Python wrappers for C++ with pybind11

We use the pybind11 library to generate Python wrappers for our C++ code. These wrappers are subject to the rules laid out in the DM Pybind11 Style Guide.

What follows is a basic step-by-step guide to writing pybind11 wrappers.

It attempts to cover the most frequently encountered patterns in LSST code. But it is not intended to be a full tutorial on pybind11. For far more detailed information please see the pybind11 documentation.

Wrapping step-by-step

To illustrate how wrapping is done we will recreate the example wrappers from the stack package template example.

Wrapping a simple class

We start by wrapping the basic ExampleOne class from the stack package template example. Its header file looks like:

#ifndef LSST_TMPL_EXAMPLEONE_H
#define LSST_TMPL_EXAMPLEONE_H

#include <ostream>
#include <string>
#include <vector>

#include "ndarray.h"

namespace lsst {
namespace tmpl {

class ExampleOne {
public:
    enum State { RED = 0, ORANGE, GREEN };

    static constexpr int someImportantConstant = 10;  ///< Important constant

    /**
     * Default constructor: default construct an ExampleOne
     */
    explicit ExampleOne() : _state(RED), _value(someImportantConstant) {}

    /**
     * Construct an ExampleOne from a filename and a state
     *
     * @param[in] fileName  name of file;
     * @param[in] state  initial state (RED, ORANGE or GREEN, default RED).
     */
    explicit ExampleOne(std::string const& fileName, State state = RED);

    /**
     * Copy constructor
     *
     * @param[in] other  the other object
     * @param[in] deep  make a deep copy
     */
    ExampleOne(ExampleOne const& other, bool deep = true);

    /**
     * Get state
     *
     * @return current state (RED, ORANGE or GREEN, default RED).
     */
    State getState() const { return _state; }

    /**
     * Set state
     *
     * @param[in] state  state
     * @param[in] state  initial state (RED, ORANGE or GREEN, default RED).
     */
    void setState(State state) { _state = state; }

    /**
     * Compute something
     *
     * @param[in] myParam some parameter
     * @return a particular value
     */
    double computeSomething(int myParam) const;

    /**
     * Compute something else
     *
     * @param[in] myFirstParam some parameter
     * @param[in] mySecondParam some other parameter
     * @return a particular value
     */
    double computeSomethingElse(int myFirstParam, double mySecondParam) const;

    /**
     * Compute something else
     *
     * @param[in] myFirstParam some parameter
     * @param[in] anotherParam some other parameter
     * @return a particular value
     */
    double computeSomethingElse(int myFirstParam, std::string anotherParam = "foo") const;

    /**
     * Compute some vector
     *
     * @return a vector with results
     */
    std::vector<int> computeSomeVector() const;

    /**
     * Do something with an input array
     *
     * @return some result
     */
    void doSomethingWithArray(ndarray::Array<int, 2, 2> const& arrayArgument);

    /**
     * Initialize something with some value
     *
     * @param someValue some value to do something with
     */
    static void initializeSomething(std::string const& someValue);

    bool operator==(ExampleOne const& other) { return _value == other._value; }
    bool operator!=(ExampleOne const& other) { return _value != other._value; }

    ExampleOne& operator+=(ExampleOne const& other) {
        _value += other._value;
        return *this;
    }

    friend std::ostream& operator<<(std::ostream&, ExampleOne const&);

private:
    State _state;  ///< Current state
    int _value;    ///< Some value
};

ExampleOne operator+(ExampleOne lhs, ExampleOne const& rhs) {
    lhs += rhs;
    return lhs;
}

std::ostream& operator<<(std::ostream& out, ExampleOne const& rhs) {
    out << "Example(" << rhs._value << ")";
    return out;
}

}}  // namespace lsst::tmpl

#endif

Adding dependencies

First we need to add some dependencies to the build.

Scons will not use pybind11 unless it is setup, so in {{pkg}}/ups/{{pkg}}.table, where {{pkg}} is the name of the package, you will need to add the dependency setupRequired(pybind11). You also need to modify the dependencies in {{pkg}}/ups/{{pkg}}.cfg, by adding "pybind11" to "buildRequired".

