Add flake8 to project

.github/workflows/pythonpackage.yml

@@ -1,7 +1,7 @@
 name: Python package
 
 on:
-  push: 
+  push:
     branches:
       - main
   pull_request:
@@ -17,22 +17,27 @@ jobs:
 
     steps:
       - uses: actions/checkout@v2
-      
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
-      
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install -e .[dev]
-      
+
       - name: Lint
         run: |
           black --check .
           mypy .
-
+
+      - name: Optional linting
+        continue-on-error: true
+        run: |
+          flake8 .
+
       - name: Test with pytest
         run: |
           pytest

setup.cfg

@@ -11,6 +11,16 @@ no_strict_optional = True
 no_site_packages = True
 ignore_missing_imports = True
 
+[flake8]
+filename =
+    ./src/*,
+    ./tests/*,
+exclude = .git, __pycache__, *.egg-info, *.json, *.conf, *.env,
+per-file-ignores =
+    __init__.py: F401,
+ignore =
+    W503
+max-line-length = 88
 
 [tool:pytest]
 python_files = test_*.py

setup.py

@@ -45,6 +45,7 @@
     extras_require={
         "dev": [
             "black",
+            "flake8",
             "mypy",
             "myst-parser",
             "pytest-dotenv",

src/isar/config/settings.py

@@ -56,23 +56,27 @@ class Settings(BaseSettings):
 
     # Determines which mission planner module is used by ISAR
     # Options: [local echo]
-    # Selecting a different mission planner module than local may require certain access rights
+    # Selecting a different mission planner module than local may require certain access
+    # rights
     MISSION_PLANNER: str = Field(default="local")
 
     # Determines which storage modules are used by ISAR
-    # Comma separated list of modules to use. Each module will be called when storing results from inspections
+    # Comma separated list of modules to use. Each module will be called when storing
+    # results from inspections
     # Options [local blob slimm]
     # Selecting a different storage module than local may require certain access rights
     STORAGE: List[str] = Field(default=["local"])
 
     # Determines whether the MQTT publishing module should be enabled or not
-    # The publishing module will attempt to connect to the MQTT broker configured in "service_connections"
+    # The publishing module will attempt to connect to the MQTT broker configured in
+    # "service_connections"
     # Options: [false true]
     MQTT_ENABLED: bool = Field(default=False)
 
     # Determines whether authentication is enabled for the API or not
     # Enabling this requires certain resources available for OAuth2 authentication
-    # Currently supported authentication is Azure AD (https://github.com/Intility/fastapi-azure-auth)
+    # Currently supported authentication is Azure AD
+    # (https://github.com/Intility/fastapi-azure-auth)
     AUTHENTICATION_ENABLED: bool = Field(default=False)
 
     # Tenant ID for the Azure tenant with your Azure Active Directory application
@@ -139,11 +143,12 @@ class Settings(BaseSettings):
         default="https://slimmingestapidev.azurewebsites.net/api/Ingest"
     )
 
-    # Whether the results should be copied directly into the SLIMM datalake or only the metadata
+    # Whether the results should be copied directly into the SLIMM datalake or only the
+    # metadata
     COPY_FILES_TO_SLIMM_DATALAKE: bool = Field(default=False)
 
-    # The configuration of this section is tightly coupled with the metadata that is submitted with the results once
-    # they have been uploaded.
+    # The configuration of this section is tightly coupled with the metadata that is
+    # submitted with the results once they have been uploaded.
 
     # Four digit code indicating facility
     PLANT_CODE: str = Field(default="1320")

src/isar/mission_planner/echo_planner.py

@@ -122,8 +122,8 @@ def _create_inspection_tasks_from_sensor_types(
 
     def _get_robot_pose(self, tag_name: str) -> Pose:
         """
-        Retrieve robot pose corresponding to inspection of a given tag. For now, this is a temporary hard-coded
-        solution.
+        Retrieve robot pose corresponding to inspection of a given tag. For now, this is
+        a temporary hard-coded solution.
         """
         predefined_pose: Pose = predefined_poses[tag_name]
 

