puda-drivers 0.0.15__py3-none-any.whl → 0.0.16__py3-none-any.whl

puda_drivers/core/serialcontroller.py

@@ -4,6 +4,7 @@ Generic Serial Controller for communicating with devices over serial ports.
 
 import time
 import logging
+import threading
 from typing import Optional, List, Tuple
 from abc import ABC, abstractmethod
 import serial
@@ -49,6 +50,9 @@ class SerialController(ABC):
         self.baudrate = baudrate
         self.timeout = timeout
         self._logger = logger
+        
+        # lock to prevent concurrent access to the serial port
+        self._lock = threading.Lock()
 
     def connect(self) -> None:
         """
@@ -103,8 +107,9 @@ class SerialController(ABC):
 
     def _send_command(self, command: str) -> None:
         """
-        Sends a custom protocol command, reads, and returns the response.
-        If a timeout occurs, it logs the error and returns None instead of raising an exception.
+        Sends a custom protocol command.
+        Note: This method should be called while holding self._lock to ensure
+        atomic command/response pairing.
         """
         if not self.is_connected or not self._serial:
             self._logger.error(
@@ -116,7 +121,6 @@ class SerialController(ABC):
 
         self._logger.info("-> Sending: %r", command)
 
-        # Send the command
         try:
             self._serial.reset_input_buffer()  # clear input buffer
             self._serial.reset_output_buffer()  # clear output buffer
@@ -130,7 +134,7 @@ class SerialController(ABC):
 
         except serial.SerialException as e:
             self._logger.error(
-                "Serial error writing or reading command '%s'. Error: %s",
+                "Serial error writing command '%s'. Error: %s",
                 command,
                 e,
             )
@@ -198,11 +202,14 @@ class SerialController(ABC):
         
         This method combines sending a command and reading its response into a
         single atomic operation, ensuring the response corresponds to the command
-        that was just sent. This is the preferred method for commands that
-        require a response.
+        that was just sent. The entire operation is protected by a lock to prevent
+        concurrent commands from interfering with each other.
+        
+        This is the preferred method for commands that require a response.
         
         Args:
             command: Command string to send (should include protocol terminator if needed)
+            value: Optional value parameter for the command
             
         Returns:
             Response string from the device
@@ -211,20 +218,22 @@ class SerialController(ABC):
             serial.SerialException: If device is not connected or communication fails
             serial.SerialTimeoutException: If no response is received within timeout
         """
-        self._send_command(self._build_command(command, value))
-        
-        # Increase timeout by 60 seconds for G28 (homing) command
-        original_timeout = self.timeout
-        if "G28" in command.upper():
-            self.timeout = original_timeout + 60
-            # Also update the serial connection's timeout if connected
-            if self.is_connected and self._serial:
-                self._serial.timeout = self.timeout
-        
-        try:
-            return self._read_response()
-        finally:
-            # Restore original timeout
-            self.timeout = original_timeout
-            if self.is_connected and self._serial:
-                self._serial.timeout = original_timeout
+        # Hold the lock for the entire send+read operation to ensure atomicity
+        # This prevents concurrent commands from mixing up responses
+        with self._lock:
+            # Increase timeout by 60 seconds for G28 (homing) command
+            original_timeout = self.timeout
+            if "G28" in command.upper():
+                self.timeout = original_timeout + 60
+                # Also update the serial connection's timeout if connected
+                if self.is_connected and self._serial:
+                    self._serial.timeout = self.timeout
+            
+            try:
+                self._send_command(self._build_command(command, value))
+                return self._read_response()
+            finally:
+                # Restore original timeout
+                self.timeout = original_timeout
+                if self.is_connected and self._serial:
+                    self._serial.timeout = original_timeout

puda_drivers/machines/first.py

@@ -159,7 +159,7 @@ class First:
         self.camera.disconnect()
         self._logger.info("Machine shutdown complete")
         
-    async def get_position(self) -> Dict[str, float]:
+    async def get_position(self) -> Dict[str, Union[Dict[str, float], int]]:
         """
         Get the current position of the machine. Both QuBot and Sartorius are queried.
         
@@ -234,7 +234,11 @@ class First:
         self.qubot.move_absolute(position=pos)
         
         # attach tip (move slowly down)
-        insert_depth = self.deck[slot].get_insert_depth()
+        labware = self.deck[slot]
+        if labware is None:
+            self._logger.error("Cannot attach tip: no labware loaded in slot '%s'", slot)
+            raise ValueError(f"No labware loaded in slot '{slot}'. Load labware before attaching tips.")
+        insert_depth = labware.get_insert_depth()
         self._logger.debug("Moving down by %s mm to insert tip", insert_depth)
         self.qubot.move_relative(
             position=Position(z=-insert_depth),
@@ -378,17 +382,24 @@ class First:
             
         Returns:
             Position with absolute coordinates
+            
+        Raises:
+            ValueError: If well is specified but no labware is loaded in the slot
         """
         # Get slot origin
         pos = self.get_slot_origin(slot)
 
