from pythran import typing

Pythran is currently part of OpenDreamKit, a project that aims at improving the open source computational mathematics ecosystem.

The goal of Pythran is indeed to improve some Python kernel computations, but there's something that actually makes Pythran difficult to use for new comers. What is it? Let's have a look at the following Python code, inspired by a stack overflow thread:

# create_grid.py

#pythran export create_grid(float [])

import numpy as np
def create_grid(x):
    N = x.shape[0]
    z = np.zeros((N, N))
    z[:,:,0] = x.reshape(-1,1)
    z[:,:,1] = x
    fast_grid = z.reshape(N*N, 3)
    return fast_grid

An attempt to compile it with Pythran would return a very long C++ template instantiation trace, with very little clue concerning the origin of the problem.

> pythran create_grid.py
In file included from /tmp/tmpP0xYa2.cpp:10:
In file included from ./pythran/pythonic/include/types/ndarray.hpp:12:
In file included from ./pythran/pythonic/include/utils/broadcast_copy.hpp:4:
./pythran/pythonic/include/types/tuple.hpp:122:25: error: array is too large (18446744073709551615 elements)
      value_type buffer[N ? N : 1];
                        ^~~~~~~~~
./pythran/pythonic/include/types/numpy_iexpr.hpp:57:26: note: in instantiation of template class 'pythonic::types::array<long, 18446744073709551615>' requested here
      array<long, value> _shape;
                         ^
[...]
                                    ^
./pythran/pythonic/include/utils/seq.hpp:19:19: note: use -ftemplate-depth=N to increase recursive template instantiation depth
    struct gens : gens<N - 1, N - 1, S...> {
                  ^
3 errors generated.
CRITICAL Cover me Jack. Jack? Jaaaaack!!!!
E: ('error: Command "clang++-3.8 -DNDEBUG -g -fwrapv -O2 -Wall -fno-strict-aliasing -g -O2 -fPIC -DUSE_GMP -DENABLE_PYTHON_MODULE -D__PYTHRAN__=2 -I./pythran -I./pythran/pythonic/patch -I/home/serge/.venvs/pythran/local/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c /tmp/tmpP0xYa2.cpp -o /tmp/tmpM2Eiso/tmp/tmpP0xYa2.o -std=c++11 -fno-math-errno -w -fwhole-program -fvisibility=hidden" failed with exit status 1',)

What we now have is a slightly friendlier message:
> pythran create_grid.py
CRITICAL You shall not pass!
E: Dimension mismatch when slicing `Array[2d, float]` (create_grid.py, line 7)

Indeed, the correct declaration for z was z = np.zeros((N, N, 3)).

A Quick Glance at Pythran Typing System

As you probably know, Python uses a dynamic type system, often called duck typing: what matters is not the type of an object, but its structure, i.e. the available methods and fields: If it walks like a duck and talks like a duck, then it's a duck. That's a kind of structural typing.

On the opposite side C++ uses a static type system, and if you adhere to OOP [1] you may require an object to derive from the Duck class to be considered a duck; That's a kind of nominal typing.

Pythran uses a trick to make both world meet: ad-hoc polymorphism, as supported in C++ through template meta programing. Upon a template instantiation, there's no type name verification, only a check that given methods and attributes make sense in the current context. And that's exactly what we need to get closer to Python typing!

This all is very nice, except in the case of a bad typing. Consider this trivial Python code:

def twice(s):
    return s * 2

integer, for instance str, list, int. The C++ equivalent would be (taking into account move semantics):

template<typename T>
auto twice(T&& s) {
    return std::forward<T>(s) * 2;
}

In Python's case, type checking is done at runtime, during a lookup in s for a __mul__ magic method. In C++ it's done at compile time, when performing instantiation of twice for a given type value of T. What lacked was a human-readable error message to warn about the coming winter. And that's exactly the topic of this post ;-)

A Few Words About MyPy

Type hints, as introduced by PEP484, make it possible to leverage on arbitrary function annotations introduced by PEP 3107 to specify the expected type of a function parameter and its resulting return type. No check occur at runtime, but a third party compiler, say MyPy can take advantage of these hints to perform an ahead-of-time check. And that's great.

