Simple Arduino script to set pins high, low, input, pull up, or analog/servo, clock in or out data, with timing/start/stop, and read all or a single pin back via serial IO. NOTE: THIS HAS BEEN REPLACED BY https://github.com/JamesNewton/Arduino_Dynamixel_Stepper_Controller

PinReadWrite.ino

/*
PinReadWrite.ino
//20170512 initial version
//20170517 uS timing (was mS), vars are longs, i2C start/stop, and clock IN data w/.
//20201002 Returns valid JSON.

Simple Arduino script to set pins high, low, input, pull up, or analog/servo, 
clock out data with timing, and read all or a single pin back via serial IO. 
Written for the tiny-circuits.com TinyDuino in the end effector of the 
Dexter robot from HDRobotic.com, but generally useful to turn the Arduino
into a tool for generating test signals, and reading back results. Not as 
powerful as the busPirate, but more flexible in some ways and much easier to
operate. Not a replacement for Firmata as this is intended to be used by a 
human directly via serial monitor or terminal, not from a program.
Commands:
#?  //return binary value of digital pin, and value for analog input if exists
    //if # and default # (set by comma command, see below) are zero or ommitted  
    //? returns all pins and analog values at once.
#I  //set pin # to an input. e.g. 3I
#P  //set pin # to an input with internal pullup. 4P
#H  //set pin # to a high output. 3H4H
#L  //set pin # to a low output. 5L4L3L
#D  //delay # microseconds between each command, with a minimum of about 47uS
#,  //comma. Saves pin # as the default pin for all commands e.g. 3,HLHLHL
#A  //set pin # to an analog output with value. Only PWM outputs will respond.
    // use with comma command e.g. 5,120A will put 120 on pin 5
#S  //Set Timer1,2 divide mode. Default 4S=244Hz, 5S is 122Hz on 3,11 61Hz on 9,10
    //has no effect on Timer0 pins 5 and 6, they stay at 244Hz
_-  //low high clocked puts out the set of low and high signals shown on # with
    // a clock on #, e.g. 5,11-__-_--_ clocks out 10010110 on pin 11, with clock 
    // pulses on pin 5. Clock is currently falling edge only. 
.   //reads data back from # while clocking #, 
    // e.g. 5L 11H 5,11-__-_--_. ......... clocks out 10010110, gets the ack, and 
    // then 8 bits of data and a final ack.
(   //I2C start with # as SDA and #, as SCL
)   //I2C stop with # as SDA and #, as SCL. Pins left floating pulled up.
    // e.g. 5,11(-__-_--_. .........) starts, 10010110, gets ack, data, ack, stop

Commands can be strung together on one line; spaces, tabs, carrage returns and line feeds 
are all ignored. If no n is specified, value previously saved by , is used.

Examples:

?
//returns something like: {"?":["10010000001111",739,625,569,525,493,470]}
// where 10010000001111 shows the binary value of each pin, from 0 to 14. Pin 0 is first
// 739,625,569,525,493,470 are the values read from each analog channel 0 to 5

1?
//returns something like: {"1":[1,459]} where 1 is the binary value of pin 1 and 
//459 is the analog value of channel 1

6?
//returns something like {"6":[0]} which is the value of pin 6 (no analog)

4L 6H 5,120A
//(nothing returned) Drives pin 4 low, pin 6 high and puts a PWM / Analog value of 120 on pin 5
//this also saves pin 5 as the default pin for all commands from now on

240A
//(nothing returned) assuming prior command was 5,120A put 240 out pin 5 as new analog value

5S 3,100A
//(nothing returned) The normal PWM output is 244Hz which is a bit to fast for servoes. 
//The S command sets the divisor for Timer1 and Timer2. 4S is the default, 5S drops the frequency
//of pins 3 and 11 to 122Hz and pins 9 and 10 to 61Hz allowing servos to work just fine.
//After 5S, 47A is center with a 1.5mS pulse width, 31A 0.5mS or far CCW, 62A is 2mS; far CW.
//So this only allows 62-31 or about 30 steps for 90' or 3' resolution. For many jobs, it's enough.

?
//assuming 5, has been recieved before, returns just the value of pin 5 and analog 5

0,
//(nothing returned) clears saved pin, ? now returns all pins.

