Blackened

openflexure_microscope/api/utilities.py

@@ -2,13 +2,19 @@ import logging
 from werkzeug.exceptions import BadRequest
 from flask import url_for, Blueprint
 
+
 def blueprint_for_module(module_name, api_ver=2, suffix=""):
-    return Blueprint(blueprint_name_for_module(module_name, api_ver=api_ver, suffix=suffix), module_name)
+    return Blueprint(
+        blueprint_name_for_module(module_name, api_ver=api_ver, suffix=suffix),
+        module_name,
+    )
+
 
 def blueprint_name_for_module(module_name, api_ver=2, suffix=""):
-    bp_name = module_name.split('.')[-1]
+    bp_name = module_name.split(".")[-1]
     return f"v{api_ver}_{bp_name}_blueprint{suffix}"
 
+
 class JsonResponse:
     def __init__(self, request):
         """

openflexure_microscope/api/v2/blueprints/actions/__init__.py

@@ -11,6 +11,7 @@ from openflexure_microscope.api.views import MicroscopeView
 
 from . import camera, stage, system
 
+
 class ActionsAPI(MicroscopeView):
     def get(self):
         return jsonify(actions_representation())

openflexure_microscope/api/v2/blueprints/actions/camera.py

@@ -10,6 +10,7 @@ class CaptureAPI(MicroscopeView):
     """
     Create a new image capture. 
     """
+
     def post(self):
         """
         Create a new image capture.
@@ -107,6 +108,7 @@ class GPUPreviewStartAPI(MicroscopeView):
     """
     Start the onboard GPU preview.
     """
+
     def post(self, operation):
         """
         Start the onboard GPU preview.
@@ -152,6 +154,7 @@ class GPUPreviewStopAPI(MicroscopeView):
     """
     Stop the onboard GPU preview.
     """
+
     def post(self, operation):
         """
         Stop the onboard GPU preview.

openflexure_microscope/api/v2/blueprints/actions/stage.py

@@ -11,6 +11,7 @@ class MoveStageAPI(MicroscopeView):
     """
     Handle stage movements. 
     """
+
     def post(self):
         """
         Set x, y and z positions of the stage.

openflexure_microscope/api/v2/blueprints/actions/system.py

@@ -7,6 +7,7 @@ class ShutdownAPI(MicroscopeView):
     """
     Attempt to shutdown the device 
     """
+
     def post(self):
         """
         Attempt to shutdown the device
@@ -23,6 +24,7 @@ class RebootAPI(MicroscopeView):
     """
     Attempt to reboot the device 
     """
+
     def post(self):
         """
         Attempt to shutdown the device

openflexure_microscope/api/v2/blueprints/plugins.py

@@ -14,6 +14,7 @@ import copy
 import logging
 import warnings
 
+
 def plugins_representation(plugin_loader_object: PluginLoader):
     """
     Generate a dictionary representation of all plugins, including Flask route URLs
@@ -33,16 +34,14 @@ def plugins_representation(plugin_loader_object: PluginLoader):
             "plugin": str(plugin),
             "views": {},
             "gui": plugin.gui,
-            "description": get_docstring(plugin)
+            "description": get_docstring(plugin),
         }
 
         for view_id, view_data in plugin.views.items():
             logging.debug(f"Representing view {view_id}")
             uri = url_for(f"v2_plugins_blueprint.{view_id}")
             # Make links dictionary if it doesn't yet exist
-            view_d = {
-                "links": {"self": uri}
-            }
+            view_d = {"links": {"self": uri}}
 
             view_d.update(description_from_view(view_data["view"]))
 
@@ -87,9 +86,7 @@ def construct_blueprint(microscope_obj):
             blueprint.add_url_rule(
                 plugin_view["rule"],
                 view_func=plugin_view["view"].as_view(
-                    plugin_view_id,
-                    microscope=microscope_obj,
-                    plugin=plugin,
+                    plugin_view_id, microscope=microscope_obj, plugin=plugin
                 ),
             )
 

openflexure_microscope/api/v2/blueprints/root.py

@@ -4,11 +4,19 @@ from openflexure_microscope.api.views import MicroscopeView
 
 from openflexure_microscope.utilities import get_docstring, bottom_level_name
 from openflexure_microscope.api.utilities import blueprint_name_for_module
-from openflexure_microscope.api.v2.blueprints import settings, status, plugins, captures, actions, streams
+from openflexure_microscope.api.v2.blueprints import (
+    settings,
+    status,
+    plugins,
+    captures,
+    actions,
+    streams,
+)
 
 # List of submodules containing create_blueprint methods using standard blueprint_for_module naming
 _root_blueprint_modules = [settings, status, plugins, captures, actions, streams]
 
