puda-drivers 0.0.11__tar.gz → 0.0.13__tar.gz

{puda_drivers-0.0.11 → puda_drivers-0.0.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: puda-drivers
-Version: 0.0.11
+Version: 0.0.13
 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
@@ -14,7 +14,8 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Classifier: Topic :: System :: Hardware
-Requires-Python: >=3.8
+Requires-Python: >=3.10
+Requires-Dist: nats-py>=2.12.0
 Requires-Dist: opencv-python>=4.12.0.88
 Requires-Dist: pyserial~=3.5
 Description-Content-Type: text/markdown
@@ -85,6 +86,7 @@ When file logging is enabled, logs are saved to timestamped files (unless a cust
 The `First` machine integrates motion control, deck management, liquid handling, and camera capabilities:
 
 ```python
+import time
 import logging
 from puda_drivers.machines import First
 from puda_drivers.core.logging import setup_logging
@@ -102,14 +104,8 @@ machine = First(
     camera_index=0,
 )
 
-# Connect all devices
-machine.connect()
-
-# Home the gantry
-machine.qubot.home()
-
-# Initialize the pipette
-machine.pipette.initialize()
+# Start up the machine (connects all controllers, homes gantry, and initializes pipette)
+machine.startup()
 
 # Load labware onto the deck
 machine.load_deck({
@@ -119,19 +115,19 @@ machine.load_deck({
 })
 
 # Start video recording
-machine.camera.start_video_recording()
+machine.start_video_recording()
 
 # Perform liquid handling operations
 machine.attach_tip(slot="A3", well="G8")
 machine.aspirate_from(slot="C2", well="A1", amount=100, height_from_bottom=10.0)
 machine.dispense_to(slot="C2", well="B4", amount=100, height_from_bottom=30.0)
-machine.drop_tip(slot="C1", well="A1")
+machine.drop_tip(slot="C1", well="A1", height_from_bottom=10)
 
 # Stop video recording
-machine.camera.stop_video_recording()
+machine.stop_video_recording()
 
-# Disconnect all devices
-machine.disconnect()
+# Shutdown the machine (gracefully disconnects all controllers)
+machine.shutdown()
 ```
 
 **Discovering Available Methods**: To explore what methods are available on any class instance, you can use Python's built-in `help()` function:
@@ -193,7 +189,7 @@ sartorius_ports = list_serial_ports(filter_desc="Sartorius")
 
 ## Requirements
 
-- Python >= 3.14
+- Python >= 3.8
 - pyserial >= 3.5
 - See `pyproject.toml` for full dependency list
 

{puda_drivers-0.0.11 → puda_drivers-0.0.13}/README.md

@@ -64,6 +64,7 @@ When file logging is enabled, logs are saved to timestamped files (unless a cust
 The `First` machine integrates motion control, deck management, liquid handling, and camera capabilities:
 
 ```python
+import time
 import logging
 from puda_drivers.machines import First
 from puda_drivers.core.logging import setup_logging
@@ -81,14 +82,8 @@ machine = First(
     camera_index=0,
 )
 
-# Connect all devices
-machine.connect()
-
-# Home the gantry
-machine.qubot.home()
-
-# Initialize the pipette
-machine.pipette.initialize()
+# Start up the machine (connects all controllers, homes gantry, and initializes pipette)
+machine.startup()
 
 # Load labware onto the deck
 machine.load_deck({
@@ -98,19 +93,19 @@ machine.load_deck({
 })
 
 # Start video recording
-machine.camera.start_video_recording()
+machine.start_video_recording()
 
 # Perform liquid handling operations
 machine.attach_tip(slot="A3", well="G8")
 machine.aspirate_from(slot="C2", well="A1", amount=100, height_from_bottom=10.0)
 machine.dispense_to(slot="C2", well="B4", amount=100, height_from_bottom=30.0)
-machine.drop_tip(slot="C1", well="A1")
+machine.drop_tip(slot="C1", well="A1", height_from_bottom=10)
 
 # Stop video recording
-machine.camera.stop_video_recording()
+machine.stop_video_recording()
 
-# Disconnect all devices
-machine.disconnect()
+# Shutdown the machine (gracefully disconnects all controllers)
+machine.shutdown()
 ```
 