src/isar/models/communication/queues/queue_io.py

@@ -3,8 +3,8 @@
 
 class QueueIO:
     """
-    Creates input and output queue. The queues are defined such that input is from api to state machine
-    while output is from state machine to api.
+    Creates input and output queue. The queues are defined such that the input is from
+    api to state machine while the output is from state machine to api.
     """
 
     def __init__(self, input_size: int = 0, output_size: int = 0):

src/isar/models/mission.py

@@ -36,7 +36,10 @@ def _set_unique_id(self) -> None:
         plant_short_name: str = settings.PLANT_SHORT_NAME
         robot_id: str = settings.ROBOT_ID
         now: datetime = datetime.utcnow()
-        self.id = f"{plant_short_name.upper()}{robot_id.upper()}{now.strftime('%d%m%Y%H%M%S%f')[:-3]}"
+        self.id = (
+            f"{plant_short_name.upper()}{robot_id.upper()} "
+            f"{now.strftime('%d%m%Y%H%M%S%f')[:-3]}"
+        )
 
     def __post_init__(self) -> None:
         if self.id is None:

src/isar/services/service_connections/mqtt/mqtt_client.py

@@ -58,7 +58,8 @@ def __init__(self, mqtt_queue: Queue) -> None:
             password = os.environ["ISAR_MQTT_PASSWORD"]
         except KeyError:
             self.logger.warning(
-                "Failed to retrieve ISAR_MQTT_PASSWORD from environment. Attempting with empty string as password."
+                "Failed to retrieve ISAR_MQTT_PASSWORD from environment. Attempting "
+                "with empty string as password."
             )
 
         self.host: str = settings.MQTT_HOST
@@ -110,7 +111,7 @@ def _on_backoff(data: dict) -> None:
     @staticmethod
     def _on_giveup(data: dict) -> None:
         logging.getLogger("mqtt_client").error(
-            "Failed to connect to MQTT Broker within set backoff strategy. Raising error."
+            "Failed to connect to MQTT Broker within set backoff strategy."
         )
 
     @backoff.on_exception(

src/isar/services/utilities/json_service.py

@@ -21,7 +21,7 @@ def to_object(json_string: str) -> SimpleNamespace:
 
 class EnhancedJSONEncoder(json.JSONEncoder):
     """
-    Custom JSONEncoder used in this project. Of special note is the ability to encode dataclasses.
+    Custom JSONEncoder with the ability to encode dataclasses.
     """
 
     def default(self, o):

src/isar/services/utilities/queue_utilities.py

@@ -15,8 +15,9 @@ class QueueUtilities:
     @staticmethod
     def check_queue(queue: Queue, queue_timeout: int = None) -> Any:
         """
-        Checks if there is a message on a queue. If a timeout is specified the function will raise a QueueTimeoutError
-        if there is no message within the timeout. If there is no timeout specified this function will block.
+        Checks if there is a message on a queue. If a timeout is specified the function
+        will raise a QueueTimeoutError if there is no message within the timeout. If
+        there is no timeout specified this function will block.
         :param queue: The queue to be checked for a message
         :param queue_timeout: Timeout in seconds
         :return: Message found on queue

src/isar/services/utilities/scheduling_utilities.py

@@ -17,8 +17,8 @@
 
 class SchedulingUtilities:
     """
-    Contains utility functions for scheduling missions from the API. The class handles required thread communication
-    through queues to the state machine.
+    Contains utility functions for scheduling missions from the API. The class handles
+    required thread communication through queues to the state machine.
     """
 
