Let's write a Minifier
Python 2.7, 2013 score
This program can be used as reference, and you are allowed to take the following code and modify it and then post it in your own solutions.
In hindsight, I maybe should have used regex for the quote handling too, but I think in its current state it may be enough to jump-start people into the problem.
Why I chose Python 2.7:  I thought it would be easier to test to see if I made the program crash via the exec keyword.
This code intakes the program as in.txt.
I figured I should at least get the ball rolling for whoever want to participate by writing a quote parser (that also happens to handle comments) and a brief example on how regex, when combined with the quote parser can really change the game in terms of complexity of this problem.
Note: there is still plenty of room for improvement in this minifier.  Like you could play around with indentation, variable names, and removing the parenthesis when they're being used my keywords, like print or yield.
import re

with open(&quot;in.txt&quot;,&quot;r&quot;) as fi:
    code = fi.read()

class QuoteHandler():
    def __init__(self):
        pass
    def loadCode(self,code):
        quoteFlag = False
        currentQuoteChar = &quot;&quot;
        ignoreNext = False
        inEndLineComment=False
        startLocation = 0

        self.reAddStrings = []

        outStr = &quot;&quot;
        
        for i, character in enumerate(code):
            if ignoreNext:
                ignoreNext = False
            elif inEndLineComment:
                if character in &quot;\r\n&quot;:
                    inEndLineComment=False
            elif character == &quot;#&quot; and not quoteFlag:
                inEndLineComment = True
            elif character in &quot;'\&quot;&quot; and (currentQuoteChar == character or not quoteFlag):
                if quoteFlag:
                    self.reAddStrings.append(code[startLocation+1:i])
                else:
                    currentQuoteChar = character
                    startLocation = i
                quoteFlag = not quoteFlag
            elif character == &quot;\\&quot;:
                ignoreNext = True
                
            if not inEndLineComment and not quoteFlag:
                outStr+=character                
        return outStr

    def find_all_locations(self,substr,code):
        return [m.start() for m in re.finditer(substr, code)]
    
    def unloadCode(self,code):
        temp = self.reAddStrings[::-1]
        for i, location in enumerate(list(self.find_all_locations('&quot;',code))[::-1]):
            code = code[:location] + &quot;\&quot;&quot; + temp[i] + code[location:]
        return code

def applyRegexes(code):#\w here?
    operatorRegexCleaner = [&quot;([\d\/*\-\&quot;=,'+{}:[\](\)])&quot;,&quot;[ \t]+&quot;,&quot;(\w)&quot;]
    regexes = [
        [''.join(operatorRegexCleaner),r&quot;\1\2&quot;],
        [''.join(operatorRegexCleaner[::-1]),r&quot;\1\2&quot;],#removes whitespace between operators
        [&quot;\n\s*\n&quot;,&quot;\n&quot;]#removes empty lines
    ]
    for regex in regexes:
        code = re.sub(regex[0],regex[1],code)
    return code

qh = QuoteHandler()
code = qh.loadCode(code)
code = applyRegexes(code)
code = qh.unloadCode(code)
print(code)
exec(code)

Output of program:
def factor(factor_number):
    for n in range(2,factor_number):
        if factor_number % n==0:    
            yield(n)
def gcd(a,b):
    &quot;&quot;&quot;Calculate the Greatest Common Divisor of a and b.

    Unless b==0, the result will have the same sign as b (so that when
    b is divided by it, the result comes out positive).
    &quot;&quot;&quot;
    while b:
         a,b=b,a%b 
    return a
class Apricot:
    def __init__(self):
        self.mold=False
    def get(self):
        return self.mold
    def update(self):
        self.mold=not self.mold
    def blue(self):return5
def tell_me_about_these_numbers(*a):
    print(&quot;%d is the first number!&quot; % a[0])
    print(&quot;{} / 3 is {}&quot;.format(a[0],a[0]/3.))
    myFavorate=Apricot()
    for number in a:
        print list(factor(number))
        myFavorate.update()
    print[gcd(a,b)for a,b in zip(a[:-1],a[1:])]
    print(myFavorate.get())
tell_me_about_these_numbers(5,6,9,45,200)
print&quot;Let's play with scope!&quot;
a,b=10,9
def randomFunction(a):
    print(a)
randomFunction(b)
print(a)
for a in range(100):
    b+=a
print(a)
print(b)
li=[]
for i in range(10):
 li.append(i*2)
print(li)
print([i*2for i in range(10)])
a=c=b=d=e=f=g=h=i=j=k=l=m=n=o=p=q=r=s=t=u=v=w=x=y=z=5
print(a)
a-=1
print(a)
g=10
print(str(10**g+5)[::-1])
def blue_fish(a):
    def blue_fish(a):
        def blue_fish(a):
            return a
        a+=1
        return blue_fish(a)
    a-=1
    return blue_fish(a)
print(blue_fish(10))
def blue_fish(a):
    if a==0:
        return&quot;0&quot;
    return&quot;1&quot; +blue_fish(a-1)
print(blue_fish(5))
blue_fish=lambda a,b,c:a*b*c
print(blue_fish(1,2,3))
blue_fish=lambda*a:reduce(lambda a,b:a*b,a)
print(blue_fish(1,2,3))
print(max([[6,1],[5,2],[4,3],[3,4],[2,5],[1,6]],key=lambda a:a[1]))
print(zip(*[[1],[2],[3],[4],[5]]))
print&quot;Now let's test to see if you handle quotes correctly:&quot;
print&quot;test \'many diffent\' \&quot;types of \&quot; quotes, even with \' \&quot; trailing quotes&quot;
print&quot;&quot;&quot;

Multi line quotes are great too!

&quot;&quot;&quot;
a=&quot;&quot;&quot; ::
one more multi-line quote won't hurt
&quot;&quot;&quot;
print a