Binding detailed example: Minuit2

Let’s try a non-trivial example: Minuit2 (6.26.10 standalone edition)

Expectations

• Be able to minimize a very simple function and get some parameters

import sys

Step 1: Get source

• Download Minuit2 source (already provided in minuit2)

Step 2: Plan interface

• You should know what the C++ looks like, and know what you want the Python to look like

• For now, let’s replicate the C++ experience

For example: a simple minimizer for \(f(x) = x^2\) (should quickly find 0 as minimum):

• Define FCN

• Setup parameters

• Minimize

• Print result

Will use print out for illustration (instead of MnPrint::SetLevel)

%%writefile SimpleFCN.h
#pragma once

#include <Minuit2/FCNBase.h>
#include <Minuit2/FunctionMinimum.h>
#include <Minuit2/MnPrint.h>
#include <Minuit2/MnMigrad.h>

#include <iostream>

using namespace ROOT::Minuit2;

class SimpleFCN : public FCNBase {
    // Always 0.5 for these sorts of fits
    
    double Up() const override {return 0.5;}
    
    // This computes whatever you are going to minimize
    double operator()(const std::vector<double> &v) const override {
        std::cout << "val = " << v.at(0) << std::endl;
        return v.at(0)*v.at(0);
    }
};

Writing SimpleFCN.h

%%writefile simpleminuit.cpp
#include "SimpleFCN.h"

int main() {
    SimpleFCN fcn;
    MnUserParameters upar;
    upar.Add("x", 1., 0.1);
    MnMigrad migrad(fcn, upar);
    FunctionMinimum min = migrad();
    std::cout << min << std::endl;
}

Writing simpleminuit.cpp

%%writefile CMakeLists.txt

cmake_minimum_required(VERSION 3.18...3.29)
project(Minuit2SimpleExamle LANGUAGES CXX)

include(FetchContent)
FetchContent_Declare(
  minuit2
  URL           https://github.com/root-project/root/archive/refs/tags/v6-26-10.tar.gz
  URL_HASH      SHA256=a84ed095252614c6e2084987fce9ce4a5a62057bfd5a4a2725123ca9f60f674f
  SOURCE_SUBDIR math/minuit2
  DOWNLOAD_NO_PROGRESS
)
FetchContent_MakeAvailable(minuit2)

add_executable(simpleminuit simpleminuit.cpp SimpleFCN.h)
target_link_libraries(simpleminuit PRIVATE Minuit2::Minuit2)

Writing CMakeLists.txt

Standard CMake configure and build (using Ninja instead of Make for speed)

!cmake -GNinja -S . -B build
!cmake --build build

-- The CXX compiler identification is GNU 11.4.0
-- Detecting CXX compiler ABI info

-- Detecting CXX compiler ABI info - done

-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done

CMake Deprecation Warning at build/_deps/minuit2-src/math/minuit2/CMakeLists.txt:7 (cmake_minimum_required):
  Compatibility with CMake < 3.10 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.


CMake Deprecation Warning at build/_deps/minuit2-src/math/minuit2/StandAlone.cmake:1 (cmake_minimum_required):
  Compatibility with CMake < 3.10 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.
Call Stack (most recent call first):
  build/_deps/minuit2-src/math/minuit2/CMakeLists.txt:250 (include)

-- Configuring done (16.9s)
-- Generating done (0.0s)
-- Build files have been written to: /home/runner/work/se-for-sci/se-for-sci/content/week09/03-pybind/build

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!./build/simpleminuit

val = 1
val = 1.001
val = 0.999
val = 1.0006
val = 0.999402
val = -8.23008e-11
val = 0.000345267
val = -0.000345267
val = -8.23008e-11
val = 0.000345267
val = -0.000345267
val = 6.90533e-05
val = -6.90535e-05

  Valid         : yes
  Function calls: 13
  Minimum value : 6.773427082e-21
  Edm           : 6.773427082e-21
  Internal parameters: 
 -8.230083282e-11
  Internal covariance matrix: 
              1
  External parameters: 
  Pos |    Name    |  type   |      Value       |    Error +/-
    0 |          x |  free   | -8.230083282e-11 | 0.7071067812

Step 3: Bind parts we need

• subclassable FCNBase

• MnUserParameters (constructor and Add(string, double, double))

• MnMigrad (constructor and operator())

• FunctionMinimum (cout)

%mkdir src

Recommended structure of a Pybind11 program

main.cpp

• Builds module

• Avoids imports (fast compile)

include <pybind11/pybind11.h>
namespace py = pybind11;

void init_part1(py::module &);
void init_part2(py::module &);