     @inject
@@ -31,9 +31,10 @@ def ready_to_start_mission(
         self,
     ) -> Tuple[bool, Optional[Tuple[StartMessage, HTTPStatus]]]:
         """
-        Checks the current mission status by communicating with the state machine thread through queues.
-        :return: (True, None) if the mission may be started. Otherwise (False, response) with a relevant response
-        message indicating the cause.
+        Checks the current mission status by communicating with the state machine thread
+        through queues.
+        :return: (True, None) if the mission may be started. Otherwise (False, response)
+        with a relevant response message indicating the cause.
         """
         self.queues.mission_status.input.put(True)
         try:
@@ -58,7 +59,8 @@ def start_mission(self, mission: Mission) -> Tuple[StartMessage, HTTPStatus]:
         """
         Starts a mission by communicating with the state machine thread through queues.
         :param mission: A Mission containing the mission tasks to be started.
-        :return: (message, status_code) is returned indicating the success and cause of the operation.
+        :return: (message, status_code) is returned indicating the success and cause of
+        the operation.
         """
         self.queues.start_mission.input.put(deepcopy(mission))
         try:

src/isar/state_machine/state_machine.py

@@ -300,7 +300,8 @@ def log_task_overview(self, mission: Mission):
         """Log an overview of the tasks in a mission"""
         task_status: str = "\n".join(
             [
-                f"{i:>3}  {type(task).__name__:<20} {str(task.id)[:8]:<32} -- {task.status}"
+                f"{i:>3}  {type(task).__name__:<20} "
+                f"{str(task.id)[:8]:<32} -- {task.status}"
                 for i, task in enumerate(mission.tasks)
             ]
         )

src/isar/state_machine/states/initiate_task.py

@@ -95,7 +95,8 @@ def _run(self):
             except RobotInvalidTaskExpection:
                 self.state_machine.current_task.status = TaskStatus.Failed
                 self.logger.warning(
-                    f"Failed to initiate {type(self.state_machine.current_task).__name__}"
+                    f"Failed to initiate "
+                    f"{type(self.state_machine.current_task).__name__}"
                     f"Invalid task: {str(self.state_machine.current_task.id)[:8]}"
                 )
                 next_state = States.InitiateTask
@@ -107,14 +108,16 @@ def _run(self):
                 self.state_machine.current_task.status = TaskStatus.Scheduled
                 next_state = States.Monitor
                 self.logger.info(
-                    f"Successfully initiated {type(self.state_machine.current_task).__name__} "
+                    f"Successfully initiated "
+                    f"{type(self.state_machine.current_task).__name__} "
                     f"task: {str(self.state_machine.current_task.id)[:8]}"
                 )
                 break
             else:
                 self.initiate_task_failure_counter += 1
                 self.logger.info(
-                    f"Initiating task failed #: {str(self.initiate_task_failure_counter)}"
+                    f"Initiating task failed #: "
+                    f"{str(self.initiate_task_failure_counter)}"
                 )
                 if (
                     self.initiate_task_failure_counter

src/isar/storage/local_storage.py

@@ -34,7 +34,8 @@ def store(self, inspection: Inspection, metadata: MissionMetadata):
                 metadata_file.write(metadata_bytes)
         except IOError as e:
             self.logger.warning(
-                f"Failed open/write for one of the following files: \n{absolute_path}\n{absolute_metadata_path}"
+                f"Failed open/write for one of the following files: \n"
+                f"{absolute_path}\n{absolute_metadata_path}"
             )
             raise StorageException from e
         except Exception as e:

src/isar/storage/slimm_storage.py

@@ -70,7 +70,8 @@ def _ingest(self, inspection, multiform_body, request_url, token):
             )
         except (RequestException, HTTPError) as e:
             self.logger.warning(
-                f"Failed to upload inspection: {inspection.id} to SLIMM due to a request exception"
+                f"Failed to upload inspection: {inspection.id} to SLIMM due to a "
+                f"request exception"
             )
             raise StorageException from e
 

src/isar/storage/uploader.py

@@ -99,15 +99,16 @@ def _upload(self, upload_item: UploaderQueueItem):
                 upload_item.increment_retry(self.max_wait_time)
                 self.logger.warning(
                     f"Storage handler: {type(upload_item.storage_handler).__name__} "
-                    f"failed to upload inspection: {str(upload_item.inspection.id)[:8]}. "
+                    f"failed to upload inspection: "
+                    f"{str(upload_item.inspection.id)[:8]}. "
                     f"Retrying in {upload_item.seconds_until_retry()}s."
                 )
             else:
                 self._internal_upload_queue.remove(upload_item)
                 self.logger.error(
                     f"Storage handler: {type(upload_item.storage_handler).__name__} "
-                    f"exceeded max retries to upload inspection: {str(upload_item.inspection.id)[:8]}. "
-                    "Aborting upload."
+                    f"exceeded max retries to upload inspection: "
+                    f"{str(upload_item.inspection.id)[:8]}. Aborting upload."
                 )
 
