I think this works

brainfuck.py

@@ -100,14 +100,17 @@ def compile(program):
     elif char == ',':
       output.read()
     elif char == '[':
+      # TODO: this won't work if there are other characters in the input
       output.jump(pairs[i], True)
     elif char == ']':
       output.jump(pairs[i], False)
   output.append('select-window -t :=0')
   return output.to_string()
 
 
-program = '++++++++[>++++[>++>+++>+++>+<<<<-]>+>+>->>+[<]<-]>>.>---.+++++++..+++.>>.<-.<.+++.------.--------.>>+.>++.'
+with open(sys.argv[1]) as f:
+  program = f.read()
+
 comp = compile(program)
 print(comp)
 with open(sys.argv[1], 'wt') as o:

main.py

@@ -174,11 +174,14 @@ def compile_if(self, func):
   cb = func.cond()
   for expr in self.body:
     expr.compile_to(func)
+    func.pop_stack()
   goto = func.goto()
   cb()
   for expr in self.orelse:
     expr.compile_to(func)
+    func.pop_stack()
   goto()
+  func.push_constant(0)
 ast.If.compile_to = compile_if
 
 def compile_boolop(self, func):
@@ -201,8 +204,10 @@ def compile_while(self, func):
   cb = func.cond()
   for expr in self.body:
     expr.compile_to(func)
+    func.pop_stack()
   func.jump(startindex)
   cb()
+  func.push_constant(0)
 ast.While.compile_to = compile_while
 
 def compile_compare(self, func):
@@ -231,6 +236,7 @@ def compile_func(self, program):
     expr.compile_to(func)
     func.pop_stack()
   if type(self.body[-1]) is not ast.Return:
+    func.push_constant(0)
     func.switch_back()
   func.write('select-window -t :=0')
 ast.FunctionDef.compile_to = compile_func
@@ -246,6 +252,7 @@ def compile_assign(self, func):
   self.value.compile_to(func)
   name = self.targets[0].id
   func.set_variable(name)
+  func.push_constant(0)
 ast.Assign.compile_to = compile_assign
 
 def compile_name(self, func):
@@ -254,6 +261,7 @@ def compile_name(self, func):
 
 ast.Eq.compile_to = lambda self, func: func.maths_op('==')
 ast.NotEq.compile_to = lambda self, func: func.maths_op('!=')
+ast.Mod.compile_to = lambda self, func: func.maths_op('%')
 ast.Lt.compile_to = lambda self, func: func.maths_op('<')
 ast.Gt.compile_to = lambda self, func: func.maths_op('>')
 ast.Add.compile_to = lambda self, func: func.maths_op('+')
@@ -303,6 +311,7 @@ def compile_module(self, program):
       expr.compile_to(program)
     else:
       expr.compile_to(program.main)
+      program.main.pop_stack()
 
   program.main.write('select-window -t :=0')
 

program.py

@@ -1,4 +1,10 @@
-def func(a):
-  return a * 2
+def is_prime(num):
+  i = 2
+  while i < num:
+    if num % i == 0:
+      return 0
+    i = i + 1
 
-print(func(5))
+  return 1
+
+print(is_prime(13))