 **Discovering Available Methods**: To explore what methods are available on any class instance, you can use Python's built-in `help()` function:
@@ -172,7 +167,7 @@ sartorius_ports = list_serial_ports(filter_desc="Sartorius")
 
 ## Requirements
 
-- Python >= 3.14
+- Python >= 3.8
 - pyserial >= 3.5
 - See `pyproject.toml` for full dependency list
 

{puda_drivers-0.0.11 → puda_drivers-0.0.13}/pyproject.toml

@@ -1,12 +1,12 @@
 [project]
 name = "puda-drivers"
-version = "0.0.11"
+version = "0.0.13"
 description = "Hardware drivers for the PUDA platform."
 readme = "README.md"
 authors = [
     { name = "zhao", email = "20024592+agentzhao@users.noreply.github.com" }
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 classifiers = [
     "Intended Audience :: Science/Research",
     "Intended Audience :: Developers",
@@ -19,6 +19,7 @@ classifiers = [
 license = "MIT"
 license-files = ["LICEN[CS]E*"]
 dependencies = [
+    "nats-py>=2.12.0",
     "opencv-python>=4.12.0.88",
     "pyserial~=3.5",
 ]

{puda_drivers-0.0.11 → puda_drivers-0.0.13}/src/puda_drivers/machines/first.py

@@ -9,7 +9,9 @@ This class demonstrates the integration of:
 
 import logging
 import time
+from pathlib import Path
 from typing import Optional, Dict, Tuple, Type, Union
+import numpy as np
 from puda_drivers.move import GCodeController, Deck
 from puda_drivers.core import Position
 from puda_drivers.transfer.liquid.sartorius import SartoriusController
@@ -118,24 +120,73 @@ class First:
             camera_index if camera_index is not None else self.DEFAULT_CAMERA_INDEX,
         )
         
-    def connect(self):
-        """Connect all controllers."""
-        self._logger.info("Connecting all controllers")
+    def startup(self):
+        """
+        Start up the machine by connecting all controllers and initializing subsystems.
+        
+        This method:
+        - Connects to all controllers (gantry, pipette, camera)
+        - Homes the gantry to establish a known position
+        - Initializes the pipette to reset it to a known state
+        
+        The machine is ready for operations after this method completes.
+        """
+        self._logger.info("Starting up machine and connecting all controllers")
         self.qubot.connect()
         self.pipette.connect()
         self.camera.connect()
         self._logger.info("All controllers connected successfully")
         
-    def disconnect(self):
-        """Disconnect all controllers."""
-        self._logger.info("Disconnecting all controllers")
+        # Home the gantry to establish known position
+        self._logger.info("Homing gantry...")
+        self.qubot.home()
+        
+        # Initialize the pipette (all pipette operations need to wait 5 seconds for completion)
+        self._logger.info("Initializing pipette...")
+        self.pipette.initialize()
+        time.sleep(5)
+        self._logger.info("Machine startup complete - ready for operations")
+        
+    def shutdown(self):
+        """
+        Gracefully shut down the machine by disconnecting all controllers.
+        
+        This method ensures all connections are properly closed and resources are released.
+        """
+        self._logger.info("Shutting down machine and disconnecting all controllers")
         self.qubot.disconnect()
         self.pipette.disconnect()
         self.camera.disconnect()
-        self._logger.info("All controllers disconnected successfully")
+        self._logger.info("Machine shutdown complete")
+        
+    def get_position(self) -> Dict[str, float]:
+        """
+        Get the current position of the machine. Both QuBot and Sartorius are queried.
+        
+        Args:
+            None
+        Returns:
+            Dictionary containing the current position of the machine and it's components.
+        """
+        qubot_position = self.qubot.get_position()
+        sartorius_position = self.pipette.get_position()
+
+        return {
+            "qubot": qubot_position.to_dict(),
+            "pipette": sartorius_position,
+        }
         
