Typos and other minor

docs/code_documentation/_build/html/_modules/pycont/controller.html

@@ -1036,7 +1036,7 @@ <h1>Source code for pycont.controller</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">go_to_volume</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">total_volume</span><span class="p">,</span> <span class="n">speed</span><span class="o">=</span><span class="n">speed</span><span class="p">,</span> <span class="n">wait</span><span class="o">=</span><span class="n">wait</span><span class="p">)</span></div>
 
     <span class="c"># valve</span>
-<div class="viewcode-block" id="C3000Controller.get_raw_valve_postion"><a class="viewcode-back" href="../../pycont.html#pycont.controller.C3000Controller.get_raw_valve_postion">[docs]</a>    <span class="k">def</span> <span class="nf">get_raw_valve_postion</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="viewcode-block" id="C3000Controller.get_raw_valve_position"><a class="viewcode-back" href="../../pycont.html#pycont.controller.C3000Controller.get_raw_valve_position">[docs]</a>    <span class="k">def</span> <span class="nf">get_raw_valve_position</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Gets the raw value of the valve&#39;s position.</span>
 
@@ -1063,7 +1063,7 @@ <h1>Source code for pycont.controller</h1><div class="highlight"><pre>
 
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">max_repeat</span><span class="p">):</span>
-            <span class="n">raw_valve_position</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_raw_valve_postion</span><span class="p">()</span>
+            <span class="n">raw_valve_position</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_raw_valve_position</span><span class="p">()</span>
             <span class="k">if</span> <span class="n">raw_valve_position</span> <span class="o">==</span> <span class="s">&#39;i&#39;</span><span class="p">:</span>
                 <span class="k">return</span> <span class="n">VALVE_INPUT</span>
             <span class="k">elif</span> <span class="n">raw_valve_position</span> <span class="o">==</span> <span class="s">&#39;o&#39;</span><span class="p">:</span>

docs/code_documentation/_build/html/genindex.html

@@ -465,7 +465,7 @@ <h2 id="G">G</h2>
   </dt>
 
 
-  <dt><a href="pycont.html#pycont.controller.C3000Controller.get_raw_valve_postion">get_raw_valve_postion() (pycont.controller.C3000Controller method)</a>
+  <dt><a href="pycont.html#pycont.controller.C3000Controller.get_raw_valve_position">get_raw_valve_position() (pycont.controller.C3000Controller method)</a>
   </dt>
 
   </dl></td>

docs/code_documentation/_build/html/pycont.html

@@ -226,8 +226,8 @@ <h1>Pycont Package<a class="headerlink" href="#pycont-package" title="Permalink
 </dd></dl>
 
 <dl class="method">
-<dt id="pycont.controller.C3000Controller.get_raw_valve_postion">
-<code class="descname">get_raw_valve_postion</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pycont/controller.html#C3000Controller.get_raw_valve_postion"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pycont.controller.C3000Controller.get_raw_valve_postion" title="Permalink to this definition">¶</a></dt>
+<dt id="pycont.controller.C3000Controller.get_raw_valve_position">
+<code class="descname">get_raw_valve_position</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pycont/controller.html#C3000Controller.get_raw_valve_position"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pycont.controller.C3000Controller.get_raw_valve_position" title="Permalink to this definition">¶</a></dt>
 <dd><p>Gets the raw value of the valve&#8217;s position.</p>
 <dl class="docutils">
 <dt>Returns:</dt>

docs/code_documentation/createsphinxproject.py

@@ -1,5 +1,6 @@
 import os
 
+
 def main():
     print("Please enter the details of the Sphinx project you wish to create.\n")
     projectName = input("Project name: ")
@@ -9,12 +10,13 @@ def main():
     sourceDir = input("Source code directory: ")
 
     try:
-        print ("Creating sphinx project...")
+        print("Creating sphinx project...")
         command = "sphinx-apidoc -F -H {0} -A {1} -V {2} -o {3} {4}".format(projectName, author, version, outputDir, sourceDir)
         print(command)
-        #os.system(command)
-    except Exception as e:
+        # os.system(command)
+    except Exception:
         print("Error when creating project.")
 
