linting and typing fixes

openflexure_microscope/api/app.py

@@ -24,7 +24,7 @@ import os
 from datetime import datetime
 
 import pkg_resources
-from flask import abort, send_file, jsonify
+from flask import abort, jsonify, send_file
 from flask_cors import CORS, cross_origin
 from labthings import create_app
 from labthings.extensions import find_extensions
@@ -39,6 +39,7 @@ from openflexure_microscope.paths import (
     OPENFLEXURE_VAR_PATH,
     logs_file_path,
 )
+
 from .openapi import add_spec_extras
 
 

openflexure_microscope/api/default_extensions/autofocus.py

@@ -7,6 +7,7 @@ from typing import Callable, Dict, List, Optional, Tuple
 import numpy as np
 from labthings import current_action, fields, find_component
 from labthings.extensions import BaseExtension
+from labthings.utilities import get_docstring, get_summary
 from labthings.views import ActionView, View
 from scipy import ndimage
 
@@ -15,7 +16,6 @@ from openflexure_microscope.devel import abort
 from openflexure_microscope.microscope import Microscope
 from openflexure_microscope.stage.base import BaseStage
 from openflexure_microscope.utilities import set_properties
-from labthings.utilities import get_docstring, get_summary
 
 ### Autofocus utilities
 
@@ -218,7 +218,7 @@ def extension_action(args=None):
                 # Run the action
                 return func(**arguments)
 
-            def get(self, *args, **kwargs):
+            def get(self, *args, **kwargs):  # pylint: disable=useless-super-delegation
                 # Explicitly wrap the `get` method to allow us to add a docstring
                 return super().get(*args, **kwargs)
 
@@ -346,7 +346,7 @@ class AutofocusExtension(BaseExtension):
         camera: BaseCamera = microscope.camera
         stage: BaseStage = microscope.stage
         if not dz:
-            dz = np.linspace(-300, 300, 7)
+            dz: List[int] = list(np.linspace(-300, 300, 7))
 
         with set_properties(stage, backlash=256), stage.lock, camera.lock:
             sharpnesses: List[float] = []

openflexure_microscope/api/default_extensions/scan.py

@@ -2,10 +2,10 @@ import datetime
 import logging
 import time
 import uuid
-import marshmallow
 from functools import reduce
 from typing import Dict, List, Optional, Tuple
 
+import marshmallow
 from labthings import (
     current_action,
     fields,

openflexure_microscope/api/v2/views/__init__.py

@@ -1,7 +1,7 @@
 from .actions import enabled_root_actions
 from .camera import *
 from .captures import *
+from .docs import *
 from .instrument import *
 from .stage import *
 from .streams import *
-from .docs import *

openflexure_microscope/api/v2/views/docs.py

@@ -1,6 +1,6 @@
-from labthings.views import View
-from labthings import current_labthing
 from flask import Response
+from labthings import current_labthing
+from labthings.views import View
 
 
 class APISpecJSONView(View):

openflexure_microscope/microscope.py

@@ -19,8 +19,8 @@ from openflexure_microscope.stage.sanga import SangaDeltaStage, SangaStage
 
 try:
     from openflexure_microscope.camera.pi import PiCameraStreamer
-except Exception as e:  # pylint: disable=W0703
+except Exception as exc:  # pylint: disable=W0703
-    logging.error(e)
+    logging.error(exc)
     logging.warning("Unable to import PiCameraStreamer")
 from labthings import CompositeLock
 

setup.py

@@ -75,6 +75,8 @@ setup(
             "pylint ~= 2.3",
             "pytest ~= 6.1.2",
             "mypy ~= 0.790",
+            "types-python-dateutil",
+            "types-setuptools",
             "poethepoet ~= 0.10.0",
             "freezegun ~= 1.0.0",
             "lxml ~= 4.6",