+
 def root_representation():
     """
     Generate a dictionar representation of all top-level blueprint rules
@@ -23,7 +31,7 @@ def root_representation():
         d[module_short_name] = {
             "name": blueprint_module.__name__,
             "description": get_docstring(blueprint_module),
-            "links": {"self": url_for(f"{blueprint_name}.{module_short_name}")}
+            "links": {"self": url_for(f"{blueprint_name}.{module_short_name}")},
         }
 
     return d

openflexure_microscope/api/v2/blueprints/status.py

@@ -7,6 +7,7 @@ from openflexure_microscope.api.utilities import blueprint_for_module
 
 from flask import Blueprint, jsonify
 
+
 class StatusAPI(MicroscopeView):
     def get(self):
         """

openflexure_microscope/api/v2/blueprints/streams.py

@@ -4,7 +4,10 @@ Top-level description of routes related to live camera stream data
 
 from openflexure_microscope.api.utilities import gen, JsonResponse
 from openflexure_microscope.api.views import MicroscopeView
-from openflexure_microscope.api.utilities import blueprint_for_module, blueprint_name_for_module
+from openflexure_microscope.api.utilities import (
+    blueprint_for_module,
+    blueprint_name_for_module,
+)
 from openflexure_microscope.utilities import description_from_view
 
 from flask import Response, Blueprint, jsonify, request, url_for
@@ -19,6 +22,7 @@ class MjpegAPI(MicroscopeView):
     """
     Real-time MJPEG stream from the microscope camera
     """
+
     def get(self):
         """
         Real-time MJPEG stream from the microscope camera
@@ -42,6 +46,7 @@ class SnapshotAPI(MicroscopeView):
     """
     Single JPEG snapshot from the camera stream
     """
+
     def get(self):
         """
         Single snapshot from the camera stream
@@ -59,16 +64,8 @@ class SnapshotAPI(MicroscopeView):
 
 
 _streams = {
-    "mjpeg": {
-        "rule": "/mjpeg",
-        "view_class": MjpegAPI,
-        "conditions": True,
-    },
-    "snapshot": {
-        "rule": "/snapshot",
-        "view_class": SnapshotAPI,
-        "conditions": True,
-    }
+    "mjpeg": {"rule": "/mjpeg", "view_class": MjpegAPI, "conditions": True},
+    "snapshot": {"rule": "/snapshot", "view_class": SnapshotAPI, "conditions": True},
 }
 
 
@@ -82,9 +79,7 @@ def streams_representation():
 
     streams = {}
     for name, stream in enabled_streams().items():
-        d = {
-            "links": {"self": url_for(f".{name}")},
-        }
+        d = {"links": {"self": url_for(f".{name}")}}
 
         d.update(description_from_view(stream["view_class"]))
 

openflexure_microscope/camera/mock.py

@@ -23,7 +23,7 @@ from openflexure_microscope.camera.base import BaseCamera
 PIL spams the logger with debug-level information. This is a pain when debugging api.app.
 We override the logging settings in api.app by setting a level for PIL here.
 """
-pil_logger = logging.getLogger('PIL')
+pil_logger = logging.getLogger("PIL")
 pil_logger.setLevel(logging.INFO)
 
 # MAIN CLASS

openflexure_microscope/plugins/default/autofocus/api.py

@@ -21,6 +21,7 @@ class AutofocusAPI(MicroscopeViewPlugin):
     """
     Run a standard autofocus
     """
+
     def post(self):
         payload = JsonResponse(request)
 
@@ -42,6 +43,7 @@ class FastAutofocusAPI(MicroscopeViewPlugin):
     """
     Run a fast autofocus
     """
+
     def post(self):
         payload = JsonResponse(request)
 

openflexure_microscope/plugins/loader.py

@@ -186,7 +186,7 @@ class PluginLoader(object):
                 plugin_object = plugin_class()
 
                 if hasattr(
-                        self, plugin_name
+                    self, plugin_name
                 ):  # If a plugin with the same name is already attached.
                     logging.warning(
                         ConColors.WARNING
@@ -197,7 +197,7 @@ class PluginLoader(object):
                     )
 
                 elif isinstance(
-                        plugin_object, BasePlugin
+                    plugin_object, BasePlugin
                 ):  # If plugin_object is an instance of MicroscopePlugin
                     # Attach plugin_object to the plugin mount
                     setattr(self, plugin_name_python_safe, plugin_object)
@@ -212,7 +212,9 @@ class PluginLoader(object):
 
                     logging.info(
                         ConColors.OKGREEN
-                        + "Plugin {} loaded as {}.".format(plugin_map, plugin_object._name)
+                        + "Plugin {} loaded as {}.".format(
+                            plugin_map, plugin_object._name
+                        )
                         + ConColors.ENDC
                     )
 
