Code cleaning

puppeteer/__init__.py

@@ -53,7 +53,7 @@ def Controller(USR_INSTRUCTIONS, Connection, cancel_switch, ConnectionStatus,
     Protocol = SetProtocol(with_device=Box, filters=user_filters,
                            and_wavelenghts=USR_INSTRUCTIONS.user_wavelengths, 
                            well_number=96, protocol_name='default_protocol')
-    BoxQueue.put([Protocol, USR_INSTRUCTIONS.QueueFile])  # Export `Protocol' before Run begins.
+    BoxQueue.put([Box, Protocol, USR_INSTRUCTIONS.QueueFile])  # Export `Protocol' before Run begins.
     # Run Protocol. `Connection' is no longer a dependency of this method as 
     # the log messages produced interfere with the GUI during a protocol run.
     Protocol.Run(assay_length=USR_INSTRUCTIONS.length,
@@ -172,19 +172,20 @@ def ExportData(Protocol, ProcessData, QueueFile, Connection, Status,
             # House keeping. Always. Test or not.
             house_keeper(Protocol._dir_info, QueueFile, Connection, BUFFER_SIZE)
 
-def CancelProtocol():
+def CancelProtocol(with_device=None, Connection=None, ConnectionStatus=None):
     """
         Cancels a running protocol with IMMEDIATE effect. The use of flags with 
         multithreading cannot cancel a running protocol until the next iteration
         be it within a minute or an hour. `CancelProtocol' soft-restarts the 
         light modulator and, therefore, protocols are cancelled immediately. 
     """
-    # Stop hardware
-    # Protocol._device._camera.close()
-    # Protocol._device._heater.stop()
-    # Protocol._device._servo.stop()
-    # Protocol._device._light_panel.stop()
-    # Restart it all...
+    Box = with_device
+    # Stop hardware. Fixes heating being left on. Note that Connection and
+    # ConnectionStatus are set to `None', meaning no logs will be reported back
+    # to the GUI.
+    if Box is not None:
+        Box.terminate_device(Connection, ConnectionStatus)
+    # Restart server (workaround, as python won't recognise BASH functions).
     LiMO_Path = "/home/client/.srv/"
     Routine=".cancel_protocol.sh"
     subprocess.call(["bash", "-c", LiMO_Path + Routine])

puppeteer/_core.py

@@ -855,7 +855,6 @@ class SetProtocol:
                 servo_state = self._device.set_filter(flt, current_pwm=servo_state)
                 # self._data_acquisition(light_range, current_time, flt,
                 #                        wavelength, singleRead)
-                print("Time between reads: " + str(round(t.time() - warmup_init_t, 3)) + "s.")
                 self._data_acquisition_triplicate(light_range, current_time, flt,
                                        wavelength, singleRead)
                 if flt == "Filter_2":

pupuicon/_corelib.py

@@ -153,17 +153,17 @@ class NetworkOperator():
                 This snippet handles short packages (<BUFFER_SIZE) to allow the
                 handshake between server and client.
             """
-           return Stream
+            return Stream
         else:
             """
                 This other snippet handles larger packages (>=BUFFER_SIZE) to
                 allow the transmission of actual data, like, say, a protocol.
             """
-           while Stream:  
+            while Stream:  
                Buffer = Connection.recv(BUFFER_SIZE)
                Stream += Buffer
                if len(Buffer) < BUFFER_SIZE : break
-           return Stream
+            return Stream
 
     def _retrieve_protocol(self, ProtocolSize, Connection, BUFFER_SIZE):
         """