     def load_labware(self, slot: str, labware_name: str):
-        """Load a labware object into a slot."""
+        """
+        Load a labware object into a slot.
+        
+        Args:
+            slot: Slot name (e.g., 'A1', 'B2')
+            labware_name: Name of the labware class to load
+        
+        Raises:
+            KeyError: If slot is not found in deck
+        """
         self._logger.info("Loading labware '%s' into slot '%s'", labware_name, slot)
         self.deck.load_labware(slot=slot, labware_name=labware_name)
         self._logger.debug("Labware '%s' loaded into slot '%s'", labware_name, slot)
@@ -161,10 +212,20 @@ class First:
         self._logger.info("Deck layout loaded successfully")
         
     def attach_tip(self, slot: str, well: Optional[str] = None):
-        """Attach a tip from a slot."""
+        """
+        Attach a tip from a slot.
+
+        Args:
+            slot: Slot name (e.g., 'A1', 'B2')
+            well: Optional well name within the slot (e.g., 'A1' for a well in a tiprack)
+        
+        Note:
+            This method is idempotent - if a tip is already attached, it will
+            log a warning and return successfully without raising an error.
+        """
         if self.pipette.is_tip_attached():
-            self._logger.error("Cannot attach tip: tip already attached")
-            raise ValueError("Tip already attached")
+            self._logger.warning("Tip already attached - skipping attachment (idempotent operation)")
+            return
         
         self._logger.info("Attaching tip from slot '%s'%s", slot, f", well '{well}'" if well else "")
         pos = self.get_absolute_z_position(slot, well)
@@ -336,6 +397,13 @@ class First:
     def get_absolute_a_position(self, slot: str, well: Optional[str] = None) -> Position:
         """
         Get the absolute position for a slot (and optionally a well within that slot) based on the origin
+        
+        Args:
+            slot: Slot name (e.g., 'A1', 'B2')
+            well: Optional well name within the slot (e.g., 'A1' for a well in a tiprack)
+            
+        Returns:
+            Position with absolute coordinates
         """
         pos = self.get_slot_origin(slot)
         
@@ -350,3 +418,86 @@ class First:
         else:
             self._logger.debug("Absolute A position for slot '%s': %s", slot, pos)
         return pos
+    
+    def start_video_recording(
+        self,
+        filename: Optional[Union[str, Path]] = None,
+        fps: Optional[float] = None
+    ) -> Path:
+        """
+        Start recording a video.
+        
+        Args:
+            filename: Optional filename for the video. If not provided, a timestamped
+                    filename will be generated. If provided without extension, .mp4 will be added.
+            fps: Optional frames per second for the video. Defaults to 30.0 if not specified.
+        
+        Returns:
+            Path to the video file where recording is being saved
+            
+        Raises:
+            IOError: If camera is not connected or recording fails to start
+            ValueError: If already recording
+        """
+        return self.camera.start_video_recording(filename=filename, fps=fps)
+    
+    def stop_video_recording(self) -> Optional[Path]:
+        """
+        Stop recording a video.
+        
+        Returns:
+            Path to the saved video file, or None if no recording was in progress
+            
+        Raises:
+            IOError: If video writer fails to release
+        """
+        return self.camera.stop_video_recording()
+    
+    def record_video(
+        self,
+        duration_seconds: float,
+        filename: Optional[Union[str, Path]] = None,
+        fps: Optional[float] = None
+    ) -> Path:
+        """
+        Record a video for a specified duration.
+        
+        Args:
+            duration_seconds: Duration of the video in seconds
+            filename: Optional filename for the video. If not provided, a timestamped
+                    filename will be generated. If provided without extension, .mp4 will be added.
+            fps: Optional frames per second for the video. Defaults to 30.0 if not specified.
+        
+        Returns:
+            Path to the saved video file
+            
+        Raises:
+            IOError: If camera is not connected or recording fails
+        """
+        return self.camera.record_video(
+            duration_seconds=duration_seconds,
+            filename=filename,
+            fps=fps
+        )
+    
+    def capture_image(
+        self, 
+        save: bool = False, 
+        filename: Optional[Union[str, Path]] = None
+    ) -> np.ndarray:
+        """
+        Capture a single image from the camera.
+        
+        Args:
+            save: If True, save the image to the captures folder
+            filename: Optional filename for the saved image. If not provided and save=True,
+                     a timestamped filename will be generated. If provided without extension,
+                     .jpg will be added.
+        
+        Returns:
+            Captured image as a numpy array (BGR format)
+            
+        Raises:
+            IOError: If camera is not connected or capture fails
+        """
+        return self.camera.capture_image(save=save, filename=filename)