Note

In this post, we use the type annotation introduced by PEP484 and used in MyPy to describe types. int is an integer, List[str] is a list of string and so on.

So, did we trade #pythran export twice(str) for def twice(s: str):? No. Did we consider the option? Yes. First there's the issue of MyPy only running on Python3. It can process Python2 code, but it runs on Python3. We've been struggling so much to keep Python2.7 compatibility in addition to the recent addition of broader Python3 support. We're not going to leave it apart without good reasons.

Note

It also turns out that the typing module has a different internal API between Python2 and Python3. This makes it quite difficult to use for my purpose. What a joy to discover this when you think you're done with all your tests :-/

No, the main problem is this MyPy issue that basically states that Numpy does not fit into the model:

Of course, the best behavior would be to provide a stub for Numpy, but some features in Numpy make it difficult to provide a good stub

Meanwhile, someone that did not read this issue wrote A Numpy stub for MyPy. It turns out that it' **is** a pain, mostly due to the flexibility of many Numpy methods.

Additionally, Pythran currently infers type inter-procedurally, while MyPy requires type annotation on every functions, to keep the problem within reasonable bounds.

But wait. MyPy author did his PhD on the subject, and he now works hand in hand with Guildo van Rossum on the subject. Is there any chance for us to do a better job? Let's be honest. There is not.

What can we do in such a situation? Take advantage of some extra assumptions Pythran can afford. We focus on scientific computing, all existing types are known (no user-defined types in Pythran) and we only need to handle small size kernels, so we can spend some extra computing resources in the process.

A Variant of Hindley-Milner for Pythran

Hindley-Milner (HM) is a relatively easy to understand type system that supports parametric polymorphism. A simple implementation has been written in Python, but not for Python, even not for the subset supported by Pythran.

The main issue comes with overloaded functions. Consider the map function: it has a varying number of parameters, and for a given number of parameters, two possible overloads exist (the first argument being None or a Callable). Some extra stuff are not as critical but also important: it's not possible to infer implicit option types (the one that comes with usage of None). Ocaml uses Some as a counterpart of None to handle this issue. but there's no such hint in Python (and we don't want to introduce one).

Still, the whole subject of typing is reaaaaaalllllly difficult, and I wanted to stick as close as possible to Hindley-Milner because of its simplicity. So what got introduced is the concept of MultiType, which is the type of an object that can hold several types at the same time. So that's not exactly a UnionType which is the type of an object that can be of one type among many. The difference exists because of the situation described by the following code:

def foo(l, m=1):
    pass

foo(1)
foo(2, 3)

In that case foo really has two types, namely Callable[[Any], None] and Callalble[[Any, Any], None]. That's what MultiType represents.

Handling Overloading

So we handle overloading through a unique object that has a specific type, a MultiType that is just a list of possible types.

Abusing from Multiype can quickly make the combinatorics of the type possibilities go wild, so we had to make a decision. Consider the following code:

def foo(x, y):
    return y in x

The in operator could be implemented as a MultiType, enumerating the possible valid signature (remember we know of all possible types in Pythran):

  • Callable[[List[T0], T0], bool], a function that takes a list of T0 and a T0 and returns a boolean,
  • Callable[[str, str], bool], a function that takes two strings and returns a boolean,

And so on, including for numpy arrays, but we'll comme back to this later and assume for now we only have these two types. So what is the type of foo? From the x in y expression, HM tells us that x can be a list of T0, and in that case y must be of type T0, or x is a string and so must be y. And in both cases, a boolean is returned.

We could consider both alternatives, follow the two type paths and in the end, compute the signature of foo as a MultiType holding the outcome of all paths. But that could mean a lot! What we do is an over-approximation: what is the common structure between List[T0] and str? Both are iterable, therefeore x must be iterable. Nothing good comes from T0 and str, and bool compared to bool results in a bool, so in the end foo takes an iterable and any value, and returns a boolean. That's not as strict as it could be, but that's definitively enough. However our type system is no longer sound (it does not reject all bad program).

