fix: Newlines before comments, removed extraneous whitespace

scripts/config_validation.py

@@ -65,6 +65,7 @@ def validate_config_recursive(user_data, default_data, annotations, key_path=[])
                 elif isinstance(default_value, dict):
                     if not validate_config_recursive(user_data[key], default_value, annotations, current_path):
                         all_valid = False
+
         # If a key from default config is not in the annotations, it's assumed required.
         elif key not in user_data:
             print(f"Key {'.'.join(current_path)} is required since not #optional but missing from the user YAML")

scripts/tmux_run.sh

@@ -16,29 +16,29 @@ if tmux has-session -t phyto-arm 2>/dev/null; then
 else
   # Create the session and name the window
   tmux new-session -d -s phyto-arm -n docker
-  
+
   # Split the window into three panes
   tmux split-window -v
   tmux split-window -v
   tmux select-layout even-vertical
-  
+
   # Select pane 1 and launch the main process in docker
   tmux select-pane -t 0
   tmux send-keys "./scripts/docker_run.sh -b $CONFIG" C-m
   tmux send-keys "./phyto-arm start main mounted_config.yaml" C-m
-  
+
   # Select pane 2 and launch the IFCB arm in the same container
   tmux select-pane -t 1
   tmux send-keys "sleep 8" C-m
   tmux send-keys "docker exec -it phyto-arm bash" C-m
   tmux send-keys "./phyto-arm start arm_ifcb ./mounted_config.yaml" C-m
-  
+
   # Select pane 3 and launch the Chanos arm in the same container
   tmux select-pane -t 2
   tmux send-keys "sleep 10" C-m
   tmux send-keys "docker exec -it phyto-arm bash" C-m
   tmux send-keys "./phyto-arm start arm_chanos ./mounted_config.yaml" C-m
-  
+
   # Attach to the session
   tmux attach -t phyto-arm
 fi

src/jvl_motor/src/jvl_motor_node.py

@@ -148,7 +148,7 @@ def main():
         msg.Motion,
         queue_size=1
     )
-    
+
     # Create services
     services = [
         rospy.Service(

src/phyto_arm/src/arm_base.py

@@ -45,6 +45,7 @@ def __init__(self, arm_name, winch_name=None):
             acquire_move_clearance = rospy.ServiceProxy('/lock_manager/acquire', LockOperation)
             release_move_clearance = rospy.ServiceProxy('/lock_manager/release', LockOperation)
             lock_op = LockOperationRequest(arm_name)
+
             # Bind lock operations to instance
             self.request_clearance = lambda: acquire_move_clearance(lock_op).success
             self.release_clearance = lambda: release_move_clearance(lock_op).success
@@ -54,6 +55,7 @@ def __init__(self, arm_name, winch_name=None):
             rospy.loginfo('Awaiting lock manager check...')
             check_lock.wait_for_service()
             rospy.loginfo('Server acquired for lock check.')
+
             # Check whether we have a dangling acquisition to release
             if check_lock(LockCheckRequest(arm_name)).has_lock:
                 rospy.logwarn('Releasing dangling lock acquisition')
@@ -76,31 +78,35 @@ def winch_busy(self):
     def send_winch_goal(self, depth, speed, callback):
         global winches_moving
         rospy.loginfo(f"Sending winch move to {depth}")
+
         # Ensure winch is enabled
         if rospy.get_param('winch/enabled') != True:
             raise ValueError('Move aborted: winch is disabled in config')
+
         # Safety check: Do not exceed depth bounds
         if depth < rospy.get_param('winch/range/min'):
             raise ValueError(f'Move aborted: depth {depth} is below min {rospy.get_param("winch/range/max")}')
         elif depth > rospy.get_param('winch/range/max'):
             raise ValueError(f'Move aborted: depth {depth} is above max {rospy.get_param("winch/range/max")}')
+
         # Set max speed if not specified
         if speed is None:
             speed = rospy.get_param('winch/max_speed')
+
         # Safety check: Speed cannot exceed max speed
         elif speed > rospy.get_param('winch/max_speed'):
             raise ValueError(f'Move aborted: speed {speed} is above max {rospy.get_param("winch/max_speed")}')
         if self.winch_busy():
             raise RuntimeError('Move aborted: winch in unexpected busy state')
         rospy.loginfo(f"All checks passed; Moving winch to {depth}")
 
-
         # Intermediate callback for ensuring move was a success and to release lock
         # before calling the task's callback
         def winch_done(state, move_result):
             try:
                 # Ensure winch move was successful
                 assert state == actionlib.GoalStatus.SUCCEEDED
+
                 # Free up semaphore for another winch movement
                 assert self.release_clearance()
                 callback(move_result)
@@ -134,15 +140,18 @@ def loop(self):
                     task = self.get_next_task(task)
                     rospy.logwarn(f'No winch; running {task.name}')
                     task.callback()
+
                 # Otherwise, move winch
                 else:
                     rospy.logwarn('Arm waiting for clearance')
+
                     # TODO: Consider replacing this with a queueing mechanism.  Requires setting up
                     # callbacks via ROS service calls. Unnecessarily complex for a 2 winch system,
                     # but might be the only way to achieve round-robin for many winches.
                     while not rospy.is_shutdown() and not self.request_clearance():
                         # Wait until central semaphore clears us to move
                         rospy.sleep(1)
+
                     # TODO: Optimize task evaluation. Currently we are blocking on the assumption that
                     # movement will be needed; this is not always the case. Not a problem for 1 or 2
                     # winches, but could get slow if the number of winches greatly exceeds the

src/phyto_arm/src/arm_chanos.py

@@ -112,6 +112,7 @@ def compute_profiler_steps():
 
 def on_profile_msg(msg):
     arm.latest_profile = msg
+
     # Find the maximal value in the profile
     argmax = max(range(len(arm.latest_profile.values)), key=lambda i: arm.latest_profile.values[i])
     arm.profiler_peak_value = arm.latest_profile.values[argmax]

src/phyto_arm/src/arm_ifcb.py

@@ -63,6 +63,7 @@ def get_next_task(self, last_task):
 