{puda_drivers-0.0.11 → puda_drivers-0.0.13}/src/puda_drivers/move/gcode.py

@@ -508,9 +508,9 @@ class GCodeController(SerialController):
         
         return self._current_position
 
-    def query_position(self) -> Position:
+    def get_position(self) -> Position:
         """
-        Query the current machine position (M114 command).
+        Get the current machine position (M114 command).
 
         Returns:
             Position containing X, Y, Z, and A positions
@@ -560,7 +560,7 @@ class GCodeController(SerialController):
         self._logger.info("Starting position synchronization check (M114).")
 
         # Query the actual machine position
-        queried_position = self.query_position()
+        queried_position = self.get_position()
 
         if not queried_position.get_axes():
             self._logger.error("Query position failed. Cannot synchronize.")

puda_drivers-0.0.13/src/puda_drivers/transfer/liquid/sartorius/__init__.py

@@ -0,0 +1,2 @@
+from .rLine import SartoriusController, SartoriusDeviceError
+from .constants import STATUS_CODES

puda_drivers-0.0.11/src/puda_drivers/transfer/liquid/sartorius/sartorius.py → puda_drivers-0.0.13/src/puda_drivers/transfer/liquid/sartorius/rLine.py

@@ -7,6 +7,7 @@ pipettes and robotic dispensers via serial communication.
 Reference: https://api.sartorius.com/document-hub/dam/download/34901/Sartorius-rLine-technical-user-manual-v1.1.pdf
 """
 
+import json
 import logging
 from typing import Optional
 from puda_drivers.core.serialcontroller import SerialController
@@ -62,14 +63,14 @@ class SartoriusController(SerialController):
             timeout: Timeout in seconds for operations. Defaults to 10.
         """
         super().__init__(port_name, baudrate, timeout)
-        self._logger = logging.getLogger(__name__)
+        self._logger = logging.getLogger('puda_drivers.transfer.liquid.sartorius')
         self._logger.info(
             "Sartorius Controller initialized with port='%s', baudrate=%s, timeout=%s",
             port_name,
             baudrate,
             timeout,
         )
-        self._tip_attached: bool
+        self._tip_attached: bool = False
         self._volume: int = 0
 
     def _build_command(self, command: str, value: Optional[str] = None) -> str:
@@ -337,7 +338,10 @@ class SartoriusController(SerialController):
         Query the current status of the pipette (DS command).
 
