fixed astra_msgs nixpkg being used incorrectly

-> python 3.13

.gitmodules

@@ -1,6 +1,3 @@
 [submodule "src/astra_description"]
 	path = src/astra_descriptions
 	url = ../astra_descriptions
-[submodule "src/astra_msgs"]
-	path = src/astra_msgs
-	url = git@github.com:SHC-ASTRA/astra_msgs.git

README.md

@@ -65,10 +65,10 @@ You can fake the presence of a Serial device (i.e., MCU) by using the following
 $ socat -dd -v pty,rawer,crnl,link=/tmp/ttyACM9 pty,rawer,crnl,link=/tmp/ttyOUT
 ```
 
-When you go to run anchor, use the `port_override` launch parameter to point it to the fake serial port, like so:
+When you go to run anchor, use the `PORT_OVERRIDE` environment variable to point it to the fake serial port, like so:
 
 ```bash
-$ ros2 launch anchor_pkg rover.launch.py port_override:=/tmp/ttyACM9
+$ PORT_OVERRIDE=/tmp/ttyACM9 ros2 launch anchor_pkg rover.launch.py
 ```
 
 ### Connecting the GuliKit Controller
@@ -121,24 +121,23 @@ A: Don't worry about it. If you had the workspace sourced, ROS2 will complain ab
 ...
 ```
 
-A: To find a microcontroller to talk to, Anchor filters through your available serial ports to find microcontrollers. If the microcontroller fails
-to respond properly, or one is not found, it will abort. There are a few possible fixes:
+A: To find a microcontroller to talk to, Anchor sends a ping to every Serial port on your computer. If it does not receive a 'pong' in less than one second, then it aborts. There are a few possible fixes:
 
 - Keep trying to run it until it works
 - Run `lsusb` to see if the microcontroller is detected by your computer.
 - Run `ls /dev/tty*0` to see if there is a valid Serial port enumerated for the microcontroller.
-- Check if you are in the `dialout` group (or whatever group shows up by running `ls -l /dev/tty*`) by using the `groups` command.
+- Check if you are in the `dialout` group (or whatever group shows up by running `ls -l /dev/tty*`).
 
 ## Packages
 
 - [anchor\_pkg](./src/anchor_pkg) - Handles Serial communication between the various other packages here and the microcontroller.
 - [arm\_pkg](./src/arm_pkg) - Relays controls and sensor data for the arm (socket and digit) between anchor and basestation/headless.
 - [astra\_descriptions](./src/astra_descriptions) - Submodule with URDF-related packages.
-- [astra\_msgs](./src/astra_msgs) - Contains custom message types for communication between basestation and the rover over ROS2.
 - [bio\_pkg](./src/bio_pkg) - Like arm_pkg, but for CITADEL and FAERIE
 - [core\_pkg](./src/core_pkg) - Like arm_pkg, but for Core
 - [headless\_pkg](./src/headless_pkg) - Simple, non-graphical controller node to work in place of basestation when controlling the rover by itself. This is autostarted with anchor to allow for setup-less control of the rover.
 - [latency\_tester](./src/latency_tester) - A temporary node to test comms latency over ROS2, Serial, and CAN.
+- [ros2\_interfaces\_pkg](./src/ros2_interfaces_pkg) - Contains custom message types for communication between basestation and the rover over ROS2. (being renamed to `astra_msgs`).
 - [servo\_arm\_twist\_pkg](./src/servo_arm_twist_pkg) - A temporary node to translate controller state from `ros2_joy` to `Twist` messages to control the Arm via IK.
 
 ## Maintainers

auto_start/auto_start_anchor.sh

@@ -14,12 +14,8 @@ echo "[INFO] Network interface is up!"
 # Your actual ROS node start command goes here
 echo "[INFO] Starting ROS node..."
 
-# Source ROS 2 Humble setup script
-if command -v nixos-rebuild; then
-    echo "[INFO] running on NixOS"
-else
-    source /opt/ros/humble/setup.bash
-fi
+# Source ROS 2 Humble setup script (if we aren't using nix)
+command -v ros2 || source /opt/ros/humble/setup.bash
 
 # Source your workspace setup script
 source $SCRIPT_DIR/../install/setup.bash

auto_start/auto_start_headless_full.sh

@@ -15,11 +15,7 @@ echo "[INFO] Network interface is up!"
 echo "[INFO] Starting ROS node..."
 
 # Source ROS 2 Humble setup script
-if command -v nixos-rebuild; then
-    echo "[INFO] running on NixOS"
-else
-    source /opt/ros/humble/setup.bash
-fi
+command -v ros2 || source /opt/ros/humble/setup.bash
 
 # Source your workspace setup script
 source $SCRIPT_DIR/../install/setup.bash

auto_start/start_rosbag.sh

@@ -17,11 +17,7 @@ done
 echo "[INFO] Network interface is up!"
 
