puda-drivers 0.0.16__py3-none-any.whl → 0.0.17__py3-none-any.whl

puda_drivers/core/serialcontroller.py

@@ -48,7 +48,7 @@ class SerialController(ABC):
         self._serial = None
         self.port_name = port_name
         self.baudrate = baudrate
-        self.timeout = timeout
+        self._timeout = timeout
         self._logger = logger
         
         # lock to prevent concurrent access to the serial port
@@ -75,7 +75,7 @@ class SerialController(ABC):
             self._serial = serial.Serial(
                 port=self.port_name,
                 baudrate=self.baudrate,
-                timeout=self.timeout,
+                timeout=self._timeout,
             )
             self._serial.flush()
             self._logger.info("Successfully connected to %s.", self.port_name)
@@ -107,19 +107,19 @@ class SerialController(ABC):
 
     def _send_command(self, command: str) -> None:
         """
-        Sends a custom protocol command.
+        Sends a command to the device.
         Note: This method should be called while holding self._lock to ensure
         atomic command/response pairing.
         """
+        self._logger.info("-> Sending: %r", command)
+
         if not self.is_connected or not self._serial:
             self._logger.error(
                 "Attempt to send command '%s' failed: Device not connected.",
                 command,
             )
             # Retain raising an error for being disconnected, as that's a connection state issue
-            raise serial.SerialException("Device not connected. Call connect() first.")
-
-        self._logger.info("-> Sending: %r", command)
+            raise serial.SerialException("Device disconnected. Call connect() first.")
 
         try:
             self._serial.reset_input_buffer()  # clear input buffer
@@ -140,7 +140,7 @@ class SerialController(ABC):
             )
             return None
 
-    def _read_response(self) -> str:
+    def _read_response(self, timeout: int = None) -> str:
         """
         Generic, blocking read that respects timeout and returns
         all data that arrived within the timeout period.
@@ -148,10 +148,13 @@ class SerialController(ABC):
         if not self.is_connected or not self._serial:
             raise serial.SerialException("Device not connected.")
 
+        if timeout is None:
+            timeout = self._timeout
+
         start_time = time.time()
         response = b""
 
-        while time.time() - start_time < self.timeout:
+        while time.time() - start_time < timeout:
             if self._serial.in_waiting > 0:
                 # Read all available bytes
                 response += self._serial.read(self._serial.in_waiting)
@@ -168,14 +171,12 @@ class SerialController(ABC):
 
         # Timeout reached - check what we got
         if not response:
-            self._logger.error("No response within %s seconds.", self.timeout)
+            self._logger.error("No response within %s seconds.", timeout)
             raise serial.SerialTimeoutException(
-                f"No response received within {self.timeout} seconds."
+                f"No response received within {timeout} seconds."
             )
 
-        # Decode once and check the decoded string
         decoded_response = response.decode("utf-8", errors="ignore").strip()
-        
         if "ok" in decoded_response.lower():
             self._logger.debug("<- Received response: %r", decoded_response)
         elif "err" in decoded_response.lower():
@@ -193,10 +194,12 @@ class SerialController(ABC):
     def _build_command(self, command: str, value: Optional[str] = None) -> str:
         """
         Build a command string according to the device protocol.
+        
+        There might be special starting and ending characters for devices
         """
-        pass
+        raise NotImplementedError
 
-    def execute(self, command: str, value: Optional[str] = None) -> str:
+    def execute(self, command: str, value: Optional[str] = None, timeout: int = None) -> str:
         """
         Send a command and read the response atomically.
         
@@ -218,22 +221,10 @@ class SerialController(ABC):
             serial.SerialException: If device is not connected or communication fails
             serial.SerialTimeoutException: If no response is received within timeout
         """
+        if timeout is None:
+            timeout = self._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
+            self._send_command(self._build_command(command, value))
+            return self._read_response(timeout=timeout)

puda_drivers/labware/trash_bin.json

@@ -20,7 +20,8 @@
       "width": 10.0,
       "height": 10.0,
       "x": 60.0,
-      "y": 42.0
+      "y": 42.0,
+      "z": 0.0
     }
   },
   "groups": [

puda_drivers/machines/first.py

@@ -176,6 +176,8 @@ class First:
             "pipette": sartorius_position,
         }
         
+    ### Labware management ###
+        
     def load_labware(self, slot: str, labware_name: str):
         """
         Load a labware object into a slot.
@@ -190,7 +192,33 @@ class First:
         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)
+
+    def remove_labware(self, slot: str):
+        """
+        Remove labware from a slot.
+        
+        Args:
+            slot: Slot name (e.g., 'A1', 'B2')
+        
+        Raises:
+            KeyError: If slot is not found in deck
+        """
+        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]]):
         """
         Load multiple labware into the deck at once.
@@ -211,6 +239,8 @@ 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.

