puda-drivers 0.0.17__tar.gz → 0.0.18__tar.gz

{puda_drivers-0.0.17 → puda_drivers-0.0.18}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: puda-drivers
-Version: 0.0.17
+Version: 0.0.18
 Summary: Hardware drivers for the PUDA platform.
-Project-URL: Homepage, https://github.com/PUDAP/puda-drivers
-Project-URL: Issues, https://github.com/PUDAP/puda-drivers/issues
+Project-URL: Homepage, https://github.com/PUDAP/puda
+Project-URL: Issues, https://github.com/PUDAP/puda/issues
 Author-email: zhao <20024592+agentzhao@users.noreply.github.com>
 License-Expression: MIT
 License-File: LICENSE
@@ -18,7 +18,6 @@ Requires-Python: >=3.10
 Requires-Dist: nats-py>=2.12.0
 Requires-Dist: opencv-python>=4.12.0.88
 Requires-Dist: pyserial~=3.5
-Requires-Dist: pytest>=9.0.2
 Description-Content-Type: text/markdown
 
 # puda-drivers
@@ -260,6 +259,9 @@ uv run pytest tests/ --cov=puda_drivers --cov-report=html
 # Build distribution packages
 uv build
 
+# cd to puda project root
+cd ...
+
 # Publish to PyPI
 uv publish
 # Username: __token__

{puda_drivers-0.0.17 → puda_drivers-0.0.18}/README.md

@@ -237,6 +237,9 @@ uv run pytest tests/ --cov=puda_drivers --cov-report=html
 # Build distribution packages
 uv build
 
+# cd to puda project root
+cd ...
+
 # Publish to PyPI
 uv publish
 # Username: __token__

{puda_drivers-0.0.17 → puda_drivers-0.0.18}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "puda-drivers"
-version = "0.0.17"
+version = "0.0.18"
 description = "Hardware drivers for the PUDA platform."
 readme = "README.md"
 authors = [
@@ -18,10 +18,14 @@ classifiers = [
 ]
 license = "MIT"
 license-files = ["LICEN[CS]E*"]
+
 dependencies = [
     "nats-py>=2.12.0",
     "opencv-python>=4.12.0.88",
     "pyserial~=3.5",
+]
+[dependency-groups]
+dev = [
     "pytest>=9.0.2",
 ]
 
@@ -30,5 +34,5 @@ requires = ["hatchling >= 1.26"]
 build-backend = "hatchling.build"
 
 [project.urls]
-Homepage = "https://github.com/PUDAP/puda-drivers"
-Issues = "https://github.com/PUDAP/puda-drivers/issues"
+Homepage = "https://github.com/PUDAP/puda"
+Issues = "https://github.com/PUDAP/puda/issues"

{puda_drivers-0.0.17 → puda_drivers-0.0.18}/src/puda_drivers/labware/labware.py

@@ -3,9 +3,8 @@
 import json
 import inspect
 from pathlib import Path
-from typing import Dict, Any
+from typing import Dict, Any, List
 from abc import ABC
-from typing import List
 from puda_drivers.core import Position
 
 

{puda_drivers-0.0.17 → puda_drivers-0.0.18}/src/puda_drivers/machines/first.py

@@ -141,10 +141,10 @@ class First:
         self._logger.info("Homing gantry...")
         self.qubot.home()
         
-        # Initialize the pipette (all pipette operations need to wait 5 seconds for completion)
+        # Initialize the pipette
         self._logger.info("Initializing pipette...")
         self.pipette.initialize()
-        time.sleep(5)
+        time.sleep(3) # need to wait for the pipette to initialize
         self._logger.info("Machine startup complete - ready for operations")
         
     def shutdown(self):
@@ -159,6 +159,8 @@ class First:
         self.camera.disconnect()
         self._logger.info("Machine shutdown complete")
         
+    ### Queue (public commands) ###
+    
     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.
@@ -175,8 +177,18 @@ class First:
             "qubot": qubot_position.to_dict(),
             "pipette": sartorius_position,
         }
+    
+    def get_deck(self):
+        """
+        Get the current deck layout.
         
-    ### Labware management ###
+        Returns:
+            Dictionary mapping slot names (e.g., "A1") to labware classes.
+        
+        Raises:
+            None
+        """
+        return self.deck.to_dict()
         
     def load_labware(self, slot: str, labware_name: str):
         """
@@ -205,19 +217,6 @@ class First:
         """
         self.deck.empty_slot(slot=slot)
         self._logger.debug("Slot '%s' emptied", slot)
-    
-    def get_deck(self):
-        """
-        Get the current deck layout.
-        
-        Returns:
-            Dictionary mapping slot names (e.g., "A1") to labware classes.
-        
-        Raises:
-            None
-        """
-        return self.deck.to_dict()
-
         
     def load_deck(self, deck_layout: Dict[str, Type[StandardLabware]]):
         """
@@ -239,8 +238,6 @@ class First:
             self.load_labware(slot=slot, labware_name=labware_name)
         self._logger.info("Deck layout loaded successfully")
         
-    ### Liquid handling ###
-        
     def attach_tip(self, slot: str, well: Optional[str] = None):
         """
         Attach a tip from a slot.
@@ -258,7 +255,7 @@ class First:
             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)
+        pos = self._get_absolute_z_position(slot, well)
         self._logger.debug("Moving to position %s for tip attachment", pos)
         # return the offset from the origin
         self.qubot.move_absolute(position=pos)
@@ -280,7 +277,7 @@ class First:
         self.qubot.home(axis="Z")
         self._logger.debug("Z axis homed after tip attachment")
         
-    def drop_tip(self, slot: str, well: str, height_from_bottom: float = 0.0):
+    def drop_tip(self, *, slot: str, well: str, height_from_bottom: float = 0.0):
         """
         Drop a tip into a slot.
         