 
-if command -v nixos-rebuild; then
-    echo "[INFO] running on NixOS"
-else
-    source /opt/ros/humble/setup.bash
-fi
+command -v ros2 || source /opt/ros/humble/setup.bash
 source $ANCHOR_WS/install/setup.bash
 [[ -f $AUTONOMY_WS/install/setup.bash ]] && source $AUTONOMY_WS/install/setup.bash
 

flake.lock

@@ -1,5 +1,29 @@
 {
   "nodes": {
+    "astra-msgs": {
+      "inputs": {
+        "nix-ros-overlay": "nix-ros-overlay",
+        "nixpkgs": [
+          "astra-msgs",
+          "nix-ros-overlay",
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1770693861,
+        "narHash": "sha256-8NBtSsKVYtd+NYt51tJ1EteC0nOTemDUBoRXbDoQAuA=",
+        "owner": "SHC-ASTRA",
+        "repo": "astra_msgs",
+        "rev": "60bbb53085b09fbdb7e848b1dd168d526d9af281",
+        "type": "github"
+      },
+      "original": {
+        "owner": "SHC-ASTRA",
+        "ref": "60bbb53085b09fbdb7e848b1dd168d526d9af281",
+        "repo": "astra_msgs",
+        "type": "github"
+      }
+    },
     "flake-utils": {
       "inputs": {
         "systems": "systems"
@@ -18,33 +42,87 @@
         "type": "github"
       }
     },
+    "flake-utils_2": {
+      "inputs": {
+        "systems": "systems_2"
+      },
+      "locked": {
+        "lastModified": 1731533236,
+        "narHash": "sha256-l0KFg5HjrsfsO/JpG+r7fRrqm12kzFHyUHqHCVpMMbI=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "11707dc2f618dd54ca8739b309ec4fc024de578b",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
     "nix-ros-overlay": {
       "inputs": {
         "flake-utils": "flake-utils",
         "nixpkgs": "nixpkgs"
       },
       "locked": {
-        "lastModified": 1761810010,
-        "narHash": "sha256-o0wJKW603SiOO373BTgeZaF6nDxegMA/cRrzSC2Cscg=",
+        "lastModified": 1770408708,
+        "narHash": "sha256-E7ZQRgGrsiuswgXnG7337ZR5s4SdZlheZjxKOQdVoH8=",
         "owner": "lopsided98",
         "repo": "nix-ros-overlay",
-        "rev": "e277df39e3bc6b372a5138c0bcf10198857c55ab",
+        "rev": "e78ba91032c7f8bdd823fbf43937cbf0f4f09747",
         "type": "github"
       },
       "original": {
         "owner": "lopsided98",
-        "ref": "master",
+        "ref": "develop",
+        "repo": "nix-ros-overlay",
+        "type": "github"
+      }
+    },
+    "nix-ros-overlay_2": {
+      "inputs": {
+        "flake-utils": "flake-utils_2",
+        "nixpkgs": "nixpkgs_2"
+      },
+      "locked": {
+        "lastModified": 1770108954,
+        "narHash": "sha256-VBj6bd4LPPSfsZJPa/UPPA92dOs6tmQo0XZKqfz/3W4=",
+        "owner": "lopsided98",
+        "repo": "nix-ros-overlay",
+        "rev": "3d05d46451b376e128a1553e78b8870c75d7753a",
+        "type": "github"
+      },
+      "original": {
+        "owner": "lopsided98",
+        "ref": "develop",
         "repo": "nix-ros-overlay",
         "type": "github"
       }
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1744849697,
-        "narHash": "sha256-S9hqvanPSeRu6R4cw0OhvH1rJ+4/s9xIban9C4ocM/0=",
-        "owner": "lopsided98",
+        "lastModified": 1759381078,
+        "narHash": "sha256-gTrEEp5gEspIcCOx9PD8kMaF1iEmfBcTbO0Jag2QhQs=",
+        "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "6318f538166fef9f5118d8d78b9b43a04bb049e4",
+        "rev": "7df7ff7d8e00218376575f0acdcc5d66741351ee",
+        "type": "github"
+      },
+      "original": {
+        "owner": "lopsided98",
+        "ref": "nix-ros",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "nixpkgs_2": {
+      "locked": {
+        "lastModified": 1759381078,
+        "narHash": "sha256-gTrEEp5gEspIcCOx9PD8kMaF1iEmfBcTbO0Jag2QhQs=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "7df7ff7d8e00218376575f0acdcc5d66741351ee",
         "type": "github"
       },
       "original": {
@@ -56,7 +134,8 @@
     },
     "root": {
       "inputs": {
-        "nix-ros-overlay": "nix-ros-overlay",
+        "astra-msgs": "astra-msgs",
+        "nix-ros-overlay": "nix-ros-overlay_2",
         "nixpkgs": [
           "nix-ros-overlay",
           "nixpkgs"
@@ -77,6 +156,21 @@
         "repo": "default",
         "type": "github"
       }
+    },
+    "systems_2": {
+      "locked": {
+        "lastModified": 1681028828,
+        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-systems",
+        "repo": "default",
+        "type": "github"
+      }
     }
   },
   "root": "root",

flake.nix

@@ -2,8 +2,10 @@
   description = "Development environment for ASTRA Anchor";
 