+
 if __name__=='__main__':
     main()

docs/code_documentation/makehtmldocs.py

@@ -1,8 +1,10 @@
 import os
 
+
 def main():
     os.system("make clean")
     os.system("make html")
 
+
 if __name__=='__main__':
     main()

pycont/controller.py

@@ -54,7 +54,7 @@
 
 #: Microstep Mode 0
 MICRO_STEP_MODE_0 = 0
-#:Microstep Mode 2
+#: Microstep Mode 2
 MICRO_STEP_MODE_2 = 2
 
 #: Number of steps in Microstep Mode 0
@@ -100,6 +100,7 @@ def __init__(self, port, baudrate=DEFAULT_IO_BAUDRATE, timeout=DEFAULT_IO_TIMEOU
         self.port = port
         self.baudrate = baudrate
         self.timeout = timeout
+        self._serial = None
 
         self.open(port, baudrate, timeout)
 
@@ -163,7 +164,7 @@ def __exit__(self, exc_type, exc_value, traceback):
 
             exc_value (Exception): The value associated with the Exception.
 
-            traceback (str): Location of where the exception occured.
+            traceback (str): Location of where the exception occurred.
 
         """
         self.close()
@@ -318,7 +319,7 @@ class C3000Controller(object):
 
         address (str): Address of the controller.
 
-        total_volume (int): Total volume of the pump.
+        total_volume (float): Total volume of the pump.
 
         micro_step_mode (int): The mode which the microstep will use, default set to MICRO_STEP_MODE_2 (2)
 
@@ -504,7 +505,7 @@ def is_initialized(self):
 
     def smart_initialize(self, valve_position=None, secure=True):
         """
-        Initialises the pump and sets all pump parammeters.
+        Initialises the pump and sets all pump parameters.
 
         Args:
             valve_position (int): Position of the valve, default set None.
@@ -733,8 +734,8 @@ def set_top_velocity(self, top_velocity, max_repeat=MAX_REPEAT_OPERATION, secure
             if secure is False:
                 return True
 
-        self.logger.debug("[PUMP {}] Too many failed attempts in set_top_velocity!".format(self.name))
-        raise ControllerRepeatedError('Repeated Error from pump {}'.format(self.name))
+        self.logger.debug(f"[PUMP {self.name}] Too many failed attempts in set_top_velocity!")
+        raise ControllerRepeatedError(f'Repeated Error from pump {self.name}')
 
     def get_top_velocity(self):
         """
@@ -943,11 +944,11 @@ def transfer(self, volume_in_ml, from_valve, to_valve, speed_in=None, speed_out=
             speed_out (int): The speed of transfer from the valve, default set to None.
 
         """
-        volume_transfered = min(volume_in_ml, self.remaining_volume)
-        self.pump(volume_transfered, from_valve, speed_in=speed_in, wait=True)
-        self.deliver(volume_transfered, to_valve, speed_out=speed_out, wait=True)
+        volume_transferred = min(volume_in_ml, self.remaining_volume)
+        self.pump(volume_transferred, from_valve, speed_in=speed_in, wait=True)
+        self.deliver(volume_transferred, to_valve, speed_out=speed_out, wait=True)
 
-        remaining_volume_to_transfer = volume_in_ml - volume_transfered
+        remaining_volume_to_transfer = volume_in_ml - volume_transferred
         if remaining_volume_to_transfer > 0:
             self.transfer(remaining_volume_to_transfer, from_valve, to_valve, speed_in, speed_out)
 
@@ -977,9 +978,9 @@ def go_to_volume(self, volume_in_ml, speed=None, wait=False, secure=True):
 
             speed (int): The speed of movement, default set to None.
 
-            wait (bool): Waits for the pump to be idle, defualt set to False.
+            wait (bool): Waits for the pump to be idle, default set to False.
 
-            secure (bool): Ensures that everything is corect, default set to True.
+            secure (bool): Ensures that everything is correct, default set to True.
 
