added docker compose

.gitmodules

@@ -1,3 +1,6 @@
 [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

auto_start/auto_start_anchor.sh

@@ -14,8 +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 we aren't using nix)
-command -v ros2 || source /opt/ros/humble/setup.bash
+# Source ROS 2 Humble setup script
+source /opt/ros/humble/setup.bash
 
 # Source your workspace setup script
 source $SCRIPT_DIR/../install/setup.bash

auto_start/auto_start_headless_full.sh

@@ -15,7 +15,7 @@ echo "[INFO] Network interface is up!"
 echo "[INFO] Starting ROS node..."
 
 # Source ROS 2 Humble setup script
-command -v ros2 || source /opt/ros/humble/setup.bash
+source /opt/ros/humble/setup.bash
 
 # Source your workspace setup script
 source $SCRIPT_DIR/../install/setup.bash

auto_start/start_rosbag.sh

@@ -17,7 +17,7 @@ done
 echo "[INFO] Network interface is up!"
 
 
-command -v ros2 || source /opt/ros/humble/setup.bash
+source /opt/ros/humble/setup.bash
 source $ANCHOR_WS/install/setup.bash
 [[ -f $AUTONOMY_WS/install/setup.bash ]] && source $AUTONOMY_WS/install/setup.bash
 

docker-compose.yml

@@ -0,0 +1,18 @@
+
+services:
+  ros2:
+    image: osrf/ros:jazzy-desktop-full
+    container_name: ros2_jazzy_gui
+    network_mode: host
+    environment:
+      - DISPLAY=${DISPLAY}
+      - QT_X11_NO_MITSHM=1
+      - XAUTHORITY=/tmp/.docker.xauth
+      - NVIDIA_VISIBLE_DEVICES=all
+      - NVIDIA_DRIVER_CAPABILITIES=all
+    volumes:
+      - /tmp/.X11-unix:/tmp/.X11-unix:rw
+      - ./ros_ws:/ros_ws
+    stdin_open: true
+    tty: true
+    privileged: true

flake.lock

@@ -1,29 +1,5 @@
 {
   "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"
@@ -42,87 +18,33 @@
         "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": 1770408708,
-        "narHash": "sha256-E7ZQRgGrsiuswgXnG7337ZR5s4SdZlheZjxKOQdVoH8=",
+        "lastModified": 1761810010,
+        "narHash": "sha256-o0wJKW603SiOO373BTgeZaF6nDxegMA/cRrzSC2Cscg=",
         "owner": "lopsided98",
         "repo": "nix-ros-overlay",
-        "rev": "e78ba91032c7f8bdd823fbf43937cbf0f4f09747",
+        "rev": "e277df39e3bc6b372a5138c0bcf10198857c55ab",
         "type": "github"
       },
       "original": {
         "owner": "lopsided98",
-        "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",
+        "ref": "master",
         "repo": "nix-ros-overlay",
         "type": "github"
       }
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1759381078,
-        "narHash": "sha256-gTrEEp5gEspIcCOx9PD8kMaF1iEmfBcTbO0Jag2QhQs=",
-        "owner": "NixOS",
-        "repo": "nixpkgs",
-        "rev": "7df7ff7d8e00218376575f0acdcc5d66741351ee",
-        "type": "github"
-      },
-      "original": {
+        "lastModified": 1744849697,
+        "narHash": "sha256-S9hqvanPSeRu6R4cw0OhvH1rJ+4/s9xIban9C4ocM/0=",
         "owner": "lopsided98",
-        "ref": "nix-ros",
         "repo": "nixpkgs",
-        "type": "github"
-      }
-    },
-    "nixpkgs_2": {
-      "locked": {
-        "lastModified": 1759381078,
-        "narHash": "sha256-gTrEEp5gEspIcCOx9PD8kMaF1iEmfBcTbO0Jag2QhQs=",
-        "owner": "NixOS",
-        "repo": "nixpkgs",
-        "rev": "7df7ff7d8e00218376575f0acdcc5d66741351ee",
+        "rev": "6318f538166fef9f5118d8d78b9b43a04bb049e4",
         "type": "github"
       },
       "original": {
@@ -134,8 +56,7 @@
     },
     "root": {
       "inputs": {
-        "astra-msgs": "astra-msgs",
-        "nix-ros-overlay": "nix-ros-overlay_2",
+        "nix-ros-overlay": "nix-ros-overlay",
         "nixpkgs": [
           "nix-ros-overlay",
           "nixpkgs"
@@ -156,21 +77,6 @@
         "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