   inputs = {
-    nix-ros-overlay.url = "github:lopsided98/nix-ros-overlay/master";
+    nix-ros-overlay.url = "github:lopsided98/nix-ros-overlay/develop";
     nixpkgs.follows = "nix-ros-overlay/nixpkgs"; # IMPORTANT!!!
+    # specify astra_msgs commit hash to the one we support
+    astra-msgs.url = "github:SHC-ASTRA/astra_msgs?ref=60bbb53085b09fbdb7e848b1dd168d526d9af281";
   };
 
   outputs =
@@ -11,6 +13,7 @@
       self,
       nix-ros-overlay,
       nixpkgs,
+      astra-msgs,
     }:
     nix-ros-overlay.inputs.flake-utils.lib.eachDefaultSystem (
       system:
@@ -24,8 +27,9 @@
         devShells.default = pkgs.mkShell {
           name = "ASTRA Anchor";
           packages = with pkgs; [
+            astra-msgs.packages.${system}.astra-msgs
             colcon
-            (python312.withPackages (
+            (python313.withPackages (
               p: with p; [
                 pyserial
                 pygame
@@ -39,6 +43,7 @@
               buildEnv {
                 paths = [
                   ros-core
+                  rqt-graph
                   ros2cli
                   ros2run
                   ros2bag
@@ -56,10 +61,12 @@
                   control-msgs
                   control-toolbox
                   moveit-core
+                  moveit-planners
                   moveit-common
                   moveit-msgs
                   moveit-ros-planning
                   moveit-ros-planning-interface
+		  moveit-ros-visualization
                   moveit-configs-utils
                   moveit-ros-move-group
                   moveit-servo
@@ -68,9 +75,9 @@
                   pilz-industrial-motion-planner
                   pick-ik
                   ompl
-                  chomp-motion-planner
                   joy
-                  # ros2-controllers nixpkg does not build :(
+                  ros2-controllers
+		  chomp-motion-planner
                 ];
               }
             )

src/anchor_pkg/anchor_pkg/anchor_node.py

@@ -1,17 +1,20 @@
-import atexit
-import glob
-import signal
-import threading
-from typing import cast
-
 import rclpy
+from rclpy.node import Node
+from rclpy.executors import ExternalShutdownException
+from std_srvs.srv import Empty
+
+import signal
+import time
+import atexit
+
 import serial
 import serial.tools.list_ports
-from rcl_interfaces.msg import ParameterDescriptor, ParameterType
-from rclpy.executors import ExternalShutdownException
-from rclpy.node import Node
-from std_msgs.msg import Header, String
+import os
+import sys
+import threading
+import glob
 
+from std_msgs.msg import String, Header
 from astra_msgs.msg import VicCAN
 
 KNOWN_USBS = [
@@ -43,23 +46,15 @@ class Anchor(Node):
         - Publish raw strings to this topic to send directly to the MCU for debugging
     """
 
-    serial_port: str | None = None  # e.g., "/dev/ttyUSB0"
-
     def __init__(self):
         # Initalize node with name
-        super().__init__("anchor_node")
+        super().__init__("anchor_node")  # previously 'serial_publisher'
 
-        self.declare_parameter(
-            "port_override",
-            "",
-            ParameterDescriptor(
-                name="port_override", type=ParameterType.PARAMETER_STRING
-            ),
-        )
+        self.serial_port: str | None = None  # e.g., "/dev/ttyUSB0"
 
         # Serial port override
-        if port_override := self.get_parameter("port_override").value:
-            self.serial_port = cast(str, port_override)  # Cast to make the linter happy
+        if port_override := os.getenv("PORT_OVERRIDE"):
+            self.serial_port = port_override
 
         ##################################################
         # Serial MCU Discovery
@@ -67,64 +62,104 @@ class Anchor(Node):
         # If there was not a port override, look for a MCU over USB for Serial.
         if self.serial_port is None:
             comports = serial.tools.list_ports.comports()
-            recog_ports = list(
+            real_ports = list(
                 filter(
-                    # Filter for ports we know that aren't invalid
-                    lambda p: (p.vid, p.pid) in KNOWN_USBS and p.device is not None,
+                    lambda p: p.vid is not None
+                    and p.pid is not None
+                    and p.device is not None,
                     comports,
                 )
             )
+            recog_ports = list(filter(lambda p: (p.vid, p.pid) in KNOWN_USBS, comports))
 
-            # Guards
-            if len(recog_ports) > 1:  # If we found too many
-                self.get_logger().fatal(
+            if len(recog_ports) == 1:  # Found singular recognized MCU
+                found_port = recog_ports[0]
+                self.get_logger().info(
+                    f"Selecting MCU '{found_port.description}' at {found_port.device}."
+                )
+                self.serial_port = found_port.device  # String, location of device file; e.g., '/dev/ttyACM0'
+            elif len(recog_ports) > 1:  # Found multiple recognized MCUs
+                # Kinda jank log message
+                self.get_logger().error(
                     f"Found multiple recognized MCUs: {[p.device for p in recog_ports].__str__()}"
                 )
-                exit(1)
-            if len(recog_ports) == 0:
-                self.get_logger().fatal(
-                    f"Found no recognized MCUs: {[p.device for p in recog_ports].__str__()}"
+                # Don't set self.serial_port; later if-statement will exit()
+            elif (
+                len(recog_ports) == 0 and len(real_ports) > 0
+            ):  # Found real ports but none recognized; i.e. maybe found an IMU or camera but not a MCU
+                self.get_logger().error(
+                    f"No recognized MCUs found; instead found {[p.device for p in real_ports].__str__()}."
                 )
-                exit(1)
+                # Don't set self.serial_port; later if-statement will exit()
+            else:  # Found jack shit
+                self.get_logger().error("No valid Serial ports specified or found.")
+                # Don't set self.serial_port; later if-statement will exit()
 