In order to make it easier to perform this approximation, we chose a dedicated representation for containers. In our type system (oh, it's named tog by the way, so in the tog type system), containers are roughly described as a tuple of (name, sized, key, value, iter):

  • a List[T0] is considered as (List, Sized, int, T0, T0)
  • a Set[T0] is considered as (Set, Sized, NoKey, T0, T0)
  • a Dict[T0, T1] is considered as (Dict, Sized, T0, T1, T0)
  • a str is considered as (Str, Sized, int, Str, Str)
  • a Generator[T0] is considered as (Generator, NoSized, NoKey, T0, T0)

As a consequence, an Iterable[T0], to be compatible with the over-approximation defined above, is a (Any, Any, Any, Any, T0).

Handling Option Types

When HM runs on the following Python code:

def foo(a):
    if a:
        n = 1
        range(n)
        return n
    else:
        return None

It runs into some troubles. The return from the True branch sets the return type of foo to int but the one from the False branch sets it to None. How could we make this unification valid? Option types are generally described as a parametric type, Optional[T0]. To be able to unify int and None, we would instead need to unify Optional[int] and None, thus marking n as Optional[int], which does not work, because range expects an int.

The solution we have adopted is to make type inference control-flow sensitive. When meeting an if, we generate a new copy of the variable environment for each branch, and we merge (not unify) the environments.

Likewise, if the condition is explicitely a check for None, as in:

if a is None:
    stuff()
else:
    return stuff(a)

the environment in the True branch holds the None type for a, and the int type in the False branch. This could be improved, as we support only a few patterns as the condition expression, there is something more generic to be done there.

This even led to improvement in our test base, as the following code was no longer correct:

def foo(x):
    v = x.get(1)
    return v + 1

Type inference computes that v is of type Optional[T0], which is not compatible with v + 1 and a PythranTypeError is raised. A compatible way to write this would be:

def foo(x):
    v = x.get(1)
    if v is None:
        pass  # or do stuff
    else:
        return v + 1

Handling Type Promotion

It's not uncommon to find this kind of code:

l = []
l.append(0)
l.append(3.14)

And there's nothing wrong with this in Python, but is this a type error for Pythran? In classical HM systems, that's a type error: [] is of type List[TO], list.append is of type Callable[[List[T0], T0], None] so unification sets T0 to int after first append, and fails upon the second append because unification between an int and a float fails.

Looking back in Python typing history, it seems that shedskin made the decision to consider it's not an error (see the blogpost announce on the topic. Several test cases of Pythran test suite would fail with a stricter typing, so let's try to achieve the same behavior as Shedskin, within HM.

The trick here is to consider a scalar as a tuple of four elements [0], one per scalar type we want to support. And then apply the following rule: the actual type of the scalar is the type of the first non variable type, starting from the lower index. Under that assumption,

  • a bool is a (T0, T1, T2, bool)
  • an int is a (T0, T1, int, T2)
  • a float is a (T0, float, T1, T2)
  • a complex is a (complex, T0, T1, T2)

When unifying an int with a float, regular unification yields (T0, float, int, T2) which is a float according to the previous definition.

If we want to enforce an int, say as argument of range, then we can define strict_int as (no-complex, no-float, int, T0) which still allows up-casting from bool to int but prevents up-casting from int to float.

Note

numpy introduces many sized type for integers, floating point numbers and complex numbers, with a set of rules to handle conversion between one and the other. As these conversions are generally possible in numpy (i.e. they dont raise a TypeError), we just use four scalar types: bool`, ``int, complex and float. long is merged into int, which also makes the Python2/3 compatibility easier.

Handling NDArray Type

numpy.ndarray is the corner stone of the numpy package. And it's super-flexible, allowing all kinds of broadcasting, reshaping, up-casting etc. Even if Pythran is far from supporting all of its features, it does support a wide set. The good news is that Pythran supports a lower version of ndarray, where the number of dimensions of an array does not change: it cannot be reshaped in place. For instance the C++ type returned by numpy.ones((10, 10)) is types::ndarray<double /*dtype*/, 2 /*nbdim*/>.

We've extended the typing module to provide NDArray. For Pythran, the Python equivalent of the above C++ type is NDArray[float, :, :].