Creating a module file

Following our rules on file naming, we start by creating a minimal module file python/lsst/TMPL/exampleOne.cc with the following content:

#include "pybind11/pybind11.h"

#include "lsst/TMPL/ExampleOne.h"

namespace py = pybind11;

namespace lsst {
namespace tmpl {

PYBIND11_PLUGIN(exampleOne) {
    py::module mod("exampleOne");

    return mod.ptr();

}}}  // lsst::tmpl

Warning

The name used for the PYBIND11_PLUGIN(...) macro must match both the name used for mod(...) and the name of the file, otherwise an ImportError will be raised.

Wrapping the class

We wrap the class using the py::class_<T> template:

PYBIND11_PLUGIN(exampleOne) {
    py::module mod("exampleOne");

    py::class_<ExampleOne, std::shared_ptr<ExampleOne>> clsExampleOne(mod, "ExampleOne");

    return mod.ptr();
}

Note

As in the example, classes should almost always have a shared_ptr holder type.

Wrapping enums

The next thing to wrap is the enum (because it is used in the constructor arguments). This is done using py::enum_:

py::class_<ExampleOne, std::shared_ptr<ExampleOne>> clsExampleOne(mod, "ExampleOne");

py::enum_<ExampleOne::State>(clsExampleOne, "State")
    .value("RED", ExampleOne::State::RED)
    .value("ORANGE", ExampleOne::State::ORANGE)
    .value("GREEN", ExampleOne::State::GREEN);

Note

We attach the enum values to the class (by passing the py::class_ object clsExampleOne as the first argument)

Note

Add .export_values() if (and only if) you need to export the values into the class scope (so they can be reached as ExampleOne.RED, in addition to ExampleOne.State.Red).

Never do this for new style scoped enum class types, since that will give them different symantics in C++ and Python.

Wrapping constructors

Constructors are added to the class using the py::init<T...> helper:

clsExampleOne.def(py::init<>());
clsExampleOne.def(py::init<std::string const&, ExampleOne::State>());
clsExampleOne.def(py::init<ExampleOne const&, bool>()); // Copy constructor

However, two of the constructors have default arguments. So we use the argument literal from pybind::literals to wrap them as keyword arguments (which following the rule on keyword arguments should almost always be done, except for non-overloaded functions taking a single argument):

clsExampleOne.def(py::init<>());
clsExampleOne.def(py::init<std::string const&, ExampleOne::State>(), "fileName"_a, "state"_a=ExampleOne::State::RED);
clsExampleOne.def(py::init<ExampleOne const&, bool>(), "other"_a, "deep"_a=true); // Copy constructor

We also need to add: using namespace pybind11::literals; at the top.

Warning

Unfortunately there is no way for pybind11 to track the value of the default argument. So be careful to dupplicate it correctly, and update it when it is changed in the code.

Getters and setters

We can wrap getState and setState as follows:

clsExampleOne.def("getState", &ExampleOne::getState);
clsExampleOne.def("setState", &ExampleOne::setState);

Following the rules on properties you may choose to add a property too:

clsExampleOne.def_property("state", &ExampleOne::getState, &ExampleOne::setState);

Wrapping (overloaded) member functions

Wrapping a member function is easy:

clsExampleOne.def("computeSomething", &ExampleOne::computeSomething);

However, when the function is overloaded we need to disambiguate the overloads. Following the rule on overload disambiguation we use C-style casts for this:

clsExampleOne.def("computeSomethingElse",
                  (double (ExampleOne::*)(int, double) const) & ExampleOne::computeSomethingElse,
                  "myFirstParam"_a, "mySecondParam"_a);
clsExampleOne.def("computeSomethingElse",
                  (double (ExampleOne::*)(int, std::string) const) &ExampleOne::computeSomethingElse,
                  "myFirstParam"_a, "anotherParam"_a="foo");

Note

In the spirit of py::init<T...>, there is also py::overload_cast<T...>. This would be really nice to use, but we can’t because it requires C++14.