-            # Everything is ok
-            found_port = recog_ports[0]
-            self.get_logger().info(
-                f"Selecting MCU '{found_port.description}' at {found_port.device}."
-            )
-            # String, location of device file; e.g., '/dev/ttyACM0'
-            self.serial_port = found_port.device
-
-        # Found a Serial port, try to open it; above code has not officially opened a Serial port
-        self.get_logger().debug(
-            f"Attempting to open Serial port '{self.serial_port}'..."
-        )
-        try:
-            self.serial_interface = serial.Serial(self.serial_port, 115200, timeout=1)
-
-            # Attempt to get name of connected MCU
-            self.serial_interface.write(b"can_relay_mode,on\n")  # can_relay_ready,[mcu]
-            mcu_name: str = ""
-            for _ in range(4):  # Sometimes it takes a sec
-                response = self.serial_interface.read_until(bytes("\n", "utf8"))
-                if b"can_relay_ready" in response:
-                    try:
-                        args: list[str] = response.decode("utf8").strip().split(",")
-                    except UnicodeDecodeError:
-                        continue  # ignore malformed responses
-                    if len(args) == 2:
-                        mcu_name = args[1]
+        # We still don't have a serial port; fall back to legacy discovery (Areeb's code)
+        # Loop through all serial devices on the computer to check for the MCU
+        if self.serial_port is None:
+            self.get_logger().warning("Falling back to legacy MCU discovery...")
+            ports = Anchor.list_serial_ports()
+            for _ in range(4):
+                if self.serial_port is not None:
                     break
-            self.get_logger().info(
-                f"MCU '{mcu_name}' is ready at '{self.serial_port}'."
-            )
+                for port in ports:
+                    try:
+                        # connect and send a ping command
+                        ser = serial.Serial(port, 115200, timeout=1)
+                        # (f"Checking port {port}...")
+                        ser.write(b"ping\n")
+                        response = ser.read_until(bytes("\n", "utf8"))
 
-        except serial.SerialException as e:
-            self.get_logger().fatal(
-                f"Could not open Serial port '{self.serial_port}' for reason:"
+                        # if pong is in response, then we are talking with the MCU
+                        if b"pong" in response:
+                            self.serial_port = port
+                            self.get_logger().info(f"Found MCU at {self.serial_port}!")
+                            break
+                    except:
+                        pass
+
+        # If port is still None then we ain't finding no mcu
+        if self.serial_port is None:
+            self.get_logger().error("Unable to find MCU. Exiting...")
+            time.sleep(1)
+            sys.exit(1)
+        # Found a Serial port, try to open it; above code has not officially opened a Serial port
+        else:
+            self.get_logger().debug(
+                f"Attempting to open Serial port '{self.serial_port}'..."
             )
-            self.get_logger().fatal(e.strerror)
-            exit(1)
+            try:
+                self.serial_interface = serial.Serial(
+                    self.serial_port, 115200, timeout=1
+                )
+
+                # Attempt to get name of connected MCU
+                self.serial_interface.write(
+                    b"can_relay_mode,on\n"
+                )  # can_relay_ready,[mcu]
+                mcu_name: str = ""
+                for _ in range(4):
+                    response = self.serial_interface.read_until(bytes("\n", "utf8"))
+                    try:
+                        if b"can_relay_ready" in response:
+                            args: list[str] = response.decode("utf8").strip().split(",")
+                            if len(args) == 2:
+                                mcu_name = args[1]
+                            break
+                    except UnicodeDecodeError:
+                        pass  # ignore malformed responses
+                self.get_logger().info(
+                    f"MCU '{mcu_name}' is ready at '{self.serial_port}'."
+                )
+
+            except serial.SerialException as e:
+                self.get_logger().error(
+                    f"Could not open Serial port '{self.serial_port}' for reason:"
+                )
+                self.get_logger().error(e.strerror)
+                time.sleep(1)
+                sys.exit(1)
 
