Deepsource fixes (#19)

* Ignore all virtual envs

* Fixed PYL-W0102

* State test_patterns

* Fix BAN-B101

* Fixed FLK-E501 regression

* Skip PYL-E1111

* Skip PYL-W0703

* Fix PYL-W0404

* Fix PYL-W0621

* Clean up unused imports

* Fix FLK-E266

* Better variable names

* Better global variable naming

* Fixed docstring utilities

* Fixed FLK-E501

* Cleaned up some trailing whitespace

* Fixed PYL-R1705

* Fixed FLK-W291

* Started adding missing docstrings

* Removed blank line whitespace

* Fix FLK-D200

* Fixed OrderedDict import

* Started fixing PYL-W0212

* Created FieldSchema for single-field data validation

* Silence PYL-W0212 (no alternative found)

* Added a note on our _get_current_object use

* Fixed some more PYL-W0212

* Fixed FLK-W293

* Fixed PYL-W0611

* Added dependency_file_paths

Author: jtc42

.deepsource.toml

@@ -1,8 +1,19 @@
 version = 1
 
+# Glob pattern of the test files
+test_patterns = [
+  "tests/**",
+  "test_*.py"
+]
+
 [[analyzers]]
 name = "python"
 enabled = true
 
+dependency_file_paths = [
+  "poetry.lock",
+  "pyproject.toml"
+]
+
   [analyzers.meta]
   runtime_version = "3.x.x"

.gitignore

@@ -102,8 +102,8 @@ celerybeat.pid
 *.sage.py
 
 # Environments
-.env
-.venv
+.env*
+.venv*
 env/
 venv/
 ENV/

examples/nested_thing.py

@@ -17,9 +17,9 @@
 
 
 class DataSet:
-    def __init__(self, xs, ys):
-        self.xs = xs
-        self.ys = ys
+    def __init__(self, x_values, y_values):
+        self.xs = x_values
+        self.ys = y_values
 
 
 class DataSetSchema(Schema):
@@ -29,19 +29,19 @@ class DataSetSchema(Schema):
 
 class MyComponent:
     def __init__(self):
-        self.id = uuid.uuid4()
+        self.id = uuid.uuid4()  # skipcq: PYL-C0103
         self.x_range = range(-100, 100)
         self.magic_denoise = 200
 
-    def noisy_pdf(self, x, mu=0.0, sigma=25.0):
+    def noisy_pdf(self, x_value, mu=0.0, sigma=25.0):
         """
         Generate a noisy gaussian function (to act as some pretend data)
         
         Our noise is inversely proportional to self.magic_denoise
         """
-        x = float(x - mu) / sigma
+        x_value = float(x_value - mu) / sigma
         return (
-            math.exp(-x * x / 2.0) / math.sqrt(2.0 * math.pi) / sigma
+            math.exp(-x_value * x_value / 2.0) / math.sqrt(2.0 * math.pi) / sigma
             + (1 / self.magic_denoise) * random.random()
         )
 
@@ -60,12 +60,15 @@ class MyComponentSchema(Schema):
 
 
 """
-Create a view to view and change our magic_denoise value, and register is as a Thing property
+Create a view to view and change our magic_denoise value,
+and register is as a Thing property
 """
 
 
-@ThingProperty  # Register this view as a Thing Property
-@PropertySchema(  # Define the data we're going to output (get), and what to expect in (post)
+# Register this view as a Thing Property
+@ThingProperty
+# Define the data we're going to output (get), and what to expect in (post)
+@PropertySchema(
     fields.Integer(
         required=True,
         example=200,

examples/properties_dictionary.py

@@ -46,7 +46,8 @@ def get_state_schema(self):
 
 
 """
-Create a view to view and change our magic_denoise value, and register is as a Thing property
+Create a view to view and change our magic_denoise value,
+and register is as a Thing property
 """
 
 
@@ -59,18 +60,18 @@ def get(self):
         """Show the current magic_denoise value"""
 
         # When a GET request is made, we'll find our attached component
-        my_component = find_component("org.labthings.example.mycomponent")
-        return my_component.get_state()
+        found_my_component = find_component("org.labthings.example.mycomponent")
+        return found_my_component.get_state()
 