STL containers

The function ExampleOne::computeSomeVector returns a std::vector<int>. Following the rule on STL containers we simply include the pybind11/stl.h header (to enable automatic conversion to and from Python containers) and wrap the function as normal:

clsExampleOne.def("computeSomeVector", &ExampleOne::computeSomeVector);

Ndarray

The function ExampleOne::doSomethingWithArray takes an ndarray::Array argument. To enable automatic conversion to and from numpy.ndarray in Python add the following includes (right below the pybind11 ones):

#include "numpy/arrayobject.h"
#include "ndarray/pybind11.h"

We also need to make sure the numpy module is imported by adding:

if (_import_array() < 0) {
        PyErr_SetString(PyExc_ImportError, "numpy.core.multiarray failed to import");
        return nullptr;
};

Then the function can be wrapped as normal:

clsExampleOne.def("doSomethingWithArray", &ExampleOne::doSomethingWithArray);

Warning

Forgetting to add _import_array is one of the most common causes of pybind11 segfaults.

Static member functions

Wrapping static member functions is trivial:

clsExampleOne.def_static("initializeSomething", &ExampleOne::initializeSomething);

Wrapping operators

According to our rule on operators we can either wrap operators directly, or use a lambda. Here we use both approaches:

clsExampleOne.def("__eq__", &ExampleOne::operator==, py::is_operator());
clsExampleOne.def("__ne__", &ExampleOne::operator!=, py::is_operator());
clsExampleOne.def("__iadd__", &ExampleOne::operator+= /* no py::is_operator() here */);
clsExampleOne.def("__add__", [](ExampleOne const & self, ExampleOne const & other) { return self + other; }, py::is_operator());

Note

• We use py::is_operator() to return NotImplemented on failure.
• We don’t use py::is_operator() for in-place operators as this can lead to confusing behavior.
• We name the lambda arguments self and other.

Custom exceptions

The example contains a custom exception (ExampleError) added by the LSST_EXCEPTION_TYPE macro:

LSST_EXCEPTION_TYPE(ExampleError, lsst::pex::exceptions::RuntimeError, ExampleError)

To wrap it we can use the declareException macro from #include "lsst/pex/exceptions/python/Exception.h":

pex::exceptions::python::declareException<ExampleError, pex::exceptions::RuntimeError>(
        mod, "ExampleError", "RuntimeError");

Finished wrapper

The end result of all the steps above looks like this:

#include "pybind11/pybind11.h"
#include "pybind11/stl.h"

#include "numpy/arrayobject.h"
#include "numpy/arrayobject.h"
#include "ndarray/pybind11.h"

#include "lsst/pex/exceptions/python/Exception.h"

#include "lsst/TMPL/ExampleOne.h"

namespace py = pybind11;
using namespace pybind11::literals;

namespace lsst {
namespace tmpl {

PYBIND11_PLUGIN(exampleOne) {
    py::module mod("exampleOne");

    if (_import_array() < 0) {
            PyErr_SetString(PyExc_ImportError, "numpy.core.multiarray failed to import");
            return nullptr;
    };

    pex::exceptions::python::declareException<ExampleError, pex::exceptions::RuntimeError>(
            mod, "ExampleError", "RuntimeError");

    py::class_<ExampleOne, std::shared_ptr<ExampleOne>> clsExampleOne(mod, "ExampleOne");

    py::enum_<ExampleOne::State>(clsExampleOne, "State")
        .value("RED", ExampleOne::State::RED)
        .value("ORANGE", ExampleOne::State::ORANGE)
        .value("GREEN", ExampleOne::State::GREEN)
        .export_values();

    clsExampleOne.def(py::init<>());
    clsExampleOne.def(py::init<std::string const&, ExampleOne::State>(), "fileName"_a, "state"_a=ExampleOne::State::RED);
    clsExampleOne.def(py::init<ExampleOne const&, bool>(), "other"_a, "deep"_a=true); // Copy constructor

    clsExampleOne.def("getState", &ExampleOne::getState);
    clsExampleOne.def("setState", &ExampleOne::setState);
    clsExampleOne.def_property("state", &ExampleOne::getState, &ExampleOne::setState);
    clsExampleOne.def("computeSomething", &ExampleOne::computeSomething);
    clsExampleOne.def("computeSomethingElse",
                      (double (ExampleOne::*)(int, double) const) & ExampleOne::computeSomethingElse,
                      "myFirstParam"_a, "mySecondParam"_a);
    clsExampleOne.def("computeSomethingElse", (double (ExampleOne::*)(int, std::string) const) &ExampleOne::computeSomethingElse, "myFirstParam"_a, "anotherParam"_a="foo");
    clsExampleOne.def("computeSomeVector", &ExampleOne::computeSomeVector);
    clsExampleOne.def("doSomethingWithArray", &ExampleOne::doSomethingWithArray);
    clsExampleOne.def_static("initializeSomething", &ExampleOne::initializeSomething);