         # Close serial port on exit
         atexit.register(self.cleanup)
@@ -170,38 +205,54 @@ class Anchor(Node):
 
     def read_MCU(self):
         """Check the USB serial port for new data from the MCU, and publish string to appropriate topics"""
-        output: str | None = None
         try:
             output = str(self.serial_interface.readline(), "utf8")
+
+            if output:
+                self.relay_fromvic(output)
+                # All output over debug temporarily
+                # self.get_logger().info(f"[MCU] {output}")
+                msg = String()
+                msg.data = output
+                self.debug_pub.publish(msg)
+                if output.startswith("can_relay_fromvic,core"):
+                    self.core_pub.publish(msg)
+                elif output.startswith("can_relay_fromvic,arm") or output.startswith(
+                    "can_relay_fromvic,digit"
+                ):  # digit for voltage readings
+                    self.arm_pub.publish(msg)
+                if output.startswith("can_relay_fromvic,citadel") or output.startswith(
+                    "can_relay_fromvic,digit"
+                ):  # digit for SHT sensor
+                    self.bio_pub.publish(msg)
+                # msg = String()
+                # msg.data = output
+                # self.debug_pub.publish(msg)
+                return
         except serial.SerialException as e:
-            self.get_logger().fatal(f"SerialException: {e}")
+            print(f"SerialException: {e}")
+            print("Closing serial port.")
+            try:
+                if self.serial_interface.is_open:
+                    self.serial_interface.close()
+            except:
+                pass
             exit(1)
         except TypeError as e:
-            self.get_logger().fatal(f"TypeError: {e}")
+            print(f"TypeError: {e}")
+            print("Closing serial port.")
+            try:
+                if self.serial_interface.is_open:
+                    self.serial_interface.close()
+            except:
+                pass
             exit(1)
         except Exception as e:
-            self.get_logger().error(f"Exception: {e}")
-
-        if output:
-            self.relay_fromvic(output)
-            msg = String()
-            msg.data = output
-
-            # All output over debug
-            self.debug_pub.publish(msg)
-
-            # Send the message to the right place
-            if output.startswith("can_relay_fromvic,core"):
-                self.core_pub.publish(msg)
-            elif output.startswith("can_relay_fromvic,arm") or output.startswith(
-                "can_relay_fromvic,digit"
-            ):  # digit for voltage readings
-                self.arm_pub.publish(msg)
-            if output.startswith("can_relay_fromvic,citadel") or output.startswith(
-                "can_relay_fromvic,digit"
-            ):  # digit for SHT sensor
-                self.bio_pub.publish(msg)
-            return
+            print(f"Exception: {e}")
+            # print("Closing serial port.")
+            # if self.ser.is_open:
+            #     self.ser.close()
+            # exit(1)
 
     def on_mock_fromvic(self, msg: String):
         """For testing without an actual MCU, publish strings here as if they came from an MCU"""
@@ -309,6 +360,6 @@ def main(args=None):
 
 if __name__ == "__main__":
     signal.signal(
-        signal.SIGTERM, lambda signum, frame: exit(0)
+        signal.SIGTERM, lambda signum, frame: sys.exit(0)
     )  # Catch termination signals and exit cleanly
     main()

src/arm_pkg/arm_pkg/arm_node.py

@@ -49,7 +49,7 @@ class SerialRelay(Node):
 
         # Create subscribers
         self.man_sub = self.create_subscription(
-            ArmManual, "/arm/control/manual", self.send_manual, 10
+            ArmManual, "/arm/control/manual", self.send_manual, 2
         )
 
         # New messages
@@ -190,7 +190,7 @@ class SerialRelay(Node):
 
         command += f"can_relay_tovic,digit,39,{msg.effector_yaw},{msg.effector_roll}\n"
 
-        # command += f"can_relay_tovic,digit,26,{msg.gripper}\n"  # no hardware rn
+        command += f"can_relay_tovic,digit,26,{msg.gripper}\n"  # no hardware rn
 
         command += f"can_relay_tovic,digit,28,{msg.laser}\n"
 

src/bio_pkg/bio_pkg/bio_node.py

@@ -1,241 +1,203 @@
-import rclpy
-from rclpy.node import Node
-import serial
+import signal
 import sys
 import threading
-import os
-import glob
 import time
-import atexit
-import signal
-from std_msgs.msg import String
-from astra_msgs.msg import BioControl
-from astra_msgs.msg import BioFeedback
+
+import rclpy
+from astra_msgs.action import BioVacuum
+from astra_msgs.msg import BioControl, BioDistributor, VicCAN
+from astra_msgs.srv import BioTestTube
+from rclpy.action import ActionServer
+from rclpy.node import Node
+from std_msgs.msg import Header, String
 
 serial_pub = None
 thread = None
 
+# used to verify the length of an incoming VicCAN feedback message
+# key is VicCAN command_id, value is expected length of data list
+viccan_citadel_msg_len_dict = {
+    # empty because not expecting any VicCAN from citadel atm
+}
+viccan_lance_msg_len_dict = {
+    # empty because not sure what VicCAN commands LANCE sends
+}
+
 
 class SerialRelay(Node):
     def __init__(self):
         # Initialize node
         super().__init__("bio_node")
 
-        # Get launch mode parameter
-        self.declare_parameter("launch_mode", "bio")
-        self.launch_mode = self.get_parameter("launch_mode").value
-        self.get_logger().info(f"bio launch_mode is: {self.launch_mode}")
-
-        # Create publishers
-        self.debug_pub = self.create_publisher(String, "/bio/feedback/debug", 10)
-        self.feedback_pub = self.create_publisher(BioFeedback, "/bio/feedback", 10)
-
-        # Create subscribers
-        self.control_sub = self.create_subscription(
-            BioControl, "/bio/control", self.send_control, 10
+        # Anchor Topics
+        self.anchor_fromvic_sub_ = self.create_subscription(
+            VicCAN, "/anchor/from_vic/bio", self.relay_fromvic, 20
+        )
+        self.anchor_tovic_pub_ = self.create_publisher(
+            VicCAN, "/anchor/to_vic/relay", 20
         )
 