         Returns:
             True (bool): The supplied volume is valid.
@@ -1022,7 +1023,7 @@ def go_to_max_volume(self, speed=None, wait=False):
         """
         self.go_to_volume(self.total_volume, speed=speed, wait=wait)
 
-    def get_raw_valve_postion(self):
+    def get_raw_valve_position(self):
         """
         Gets the raw value of the valve's position.
 
@@ -1049,7 +1050,7 @@ def get_valve_position(self, max_repeat=MAX_REPEAT_OPERATION):
 
         """
         for i in range(max_repeat):
-            raw_valve_position = self.get_raw_valve_postion()
+            raw_valve_position = self.get_raw_valve_position()
             if raw_valve_position == 'i':
                 return VALVE_INPUT
             elif raw_valve_position == 'o':

pycont/pump_protocol.py

@@ -189,7 +189,7 @@ def forge_initialize_valve_left_packet(self, operand_value=0):
         Creates a packet for initialising the left valve.
 
         Args:
-            operand_value (int): The value of the supplied operand, 0 by defualt.
+            operand_value (int): The value of the supplied operand, 0 by default.
 
         Returns:
             DTInstructionPacket: The packet created for initialising the left valve.
@@ -328,7 +328,7 @@ def forge_eeprom_lowlevel_config_packet(self, sub_command=20, operand_value="pyc
         dtcommand = dtprotocol.DTCommand(CMD_EEPROM_LOWLEVEL_CONFIG, str(sub_command) + "_" + str(operand_value))
         return self.forge_packet(dtcommand, execute=False)
 
-    def forge_valve_input_packet(self, operand_value=None):
+    def forge_valve_input_packet(self):
         """
         Creates a packet for the input into a valve on the device.
 
@@ -368,13 +368,10 @@ def forge_valve_extra_packet(self):
         """
         return self.forge_packet(dtprotocol.DTCommand(CMD_VALVE_EXTRA))
 
-    def forge_valve_6way_packet(self, valve_position, operand_value=None):
+    def forge_valve_6way_packet(self, valve_position):
         """
         Creates a packet for the 6way valve on the device.
 
-        Args:
-            operand_value (int): The value of the supplied operand, None by default.
-
         Returns:
             DTInstructionPacket: The packet created for the input into a valve on the device.
 

tests/pycont_6way_test.py

@@ -9,11 +9,12 @@
 import time
 
 import logging
-logging.basicConfig(level=logging.INFO)
 
 # simply import the module
 import pycont.controller
 
+logging.basicConfig(level=logging.INFO)
+
 # link to your config file
 SETUP_CONFIG_FILE = './pump_setup_config_6way.json'
 
@@ -96,7 +97,7 @@
 # They are '1', '2', '3', '4', '5', '6', all are in the list pycont.controller.VALVE_6WAY_LIST
 for valve_position in pycont.controller.VALVE_6WAY_LIST:
     controller.pumps['water'].set_valve_position(valve_position)
-    controller.acetone.set_valve_position(valve_position)  ## this is another way to call the pump
+    controller.acetone.set_valve_position(valve_position)  # This is another way to call the pump
     time.sleep(1)  # just to pause so that you can hear the sound of valve movements
 
 # of course you can change all the valve position at once

tests/pycont_test.py

@@ -3,18 +3,19 @@
 import time
 
 import logging
-logging.basicConfig(level=logging.INFO)
 
 # simply import the module
 import pycont.controller
 
+logging.basicConfig(level=logging.INFO)
+
 # link to your config file
 SETUP_CONFIG_FILE = './pump_setup_config.json'
 
 # and load the config file in a MultiPumpController
 controller = pycont.controller.MultiPumpController.from_configfile(SETUP_CONFIG_FILE)
 
-# initialize the pumps in a smart way, if they are already initialized we do not want to reinitialize them because they got back to zero position
+# Initialize the pumps in a smart way, if they are already initialized we do not want to reinitialize them because they got back to zero position
 controller.smart_initialize()
 
 # individual pumps can be accessed in two ways: