In case you have the original Arduino bootloader which you want to execute as a part of the reset, you can do a SW reset by jumping to the bootloader reset address (0x7800 on ATmega328p boards)

void reset() { asm volatile ("jmp 0x7800"); }

The watchdog reset approach will not work because of a bug in the bootloader. Here's a note from ATmega328P Datasheet page 45:

Note: If the watchdog is accidentally enabled, for example by a runaway pointer or brown-out condition, the device will be reset and the watchdog timer will stay enabled. If the code is not set up to handle the watchdog, this might lead to an eternal loop of time-out resets. To avoid this situation, the application software should always clear the watchdog system reset flag (WDRF) and the WDE control bit in the initialization routine, even if the watchdog is not in use.

This is exactly what will happen after a watchdog reset on a system with Arduino bootloader.

If you want to control your Arduino board with a Python script you need to first establish a Serial communication and then create a simple protocol to send your commands from Python script to Arduino. For the reset part in Arduino, there are some ways to do it and I prefer to using a watchdog timeout.

Arduino Code:

#include <avr/wdt.h>


void setup()
{
    MCUSR = 0;  // clear out any flags of prior resets.
    Serial.begin(9600);
}

// read a command from serial and do proper action
void read_command()
{
    String command;
    if (Serial.available())
    {
        command = Serial.readString();
        Serial.print("Received Command: ");
        Serial.println(command);
        // do proper work with command
        if (command == "RST")
        {
            Serial.println("Arduino is Reseting...");
            // reset board
            wdt_enable(WDTO_15MS); // turn on the WatchDog and don't stroke it.
            for(;;) { 
            // do nothing and wait for the eventual...
            } 
        }
    }
}

void loop()
{
    // get new commands
    read_command();
    delay(1000);
}

Python Script:

import serial
from time import sleep


# remember to set this value to a proper serial port name
ser = serial.Serial('COM1', 9600)
ser.open()
# flush serial for unprocessed data
ser.flushInput()
while True:
   command = "RST"
   ser.write(command.encode())
   """
   # use below code if you want to take commands from user
   command = input("Enter your command: ")
   if command:
      command += "\r\n"
      ser.write(command.encode())
   """
   ser.flushInput()
   sleep(3)

I had the same problem on two Arduinos (one Uno, and one Modern Device Freeduino/USB Host board) and the window between reset and the beginning of serial port usage was so small that it was impossible to upload.

I finally fixed the problem by purchasing another Arduino Uno and building an ISP cable per these instructions, and using it to flash the Bare Bones app from the examples into each inaccessible board, using Arduino IDE version 0023, following these instructions to change preferences.txt. (Be sure to save the original file before editing it so you can replace it after you've rescued your Arduino.)

It took one quick upload to fix each board. Such a fast fix after so much grief. You might not want to purchase another Arduino, but consider these benefits:

• You can overwrite the bootloader on your Arduino to gain more space.
• Once the bootloader is overwritten, the board will boot faster.
• Supposedly you can program raw AVRs for special projects, but I have not tried this: Google for ArduinoISP
• It will quickly fix Arduinos that you block in the future.
• You can now safely experiment to find ways to prevent serial port usage from locking up the device in the future.