 # Global reference to action provided by other node
 ifcb_runner = None
+
 # Global reference to arm state
 arm = None
 
@@ -79,24 +80,29 @@ def on_profile_msg(msg):
 def wiz_to_rostime(hhmm_time):
     # Today's time
     today_time = datetime.now().time()
+
     # Convert HH:MM to a timestamp
     wiz_time = datetime.strptime(hhmm_time, "%H:%M").time()
     wiz_date = datetime.now().date()
+
     # wiz_time should always come after the current time, even if it's the next day
     if wiz_time < today_time:
         wiz_date = datetime.now().date() + timedelta(days=1)
     unix_timestamp = datetime.combine(wiz_date, wiz_time).timestamp()
+
     # Create a rospy.Time object
     return rospy.Time.from_sec(unix_timestamp)
 
 
 def find_next_wiz_time():
     # Get array of HH:MM times
     wiz_probe_times = rospy.get_param('tasks/wiz_probe/times')
+
     # Find the next time
     next_time = None
     for wiz_time in wiz_probe_times:
         wiz_time = wiz_to_rostime(wiz_time)
+
         # wiz_time will always be in the future, just find the earliest one
         if next_time is None or wiz_time < next_time:
             next_time = wiz_time
@@ -106,6 +112,7 @@ def find_next_wiz_time():
 # Check if it's time to run the wiz probe routine
 def its_wiz_time():
     prep_window = rospy.Duration(60*rospy.get_param('tasks/wiz_probe/preparation_window'))
+
     # If we're within the preparation window, it's wizin' time
     if (find_next_wiz_time() - rospy.Time.now()) <= prep_window:
         return True
@@ -135,16 +142,19 @@ def compute_wiz_depth(peak_depth):
 def await_wiz_probe(callback):
     # Find the next time to run the wiz probe
     next_time = find_next_wiz_time()
+
     # Ensure we're still in the preparation window
     prep_window = rospy.Duration(60*rospy.get_param('tasks/wiz_probe/preparation_window'))
     preptime_remaining = next_time - rospy.Time.now()
     if preptime_remaining > prep_window:
         raise ValueError(f'Next wiz time is {preptime_remaining.to_sec()}s away, should be less than \
                           {prep_window.to_sec()}s. Preparation window likely too short.')
+
     # Wait for the rest of the window + the wiz probe duration
     rospy.loginfo('Waiting for wiz probe to finish')
     wiz_duration = 60*rospy.get_param('tasks/wiz_probe/duration')
     rospy.sleep(wiz_duration + preptime_remaining.to_sec())
+
     # TODO: Run IFCB while waiting
     rospy.loginfo('Wiz probe wait time complete')
     callback()
@@ -193,6 +203,7 @@ def handle_downcast(move_result):
     while arm.latest_profile is None or \
         arm.latest_profile.goal_uuid != move_result.uuid:
         notified = arm.profile_activity.wait(60)
+
         # For short downcasts profiling will likely fail; switch to scheduled depth
         if not notified:
             rospy.logwarn('No profile data received')

src/phyto_arm/src/mocks/mock_ctd.py

@@ -9,11 +9,13 @@
 
 def generate_mock_ctd():
     ctd = Ctd()
+
     # Generate random or fixed values for CTD parameters
     ctd.conductivity = random.uniform(0, 5)  # Example random value, in S/m
     ctd.temperature = random.uniform(-2, 30)  # Example random value, in Celsius
     ctd.pressure = random.uniform(0, 600)  # Example random value, in dbar
     ctd.sound_speed = random.uniform(1400, 1600)  # Example random value, in m/s
+
     # Set covariance fields to -1, indicating "not valid"
     ctd.conductivity_covar = ctd.temperature_covar = ctd.pressure_covar = \
         ctd.salinity_covar = ctd.sound_speed_covar = -1
@@ -36,6 +38,7 @@ def main():
     global depth_pub
     rospy.init_node('mock_sensor_node')
     rospy.logwarn(f'Starting mock sensor node {rospy.get_name()}')
+
     # Subscribe to the mock depth topic from the 'mock_winch'
     rospy.Subscriber("mock_depth", Float64, depth_callback)
 

src/phyto_arm/src/winch_node.py

@@ -134,6 +134,7 @@ async def move_to_depth(server, goal):
         asyncio.create_task(depth.wait()): "depth status",
         asyncio.create_task(motor.wait()): "motor status"
     }
+
     # Get an initial depth fix and motor status message
     _, pending = await asyncio.wait(tasks.keys(), timeout=2.0, return_when=asyncio.ALL_COMPLETED)
 
@@ -169,6 +170,7 @@ async def move_to_depth(server, goal):
     # Velocity function
     max_speed = rospy.get_param('~max_speed' )
     half_speed_dist = rospy.get_param('~half_speed_dist')
+
     # Assert both are not None
     assert max_speed is not None and half_speed_dist is not None, 'Winch speed config invalid'
     assert goal.velocity < max_speed, 'Goal velocity exceeds max speed'

src/rbr_maestro3_ctd/src/rbr_maestro3_node.py

@@ -99,7 +99,7 @@ async def main():
         # Set covariance fields to -1, the standard "not valid" value
         ctd.conductivity_covar = ctd.temperature_covar = ctd.pressure_covar = \
             ctd.salinity_covar = ctd.sound_speed_covar = -1
-        
+
         # Construct the DepthPressure message
         dp = DepthPressure()
         dp.depth = depth