1000D 5,LHLHLHL
//(nothing returned) delay is 1 millisecond between commands. So pin 5 pulse 3 times at ~200Hz
//Actually about 1.04mS because of the time it takes to recieve and interpret each command. 
//The delay command is also useful for making sure all the commands on a line arrive before they are 
//excecuted. e.g.:
10000D 3D 5,LHLHL?
//will put out 2 pulses at 50uS per pulse or 10KHz without the 10000D, they are 163uS
//The time it takes to interpret a command is about 47uS so 3D makes it 50. For 100uS
//53D would work. Take the uS delay you want and subtract 47.
//With larger delays, the error is consistant but has relativly less effect.
// Note that the CYCLE_DELAY is not used as long as new characters are available.

*/

#define ANALOG_PINS 6
#define DIGITAL_PINS 14
//#define BAUD_RATE 57600
//might not work at 115200
#define BAUD_RATE 115200
#define CYCLE_DELAY 100

unsigned long n,p,d;
char cmd;

/*
https://playground.arduino.cc/Code/PwmFrequency
Pins 9 and 10 run at 31250Hz from Timer1 which is only used for servo. 
3 and 11 are on Timer2, 5 and 6 on Timer0. These are also used for delay, millis, etc...

So limiting our changes to Timer1 and pins 9 and 10 allows us to still have timing.
 switch(divisor) {
      case 1: mode = 0x01; break;   //31250Hz
      case 8: mode = 0x02; break;   //3906.25Hz
      case 64: mode = 0x03; break;  //488.28125Hz //default?
      case 256: mode = 0x04; break; //122.0703125Hz
      case 1024: mode = 0x05; break;//30.517578125Hz
    }
      TCCR1B = TCCR1B & 0b11111000 | mode;

https://www.arduino.cc/en/Tutorial/SecretsOfArduinoPWM
Says only Timer0 is used for delay and millis... 
We can try changing 3 and 11 on Timer2 
Different divisors, so compensate
T2  T1 / Freq
0x01 1 1 31250
0x02 2 8 3906.25
0x03 2 32  976.5625
0x04 3 64  488.28125 //default?
0x05 3 128 244.140625
0x06 4 256 122.0703125
0x07 5 1024  30.517578125
TCCR2B = TCCR2B & 0b11111000 | mode;

if (n>2) n--; //1,2,2,3,4,5,6
if (n>3) n--; //1,2,2,3,3,4,5

formula is f = clock / (510 * mode) where clock=16MHz

If you mess with TCCR0B, delay can be compensated as follows
0x01: delay(64000) or 64000 millis() ~ 1 second
0x02: delay(8000) or 8000 millis() ~ 1 second
0x03: delay(1000) or 1000 millis() ~ 1 second //default
0x04: delay(250) or 250 millis() ~ 1 second
0x05: delay(62) or 62 millis() ~ 1 second
(Or 63 if you need to round up.  The number is actually 62.5)

void setPin9_10PWMFreq(freq) {
  
}

*/

void delayus(unsigned long us) {
  if (us>10000) { //can't delayMicroseconds() more than 16838
    delay(us/10000);
    us=us % 10000;
    }
  delayMicroseconds(us);
  }

void setup() {
  Serial.begin(BAUD_RATE);
  n=0; //number
  p=0; //pin number
  d=2; //delay. Default is 2uS or 250KHz
 }