puda_drivers/move/deck.py

@@ -1,5 +1,6 @@
 # src/puda_drivers/move/deck.py
 
+import json
 from puda_drivers.labware import StandardLabware
 
 
@@ -29,6 +30,20 @@ class Deck:
         if slot.upper() not in self.slots:
             raise KeyError(f"Slot {slot} not found in deck")
         self.slots[slot.upper()] = StandardLabware(labware_name=labware_name)
+    
+    def empty_slot(self, slot: str):
+        """
+        Empty a slot (remove labware from it).
+        
+        Args:
+            slot: Slot name (e.g., 'A1', 'B2')
+        
+        Raises:
+            KeyError: If slot is not found in deck
+        """
+        if slot.upper() not in self.slots:
+            raise KeyError(f"Slot {slot} not found in deck")
+        self.slots[slot.upper()] = None
         
     def __str__(self):
         """
@@ -44,4 +59,23 @@ class Deck:
 
     def __getitem__(self, key):
         """Allows syntax for: my_deck['B4']"""
-        return self.slots[key.upper()]
+        return self.slots[key.upper()]
+ 
+    def to_dict(self) -> dict:
+        """
+        Return the deck layout as a dictionary.
+        """
+        deck_data = {}
+        for slot, labware in self.slots.items():
+            if labware is None:
+                deck_data[slot] = None
+            else:
+                deck_data[slot] = labware.name
+        return deck_data
+
+    def to_json(self) -> str:
+        """
+        Return the deck layout as a JSON string.
+        """
+        # Re-use the logic from to_dict() so you don't have to update it in two places
+        return json.dumps(self.to_dict(), indent=2)

puda_drivers/move/gcode.py

@@ -296,7 +296,7 @@ class GCodeController(SerialController):
             home_target = "All"
 
         self._logger.info("[%s] homing axis/axes: %s **", cmd, home_target)
-        self.execute(cmd)
+        self.execute(command=cmd, timeout=90) # 90 seconds timeout for homing
         self._logger.info("Homing of %s completed.\n", home_target)
 
         # Update internal position (optimistic zeroing)
@@ -554,7 +554,7 @@ class GCodeController(SerialController):
             self._logger.info("Query position complete. Retrieved positions: %s", position)
             return position
         except asyncio.TimeoutError:
-            self._logger.warning(
+            self._logger.info(
                 "M114 command timed out after 1 second. Falling back to internal position."
             )
             return self.get_internal_position()

{puda_drivers-0.0.16.dist-info → puda_drivers-0.0.17.dist-info}/METADATA

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: puda-drivers
-Version: 0.0.16
+Version: 0.0.17
 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
+Project-URL: Homepage, https://github.com/PUDAP/puda-drivers
+Project-URL: Issues, https://github.com/PUDAP/puda-drivers/issues
 Author-email: zhao <20024592+agentzhao@users.noreply.github.com>
 License-Expression: MIT
 License-File: LICENSE
@@ -18,6 +18,7 @@ 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
@@ -40,14 +41,6 @@ Hardware drivers for the PUDA (Physical Unified Device Architecture) platform. T
 pip install puda-drivers
 ```
 
-### From Source
-
-```bash
-git clone https://github.com/zhao-bears/puda-drivers.git
-cd puda-drivers
-pip install -e .
-```
-
 ## Quick Start
 
 ### Logging Configuration
@@ -197,22 +190,70 @@ sartorius_ports = list_serial_ports(filter_desc="Sartorius")
 
 ### Setup Development Environment
 
-First, install `uv` if you haven't already. See the [uv installation guide](https://docs.astral.sh/uv/getting-started/installation/) for platform-specific instructions.
+This package is part of a UV workspace monorepo. First, install `uv` if you haven't already. See the [uv installation guide](https://docs.astral.sh/uv/getting-started/installation/) for platform-specific instructions.
+
+**From the repository root:**
 
 ```bash
-# Create virtual environment
-uv venv
+# Or install dependencies for all workspace packages
+uv sync --all-packages
+```
+
+This will:
+- Create a virtual environment at the repository root (`.venv/`)
+- Install all dependencies for all workspace packages
+- Install `puda-drivers` and other workspace packages in editable mode automatically
 