-        # Create a publisher for telemetry
-        self.telemetry_pub_timer = self.create_timer(1.0, self.publish_feedback)
+        self.anchor_sub = self.create_subscription(
+            String, "/anchor/bio/feedback", self.anchor_feedback, 10
+        )
+        self.anchor_pub = self.create_publisher(String, "/anchor/relay", 10)
 
-        # Topics used in anchor mode
-        if self.launch_mode == "anchor":
-            self.anchor_sub = self.create_subscription(
-                String, "/anchor/bio/feedback", self.anchor_feedback, 10
-            )
-            self.anchor_pub = self.create_publisher(String, "/anchor/relay", 10)
+        self.distributor_sub = self.create_subscription(
+            BioDistributor,
+            "/bio/control/distributor",
+            self.distributor_callback,
+            10,
+        )
 
-        self.bio_feedback = BioFeedback()
+        # Services
+        self.test_tube_service = self.create_service(
+            BioTestTube, "/bio/control/test_tube", self.test_tube_callback
+        )
 
-        # Search for ports IF in 'arm' (standalone) and not 'anchor' mode
-        if self.launch_mode == "bio":
-            # Loop through all serial devices on the computer to check for the MCU
-            self.port = None
-            for i in range(2):
-                try:
-                    # connect and send a ping command
-                    set_port = (
-                        "/dev/ttyACM0"  # MCU is controlled through GPIO pins on the PI
-                    )
-                    ser = serial.Serial(set_port, 115200, timeout=1)
-                    # print(f"Checking port {port}...")
-                    ser.write(b"ping\n")
-                    response = ser.read_until("\n")
-
-                    # if pong is in response, then we are talking with the MCU
-                    if b"pong" in response:
-                        self.port = set_port
-                        self.get_logger().info(f"Found MCU at {set_port}!")
-                        break
-                except:
-                    pass
-
-            if self.port is None:
-                self.get_logger().info(
-                    "Unable to find MCU... please make sure it is connected."
-                )
-                time.sleep(1)
-                sys.exit(1)
-
-            self.ser = serial.Serial(self.port, 115200)
-            atexit.register(self.cleanup)
+        # Actions
+        self._action_server = ActionServer(
+            self, BioVacuum, "/bio/actions/vacuum", self.execute_vacuum
+        )
 
     def run(self):
         global thread
         thread = threading.Thread(target=rclpy.spin, args=(self,), daemon=True)
         thread.start()
 
-        # if in arm mode, will need to read from the MCU
-
         try:
             while rclpy.ok():
-                if self.launch_mode == "bio":
-                    if self.ser.in_waiting:
-                        self.read_mcu()
-                    else:
-                        time.sleep(0.1)
+                time.sleep(0.1)
         except KeyboardInterrupt:
             pass
-        finally:
-            self.cleanup()
-
-    # Currently will just spit out all values over the /arm/feedback/debug topic as strings
-    def read_mcu(self):
-        try:
-            output = str(self.ser.readline(), "utf8")
-            if output:
-                self.get_logger().info(f"[MCU] {output}")
-                msg = String()
-                msg.data = output
-                self.debug_pub.publish(msg)
-        except serial.SerialException:
-            self.get_logger().info("SerialException caught... closing serial port.")
-            if self.ser.is_open:
-                self.ser.close()
-            pass
-        except TypeError as e:
-            self.get_logger().info(f"TypeError: {e}")
-            print("Closing serial port.")
-            if self.ser.is_open:
-                self.ser.close()
-            pass
-        except Exception as e:
-            print(f"Exception: {e}")
-            print("Closing serial port.")
-            if self.ser.is_open:
-                self.ser.close()
-            pass
-
-    def send_ik(self, msg):
-        pass
 
     def send_control(self, msg: BioControl):
-        # CITADEL Control Commands
-        ################
-
-        # Chem Pumps, only send if not zero
-        if msg.pump_id != 0:
-            command = (
-                "can_relay_tovic,citadel,27,"
-                + str(msg.pump_id)
-                + ","
-                + str(msg.pump_amount)
-                + "\n"
-            )
-            self.send_cmd(command)
-        # Fans, only send if not zero
-        if msg.fan_id != 0:
-            command = (
-                "can_relay_tovic,citadel,40,"
-                + str(msg.fan_id)
-                + ","
-                + str(msg.fan_duration)
-                + "\n"
-            )
-            self.send_cmd(command)
-        # Servos, only send if not zero
-        if msg.servo_id != 0:
-            command = (
-                "can_relay_tovic,citadel,25,"
-                + str(msg.servo_id)
-                + ","
-                + str(int(msg.servo_state))
-                + "\n"
-            )
-            self.send_cmd(command)
-
-        # LSS (SCYTHE)
-        command = "can_relay_tovic,citadel,24," + str(msg.bio_arm) + "\n"
-        # self.send_cmd(command)
-
-        # Vibration Motor
-        command += "can_relay_tovic,citadel,26," + str(msg.vibration_motor) + "\n"
-        # self.send_cmd(command)
-
-        # FAERIE Control Commands
-        ################
-
-        # To be reviewed before use#
-
-        # Laser
-        command += "can_relay_tovic,digit,28," + str(msg.laser) + "\n"
-        # self.send_cmd(command)
-
-        # Drill (SCABBARD)
-        command += f"can_relay_tovic,digit,19,{msg.drill:.2f}\n"
-        # self.send_cmd(command)
-
-        # Bio linear actuator
-        command += "can_relay_tovic,digit,42," + str(msg.drill_arm) + "\n"
-        self.send_cmd(command)
+        print("todo")
 