     # Main function to handle PUT requests (update)
     def put(self, new_property_value):
         """Change the current magic_denoise value"""
 
         # Find our attached component
-        my_component = find_component("org.labthings.example.mycomponent")
+        found_my_component = find_component("org.labthings.example.mycomponent")
 
         # Apply the new value
-        return my_component.set_state(new_property_value)
+        return found_my_component.set_state(new_property_value)
 
 
 # Create LabThings Flask app

examples/simple_thing.py

@@ -8,9 +8,7 @@
     ThingProperty,
     PropertySchema,
     use_args,
-    use_body,
     marshal_task,
-    marshal_with,
 )
 from labthings.server.view import View
 from labthings.server.find import find_component
@@ -64,12 +62,15 @@ def average_data(self, n: int):
 
 
 """
-Create a view to view and change our magic_denoise value, and register is as a Thing property
+Create a view to view and change our magic_denoise value,
+and register is as a Thing property
 """
 
 
-@ThingProperty  # Register this view as a Thing Property
-@PropertySchema(  # Define the data we're going to output (get), and what to expect in (post)
+# Register this view as a Thing Property
+@ThingProperty
+# Define the data we're going to output (get), and what to expect in (post)
+@PropertySchema(
     fields.Integer(
         required=True,
         example=200,
@@ -125,7 +126,8 @@ def get(self):
 
 @ThingAction
 class MeasurementAction(View):
-    # Expect JSON parameters in the request body. Pass to post function as dictionary argument.
+    # Expect JSON parameters in the request body.
+    # Pass to post function as dictionary argument.
     @use_args(
         {
             "averages": fields.Integer(

labthings/core/lock.py

@@ -5,14 +5,15 @@
 
 class StrictLock(object):
     """
-    Class that behaves like a Python RLock, but with stricter timeout conditions and custom exceptions.
+    Class that behaves like a Python RLock,
+    but with stricter timeout conditions and custom exceptions.
 
     Args:
-        timeout (int): Time, in seconds, lock acquisition will wait before raising an exception
+        timeout (int): Time in seconds acquisition will wait before raising an exception
 
     Attributes:
         _lock (:py:class:`threading.RLock`): Parent RLock object
-        timeout (int): Time, in seconds, lock acquisition will wait before raising an exception
+        timeout (int): Time in seconds acquisition will wait before raising an exception
     """
 
     def __init__(self, timeout=1):
@@ -46,11 +47,11 @@ class CompositeLock(object):
 
     Args:
         locks (list): List of parent RLock objects
-        timeout (int): Time, in seconds, lock acquisition will wait before raising an exception
+        timeout (int): Time in seconds acquisition will wait before raising an exception
 
     Attributes:
         locks (list): List of parent RLock objects
-        timeout (int): Time, in seconds, lock acquisition will wait before raising an exception
+        timeout (int): Time in seconds acquisition will wait before raising an exception
     """
 
     def __init__(self, locks, timeout=1):

labthings/core/tasks/pool.py

@@ -63,8 +63,8 @@ def tasks():
     Returns:
         list: List of tasks in default taskmaster
     """
-    global _default_task_master
-    return _default_task_master.tasks
+    global DEFAULT_TASK_MASTER
+    return DEFAULT_TASK_MASTER.tasks
 
 
 def dict():
@@ -73,8 +73,8 @@ def dict():
     Returns:
         dict: Dictionary of tasks in default taskmaster
     """
-    global _default_task_master
-    return _default_task_master.dict
+    global DEFAULT_TASK_MASTER
+    return DEFAULT_TASK_MASTER.dict
 
 
 def states():
@@ -83,38 +83,65 @@ def states():
     Returns:
         dict: Dictionary of task states in default taskmaster
     """
-    global _default_task_master
-    return _default_task_master.states
+    global DEFAULT_TASK_MASTER
+    return DEFAULT_TASK_MASTER.states
 
 
 def cleanup_tasks():
-    global _default_task_master
-    return _default_task_master.cleanup()
+    """Remove all finished tasks from the task list"""
+    global DEFAULT_TASK_MASTER
+    return DEFAULT_TASK_MASTER.cleanup()
 
 
 def remove_task(task_id: str):
-    global _default_task_master
-    return _default_task_master.remove(task_id)
+    """Remove a particular task from the task list
+
+    Arguments:
+        task_id {str} -- ID of the target task
+    """
+    global DEFAULT_TASK_MASTER
+    return DEFAULT_TASK_MASTER.remove(task_id)
 