PYBIND11_MODULE(mymodule, m) {
    m.doc() = "Real code would never have such poor documentation...";
    init_part1(m);
    init_part2(m);
}

%%writefile src/pyminuit2.cpp

#include <pybind11/pybind11.h>

namespace py = pybind11;

void init_FCNBase(py::module &);
void init_MnUserParameters(py::module &);
void init_MnMigrad(py::module &);
void init_FunctionMinimum(py::module &);

PYBIND11_MODULE(minuit2, m) {
    init_FCNBase(m);
    init_MnUserParameters(m);
    init_MnMigrad(m);
    init_FunctionMinimum(m);
}

Writing src/pyminuit2.cpp

We will put all headers in a collective header (not a good idea unless you are trying to show files one per slide).

%%writefile src/PyHeader.h
#pragma once
#include <pybind11/pybind11.h>
#include <pybind11/functional.h>
#include <pybind11/numpy.h>
#include <pybind11/stl.h>

#include <Minuit2/FCNBase.h>
#include <Minuit2/MnMigrad.h>
#include <Minuit2/MnApplication.h>
#include <Minuit2/MnUserParameters.h>
#include <Minuit2/FunctionMinimum.h>

namespace py = pybind11;
using namespace pybind11::literals;
using namespace ROOT::Minuit2;

Writing src/PyHeader.h

Overloads

• Pure virtual methods cannot be instantiated in C++

• Have to provide “Trampoline class” to provide Python class

%%writefile src/FCNBase.cpp
#include "PyHeader.h"
class PyFCNBase : public FCNBase {
   public:
     using FCNBase::FCNBase;

     double operator()(const std::vector<double> &v) const override {
         PYBIND11_OVERLOAD_PURE_NAME(
             double, FCNBase, "__call__", operator(), v);}

     double Up() const override {
         PYBIND11_OVERLOAD_PURE(double, FCNBase, Up, );}
 };
void init_FCNBase(py::module &m) {
    py::class_<FCNBase, PyFCNBase>(m, "FCNBase")
         .def(py::init<>())
         .def("__call__", &FCNBase::operator())
         .def("Up", &FCNBase::Up);
}

Writing src/FCNBase.cpp

Overloaded function signatures:

• C++11 syntax: (bool (MnUserParameters::*)(const std::string &, double)) &MnUserParameters::Add

• C++14 syntax: py::overload_cast<const std::string &, double>(&MnUserParameters::Add)

%%writefile src/MnUserParameters.cpp
#include "PyHeader.h"

void init_MnUserParameters(py::module &m) {
    py::class_<MnUserParameters>(m, "MnUserParameters")
        .def(py::init<>())
        .def("Add", (bool (MnUserParameters::*)(const std::string &, double)) &MnUserParameters::Add)
        .def("Add", (bool (MnUserParameters::*)(const std::string &, double, double)) &MnUserParameters::Add)
    ;
}

Writing src/MnUserParameters.cpp

Adding default arguments (and named arguments)

• Using ""_a literal, names and even defaults can be added

%%writefile src/MnMigrad.cpp
#include "PyHeader.h"
        
void init_MnMigrad(py::module &m) {
    py::class_<MnApplication>(m, "MnApplication")
        .def("__call__",
             &MnApplication::operator(),
             "Minimize the function, returns a function minimum",
             py::arg("maxfcn")    = 0,
             "tolerance"_a = 0.1);
    
    py::class_<MnMigrad, MnApplication>(m, "MnMigrad")
        .def(py::init<const FCNBase &, const MnUserParameters &, unsigned int>(),
             "fcn"_a, "par"_a, "stra"_a = 1)
    ;
}    

Writing src/MnMigrad.cpp

Lambda functions

• Pybind11 accepts lambda functions, as well

%%writefile src/FunctionMinimum.cpp
#include "PyHeader.h"

#include <sstream>
#include <Minuit2/MnPrint.h>

void init_FunctionMinimum(py::module &m) {
    py::class_<FunctionMinimum>(m, "FunctionMinimum")
        .def("__str__", [](const FunctionMinimum &self) {
            std::stringstream os;
            os << self;
            return os.str();
        })
    ;
}

Writing src/FunctionMinimum.cpp

%%writefile CMakeLists.txt

cmake_minimum_required(VERSION 3.18...3.25)
project(Minuit2SimpleExamle LANGUAGES CXX)

set(CMAKE_POSITION_INDEPENDENT_CODE ON)

include(FetchContent)
FetchContent_Declare(
  minuit2
  URL           https://github.com/root-project/root/archive/refs/tags/v6-26-10.tar.gz
  URL_HASH      SHA256=a84ed095252614c6e2084987fce9ce4a5a62057bfd5a4a2725123ca9f60f674f
  SOURCE_SUBDIR math/minuit2
  DOWNLOAD_NO_PROGRESS
  EXCLUDE_FROM_ALL
)
FetchContent_MakeAvailable(minuit2)

set(PYBIND11_FINDPYTHON ON)
find_package(pybind11)

file(GLOB OUTPUT src/*.cpp)
pybind11_add_module(minuit2 ${OUTPUT})
target_link_libraries(minuit2 PUBLIC Minuit2::Minuit2)

install(TARGETS minuit2 DESTINATION .)