void loop(){
  while (Serial.available() > 0) { //if data has arrived
    int c = Serial.read(); //get the data
    if ('0' <= c && c <= '9') { //if it's a digit
      n = (c-'0') + n*10; //add it to n, shift n up 1 digit
      continue; //and loop
      }
    cmd = char(c); //wasn't a number, must be a command
    if (' '==cmd || '\t'==cmd) { continue;} //whitespace does nothing
    if (','==cmd) { p=n; n=0; continue;} //save n to p, clear n, loop
    if (0==n) {n=p; } //if we don't have a value, use the prevous pin number
    switch (cmd) {
      case '?': //get information
        Serial.print("{"); //optional, just to signal start of data
        if (0==n) { //if we didn't have a number selecting a pin
          Serial.print("\"?\":[\""); //optional, just to signal start of data
          for (int p = 0; p < DIGITAL_PINS; p++) { //get all the pins
            //n = digitalRead(p) + n<<1;   //convert to binary number
            Serial.print(digitalRead(p));//and also print.
            }
          Serial.print("\"");
          //Serial.print(n); //print the binary value of all pins
          for (int p = 0; p < ANALOG_PINS; p++) { //also check all the analog
            Serial.print(",");
            Serial.print(analogRead(p));
            }
          }
        else {
         Serial.print("\"");
         Serial.print(n);
         Serial.print("\":[");
         Serial.print(digitalRead(n)); //just that one pin
         if (ANALOG_PINS > n) { //if there is an analog channel
            Serial.print(",");
            Serial.print(analogRead(p)); //also return it
            }
         }
        Serial.println("]}");
        break;
      case '-': 
      case 'H': //set pin n output high
        pinMode(n,OUTPUT);
        digitalWrite(n,HIGH);
        break;
      case '_': 
      case 'L': //set pin n output low
        pinMode(n,OUTPUT);
        digitalWrite(n,LOW);
        break;
      case 'I': //set pin n input
        pinMode(n,INPUT);
        break;
      case 'P': //set pin n input with pullup
        pinMode(n,INPUT_PULLUP);
        break;
      case '.': //clock in data from n via p
        pinMode(n,INPUT_PULLUP); //make n input with pull now
        break;
      case '(': //I2C start, data low while clock high
        pinMode(n,OUTPUT);
        digitalWrite(n,HIGH); //data high
        pinMode(p,OUTPUT); //setup clock (if not already)
        digitalWrite(p,HIGH); //send clock high
        delayus(d); //wait
        digitalWrite(n,LOW); //data low
        delayus(d); //wait
        digitalWrite(p,LOW); //send clock low
        continue; //no further processing
        break;
      case ')': //I2C stop, data low while clock high
        pinMode(n,OUTPUT); //data may be floating high (input from slave)
        digitalWrite(n,LOW); //so we need to drive it low
        pinMode(p,OUTPUT); //setup clock (if not already)
        digitalWrite(p,LOW); //send clock high
        delayus(d);
        pinMode(p,INPUT_PULLUP); //clock floats high
        delayus(d);
        pinMode(n,INPUT_PULLUP); //data floats high
        continue; //no further processing
        break;
      case 'A': //set pin p to analog output value n
        pinMode(p,OUTPUT);
        analogWrite(p,n);
        break;
      case 'D': //delay n ms per instruction
        d=n;
        break;
      case 'S': //PWM speed 5 allows servos, 4 is default.
        TCCR2B = TCCR2B & 0b11111000 | n; // Timer2, pins 3 and 11
        //Compensate, 
        if (n>2) n--; //1,2,2,3,4,5,6
        if (n>3) n--; //1,2,2,3,3,4,5
        TCCR1B = TCCR1B & 0b11111000 | n; // Timer1, pins 9 and 10
        break;
      case '\n': 
      case '\r':
        n=0; cmd=0; //clear command and value at end of line.
        continue; //loop now, no delay
        break; //shouldn't get here
      default:
        Serial.print("\"");
        Serial.print(n);
        Serial.print(cmd);
        Serial.println("?\"");
      }
    if ('0'>cmd || '_'==cmd) {//was it punctuation?
      digitalWrite(p,HIGH); //raise the clock
      pinMode(p,OUTPUT); 
      delayus(d/2); //half delay
      if ('.'==cmd) {Serial.print(digitalRead(n));}
      digitalWrite(p,LOW); //drop the clock
      delayus(d/2); //half delay
      }
    else {
      n=0; //zero out value for next command.
      delayus(d); //wait a bit for the next cycle.
      }
    //p is NOT cleared, so you can keep sending new commands only
    cmd=0; //done with command.
    }
  delayus(CYCLE_DELAY);
  }

Updated to return valid JSON in all cases.
Unknown command result in a string (which is valid) e.g. "a" will return "0a?"
"?" or "0,?" (if a default has been previously set) returns {"?":["10010000001111",739,625,569,525,493,470]}
Numbers which could be an analog port or a digital port return e.g. {"2":[0,431]} and if there is only a digital port, e.g. {"10":[1]}

For a much more advanced version with support for Dynamixel servos and Stepper motors, see:
https://github.com/JamesNewton/Arduino_Dynamixel_Controller