 
 # Operations on the current task
 
 
 def current_task():
+    """Return the Task instance in which the caller is currently running.
+
+    If this function is called from outside a Task thread, it will return None.
+
+    Returns:
+        TaskThread -- Currently running Task thread.
+    """
     current_task_thread = threading.current_thread()
     if not isinstance(current_task_thread, TaskThread):
         return None
     return current_task_thread
 
 
 def update_task_progress(progress: int):
+    """Update the progress of the Task in which the caller is currently running.
+
+    If this function is called from outside a Task thread, it will do nothing.
+
+    Arguments:
+        progress {int} -- Current progress, in percent (0-100)
+    """
     if current_task():
         current_task().update_progress(progress)
     else:
         logging.info("Cannot update task progress of __main__ thread. Skipping.")
 
 
 def update_task_data(data: dict):
+    """Update the data of the Task in which the caller is currently running.
+
+    If this function is called from outside a Task thread, it will do nothing.
+
+    Arguments:
+        data {dict} -- Additional data to merge with the Task data
+    """
     if current_task():
         current_task().update_data(data)
     else:
@@ -132,7 +159,7 @@ def taskify(f):
 
     @wraps(f)
     def wrapped(*args, **kwargs):
-        task = _default_task_master.new(
+        task = DEFAULT_TASK_MASTER.new(
             f, *args, **kwargs
         )  # Append to parent object's task list
         task.start()  # Start the function
@@ -142,4 +169,4 @@ def wrapped(*args, **kwargs):
 
 
 # Create our default, protected, module-level task pool
-_default_task_master = TaskMaster()
+DEFAULT_TASK_MASTER = TaskMaster()

labthings/core/tasks/thread.py

@@ -14,7 +14,7 @@ class ThreadTerminationError(SystemExit):
 
 
 class TaskThread(threading.Thread):
-    def __init__(self, target=None, name=None, args=(), kwargs={}, daemon=True):
+    def __init__(self, target=None, name=None, args=None, kwargs=None, daemon=True):
         threading.Thread.__init__(
             self,
             group=None,
@@ -24,6 +24,11 @@ def __init__(self, target=None, name=None, args=(), kwargs={}, daemon=True):
             kwargs=kwargs,
             daemon=daemon,
         )
+        # Handle arguments
+        if args is None:
+            args = ()
+        if kwargs is None:
+            kwargs = {}
 
         # A UUID for the TaskThread (not the same as the threading.Thread ident)
         self._ID = uuid.uuid4()  # Task ID
@@ -96,7 +101,7 @@ def wrapped(*args, **kwargs):
             try:
                 self._return_value = f(*args, **kwargs)
                 self._status = "success"
-            except Exception as e:
+            except Exception as e:  # skipcq: PYL-W0703
                 logging.error(e)
                 logging.error(traceback.format_exc())
                 self._return_value = str(e)
@@ -133,7 +138,11 @@ def wait(self):
     def async_raise(self, exc_type):
         """Raise an exception in this thread."""
         # Should only be called on a started thread, so raise otherwise.
-        assert self.ident is not None, "Only started threads have thread identifier"
+        if self.ident is None:
+            raise RuntimeError(
+                "Cannot halt a thread that hasn't started. "
+                "No valid running thread identifier."
+            )
 
         # If the thread has died we don't want to raise an exception so log.
         if not self.is_alive():
@@ -166,7 +175,7 @@ def _is_thread_proc_running(self):
         Returns:
             bool: If _thread_proc is currently running
         """
-        could_acquire = self._running_lock.acquire(0)
+        could_acquire = self._running_lock.acquire(False)  # skipcq: PYL-E1111
         if could_acquire:
             self._running_lock.release()
             return False