         # relative well position from slot origin
         if well:
-            well_pos = self.deck[slot].get_well_position(well).get_xy()
+            labware = self.deck[slot]
+            if labware is None:
+                self._logger.error("Cannot get well position: no labware loaded in slot '%s'", slot)
+                raise ValueError(f"No labware loaded in slot '{slot}'. Load labware before accessing wells.")
+            well_pos = labware.get_well_position(well).get_xy()
             # the deck is rotated 90 degrees clockwise for this machine
             pos += well_pos.swap_xy()
             # get z
-            pos += Position(z=self.deck[slot].get_height() - self.CEILING_HEIGHT)
+            pos += Position(z=labware.get_height() - self.CEILING_HEIGHT)
             self._logger.debug("Absolute Z position for slot '%s', well '%s': %s", slot, well, pos)
         else:
             self._logger.debug("Absolute Z position for slot '%s': %s", slot, pos)
@@ -404,15 +415,22 @@ class First:
             
         Returns:
             Position with absolute coordinates
+            
+        Raises:
+            ValueError: If well is specified but no labware is loaded in the slot
         """
         pos = self.get_slot_origin(slot)
         
         if well:
-            well_pos = self.deck[slot].get_well_position(well).get_xy()
+            labware = self.deck[slot]
+            if labware is None:
+                self._logger.error("Cannot get well position: no labware loaded in slot '%s'", slot)
+                raise ValueError(f"No labware loaded in slot '{slot}'. Load labware before accessing wells.")
+            well_pos = labware.get_well_position(well).get_xy()
             pos += well_pos.swap_xy()
             
             # get a
-            a = Position(a=self.deck[slot].get_height() - self.CEILING_HEIGHT)
+            a = Position(a=labware.get_height() - self.CEILING_HEIGHT)
             pos += a
             self._logger.debug("Absolute A position for slot '%s', well '%s': %s", slot, well, pos)
         else:

puda_drivers/move/gcode.py

@@ -514,6 +514,9 @@ class GCodeController(SerialController):
 
         This method can be called even when the machine is moving from other commands,
         as it runs the blocking serial communication in a separate thread.
+        
+        If the M114 command takes more than 1 second to respond, falls back to
+        returning the internally tracked position instead.
 
         Returns:
             Position containing X, Y, Z, and A positions
@@ -523,28 +526,38 @@ class GCodeController(SerialController):
         """
         self._logger.info("Querying current machine position (M114).")
         # Run the blocking execute call in a thread pool to allow concurrent operations
-        res: str = await asyncio.to_thread(self.execute, "M114")
-
-        # Extract position values using regex
-        pattern = re.compile(r"([XYZA]):(-?\d+\.\d+)")
-        matches = pattern.findall(res)
+        # with a 1 second timeout - if it takes longer, fall back to internal position
+        try:
+            res: str = await asyncio.wait_for(
+                asyncio.to_thread(self.execute, "M114"),
+                timeout=1.0
+            )
+            
+            # Extract position values using regex
+            pattern = re.compile(r"([XYZA]):(-?\d+\.\d+)")
+            matches = pattern.findall(res)
 
-        position_data: Dict[str, float] = {}
+            position_data: Dict[str, float] = {}
 
-        for axis, value_str in matches:
-            try:
-                position_data[axis.lower()] = float(value_str)
-            except ValueError:
-                self._logger.error(
-                    "Failed to convert position value '%s' for axis %s to float.",
-                    value_str,
-                    axis,
-                )
-                continue
-
-        position = Position.from_dict(position_data)
-        self._logger.info("Query position complete. Retrieved positions: %s", position)
-        return position
+            for axis, value_str in matches:
+                try:
+                    position_data[axis.lower()] = float(value_str)
+                except ValueError:
+                    self._logger.error(
+                        "Failed to convert position value '%s' for axis %s to float.",
+                        value_str,
+                        axis,
+                    )
+                    continue
+
+            position = Position.from_dict(position_data)
+            self._logger.info("Query position complete. Retrieved positions: %s", position)
+            return position
+        except asyncio.TimeoutError:
+            self._logger.warning(
+                "M114 command timed out after 1 second. Falling back to internal position."
+            )
+            return self.get_internal_position()
 
     def _sync_position(self) -> Tuple[bool, Position]:
         """

{puda_drivers-0.0.15.dist-info → puda_drivers-0.0.16.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: puda-drivers
-Version: 0.0.15
+Version: 0.0.16
 Summary: Hardware drivers for the PUDA platform.
 Project-URL: Homepage, https://github.com/zhao-bears/puda-drivers
 Project-URL: Issues, https://github.com/zhao-bears/puda-drivers/issues

