How to make data sent by Python (via serial connection) wait for Arduino to finish current task?
If I'm getting things right, your program fails in the above:
  
  when you send the first message in python, you set state = 0. In
  arduino you enter the serialEvent function and while is triggered. You
  get the first char and send it through Serial.print (but this char
  will be send to python!!!). For the sake of example let's say the
  first char you get from cvs is '2'. At this point let's hold on a
  sec and look what happens in python. State was '0' but as you have
  used in arduino Serial.print(ch); now state will be updated with
  '2'. This will cause no more triggers of the if-else statements in
  python.
  
  edit:
  
  By now, and also as a debug, add this lines at your code:

if state == '0': # Wait for Arduino to be ready
    state = ser.read()
    if state != '1':
        print "state: " + state
        state = '0'

  
  However if csv file contains '1's values this will also cause a
  problem. Do you really need that Serial.print(ch) in arduino?


EDIT The new version since comments
Basically if you are trying to do things before new coordinates, you have to do things in a sequential way. You only ask for info after making all the moves. This is the code I've used to test.
Note: I had to adapt your code because was missing the complete arduino code to test it. So I kinda simulated the motor moving etc with delays. Please adapt to your original code

#include &lt;string.h&gt;

bool coord_complete = false;
byte stepper1_disToGo = 0, stepper2_disToGo = 0;
// debug things
int led = 13;
bool led_state = true, x_complete, y_complete;
char coord_string[256];
int index = 0, x_new = 0, y_new = 0;



void setup() {
  // put your setup code here, to run once:
  Serial.begin(9600);
  pinMode(led, OUTPUT);
  memset(&amp;coord_string, 0, sizeof(coord_string));
}

void loop() {

  serialData(); //ask and process more data

  /*
    // Steps to move from currrent to new point
    target1 = steps(x_current, y_current, x_new, y_new, 1);
    target2 = steps(x_current, y_current, x_new, y_new, 2);

    // Start moving
    stepper1.move(target1);
    stepper2.move(target2);

    // Update current position
    x_current = x_new;
    y_current = y_new;

    // Reset variables
    x_complete = false;
    y_complete = false;
  */
  delay(2000); //replace to simulate actions
  stepper1_disToGo = 10;
  stepper2_disToGo = 10;
  coord_complete = false;

  // replaced to simulate
  /*
    // Stay in while loop until steppermotors is done
    while ((stepper1.distanceToGo() != 0) &amp;&amp; (stepper2.distanceToGo() != 0)) {
    stepper1.run();
    stepper2.run();
    }
  */
  while ((stepper1_disToGo != 0) || (stepper2_disToGo != 0)) {
    stepper1_disToGo --;
    stepper2_disToGo --;
    digitalWrite(led, led_state); // is moving!!!!
    delay(100);
    led_state = !led_state;
  }
}

/*
   you try to use the serialEvent  but the structure of
   your code and the verifications make it act like sequential.
   If you only want to make things after all steps are done there
   is no need for the serialEvent function
*/
void serialData() {
  /*
     This will never be false because you are stuck in the while

    // EDIT : PUT SERIAL.WRITE INSIDE IF STATEMENT //
    if((stepper1.distanceToGo() == 0) &amp;&amp; (stepper2.distanceToGo() == 0)){
    Serial.write('1'); // Tell Python that Arduino is ready for one more line
    }
  */
  //EDIT: wait for info
  while (Serial.available() &lt; 1) {
    Serial.write('1'); /// Tell Python that Arduino is ready for one more line
    delay(500);// ask for info sometimes
  }
  while (Serial.available()) {
    char ch = Serial.read(); // Get new character

    // If digit; add it to coord_string
    if (isDigit(ch)) {
      coord_string[index++] = ch;

      // Else if ch is ","; then rename to x_new
    } else if (ch == ',') {
      coord_string[index++] = NULL;                   // Finish coord_string
      x_new = atoi(coord_string);                     // Convert to integer
      x_complete = true;                              // Change x_complete to true
      index = 0;                                      // Reset index
      memset(coord_string, 0, sizeof(coord_string));  // Reset coord_string

      // Else if ch is a new line; then rename as y_new
    } else if (ch == ';') {
      coord_string[index++] = NULL;
      y_new = atoi(coord_string);
      y_complete = true;
      index = 0;
      memset(coord_string, 0, sizeof(coord_string));
    }
    //EDIT: change to AND verification
    // Ends while-loop when true
    coord_complete = x_complete &amp;&amp; y_complete;
  }
}


The structure of your loop should be:


ask for data and wait for it
Read data and parse it
Calculate steps needed
move servos till new positions
repeat


this should be your new code more or less if no mistakes were made because can't really test this version (is missing the variables declarations setup, includes etc...)

void loop() {

  serialData(); //ask and process more data
  // Steps to move from currrent to new point
  target1 = steps(x_current, y_current, x_new, y_new, 1);
  target2 = steps(x_current, y_current, x_new, y_new, 2);

  // Start moving
  stepper1.move(target1);
  stepper2.move(target2);

  // Update current position
  x_current = x_new;
  y_current = y_new;

  // Reset variables
  x_complete = false;
  y_complete = false;
  coord_complete = false;

  // Stay in while loop until steppermotors is done
  while ((stepper1.distanceToGo() != 0) &amp;&amp; (stepper2.distanceToGo() != 0)) {
    stepper1.run();
    stepper2.run();
  }
}

void serialData() {

  //EDIT: wait for info
  while (Serial.available() &lt; 1) {
    Serial.write('1'); /// Tell Python that Arduino is ready for one more line
    delay(500);// ask for info sometimes
  }
  // we got info!!!
  while (Serial.available()) {
    char ch = Serial.read(); // Get new character

    // If digit; add it to coord_string
    if (isDigit(ch)) {
      coord_string[index++] = ch;

      // Else if ch is ","; then rename to x_new
    } else if (ch == ',') {
      coord_string[index++] = NULL;                   // Finish coord_string
      x_new = atoi(coord_string);                     // Convert to integer
      x_complete = true;                              // Change x_complete to true
      index = 0;                                      // Reset index
      memset(coord_string, 0, sizeof(coord_string));  // Reset coord_string

      // Else if ch is a new line; then rename as y_new
    } else if (ch == ';') {
      coord_string[index++] = NULL;
      y_new = atoi(coord_string);
      y_complete = true;
      index = 0;
      memset(coord_string, 0, sizeof(coord_string));
    }
    //EDIT: change to AND verification
    // Ends while-loop when true
    coord_complete = x_complete &amp;&amp; y_complete;
  }
}