-# Activate virtual environment
+**Using the package:**
+
+```bash
+# Run Python scripts with workspace context (recommended, works from anywhere in the workspace)
+uv run python your_script.py
+
+# Or activate the virtual environment (from repository root where .venv is located)
 source .venv/bin/activate  # On Windows: .venv\Scripts\activate
+python your_script.py
+```
+
+**Adding dependencies:**
 
-# Install dependencies
-uv sync
+```bash
+# From the package directory
+cd libs/drivers
+uv add some-package
 
-# Install package in editable mode
-pip install -e .
+# Or from repository root
+uv add --package puda-drivers some-package
 ```
 
+**Note:** Workspace packages are automatically installed in editable mode, so code changes are immediately available without reinstalling.
+
+### Testing
+
+Run tests using pytest with `uv run`:
+
+```bash
+# Run all tests
+uv run pytest tests/
+
+# Run a specific test file
+uv run pytest tests/test_deck.py
+
+# Run a specific test class
+uv run pytest tests/test_deck.py::TestDeckToDict
+
+# Run a specific test function
+uv run pytest tests/test_deck.py::TestDeckToDict::test_to_dict_empty_deck
+
+# Run with verbose output
+uv run pytest tests/ -v
+
+# Run with coverage report
+uv run pytest tests/ --cov=puda_drivers --cov-report=html
+```
+
+**Note:** Make sure you're in the `libs/drivers` directory or use the full path to the tests directory when running pytest commands.
+
 ### Building and Publishing
 
 ```bash

{puda_drivers-0.0.16.dist-info → puda_drivers-0.0.17.dist-info}/RECORD

@@ -3,19 +3,19 @@ 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=aIyEpA8J4R7yBfIq0roMqbD-nxEwuwaB8c_7zaOXg_A,9100
+puda_drivers/core/serialcontroller.py,sha256=8Yf9DYIhtQTIVGB1Pm6COa6qgJcM0ZxdGwOGW8Om9ss,8654
 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
 puda_drivers/labware/labware.py,sha256=hZhOzSyb1GP_bm1LvQsREx4YSqLCWBTKNWDgDqfFavI,5317
 puda_drivers/labware/opentrons_96_tiprack_300ul.json,sha256=jmNaworu688GEgFdxMxNRSaEp4ZOg9IumFk8bVHSzYY,19796
 puda_drivers/labware/polyelectric_8_wellplate_30000ul.json,sha256=esu2tej0ORs7Pfd4HwoQVUpU5mPvp2AYzE3zsCC2FDk,3104
-puda_drivers/labware/trash_bin.json,sha256=Hk4MXO48P28jG7F87DUd9Ja4c_P7kAy3karPQ965i9Y,580
+puda_drivers/labware/trash_bin.json,sha256=6dH0prXKJVXMRm096rPSiJgMr0nPRtHUKo7Z6xIxdnA,596
 puda_drivers/machines/__init__.py,sha256=zmIk_r2T8nbPA68h3Cko8N6oL7ncoBpmvhNcAqzHmc4,45
-puda_drivers/machines/first.py,sha256=5xFjMwCHM4wZz2_VjEMXPMyXndtXjcnt1WL_GWSSRbs,20725
+puda_drivers/machines/first.py,sha256=GYYEUGi6xx6ev-ByX-_y9_GnMaBdhPCeiu-bCnKDZw0,21417
 puda_drivers/move/__init__.py,sha256=NKIKckcqgyviPM0EGFcmIoaqkJM4qekR4babfdddRzM,96
-puda_drivers/move/deck.py,sha256=yq2B4WMqj0hQvHt8HoJskP10u1DUyKwUnjP2c9gJ174,1397
-puda_drivers/move/gcode.py,sha256=nS1dmt90_89BUjlHh0VNqGLeRhyIdJ4-8Ps_7YlW-B0,23735
+puda_drivers/move/deck.py,sha256=CprlB8i9jvNImrc5IpHUZSSvvFe8uei76fNQ4iN6n34,2394
+puda_drivers/move/gcode.py,sha256=ioqRS-Kom5S7Pyp9-wg4MRXGIbIDEz7SsihBBOM2m30,23784
 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-0.0.16.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,,
+puda_drivers-0.0.17.dist-info/METADATA,sha256=YFBVlnKBI0al6Z6F9w0urGImcN133jmzsJVTcojNfEc,8420
+puda_drivers-0.0.17.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+puda_drivers-0.0.17.dist-info/licenses/LICENSE,sha256=7EI8xVBu6h_7_JlVw-yPhhOZlpY9hP8wal7kHtqKT_E,1074
+puda_drivers-0.0.17.dist-info/RECORD,,