    clsExampleOne.def("__eq__", &ExampleOne::operator==, py::is_operator());
    clsExampleOne.def("__ne__", &ExampleOne::operator!=, py::is_operator());
    clsExampleOne.def("__iadd__", &ExampleOne::operator+=);
    clsExampleOne.def("__add__", [](ExampleOne const & self, ExampleOne const & other) { return self + other; }, py::is_operator());

    return mod.ptr();
}

}}  // lsst::tmpl

Moving on

In this section we are going to look at some more advanced wrapping. In particular inheritance and templates We shall also cover how to add pure Python members to wrapped C++ classes.

We wrap the following two header files from the templates package, ExampleTwo.h:

#ifndef LSST_TMPL_EXAMPLETWO_H
#define LSST_TMPL_EXAMPLETWO_H

namespace lsst {
namespace tmpl {

class ExampleBase {
public:
    virtual int someMethod(int value) { return value + 1; }

    virtual double someOtherMethod() = 0;

    virtual ~ExampleBase() = default;
};

class ExampleTwo : public ExampleBase {
public:
    ExampleTwo() = default;

    double someOtherMethod() override {
        return 4.0;
    }
};

}
}  // namespace lsst::tmpl

#endif

and ExampleThree.h:

#ifndef LSST_TMPL_EXAMPLETHREE_H
#define LSST_TMPL_EXAMPLETHREE_H

#include "lsst/TMPL/ExampleTwo.h"

namespace lsst {
namespace tmpl {

template <typename T>
class ExampleThree : public ExampleBase {
public:
    ExampleThree(T value) : _value(value) { }

    double someOtherMethod() override {
        return static_cast<double>(_value);
    }
private:
    T _value;
};

}
}  // namespace lsst::tmpl

#endif

Create wrapper files

Again following our rules on file naming we create a basic file for the wrapper python/lsst/TMPL/exampleTwo.cc (note that this file will later move to a subpackage):

#include "pybind11/pybind11.h"

#include "lsst/TMPL/ExampleTwo.h"

namespace py = pybind11;
using namespace pybind11::literals;

namespace lsst {
namespace tmpl {

PYBIND11_PLUGIN(exampleTwo) {
    py::module mod("exampleTwo");

    return mod.ptr();
}

}}  // lsst::tmpl

And the same for exampleThree.cc.

Note

If any of this looks unfamilliar please see “Wrapping a simple class” first.

Inheritance

ExampleTwo.h defines two classes (ExampleBase and ExampleTwo) which we wrap as follows:

py::class_<ExampleBase, std::shared_ptr<ExampleBase>> clsExampleBase(mod, "ExampleBase");
clsExampleBase.def("someMethod", &ExampleBase::someMethod);

py::class_<ExampleTwo, std::shared_ptr<ExampleTwo>, ExampleBase> clsExampleTwo(mod, "ExampleTwo");

clsExampleTwo.def(py::init<>());
clsExampleTwo.def("someOtherMethod", &ExampleTwo::someOtherMethod);

There are two subtleties:

• ExampleTwo inherits from ExampleBase. To indicate this we list ExampleBase as a template parameter when declaring clsExampleTwo. If ExampleTwo had additional base classes they would all be listed here.
• ExampleBase is abstract and therefore in pybind11 cannot have a constructor (even if it is present in C++).

Templates

Now we move on to ExampleThree. This is a class template. Following this rule we declare its wrapper in a function declareExampleThree (that is itself templated on the same type, although the latter is not required):

namespace {

template <typename T>
static void declareExampleThree(py::module & mod, std::string const & suffix) {
    using Class = ExampleThree<T>;
    using PyClass = py::class_<Class, std::shared_ptr<Class>, ExampleBase>;

    PyClass cls(mod, ("ExampleThree" + suffix).c_str());

    cls.def(py::init<T>());
    cls.def("someOtherMethod", &Class::someOtherMethod);
}

}

PYBIND11_PLUGIN(exampleThree) {
    py::module::import("exampleTwo");  // See Cross module imports

    py::module mod("exampleThree");

    declareExampleThree<int>(mod, "I");
    declareExampleThree<double>(mod, "D");

    return mod.ptr();
}

Note

• We follow this rule and stick the declare function in an annonymous namespace;
• We use the alias rules for types and pybind11 class objects to minimize typing;
• A suffix is appended to the name of the class in Python. Commonly used suffixes are:
  • I for int,
  • L for long,
  • F for float,
  • D for double and
  • U for unsigned int.