     def send_cmd(self, msg: str):
-        if (
-            self.launch_mode == "anchor"
-        ):  # if in anchor mode, send to anchor node to relay
-            output = String()
-            output.data = msg
-            self.anchor_pub.publish(output)
-        elif self.launch_mode == "bio":  # if in standalone mode, send to MCU directly
-            self.get_logger().info(f"[Bio to MCU] {msg}")
-            self.ser.write(bytes(msg, "utf8"))
+        # send to anchor node to relay
+        output = String()
+        output.data = msg
+        self.anchor_pub.publish(output)
+
+    def relay_fromvic(self, msg: VicCAN):
+        # self.get_logger().info(msg)
+        if msg.mcu_name == "citadel":
+            self.process_fromvic_citadel(msg)
+
+    def process_fromvic_citadel(self, msg: VicCAN):
+        # Check message len to prevent crashing on bad data
+        if msg.command_id in viccan_citadel_msg_len_dict:
+            expected_len = viccan_citadel_msg_len_dict[msg.command_id]
+            if len(msg.data) != expected_len:
+                self.get_logger().warning(
+                    f"Ignoring VicCAN message with id {msg.command_id} due to unexpected data length (expected {expected_len}, got {len(msg.data)})"
+                )
+            return
 
     def anchor_feedback(self, msg: String):
         output = msg.data
         parts = str(output.strip()).split(",")
-        # self.get_logger().info(f"[Bio Anchor] {msg.data}")
+        self.get_logger().info(f"[Bio Anchor] {msg.data}")
+        # no data planned to be received from citadel, not sure about lance
 
-        if output.startswith(
-            "can_relay_fromvic,citadel,54"
-        ):  # bat, 12, 5, Voltage readings * 100
-            self.bio_feedback.bat_voltage = float(parts[3]) / 100.0
-            self.bio_feedback.voltage_12 = float(parts[4]) / 100.0
-            self.bio_feedback.voltage_5 = float(parts[5]) / 100.0
-        elif output.startswith("can_relay_fromvic,digit,57"):
-            self.bio_feedback.drill_temp = float(parts[3])
-            self.bio_feedback.drill_humidity = float(parts[4])
+    def distributor_callback(self, msg: BioDistributor):
+        distributor_arr = msg.distributor_id
+        vic_cmd = VicCAN(
+            header=Header(stamp=self.get_clock().now().to_msg()),
+            mcu_name="citadel",
+            command_id=40,
+            data=[
+                clamp_short(distributor_arr[0]),
+                clamp_short(distributor_arr[1]),
+                clamp_short(distributor_arr[2]),
+                0,
+            ],
+        )
+        self.anchor_tovic_pub_.publish(vic_cmd)
 
-    def publish_feedback(self):
-        self.feedback_pub.publish(self.bio_feedback)
+    def test_tube_callback(self, request, response):
+        tubes_cmd = VicCAN(
+            header=Header(stamp=self.get_clock().now().to_msg()),
+            mcu_name="citadel",
+            command_id=40,
+            data=[
+                float(int.from_bytes(request.tube_id)),
+                float(request.milliliters),
+            ],
+        )
+        self.anchor_tovic_pub_.publish(tubes_cmd)
+        return response
 
-    @staticmethod
-    def list_serial_ports():
-        return glob.glob("/dev/ttyUSB*") + glob.glob("/dev/ttyACM*")
-        # return glob.glob("/dev/tty[A-Za-z]*")
+    def execute_vacuum(self, goal_handle):
+        valve_id = int.from_bytes(goal_handle.request.valve_id)
+        duty = int.from_bytes(goal_handle.request.fan_duty_cycle_percent)
+        total = goal_handle.request.fan_time_ms
 