Overwriting CMakeLists.txt

We can use this CMakeLists from scikit-build-core:

%%writefile pyproject.toml

[build-system]
requires = ["scikit-build-core>=0.8", "pybind11>=2.10"]
build-backend = "scikit_build_core.build"

[project]
name = "minuit2"
version = "6.26.10"

Writing pyproject.toml

!{sys.executable} -m pip wheel . -v

Processing /home/runner/work/se-for-sci/se-for-sci/content/week09/03-pybind
  Running command pip subprocess to install build dependencies

  Using pip 24.2 from /home/runner/work/se-for-sci/se-for-sci/.pixi/envs/default/lib/python3.12/site-packages/pip (python 3.12)

  Collecting scikit-build-core>=0.8
    Obtaining dependency information for scikit-build-core>=0.8 from https://files.pythonhosted.org/packages/88/fe/90476c4f6a1b2f922efa00d26e876dd40c7279e28ec18f08f0851ad21ba6/scikit_build_core-0.10.7-py3-none-any.whl.metadata
    Downloading scikit_build_core-0.10.7-py3-none-any.whl.metadata (21 kB)

  Collecting pybind11>=2.10
    Obtaining dependency information for pybind11>=2.10 from https://files.pythonhosted.org/packages/13/2f/0f24b288e2ce56f51c920137620b4434a38fd80583dbbe24fc2a1656c388/pybind11-2.13.6-py3-none-any.whl.metadata
    Downloading pybind11-2.13.6-py3-none-any.whl.metadata (9.5 kB)

  Collecting packaging>=21.3 (from scikit-build-core>=0.8)
    Obtaining dependency information for packaging>=21.3 from https://files.pythonhosted.org/packages/88/ef/eb23f262cca3c0c4eb7ab1933c3b1f03d021f2c48f54763065b6f0e321be/packaging-24.2-py3-none-any.whl.metadata
    Downloading packaging-24.2-py3-none-any.whl.metadata (3.2 kB)
  Collecting pathspec>=0.10.1 (from scikit-build-core>=0.8)
    Obtaining dependency information for pathspec>=0.10.1 from https://files.pythonhosted.org/packages/cc/20/ff623b09d963f88bfde16306a54e12ee5ea43e9b597108672ff3a408aad6/pathspec-0.12.1-py3-none-any.whl.metadata
    Downloading pathspec-0.12.1-py3-none-any.whl.metadata (21 kB)
  Downloading scikit_build_core-0.10.7-py3-none-any.whl (165 kB)
  Downloading pybind11-2.13.6-py3-none-any.whl (243 kB)
  Downloading packaging-24.2-py3-none-any.whl (65 kB)

  Downloading pathspec-0.12.1-py3-none-any.whl (31 kB)

  Installing collected packages: pybind11, pathspec, packaging, scikit-build-core
    Creating /tmp/pip-build-env-651oruzt/overlay/bin
    changing mode of /tmp/pip-build-env-651oruzt/overlay/bin/pybind11-config to 755

  Successfully installed packaging-24.2 pathspec-0.12.1 pybind11-2.13.6 scikit-build-core-0.10.7

  Installing build dependencies ... ?25l?25hdone
  Running command Getting requirements to build wheel

  Getting requirements to build wheel ... ?25l?25hdone
  Running command Preparing metadata (pyproject.toml)

  *** scikit-build-core 0.10.7 using CMake 3.31.0 (metadata_wheel)
  2024-11-20 23:57:28,967 - scikit_build_core - WARNING - No license files found, set wheel.license-files to [] to suppress this warning
  Preparing metadata (pyproject.toml) ... ?25l?25hdone
Building wheels for collected packages: minuit2

  Running command Building wheel for minuit2 (pyproject.toml)

  *** scikit-build-core 0.10.7 using CMake 3.31.0 (wheel)
  2024-11-20 23:57:29,101 - scikit_build_core - WARNING - No license files found, set wheel.license-files to [] to suppress this warning
  *** Configuring CMake...
  loading initial cache file /tmp/tmpgn0p2f72/build/CMakeInit.txt

  -- The CXX compiler identification is GNU 11.4.0

  -- Detecting CXX compiler ABI info

  -- Detecting CXX compiler ABI info - done
  -- Check for working CXX compiler: /usr/bin/g++ - skipped
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done

  CMake Deprecation Warning at /tmp/tmpgn0p2f72/build/_deps/minuit2-src/math/minuit2/CMakeLists.txt:7 (cmake_minimum_required):
    Compatibility with CMake < 3.10 will be removed from a future version of
    CMake.