@@ -2,10 +2,8 @@
   description = "Development environment for ASTRA Anchor";
 
   inputs = {
-    nix-ros-overlay.url = "github:lopsided98/nix-ros-overlay/develop";
+    nix-ros-overlay.url = "github:lopsided98/nix-ros-overlay/master";
     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 =
@@ -13,7 +11,6 @@
       self,
       nix-ros-overlay,
       nixpkgs,
-      astra-msgs,
     }:
     nix-ros-overlay.inputs.flake-utils.lib.eachDefaultSystem (
       system:
@@ -27,9 +24,8 @@
         devShells.default = pkgs.mkShell {
           name = "ASTRA Anchor";
           packages = with pkgs; [
-            astra-msgs.packages.${system}.astra-msgs
             colcon
-            (python313.withPackages (
+            (python312.withPackages (
               p: with p; [
                 pyserial
                 pygame
@@ -43,7 +39,6 @@
               buildEnv {
                 paths = [
                   ros-core
-                  rqt-graph
                   ros2cli
                   ros2run
                   ros2bag
@@ -61,12 +56,10 @@
                   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
@@ -75,9 +68,9 @@
                   pilz-industrial-motion-planner
                   pick-ik
                   ompl
+                  chomp-motion-planner
                   joy
-                  ros2-controllers
-		  chomp-motion-planner
+                  # ros2-controllers nixpkg does not build :(
                 ];
               }
             )

src/anchor_pkg/anchor_pkg/anchor_node.py

@@ -1,6 +1,5 @@
 import rclpy
 from rclpy.node import Node
-from rclpy.executors import ExternalShutdownException
 from std_srvs.srv import Empty
 
 import signal
@@ -8,7 +7,6 @@ import time
 import atexit
 
 import serial
-import serial.tools.list_ports
 import os
 import sys
 import threading
@@ -17,156 +15,70 @@ import glob
 from std_msgs.msg import String, Header
 from astra_msgs.msg import VicCAN
 
-KNOWN_USBS = [
-    (0x2E8A, 0x00C0),  # Raspberry Pi Pico
-    (0x1A86, 0x55D4),  # Adafruit Feather ESP32 V2
-    (0x10C4, 0xEA60),  # DOIT ESP32 Devkit V1
-    (0x1A86, 0x55D3),  # ESP32 S3 Development Board
-]
+serial_pub = None
+thread = None
 
 
-class Anchor(Node):
-    """
-    Publishers:
-    * /anchor/from_vic/debug
-        - Every string received from the MCU is published here for debugging
-    * /anchor/from_vic/core
-        - VicCAN messages for Core node
-    * /anchor/from_vic/arm
-        - VicCAN messages for Arm node
-    * /anchor/from_vic/bio
-        - VicCAN messages for Bio node
+"""
+Publishers:
+  * /anchor/from_vic/debug
+    - Every string received from the MCU is published here for debugging
+  * /anchor/from_vic/core
+    - VicCAN messages for Core node
+  * /anchor/from_vic/arm
+    - VicCAN messages for Arm node
+  * /anchor/from_vic/bio
+    - VicCAN messages for Bio node
 
