Prime number checker in Python 3 - follow-up
0. Overview

Your code is well written and what it does is clear. However I will argue that if you want a drastic increase in performance, you need to switch your algorithm. Testing primality can be done in polynomial time, but is generally a problem which requires sophisticated math. The problem can be solved in polynomal time as shown by the AKS_primality_test. However there are far faster algorithms than this one. As you can see, it is not the easiest thing to understand without a background in higher mathematics.


A review of your algorithm
Show a probabilistic approach
Compare your algorithm, the probabilistic, and the isprime function from the primefac package.


1. Review

As your code is fairly short, there is not much to comment on. I really like that you use a docstring in the beginning of your code to document it. The code looks good.


Use the if __name__ == "__main__": module. It makes it easier to test and easier to import.
Some of the comments are unnecessary and there is too much space in the last return.
The num &lt;= 1 is a bit strange. It catches everything from inputing \$0\$ and \$1\$ to negative and decimal numbers. In my opinion it is better to treat negative numbers and non-integers with an error instead. Then we can explicitly remove \$0\$ and \$1\$ as special cases.  


One way to handle this could be 

try:
    int(num)
except ValueError:
    raise ValueError("Ops. Input must be a positive integer")
if int(num) != num or num &lt; 0:
    raise ValueError("Ops. Input must be a positive integer")

if num in [0, 1]: return False


The last line could also have been written as

if num &lt;= 1: return False


Since we have already tested that num =&gt; 0. However I prefer the first version as it is much clearer what it actually checks. You should always try to make it as clear as possible what you want to catch.

1.1 Some improvements on the algorithm

Say you check some number with your algorithm. If the number is not divisible by \$3\$ you do not need to ever check any multiples of \$3\$ again. Yet your code checks \$6\$, \$9\$ and so forth. A better approach would be to iterate over the numbers not divisible by \$2\$ or \$3\$. This removes the checking of \$2/3\$ of all numbers in comparison to only removing \$1/2\$. So, what numbers are not divisible by \$3\$ or \$2\$? Well all numbers are on the form \$6k+1\$, \$6k+2\$, \$6k+3\$, \$6k+4\$ or \$6k+5\$. Since they are either \$0\$, \$1\$, \$2\$, \$3\$, \$4\$ or \$5\$ numbers away from being a multiple of \$6\$. This means that only numbers on the form \$6k+1\$ or \$6k+5\$ are not divisible by \$2\$ or \$3\$.

Implementation is simple increase counter by \$6\$, test \$+1\$ and \$+5\$.

primes_to_remove = [2, 3, 5]
for prime in primes_to_remove:
    if num == prime: return True
    elif num % prime == 0: return False

# Look for a factor
limit = int(num**(0.5))+1
for multiple in range(6, int(num**(0.5))+1, 6):
    for k in [1, 5]:
        # If there is a factor
        if num % (multiple+k) == 0:
            # Its not a prime number
            return False


This can further be generalized by removing [2, 3, 5] as shown below

primes_to_remove = [2, 3, 5, 7, 11, 13, 19, 23, 29]
for prime in primes_to_remove:
    if num == prime: return True
    elif num % prime == 0: return False

# Look for a factor
limit = int(num**(0.5))+1
for multiple in range(30, int(num**(0.5))+1, 30):
    for k in [1, 7, 11, 13, 19, 23, 29]:
        # If there is a factor
        if num % (multiple+k) == 0:
            # Its not a prime number
            return False
return True


This idea of removing the first primes can again be modified into removing [2,3,5,7] and then check the remaining numbers. However the advantages of this method quickly diminish for larger primes as we are removing fewer and fewer numbers. As a last example, it is possible to only iterate over the primes. From the primesieve library we can import a prime generator.

from primesieve import Iterator

def is_prime_primegenerator(num):
    it = Iterator()
    prime = it.next_prime()

    # Iterate over the primes below sqrt(n)
    limit = int(num**(0.5))+1
    while prime &lt; limit:
        prime = it.next_prime()
        if num % prime == 0:
            print num, prime
            return False
    return True


This is the best we can do following down your path of checking primes from the smallest to the largest. It assumes however that the next_prime() is extremely fast. Which it luckily is. 

Using the 235 version of the sieve above, it gave me a \$2.5\$ times speed increase of your code. Putting it all together gives

def is_prime(num):
    '''Calculates whether num is a prime number,
    if it is return True otherwise return Flase'''

    try:
        int(num)
    except ValueError:
        raise ValueError("Ops. Input must be a positive integer")
    if int(num) != num or num &lt; 0:
        raise ValueError("Ops. Input must be a positive integer")

    # SPECIALCASE: These are special cases that are not primes
    if num in [0, 1]: return False

    primes_to_remove = [2, 3, 5, 7, 11, 13, 17, 19, 23, 29]
    for prime in primes_to_remove:
        if num == prime: return True
        elif num % prime == 0: return False

    # Look for a factor
    limit = int(num**(0.5))+1
    for multiple in range(30, int(num**(0.5))+1, 30):
        for k in [1, 7, 11, 13, 19, 23, 29]:
            # If there is a factor
            if num % (multiple+k) == 0:
                # Its not a prime number
                return False
    return True

if __name__ == '__main__':
    print is_prime(600851)


Using some quick comparisons it seems that the 235 version is the fastest for solving larger primes while 23 and the naive are pretty similar in running times.

               naive   23    235    primes
600851475151 | 117ms   71ms  40ms   19ms


2. Probabilistic primality test

A short explanation can be found on Wikipedia.