     def _process_upload_queue(self):

src/robot_interface/models/geometry/frame.py

@@ -3,7 +3,8 @@
 
 class Frame(str, Enum):
     """
-    Robot frame implies the local frame on the operating robot. This will depend on the robots internal mapping.
+    Robot frame implies the local frame on the operating robot. This will depend on the
+    robots internal mapping.
     Asset frame is the frame of the asset which the robot operates in.
     """
 

src/robot_interface/models/geometry/orientation.py

@@ -11,9 +11,10 @@
 @dataclass
 class Orientation:
     """
-    This class represents an orientation using quaternions. The quaternion is used throughout the project.
-    Methods that utilize Euler angles will all follow the yaw, pitch, roll convention which rotates around the ZYX axis
-    with intrinsic rotations.
+    This class represents an orientation using quaternions. The quaternion is used
+    throughout the project.
+    Methods that utilize Euler angles will all follow the yaw, pitch, roll convention
+    which rotates around the ZYX axis with intrinsic rotations.
     """
 
     x: float
@@ -42,8 +43,8 @@ def as_euler(
         wrap_angles: bool = False,
     ) -> list:
         """
-        Retrieve the orientation as yaw, pitch, roll Euler coordinates. This function uses the ZYX intrinsic rotations
-        as standard convention.
+        Retrieve the orientation as yaw, pitch, roll Euler coordinates. This function
+        uses the ZYX intrinsic rotations as standard convention.
         :param degrees: Set to true to retrieve angles as degrees.
         :return: List of euler angles [yaw, pitch, roll]
         """

src/robot_interface/models/mission/task.py

@@ -63,7 +63,7 @@ class InspectionTask(Task):
 @dataclass
 class MotionTask(Task):
     """
-    Base class for all tasks which should cause the robot to move, but not return a result.
+    Base class for all tasks which should move the robot, but not return a result.
     """
 
     pass

tests/integration/turtlebot/test_successful_mission.py

@@ -94,7 +94,7 @@ def test_successful_mission(
 
     _id: int = 2
 
-    response = client.post(
+    _ = client.post(
         f"schedule/start-mission?ID={_id}",
         headers={"Authorization": "Bearer {}".format(access_token)},
     )

tests/isar/apis/scheduler/test_scheduler_routes.py

@@ -5,7 +5,6 @@
 import pytest
 
 from isar.apis.security.authentication import Authenticator
-from isar.config.settings import robot_settings
 from isar.mission_planner.local_planner import LocalPlanner
 from isar.mission_planner.mission_planner_interface import MissionPlannerError
 from isar.models.communication.messages import (

tests/isar/models/communication/test_queues.py

@@ -7,18 +7,18 @@ def test_queues(self):
         assert queues.start_mission is not None
         assert (
             queues.start_mission.input is not None
-            and queues.start_mission.input.maxsize is 1
+            and queues.start_mission.input.maxsize == 1
         )
         assert (
             queues.start_mission.output is not None
-            and queues.start_mission.output.maxsize is 1
+            and queues.start_mission.output.maxsize == 1
         )
         assert queues.stop_mission is not None
         assert (
             queues.stop_mission.input is not None
-            and queues.stop_mission.input.maxsize is 1
+            and queues.stop_mission.input.maxsize == 1
         )
         assert (
             queues.stop_mission.output is not None
-            and queues.stop_mission.output.maxsize is 1
+            and queues.stop_mission.output.maxsize == 1
         )

tests/isar/services/readers/test_base_reader.py

@@ -1,5 +1,4 @@
 from dataclasses import asdict
-from pathlib import Path
 from typing import Any
 
 import pytest