And as we want it to be compatible with the way we defined an Iterable, an NDArray is actually a:

  • List[T0] is considered as (List, Sized, int, T0, T0)
  • Dict[T0, T1] is considered as (Dict, Sized, T0, T1, T0)
  • ...
  • NDArray[complex, :] is considered as (Array, Sized, T0, complex, complex)
  • NDArray[complex, :, :] is considered as (Array, Sized, T0, complex, NDArray[complex, :])
  • NDArray[complex, :, :, :] is considered as (Array, Sized, T0, complex, NDArray[complex, :, :])

That's a recursive definition, and that's pretty useful when used with our MultiType resolution. If we need to merge an NDArray[complex, :, :] and an NDArray[complex, :, :, :], we end up with (Array, Sized, T0, complex, (Array, Sized, T1, complex, T1)) which actually means an array of complex with at least two dimensions.

Testing the Brew

Let's be honest: the tog type system is more the result of tinkering than great research. Type systems is a complex field and I did my best to apply what I learned during my bibliography on the subject, but it still falls short in various places. So instead of a formal proof, here is some testing results :-).

First, the whole test suite passes without much modifications. It helped to spot a few errors in the tests, mostly code that was incorrect with respect to option types. We also updated the way we specify tests input type to rely on PEP484. A typical Pythran unit-test now looks like:

def test_shadow_import2(self):
    self.run_test(
        '''def shadow_import2(s):
               for set in s : set.add(1)''',
        [{1},{2}],
        shadow_import2=[List[Set[int]]]
    )

where the List[Set[int]] expression describes the type for which the code must be instantiated.

The following code sample is adapted from the MyPy example page. It requires a type comment to be correctly typed, while Pythran correctly type checks it without annotation.

def wc(content):
    d = {}

    for word in content.split():
        d[word] = d.get(word, 0) + 1

    # Use list comprehension
    l = [(freq, word) for word, freq in d.items()]

    return sorted(l)

If we turn the 1 into "1", we get the following error:

> pythran wc.py
CRITICAL You shall not pass!
E: Invalid operand for `+`: `int` and `str` (wc.py, line 5)

And if we remove the 0, d.get(word) may return None and the error message becomes:

> pythran wc.py
CRITICAL You shall not pass!
E: Invalid operand for `+`: `Option[T0]` and `int` (wc.py, line 5)

Great!

Considering Numpy functions, we don't model all of them in tog, but we can still detect several interesting errors. For instance on a gaussian kernel (error-safe version from stackexchange):

import numpy as np
def vectorized_RBF_kernel(X, sigma):
    X2 = np.sum(np.multiply(X, X), 1) # sum colums of the matrix
    K0 = X2 + X2.T - 2 * X * X.T
    K = np.power(np.exp(-1.0 / sigma**2), K0)
    return K

def badcall(s):
    return vectorized_RBF_kernel(2, s)

Pythran correctly catches the error on vectorized_RBF_kernel call:

> pythran gaussian.py
CRITICAL You shall not pass!
E: Invalid argument type for function call to `Callable[[int, T3], ...]`, tried Callable[[Array[1 d+, T0], T1], Array[1 d+, T2]] (gaussian.py, line 9)

Conclusion

I'm still not satisfied with the tog engine: it's relatively slow, not as accurate as I'd like it to be, and it's just a type checker: another (simpler) type engine is used to generate the actual C++ code. That's a lot of not very enthusiastic concluding remarks, but... I'm French :-)

On the good side, I happened to learn a lot about typing and about Python, while developing this. And Pythran is in a much better shape now, much more usable, easier to maintain too, so that was worth the effort :-)

Acknowledgments

As usual, I'd like to thanks Pierrick Brunet for all his help. He keeps feeding me with relevant insights, criticisms and great ideas. Thanks to OpenDreamKit for sponsoring that work, and in particular to Logilab for their support. Thanks to Lancelot Six, w1gz and Nicolas M. ThiƩry for proof reading this post too :-)

And last, I'm in debt to all Pythran users for keeping the motivation high!

[0]That could be more actually, for instance to distinguish single precision float from double prcesion float, the float32 and float64 from numpy. But four types is enough for the envisonned type checking.
[1]The OOP style in C++ is not enforced by the Standard Library as much as it is in the Java SDK though.