@@ -228,7 +230,9 @@ class BasePlugin:
     """
 
     def __init__(self):
-        self._views = {}  # Key: Full, Python-safe ID. Val: Original rule, and view class
+        self._views = (
+            {}
+        )  # Key: Full, Python-safe ID. Val: Original rule, and view class
         self._rules = {}  # Key: Original rule. Val: View class
         self._gui = None
 
@@ -258,10 +262,7 @@ class BasePlugin:
         view_id = cleaned_rule.replace("/", "_")
 
         # Store route information in a dictionary
-        d = {
-            "rule": full_rule,
-            "view": view_class
-        }
+        d = {"rule": full_rule, "view": view_class}
 
         # Add view to private views dictionary
         self._views[view_id] = d
@@ -276,17 +277,13 @@ class BasePlugin:
         api_gui = copy.deepcopy(self._gui)
         api_gui["id"] = self._name
 
-        if "forms" in api_gui and isinstance(
-                api_gui["forms"], list
-        ):
+        if "forms" in api_gui and isinstance(api_gui["forms"], list):
             for form in api_gui["forms"]:
                 if "route" in form and form["route"] in self._rules.keys():
                     form["route"] = self._rules[form["route"]]["rule"]
                 else:
                     logging.warn(
-                        "No valid expandable route found for {}".format(
-                            form["route"]
-                        )
+                        "No valid expandable route found for {}".format(form["route"])
                     )
         return api_gui
 
@@ -317,7 +314,7 @@ class BasePlugin:
         if module is None or module == str.__class__.__module__:
             return self.__class__.__name__  # Avoid reporting __builtin__
         else:
-            return module + '.' + self.__class__.__name__
+            return module + "." + self.__class__.__name__
 
 
 class MicroscopePlugin(BasePlugin):

openflexure_microscope/stage/sangaboard/extensible_serial_instrument.py

@@ -213,7 +213,9 @@ class ExtensibleSerialInstrument(object):
                 return self.read_multiline(termination_line)
             else:
                 logging.debug("Reading response...")
-                line = self.readline().strip()  # question: should we strip the final newline?
+                line = (
+                    self.readline().strip()
+                )  # question: should we strip the final newline?
                 logging.debug(f"Read finished. Got {line}")
                 return line
 
@@ -223,7 +225,7 @@ class ExtensibleSerialInstrument(object):
         response_string=r"%d",
         re_flags=0,
         parse_function=None,
-        **kwargs
+        **kwargs,
     ):
         """
         Perform a query, returning a parsed form of the response.

openflexure_microscope/utilities.py

@@ -5,23 +5,23 @@ from collections import abc
 from functools import reduce
 from contextlib import contextmanager
 
+
 def bottom_level_name(obj):
-    return obj.__name__.split('.')[-1]
+    return obj.__name__.split(".")[-1]
+
 
 def description_from_view(view_class):
     methods = []
     for method_key in ["get", "post", "put", "delete"]:
         if hasattr(view_class, method_key):
             methods.append(method_key.upper())
-    brief_description = get_docstring(view_class).partition('\n')[0].strip()
+    brief_description = get_docstring(view_class).partition("\n")[0].strip()
 
-    d = {
-        "methods": methods,
-        "description": brief_description
-    }
+    d = {"methods": methods, "description": brief_description}
 
     return d
 
+
 def get_docstring(obj):
     ds = obj.__doc__
     if ds:
@@ -29,13 +29,16 @@ def get_docstring(obj):
     else:
         return ""
 
+
 def camel_to_snake(name):
-    s1 = re.sub('(.)([A-Z][a-z]+)', r'\1_\2', name)
-    return re.sub('([a-z0-9])([A-Z])', r'\1_\2', s1).lower()
+    s1 = re.sub("(.)([A-Z][a-z]+)", r"\1_\2", name)
+    return re.sub("([a-z0-9])([A-Z])", r"\1_\2", s1).lower()
+
 
 def camel_to_spine(name):
-    s1 = re.sub('(.)([A-Z][a-z]+)', r'\1-\2', name)
-    return re.sub('([a-z0-9])([A-Z])', r'\1-\2', s1).lower()
+    s1 = re.sub("(.)([A-Z][a-z]+)", r"\1-\2", name)
+    return re.sub("([a-z0-9])([A-Z])", r"\1-\2", s1).lower()
+
 
 @contextmanager
 def set_properties(obj, **kwargs):