  Probabilistic tests
  
  Probabilistic tests are more rigorous than heuristics in that they
  provide provable bounds on the probability of being fooled by a
  composite number. Many popular primality tests are probabilistic
  tests. These tests use, apart from the tested number \$n\$, some other
  numbers a which are chosen at random from some sample space; the usual
  randomized primality tests never report a prime number as composite,
  but it is possible for a composite number to be reported as prime. The
  probability of error can be reduced by repeating the test with several
  independently chosen values of a; for two commonly used tests, for any
  composite \$n\$ at least half the a's detect n's compositeness, so \$k\$
  repetitions reduce the error probability to at most \$2^{−k}\$, which can be
  made arbitrarily small by increasing \$k\$.
  
  The basic structure of randomized primality tests is as follows:
  
  
  Randomly pick a number \$a\$.
  Check some equality (corresponding to the chosen test) involving \$a\$ and the given number \$n\$. If the equality fails to hold true, then \$n\$
  is a composite number, a is known as a witness for the
  compositeness, and the test stops.
  Repeat from step 1 until the required accuracy is achieved.
  
  
  After one or more iterations, if \$n\$ is not found to be a composite
  number, then it can be declared probably prime.


The important bit is the three steps at the bottom. We put our number through some test and if it passes there is a \$1/2\$ chance of it being composite. After passing \$k\$ tests, the chances of being composite is \$2^{-k}\$. When big banks check for primality they often use a probabilistic prime test where \$k\$ is around \$80\$. The chances of a composite passing \$80\$ tests is just

$$
P_{80}(\text{composite}) = 2^{-80} = \frac{1}{1208925819614629174706176}
$$

So if you test \$1208925819614629174706176\$ numbers, on average one of them will be a composite passing all the tests. Below I will show a simple implementation of the Miller-Rabin primality test. It is one of the fastest and simplest ways to implement a primetest. This algorithm can be divided into three steps:


Generate a small list of primes below some limit (I used 1 million)
Check if the prime number is even, and some other small tests. Then check if it is in the primeset. 
If the prime is bigger than the limit apply the Miller-Rabin primality test \$25\$ times. The number \$25\$ is arbitrary, however it does not need to be particularly big as the chances of a composite slipping through is \$2^{-k}\$.


The reason for step 1 is both because it is faster, but also because the Miller-Rabin test have a harder time detecting small primes. I imported the fastest prime_generator I could find through google. However if you allow for external libaries primesieve is faster. However generating primes is just a small part of the excecution time, and not worth optimizing further.
\${}{}\$

import numpy as np

def primesbelow(n):
    # https://stackoverflow.com/questions/2068372/fastest-way-to-list-all-primes-below-n-in-python/3035188#3035188
    """ Input n&gt;=6, Returns a array of primes, 2 &lt;= p &lt; n """
    sieve = np.ones(n/3 + (n%6==2), dtype=np.bool)
    sieve[0] = False
    for i in xrange(int(n**0.5)/3+1):
        if sieve[i]:
            k=3*i+1|1
            sieve[      ((k*k)/3)      ::2*k] = False
            sieve[(k*k+4*k-2*k*(i&amp;1))/3::2*k] = False
    return np.r_[2,3,((3*np.nonzero(sieve)[0]+1)|1)]


smallprimeset = set(primesbelow(100000))
_smallprimeset = 100000

def isprime(n, precision=25):
    # http://en.wikipedia.org/wiki/Miller-Rabin_primality_test#Algorithm_and_running_time
    try:
        n = abs(int(n))
    except ValueError:
        print("Input must be a non-negative integer")
    if n in [0, 1]:
        return False
    elif n in [2, 3, 5]:
        return True
    elif n % 2 == 0:
        return False
    elif n &lt; _smallprimeset:
        return n in smallprimeset

# Miller-Rabin primality test

d = n - 1
s = 0
while d % 2 == 0:
    d //= 2
    s += 1

for repeat in range(precision):
    a = random.randrange(2, n - 2)
    x = pow(a, d, n)

    if x == 1 or x == n - 1: continue

    for r in range(s - 1):
        x = pow(x, 2, n)
        if x == 1: return False
        if x == n - 1: break
    else: return False
return True


3. Comparison

I used 


pip install primefac



To be able to use the isprime function from the primefac package. Then I did some simple primality testing on a few semi-large numbers. 

All the tests where done a \$100\$ times and then i took the average. I did a \$1000\$ averages for Miller-Rabin and primefac for better accuracy. There is no need to test composite numbers, because all the implementations stop once a prime has been found. All the tests are therefore done on primes.

    number              naive             23       235    primegen     miller    primefac
    -----------------------------------------------------------------------------------------
             60085159     0.69 ms    1.09 ms   0.47 ms     1.02 ms    0.25 ms    0.24 ms
           6008514763       22 ms      61 ms      7 ms      3.8 ms   0.104 ms    0.070 ms
          60085147517       56 ms      30 ms     12 ms      6.5 ms   0.072 ms    0.090 ms
         600851475151      283 ms     281 ms    155 ms     56 ms     0.364 ms    0.331ms
    99194853094755497   117328 ms  113053 ms  58010 ms  19117 ms     0.638 ms    0.239180 ms
    -----------------------------------------------------------------------------------------


As you can see you do fairly well for small values. For \$60085159\$ your code is about \$2.75\$ times as slow as the Miller-Rabin. However as the values increase so does the difference. For \$600851475151\$ your code is about \$777\$ times slower. Finally for \$99194853094755497\$ the Miller-Rabin is \$183899\$ times faster.

There might be something wrong with my testing since the 23-version is about as fast as the naive implementation (yours). However the 235 is a simple speed increase. If you want a drastic improvement however you need to switch to another implementation. Either use a library which has a builtin isprime function, or use a probabilistic approach: Fermat primality test, Miller-Rabin, Solovay-Strassen primality test, Frobenius primality are just some of the many fast implementations.