{puda_drivers-0.0.15.dist-info → puda_drivers-0.0.16.dist-info}/RECORD

@@ -3,7 +3,7 @@ puda_drivers/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 puda_drivers/core/__init__.py,sha256=XbCdXsU6NMDsmEAtavAGiSZZPla5d7zc2L7Qx9qKHdY,214
 puda_drivers/core/logging.py,sha256=prOeJ3CGEbm37TtMRyAOTQQiMU5_ImZTRXmcUJxkenc,2892
 puda_drivers/core/position.py,sha256=f4efmDSrKKCtqrR-GUJxVitPG20MiuGSDOWt-9TVISk,12628
-puda_drivers/core/serialcontroller.py,sha256=38mKas1iJaOkAE0_V4tmqgZz7RxMMEWfGqA0Ma_Dt2A,8604
+puda_drivers/core/serialcontroller.py,sha256=aIyEpA8J4R7yBfIq0roMqbD-nxEwuwaB8c_7zaOXg_A,9100
 puda_drivers/cv/__init__.py,sha256=DYiPwYOLSUsZ9ivWiHoMGGD3MZ3Ygu9qLYja_OiUodU,100
 puda_drivers/cv/camera.py,sha256=Tzxt1h3W5Z8XFanud_z-PhhJ2UYsC4OEhcak9TVu8jM,16490
 puda_drivers/labware/__init__.py,sha256=RlRxrJn2zyzyxv4c1KGt8Gmxv2cRO8V4zZVnnyL-I00,288
@@ -12,10 +12,10 @@ puda_drivers/labware/opentrons_96_tiprack_300ul.json,sha256=jmNaworu688GEgFdxMxN
 puda_drivers/labware/polyelectric_8_wellplate_30000ul.json,sha256=esu2tej0ORs7Pfd4HwoQVUpU5mPvp2AYzE3zsCC2FDk,3104
 puda_drivers/labware/trash_bin.json,sha256=Hk4MXO48P28jG7F87DUd9Ja4c_P7kAy3karPQ965i9Y,580
 puda_drivers/machines/__init__.py,sha256=zmIk_r2T8nbPA68h3Cko8N6oL7ncoBpmvhNcAqzHmc4,45
-puda_drivers/machines/first.py,sha256=cqK8Gwk89nTweVTImhHU1RimtvDn4En36qV_ZanMGIU,19701
+puda_drivers/machines/first.py,sha256=5xFjMwCHM4wZz2_VjEMXPMyXndtXjcnt1WL_GWSSRbs,20725
 puda_drivers/move/__init__.py,sha256=NKIKckcqgyviPM0EGFcmIoaqkJM4qekR4babfdddRzM,96
 puda_drivers/move/deck.py,sha256=yq2B4WMqj0hQvHt8HoJskP10u1DUyKwUnjP2c9gJ174,1397
-puda_drivers/move/gcode.py,sha256=GNbFkGgXcr0vBXXWbM96aRkkdQsTiqLCA56V-z3ebYs,23102
+puda_drivers/move/gcode.py,sha256=nS1dmt90_89BUjlHh0VNqGLeRhyIdJ4-8Ps_7YlW-B0,23735
 puda_drivers/move/grbl/__init__.py,sha256=vBeeti8DVN2dACi1rLmHN_UGIOdo0s-HZX6mIepLV5I,98
 puda_drivers/move/grbl/api.py,sha256=loj8_Vap7S9qaD0ReHhgxr9Vkl6Wp7DGzyLkZyZ6v_k,16995
 puda_drivers/move/grbl/constants.py,sha256=4736CRDzLGWVqGscLajMlrIQMyubsHfthXi4RF1CHNg,9585
@@ -23,7 +23,7 @@ puda_drivers/transfer/liquid/sartorius/__init__.py,sha256=7fljIbu0KkumsI3NI3O64d
 puda_drivers/transfer/liquid/sartorius/api.py,sha256=jxwIJmY2k1K2ts6NC2ZgFTe4MOiH8TGnJeqYOqNa3rE,28250
 puda_drivers/transfer/liquid/sartorius/constants.py,sha256=mcsjLrVBH-RSodH-pszstwcEL9wwbV0vOgHbGNxZz9w,2770
 puda_drivers/transfer/liquid/sartorius/rLine.py,sha256=FWEFO9tZN3cbneiozXRs77O-47Jg_8vYzWJvUrWpYxA,14531
-puda_drivers-0.0.15.dist-info/METADATA,sha256=CBB25oLMTKaHkRqnPsrr80dDLenQxKa_OQoZo0GTSno,7102
-puda_drivers-0.0.15.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-puda_drivers-0.0.15.dist-info/licenses/LICENSE,sha256=7EI8xVBu6h_7_JlVw-yPhhOZlpY9hP8wal7kHtqKT_E,1074
-puda_drivers-0.0.15.dist-info/RECORD,,
+puda_drivers-0.0.16.dist-info/METADATA,sha256=kD7z3BQmYQAihFsf7T_f_iL3ttiLyY4nDegdEfmuElk,7102
+puda_drivers-0.0.16.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+puda_drivers-0.0.16.dist-info/licenses/LICENSE,sha256=7EI8xVBu6h_7_JlVw-yPhhOZlpY9hP8wal7kHtqKT_E,1074
+puda_drivers-0.0.16.dist-info/RECORD,,