Cross module imports

The import statement:

py::module::import("exampleTwo");

in the previous example is present because ExampleThree depends on ExampleBase which is defined in a different module (i.e. exampleTwo).

Thus, if you forget to add the import statement, the type ExampleBase is unknown if exampleThree happens to be imported before exampleTwo.

Adding these import statements in the C++ wrapper, rather than relying on import order in __init__ in Python, follows our rule on import.

Finished wrappers (C++ part)

The end results for the C++ part of the wrappers (see next for the Python part) are exampleTwo.cc:

#include "pybind11/pybind11.h"

#include "lsst/TMPL/ExampleTwo.h"

namespace py = pybind11;
using namespace pybind11::literals;

namespace lsst {
namespace tmpl {

PYBIND11_PLUGIN(exampleTwo) {
    py::module mod("exampleTwo");

    py::class_<ExampleBase, std::shared_ptr<ExampleBase>> clsExampleBase(mod, "ExampleBase");
    clsExampleBase.def("someMethod", &ExampleBase::someMethod);

    py::class_<ExampleTwo, std::shared_ptr<ExampleTwo>, ExampleBase> clsExampleTwo(mod, "ExampleTwo");
    clsExampleTwo.def(py::init<>());
    clsExampleTwo.def("someOtherMethod", &ExampleTwo::someOtherMethod);

    return mod.ptr();
}

}}  // lsst::tmpl

and exampleThree.cc:

#include "pybind11/pybind11.h"

#include "lsst/TMPL/ExampleThree.h"

namespace py = pybind11;
using namespace pybind11::literals;

namespace lsst {
namespace tmpl {
namespace {

template <typename T>
static void declareExampleThree(py::module & mod, std::string const & suffix) {
    using Class = ExampleThree<T>;
    using PyClass = py::class_<Class, std::shared_ptr<Class>, ExampleBase>;

    PyClass cls(mod, ("ExampleThree" + suffix).c_str());

    cls.def(py::init<T>());
    cls.def("someOtherMethod", &Class::someOtherMethod);
}

}

PYBIND11_PLUGIN(exampleThree) {
    py::module mod("exampleThree");

    py::module::import("exampleTwo");

    declareExampleThree<float>(mod, "F");
    declareExampleThree<double>(mod, "D");

    return mod.ptr();
}

}}  // lsst::tmpl

Adding pure Python members

Sometimes it is necessary to add pure Python members to a wrapped C++ class. Following our structure and naming convention for this, we move exampleTwo.cc to a new subpackage (exampleTwo) and add an __init__.py file with the following content:

from __future__ import absolute_import

from .exampleTwo import *
from .exampleTwoContinued import *

The pure Python code then goes into exampleTwo/exampleTwoContinued.py. We shall use the continueClass decorator to reopen the class and add a new method:

from __future__ import absolute_import
from lsst.utils import continueClass

from .exampleTwo import ExampleTwo

__all__ = [] # import for side effects

@continueClass
class ExampleTwo:

    def someExtraFunction(self, x):
        return x + self.someOtherMethod()

Grouping templated types with an ABC

Using the TemplateMeta metaclass from lsst.utils we can group templated types together with a single abstract base class.

This gives users a familiar interface to work with templated types. It allows them to do isinstance(my_object, ExampleThree) and create an ExampleThreeF type using ExampleThree(dtype=np.float32).

As with ExampleTwo, first move the module into its own subpackage. Create the appropriate __init__.py file, and put the following in exampleThree/exampleThreeContinued.py:

from __future__ import absolute_import
import numpy as np

from lsst.utils import TemplateMeta
from .exampleThree import ExampleThreeF, ExampleThreeD

__all__ = [] # import for side effects

class ExampleThree(metaclass=TemplateMeta):
    pass

ExampleThree.register(np.float32, ExampleThreeF)
ExampleThree.register(np.float64, ExampleThreeD)
ExampleThree.alias("F", ExampleThreeF)
ExampleThree.alias("D", ExampleThreeD)