-    Subscribers:
-    * /anchor/from_vic/mock_mcu
-        - For testing without an actual MCU, publish strings here as if they came from an MCU
-    * /anchor/to_vic/relay
-        - Core, Arm, and Bio publish VicCAN messages to this topic to send to the MCU
-    * /anchor/to_vic/relay_string
-        - Publish raw strings to this topic to send directly to the MCU for debugging
-    """
+Subscribers:
+  * /anchor/from_vic/mock_mcu
+    - For testing without an actual MCU, publish strings here as if they came from an MCU
+  * /anchor/to_vic/relay
+    - Core, Arm, and Bio publish VicCAN messages to this topic to send to the MCU
+  * /anchor/to_vic/relay_string
+    - Publish raw strings to this topic to send directly to the MCU for debugging
+"""
 
+
+class SerialRelay(Node):
     def __init__(self):
         # Initalize node with name
         super().__init__("anchor_node")  # previously 'serial_publisher'
 
-        self.serial_port: str | None = None  # e.g., "/dev/ttyUSB0"
-
-        # Serial port override
-        if port_override := os.getenv("PORT_OVERRIDE"):
-            self.serial_port = port_override
-
-        ##################################################
-        # Serial MCU Discovery
-
-        # 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()
-            real_ports = list(
-                filter(
-                    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))
-
-            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__()}"
-                )
-                # 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__()}."
-                )
-                # 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()
-
-        # 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
-                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"))
+        self.port = None
+        if port_override := os.getenv("PORT_OVERRIDE"):
+            self.port = port_override
+        ports = SerialRelay.list_serial_ports()
+        for i in range(4):
+            if self.port is not None:
+                break
+            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"))
 
-                        # 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 pong is in response, then we are talking with the MCU
+                    if b"pong" in response:
+                        self.port = port
+                        self.get_logger().info(f"Found MCU at {self.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...")
+        if self.port is None:
+            self.get_logger().info("Unable to find MCU...")
             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}'..."
-            )
-            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
+        self.ser = serial.Serial(self.port, 115200)
+        self.get_logger().info(f"Enabling Relay Mode")
+        self.ser.write(b"can_relay_mode,on\n")
         atexit.register(self.cleanup)
 
-        ##################################################
-        # ROS2 Topic Setup
-
         # New pub/sub with VicCAN
         self.fromvic_debug_pub_ = self.create_publisher(
             String, "/anchor/from_vic/debug", 20
@@ -203,10 +115,22 @@ class Anchor(Node):
             String, "/anchor/relay", self.on_relay_tovic_string, 10
         )
 
+    def run(self):
+        # This thread makes all the update processes run in the background
+        global thread
+        thread = threading.Thread(target=rclpy.spin, args={self}, daemon=True)
+        thread.start()
+
+        try:
+            while rclpy.ok():
+                self.read_MCU()  # Check the MCU for updates
+        except KeyboardInterrupt:
+            sys.exit(0)
+
     def read_MCU(self):
         """Check the USB serial port for new data from the MCU, and publish string to appropriate topics"""
         try:
-            output = str(self.serial_interface.readline(), "utf8")
+            output = str(self.ser.readline(), "utf8")
 
             if output:
                 self.relay_fromvic(output)
@@ -232,20 +156,14 @@ class Anchor(Node):
         except serial.SerialException as e:
             print(f"SerialException: {e}")
             print("Closing serial port.")
-            try:
-                if self.serial_interface.is_open:
-                    self.serial_interface.close()
-            except:
-                pass
+            if self.ser.is_open:
+                self.ser.close()
             exit(1)
         except TypeError as e:
             print(f"TypeError: {e}")
             print("Closing serial port.")
-            try:
-                if self.serial_interface.is_open:
-                    self.serial_interface.close()
-            except:
-                pass
+            if self.ser.is_open:
+                self.ser.close()
             exit(1)
         except Exception as e:
             print(f"Exception: {e}")
@@ -266,7 +184,7 @@ class Anchor(Node):
             output += f",{round(num, 7)}"  # limit to 7 decimal places
         output += "\n"
         # self.get_logger().info(f"VicCAN relay to MCU: {output}")
-        self.serial_interface.write(bytes(output, "utf8"))
+        self.ser.write(bytes(output, "utf8"))
 
     def relay_fromvic(self, msg: str):
         """Relay a string message from the MCU to the appropriate VicCAN topic"""
@@ -328,7 +246,7 @@ class Anchor(Node):
         """Relay a raw string message to the MCU for debugging"""
         message = msg.data
         # self.get_logger().info(f"Sending command to MCU: {msg}")
-        self.serial_interface.write(bytes(message, "utf8"))
+        self.ser.write(bytes(message, "utf8"))
 