@@ -301,7 +298,7 @@ class First:
             raise ValueError("Tip not attached")
         
         self._logger.info("Dropping tip into slot '%s', well '%s'", slot, well)
-        pos = self.get_absolute_z_position(slot, well)
+        pos = self._get_absolute_z_position(slot, well)
         # add height from bottom
         pos += Position(z=height_from_bottom)
         # move up by the tip length
@@ -315,7 +312,7 @@ class First:
         self.pipette.set_tip_attached(attached=False)
         self._logger.info("Tip dropped successfully")
         
-    def aspirate_from(self, slot:str, well:str, amount:int, height_from_bottom: float = 0.0):
+    def aspirate_from(self, *, slot: str, well: str, amount: int, height_from_bottom: float = 0.0):
         """
         Aspirate a volume of liquid from a slot.
         
@@ -337,7 +334,7 @@ class First:
             raise ValueError("Tip not attached")
         
         self._logger.info("Aspirating %d µL from slot '%s', well '%s'", amount, slot, well)
-        pos = self.get_absolute_z_position(slot, well)
+        pos = self._get_absolute_z_position(slot, well)
         # add height from bottom
         pos += Position(z=height_from_bottom)
         self._logger.debug("Moving Z axis to position %s", pos)
@@ -348,7 +345,7 @@ class First:
         time.sleep(5)
         self._logger.info("Aspiration completed: %d µL from slot '%s', well '%s'", amount, slot, well)
         
-    def dispense_to(self, slot:str, well:str, amount:int, height_from_bottom: float = 0.0):
+    def dispense_to(self, *, slot: str, well: str, amount: int, height_from_bottom: float = 0.0):
         """
         Dispense a volume of liquid to a slot.
         
@@ -370,7 +367,7 @@ class First:
             raise ValueError("Tip not attached")
         
         self._logger.info("Dispensing %d µL to slot '%s', well '%s'", amount, slot, well)
-        pos = self.get_absolute_z_position(slot, well)
+        pos = self._get_absolute_z_position(slot, well)
         # add height from bottom
         pos += Position(z=height_from_bottom)
         self._logger.debug("Moving Z axis to position %s", pos)
@@ -380,8 +377,93 @@ class First:
         self.pipette.dispense(amount=amount)
         time.sleep(5)
         self._logger.info("Dispense completed: %d µL to slot '%s', well '%s'", amount, slot, well)
+    
+    def start_video_recording(
+        self,
+        filename: Optional[Union[str, Path]] = None,
+        fps: Optional[float] = None
+    ) -> Path:
+        """
+        Start recording a video.
         
-    def get_slot_origin(self, slot: str) -> Position:
+        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)
+    
+    ### Private methods ###
+    
+    def _get_slot_origin(self, slot: str) -> Position:
         """
         Get the origin coordinates of a slot.
         
@@ -402,7 +484,7 @@ class First:
         self._logger.debug("Slot origin for '%s': %s", slot, pos)
         return pos
     
-    def get_absolute_z_position(self, slot: str, well: Optional[str] = None) -> Position:
+    def _get_absolute_z_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
         
@@ -417,7 +499,7 @@ class First:
             ValueError: If well is specified but no labware is loaded in the slot
         """
         # Get slot origin
-        pos = self.get_slot_origin(slot)
+        pos = self._get_slot_origin(slot)
 
         # relative well position from slot origin
         if well:
@@ -435,7 +517,7 @@ class First:
             self._logger.debug("Absolute Z position for slot '%s': %s", slot, pos)
         return pos
     
-    def get_absolute_a_position(self, slot: str, well: Optional[str] = None) -> Position:
+    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
         
@@ -449,7 +531,7 @@ class First:
         Raises:
             ValueError: If well is specified but no labware is loaded in the slot
         """
-        pos = self.get_slot_origin(slot)
+        pos = self._get_slot_origin(slot)
         
         if well:
             labware = self.deck[slot]
@@ -467,85 +549,22 @@ class First:
             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)
+    ### Control (immediate commands) ###
     
-    def stop_video_recording(self) -> Optional[Path]:
+    def pause(self):
         """
-        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
+        Pause the execution of queued commands.
         """
-        return self.camera.stop_video_recording()
+        print("Pausing machine")
     
-    def record_video(
-        self,
-        duration_seconds: float,
-        filename: Optional[Union[str, Path]] = None,
-        fps: Optional[float] = None
-    ) -> Path:
+    def resume(self):
         """
-        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
+        Resume the execution of queued commands.
         """
-        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:
+        print("Resuming machine")
+
+    def cancel(self):
         """
-        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
+        Cancel the execution of queued commands.
         """
-        return self.camera.capture_image(save=save, filename=filename)
+        print("Cancelling machine")