         Returns:
-            Status code character (single character string)
+            JSON string containing status information with keys:
+            - status_code: Status code character
+            - status_message: Human-readable status message (if known)
+            - is_known: Boolean indicating if status code is recognized
 
         Raises:
             SartoriusDeviceError: If the status query fails
@@ -351,15 +355,22 @@ class SartoriusController(SerialController):
             )
 
         status_code = response[1]
+        status_data = {
+            "status_code": status_code,
+            "is_known": status_code in STATUS_CODES
+        }
+        
         if status_code in STATUS_CODES:
             status_message = STATUS_CODES[status_code]
+            status_data["status_message"] = status_message
             self._logger.info("Pipette Status Code [%s]: %s\n", status_code, status_message)
         else:
+            status_data["status_message"] = None
             self._logger.warning(
                 "Pipette Status Code [%s]: Unknown Status Code\n", status_code
             )
 
-        return status_code
+        return json.dumps(status_data)
     
     def get_position(self) -> int:
         """

{puda_drivers-0.0.11 → puda_drivers-0.0.13}/tests/first.py

@@ -1,6 +1,7 @@
 """Test script for the First machine driver."""
 
 import random
+import time
 import logging
 from puda_drivers.machines import First
 from puda_drivers.labware import get_available_labware
@@ -8,7 +9,7 @@ from puda_drivers.core import setup_logging
 
 setup_logging(
     enable_file_logging=False,
-    log_level=logging.DEBUG,  # Use logging.DEBUG to see all (DEBUG, INFO, WARNING, ERROR, CRITICAL) logs
+    log_level=logging.INFO,  # Use logging.DEBUG to see all (DEBUG, INFO, WARNING, ERROR, CRITICAL) logs
 )
 
 if __name__ == "__main__":
@@ -34,15 +35,15 @@ if __name__ == "__main__":
     print(machine.deck)
     print(machine.deck["C2"])
 
-    machine.connect()
-    machine.qubot.home()
-    machine.pipette.initialize()
+    machine.startup()  # Connects all controllers, homes gantry, and initializes pipette
     
-    machine.camera.start_video_recording()
+    # machine.record_video(duration_seconds=10, filename="test.mp4")
+    machine.start_video_recording()
     machine.attach_tip(slot="A3", well="G8")
     machine.aspirate_from(slot="C2", well="A1", amount=100, height_from_bottom=10)
+    # machine.capture_image()
     machine.dispense_to(slot="C2", well="B4", amount=100, height_from_bottom=50)
-    machine.drop_tip(slot="C1", well="A1")
+    machine.drop_tip(slot="C1", well="A1", height_from_bottom=10)
     
     # tiprack_wells = machine.deck["A3"].wells
     # # get pick up pipette one by one and drop it in the trash bin
@@ -58,7 +59,7 @@ if __name__ == "__main__":
     #     machine.drop_tip("C1", "A1")
 
 
-    machine.camera.stop_video_recording()
+    machine.stop_video_recording()
     
-    # Disconnect machine
-    machine.disconnect()
+    # Shutdown machine
+    machine.shutdown()

puda_drivers-0.0.13/uv.lock

@@ -0,0 +1,114 @@
+version = 1
+revision = 3
+requires-python = ">=3.10"
+
+[[package]]
+name = "nats-py"
+version = "2.12.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/71/c5/2564d917503fe8d68fe630c74bf6b678fbc15c01b58f2565894761010f57/nats_py-2.12.0.tar.gz", hash = "sha256:2981ca4b63b8266c855573fa7871b1be741f1889fd429ee657e5ffc0971a38a1", size = 119821, upload-time = "2025-10-31T05:27:31.247Z" }
+
+[[package]]
+name = "numpy"
+version = "2.2.6"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/76/21/7d2a95e4bba9dc13d043ee156a356c0a8f0c6309dff6b21b4d71a073b8a8/numpy-2.2.6.tar.gz", hash = "sha256:e29554e2bef54a90aa5cc07da6ce955accb83f21ab5de01a62c8478897b264fd", size = 20276440, upload-time = "2025-05-17T22:38:04.611Z" }
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puda_drivers-0.0.11/src/puda_drivers/transfer/liquid/sartorius/__init__.py

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-from .constants import STATUS_CODES

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