     @staticmethod
     def list_serial_ports():
@@ -336,29 +254,28 @@ class Anchor(Node):
 
     def cleanup(self):
         print("Cleaning up before terminating...")
-        if self.serial_interface.is_open:
-            self.serial_interface.close()
+        if self.ser.is_open:
+            self.ser.close()
+
+
+def myexcepthook(type, value, tb):
+    print("Uncaught exception:", type, value)
+    if serial_pub:
+        serial_pub.cleanup()
 
 
 def main(args=None):
-    try:
-        rclpy.init(args=args)
-        anchor_node = Anchor()
+    rclpy.init(args=args)
+    sys.excepthook = myexcepthook
 
-        thread = threading.Thread(target=rclpy.spin, args=(anchor_node,), daemon=True)
-        thread.start()
+    global serial_pub
 
-        rate = anchor_node.create_rate(100)  # 100 Hz -- arbitrary rate
-        while rclpy.ok():
-            anchor_node.read_MCU()  # Check the MCU for updates
-            rate.sleep()
-    except (KeyboardInterrupt, ExternalShutdownException):
-        print("Caught shutdown signal, shutting down...")
-    finally:
-        rclpy.try_shutdown()
+    serial_pub = SerialRelay()
+    serial_pub.run()
 
 
 if __name__ == "__main__":
+    # signal.signal(signal.SIGTSTP, lambda signum, frame: sys.exit(0))  # Catch Ctrl+Z and exit cleanly
     signal.signal(
         signal.SIGTERM, lambda signum, frame: sys.exit(0)
     )  # Catch termination signals and exit cleanly

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, 2
+            ArmManual, "/arm/control/manual", self.send_manual, 10
         )
 
         # 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

@@ -1,203 +1,241 @@
-import signal
+import rclpy
+from rclpy.node import Node
+import serial
 import sys
 import threading
+import os
+import glob
 import time
-
-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
+import atexit
+import signal
+from std_msgs.msg import String
+from astra_msgs.msg import BioControl
+from astra_msgs.msg import BioFeedback
 
 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")
 
-        # 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
+        # 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
         )
 
-        self.anchor_sub = self.create_subscription(
-            String, "/anchor/bio/feedback", self.anchor_feedback, 10
-        )
-        self.anchor_pub = self.create_publisher(String, "/anchor/relay", 10)
+        # Create a publisher for telemetry
+        self.telemetry_pub_timer = self.create_timer(1.0, self.publish_feedback)
 
-        self.distributor_sub = self.create_subscription(
-            BioDistributor,
-            "/bio/control/distributor",
-            self.distributor_callback,
-            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)
 
-        # Services
-        self.test_tube_service = self.create_service(
-            BioTestTube, "/bio/control/test_tube", self.test_tube_callback
-        )
+        self.bio_feedback = BioFeedback()
 
-        # Actions
-        self._action_server = ActionServer(
-            self, BioVacuum, "/bio/actions/vacuum", self.execute_vacuum
-        )
+        # 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)
 
     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():
-                time.sleep(0.1)
+                if self.launch_mode == "bio":
+                    if self.ser.in_waiting:
+                        self.read_mcu()
+                    else:
+                        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):
-        print("todo")
+        # 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)
 
     def send_cmd(self, msg: str):
-        # 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
+        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"))
 
     def anchor_feedback(self, msg: String):
         output = msg.data
         parts = str(output.strip()).split(",")
-        self.get_logger().info(f"[Bio Anchor] {msg.data}")
-        # no data planned to be received from citadel, not sure about lance
+        # self.get_logger().info(f"[Bio Anchor] {msg.data}")
 
