_pydantic.shared import DATETIME_RFC339
 
 
 def resolve_links(links: list, base_url: str) -> List[Dict]:

stac_api/models/schemas.py

@@ -8,14 +8,11 @@
 from typing import Any, Callable, Dict, List, Optional, Set, Union
 
 import sqlalchemy as sa
-from shapely.geometry import Polygon as ShapelyPolygon
-from shapely.geometry import shape
-
 from geojson_pydantic.geometries import Polygon
 from pydantic import Field, ValidationError, root_validator
 from pydantic.error_wrappers import ErrorWrapper
-from stac_api import config
-from stac_api.models.decompose import CollectionGetter, ItemGetter
+from shapely.geometry import Polygon as ShapelyPolygon
+from shapely.geometry import shape
 from stac_pydantic import Collection as CollectionBase
 from stac_pydantic import Item as ItemBase
 from stac_pydantic.api import Search
@@ -24,6 +21,9 @@
 from stac_pydantic.shared import Link
 from stac_pydantic.utils import AutoValueEnum
 
+from stac_api import config
+from stac_api.models.decompose import CollectionGetter, ItemGetter
+
 # Be careful: https://github.com/samuelcolvin/pydantic/issues/1423#issuecomment-642797287
 NumType = Union[float, int]
 

tox.ini

@@ -0,0 +1,17 @@
+# Linter configs
+[flake8]
+ignore = D203
+exclude = .git,__pycache__,docs/source/conf.py,old,build,dist
+max-complexity = 12
+max-line-length = 90
+
+[mypy]
+no_strict_optional = true
+ignore_missing_imports = True
+
+[tool:isort]
+profile=black
+known_arturo=arturo
+known_first_party = stac_api
+known_third_party = rasterio,stac-pydantic,sqlalchemy,geoalchemy2,fastapi
+sections=FUTURE,STDLIB,THIRDPARTY,ARTURO,FIRSTPARTY,LOCALFOLDER