-    def cleanup(self):
-        print("Cleaning up...")
-        try:
-            if self.ser.is_open:
-                self.ser.close()
-        except Exception as e:
-            exit(0)
+        # open valve
+        self.anchor_tovic_pub_.publish(
+            VicCAN(
+                header=Header(stamp=self.get_clock().now().to_msg()),
+                mcu_name="citadel",
+                command_id=40,
+                data=[float(valve_id)],
+            )
+        )
+
+        # set fan duty cycle
+        self.anchor_tovic_pub_.publish(
+            VicCAN(
+                header=Header(stamp=self.get_clock().now().to_msg()),
+                mcu_name="citadel",
+                command_id=19,
+                data=[float(duty)],
+            )
+        )
+
+        feedback = BioVacuum.Feedback()
+        start = time.time()
+
+        while True:
+            elapsed = int((time.time() - start) * 1000)
+            remaining = max(0, total - elapsed)
+
+            feedback.fan_time_remaining_ms = remaining
+            goal_handle.publish_feedback(feedback)
+
+            if remaining == 0:
+                break
+
+            time.sleep(0.1)
+
+        # stop fan
+        self.anchor_tovic_pub_.publish(
+            VicCAN(
+                header=Header(stamp=self.get_clock().now().to_msg()),
+                mcu_name="citadel",
+                command_id=19,
+                data=[0.0],
+            )
+        )
+
+        # close valve
+        self.anchor_tovic_pub_.publish(
+            VicCAN(
+                header=Header(stamp=self.get_clock().now().to_msg()),
+                mcu_name="citadel",
+                command_id=40,
+                data=[-1.0],
+            )
+        )
+
+        goal_handle.succeed()
+        return BioVacuum.Result()
+
+
+def clamp_short(x: int) -> int:
+    return max(-32768, min(32767, x))
 
 
 def myexcepthook(type, value, tb):
     print("Uncaught exception:", type, value)
-    if serial_pub:
-        serial_pub.cleanup()
 
 
 def main(args=None):

src/core_pkg/core_pkg/core_node.py

@@ -31,14 +31,14 @@ CORE_WHEEL_RADIUS = 0.171  # meters
 CORE_GEAR_RATIO = 100.0  # Clucky: 100:1, Testbed: 64:1
 
 control_qos = qos.QoSProfile(
-    history=qos.QoSHistoryPolicy.KEEP_LAST,
+    # history=qos.QoSHistoryPolicy.KEEP_LAST,
     depth=2,
-    reliability=qos.QoSReliabilityPolicy.BEST_EFFORT,
-    durability=qos.QoSDurabilityPolicy.VOLATILE,
-    deadline=Duration(seconds=1),
-    lifespan=Duration(nanoseconds=500_000_000),  # 500ms
-    liveliness=qos.QoSLivelinessPolicy.SYSTEM_DEFAULT,
-    liveliness_lease_duration=Duration(seconds=5),
+    # reliability=qos.QoSReliabilityPolicy.BEST_EFFORT,
+    # durability=qos.QoSDurabilityPolicy.VOLATILE,
+    # deadline=Duration(seconds=1),
+    # lifespan=Duration(nanoseconds=500_000_000),  # 500ms
+    # liveliness=qos.QoSLivelinessPolicy.SYSTEM_DEFAULT,
+    # liveliness_lease_duration=Duration(seconds=5),
 )
 
 # Used to verify the length of an incoming VicCAN feedback message

src/core_pkg/core_pkg/core_ptz.py

@@ -1,25 +1,24 @@
 #!/usr/bin/env python3
+import rclpy
+from rclpy.node import Node
 import asyncio
+from concurrent.futures import ThreadPoolExecutor
 import signal
 import sys
 import threading
 import time
-from concurrent.futures import ThreadPoolExecutor
 
-import rclpy
-from rclpy.node import Node
 from std_msgs.msg import String
-
 from astra_msgs.msg import PtzControl, PtzFeedback
 
 # Import the SIYI SDK
 from core_pkg.siyi_sdk import (
-    AttitudeData,
-    CommandID,
-    DataStreamFrequency,
-    DataStreamType,
-    SingleAxis,
     SiyiGimbalCamera,
+    CommandID,
+    DataStreamType,
+    DataStreamFrequency,
+    SingleAxis,
+    AttitudeData,
 )
 
 
@@ -263,7 +262,7 @@ class PtzNode(Node):
             f"[{self.get_clock().now().nanoseconds / 1e9:.2f}] PTZ Node: {message_text}"
         )
         self.debug_pub.publish(msg)
-        self.get_logger().debug(message_text)
+        self.get_logger().info(message_text)
 
     def run_async_func(self, coro):
         """Run an async function in the event loop."""

src/headless_pkg/src/headless_node.py

@@ -35,14 +35,14 @@ ARM_STOP_MSG = ArmManual()  # "
 BIO_STOP_MSG = BioControl()  # "
 
 control_qos = qos.QoSProfile(
-    history=qos.QoSHistoryPolicy.KEEP_LAST,
+    # history=qos.QoSHistoryPolicy.KEEP_LAST,
     depth=2,
-    reliability=qos.QoSReliabilityPolicy.BEST_EFFORT,
-    durability=qos.QoSDurabilityPolicy.VOLATILE,
-    deadline=Duration(seconds=1),
-    lifespan=Duration(nanoseconds=500_000_000),  # 500ms
-    liveliness=qos.QoSLivelinessPolicy.SYSTEM_DEFAULT,
-    liveliness_lease_duration=Duration(seconds=5),
+    # reliability=qos.QoSReliabilityPolicy.BEST_EFFORT,
+    # durability=qos.QoSDurabilityPolicy.VOLATILE,
+    # deadline=Duration(seconds=1),
+    # lifespan=Duration(nanoseconds=500_000_000),  # 500ms
+    # liveliness=qos.QoSLivelinessPolicy.SYSTEM_DEFAULT,
+    # liveliness_lease_duration=Duration(seconds=5),
 )
 
 CORE_MODE = "twist"  # "twist" or "duty"