-    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)
+        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 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
+    def publish_feedback(self):
+        self.feedback_pub.publish(self.bio_feedback)
 
-    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
+    @staticmethod
+    def list_serial_ports():
+        return glob.glob("/dev/ttyUSB*") + glob.glob("/dev/ttyACM*")
+        # return glob.glob("/dev/tty[A-Za-z]*")
 
-        # 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 cleanup(self):
+        print("Cleaning up...")
+        try:
+            if self.ser.is_open:
+                self.ser.close()
+        except Exception as e:
+            exit(0)
 
 
 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/headless_pkg/src/headless_node.py

@@ -1,6 +1,5 @@
 import rclpy
 from rclpy.node import Node
-from rclpy.executors import ExternalShutdownException
 from rclpy import qos
 from rclpy.duration import Duration
 
@@ -12,8 +11,6 @@ import os
 import sys
 import threading
 import glob
-import pwd
-import grp
 from math import copysign
 
 from std_msgs.msg import String
@@ -35,14 +32,14 @@ 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"
@@ -74,36 +71,9 @@ class Headless(Node):
             print("No gamepad found. Waiting...")
 
         # Initialize the gamepad
-        id = 0
-        while True:
-            self.num_gamepads = pygame.joystick.get_count()
-            if id >= self.num_gamepads:
-                self.get_logger().fatal("Ran out of controllers to try")
-                sys.exit(1)
-
-            try:
-                self.gamepad = pygame.joystick.Joystick(id)
-                self.gamepad.init()
-            except Exception as e:
-                self.get_logger().error("Error when initializing gamepad")
-                self.get_logger().error(e)
-                id += 1
-                continue
-            print(f"Gamepad Found: {self.gamepad.get_name()}")
-
-            if self.gamepad.get_numhats() == 0 or self.gamepad.get_numaxes() < 5:
-                self.get_logger().error("Controller not correctly initialized.")
-                if not is_user_in_group("input"):
-                    self.get_logger().warning(
-                        "If using NixOS, you may need to add yourself to the 'input' group."
-                    )
-                if is_user_in_group("plugdev"):
-                    self.get_logger().warning(
-                        "If using NixOS, you may need to remove yourself from the 'plugdev' group."
-                    )
-            else:
-                break
-            id += 1
+        self.gamepad = pygame.joystick.Joystick(0)
+        self.gamepad.init()
+        print(f"Gamepad Found: {self.gamepad.get_name()}")
 
         self.create_timer(0.15, self.send_controls)
 
@@ -145,7 +115,7 @@ class Headless(Node):
                 sys.exit(0)
 
         # Check if controller is still connected
-        if pygame.joystick.get_count() != self.num_gamepads:
+        if pygame.joystick.get_count() == 0:
             print("Gamepad disconnected. Exiting...")
             # Send one last zero control message
             self.core_publisher.publish(CORE_STOP_MSG)
@@ -326,34 +296,11 @@ def deadzone(value: float, threshold=0.05) -> float:
     return value
 
 
-def is_user_in_group(group_name: str) -> bool:
-    # Copied from https://zetcode.com/python/os-getgrouplist/
-    try:
-        username = os.getlogin()
-
-        # Get group ID from name
-        group_info = grp.getgrnam(group_name)
-        target_gid = group_info.gr_gid
-
-        # Get user's groups
-        user_info = pwd.getpwnam(username)
-        user_groups = os.getgrouplist(username, user_info.pw_gid)
-
-        return target_gid in user_groups
-    except KeyError:
-        return False
-
-
 def main(args=None):
-    try:
-        rclpy.init(args=args)
-
-        node = Headless()
-        rclpy.spin(node)
-    except (KeyboardInterrupt, ExternalShutdownException):
-        print("Caught shutdown signal. Exiting...")
-    finally:
-        rclpy.shutdown()
+    rclpy.init(args=args)
+    node = Headless()
+    rclpy.spin(node)
+    rclpy.shutdown()
 
 
 if __name__ == "__main__":