    Update the VERSION argument <min> value or use a ...<max> suffix to tell
    CMake that the project does not need compatibility with older versions.

  
  CMake Deprecation Warning at /tmp/tmpgn0p2f72/build/_deps/minuit2-src/math/minuit2/StandAlone.cmake:1 (cmake_minimum_required):
    Compatibility with CMake < 3.10 will be removed from a future version of
    CMake.

    Update the VERSION argument <min> value or use a ...<max> suffix to tell
    CMake that the project does not need compatibility with older versions.
  Call Stack (most recent call first):
    /tmp/tmpgn0p2f72/build/_deps/minuit2-src/math/minuit2/CMakeLists.txt:250 (include)

  

  -- Found Python: /home/runner/work/se-for-sci/se-for-sci/.pixi/envs/default/bin/python (found suitable version "3.12.7", minimum required is "3.7") found components: Interpreter Development.Module Development.Embed

  -- Performing Test HAS_FLTO

  -- Performing Test HAS_FLTO - Success
  -- Found pybind11: /home/runner/work/se-for-sci/se-for-sci/.pixi/envs/default/lib/python3.12/site-packages/pybind11/include (found version "2.13.6")
  -- Configuring done (17.3s)

  -- Generating done (0.0s)
  -- Build files have been written to: /tmp/tmpgn0p2f72/build
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  *** Installing project into wheel...
  -- Install configuration: "Release"
  -- Installing: /tmp/tmpgn0p2f72/wheel/platlib/./minuit2.cpython-312-x86_64-linux-gnu.so
  *** Making wheel...

  *** Created minuit2-6.26.10-cp312-cp312-linux_x86_64.whl

  Building wheel for minuit2 (pyproject.toml) ... ?25l?25hdone
  Created wheel for minuit2: filename=minuit2-6.26.10-cp312-cp312-linux_x86_64.whl size=245485 sha256=7970c8c44b74f1f17d1887a435c5f0557f936312c42395abb0d91e7b21fc8f1b
  Stored in directory: /home/runner/.cache/pip/wheels/a4/eb/74/ff000d32154f6bcbd24e7b0472e3ff3daedae47ddc6c6bc9b6
Successfully built minuit2

Usage

We can now use our module! We’ll just grab the file we need out of the wheel instead of installing it:

import zipfile
from pathlib import Path

with zipfile.ZipFile(*Path.cwd().glob("minuit2-6.26.10-*.whl")) as f:
    for member in f.filelist:
        print(member.filename)
        if member.filename.startswith("minuit2."):
            f.extract(member, ".")

minuit2.cpython-312-x86_64-linux-gnu.so
minuit2-6.26.10.dist-info/METADATA
minuit2-6.26.10.dist-info/WHEEL
minuit2-6.26.10.dist-info/RECORD

import minuit2


class SimpleFCN(minuit2.FCNBase):
    def Up(self):
        return 0.5

    def __call__(self, v):
        print("val =", v[0])
        return v[0] ** 2

fcn = SimpleFCN()
upar = minuit2.MnUserParameters()
upar.Add("x", 1.0, 0.1)
migrad = minuit2.MnMigrad(fcn, upar)
minimum = migrad()

val = 1.0
val = 1.001
val = 0.999
val = 1.0005980198587356
val = 0.9994019801412644
val = -8.230083281546285e-11
val = 0.00034526688527999595
val = -0.0003452670498816616
val = -8.230083281546285e-11
val = 0.00034526688527999595
val = -0.0003452670498816616
val = 6.905331121533294e-05
val = -6.905347581699857e-05

print(minimum)

  Valid         : yes
  Function calls: 13
  Minimum value : 6.773427082e-21
  Edm           : 6.773427082e-21
  Internal parameters: 
 -8.230083282e-11
  Internal covariance matrix: 
              1
  External parameters: 
  Pos |    Name    |  type   |      Value       |    Error +/-
    0 |          x |  free   | -8.230083282e-11 | 0.7071067812

Done

• See GooFit’s built in Minuit2 bindings for a more complete example

• Pybind11 bindings can talk to each other at the C level!