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Testing and timing compared to NumPy#288

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53 changes: 53 additions & 0 deletions.github/workflows/check.yml
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name: check

on:
workflow_dispatch:
pull_request:
push:
branches:
- main

jobs:

standard:

strategy:
fail-fast: false
matrix:
runs-on: [ubuntu-latest, macos-latest, windows-latest]

defaults:
run:
shell: bash -l {0}

name: ${{ matrix.runs-on }} • x64 ${{ matrix.args }}
runs-on: ${{ matrix.runs-on }}

steps:

- name: Basic GitHub action setup
uses: actions/checkout@v3

- name: Set conda environment
uses: mamba-org/provision-with-micromamba@main
with:
environment-file: environment-dev.yml
environment-name: myenv
cache-env: true
extra-specs: |
prettytable
setuptools_scm
scikit-build
xsimd

- name: Set dummy version
run: echo "SETUPTOOLS_SCM_PRETEND_VERSION=0.0" >> $GITHUB_ENV

- name: Build and install Python module
working-directory: python-module
run: |
SKBUILD_CONFIGURE_OPTIONS="-DUSE_XSIMD=1" python -m pip install . -v

- name: Run Python tests
working-directory: python-module
run: python -m unittest discover tests
53 changes: 53 additions & 0 deletions.github/workflows/profile.yml
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name: profile

on:
workflow_dispatch:
pull_request:
push:
branches:
- main

jobs:

standard:

strategy:
fail-fast: false
matrix:
runs-on: [ubuntu-latest, macos-latest, windows-latest]

defaults:
run:
shell: bash -l {0}

name: ${{ matrix.runs-on }} • x64 ${{ matrix.args }}
runs-on: ${{ matrix.runs-on }}

steps:

- name: Basic GitHub action setup
uses: actions/checkout@v3

- name: Set conda environment
uses: mamba-org/provision-with-micromamba@main
with:
environment-file: environment-dev.yml
environment-name: myenv
cache-env: true
extra-specs: |
prettytable
setuptools_scm
scikit-build
xsimd

- name: Set dummy version
run: echo "SETUPTOOLS_SCM_PRETEND_VERSION=0.0" >> $GITHUB_ENV

- name: Build and install Python module
working-directory: python-module
run: |
SKBUILD_CONFIGURE_OPTIONS="-DUSE_XSIMD=1" python -m pip install . -v

- name: Run Python profiling
working-directory: python-module
run: python -m unittest discover profiling
2 changes: 2 additions & 0 deletions.gitignore
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_skbuild

# Prerequisites
*.d

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4 changes: 2 additions & 2 deletionsenvironment-dev.yml
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Expand Up@@ -5,9 +5,9 @@ dependencies:
# Build dependencies
- cmake
# Host dependencies
- xtensor=0.24.0
- xtensor >=0.24.0
- numpy
- pybind11=2.4.3
- pybind11 >=2.4.3
# Test dependencies
- pytest

63 changes: 63 additions & 0 deletionspython-module/CMakeLists.txt
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cmake_minimum_required(VERSION 3.18..3.21)

project(xt)

# The C++ functions are build to a library with name "_${PROJECT_NAME}"
# The Python library simply loads all functions
set(PYPROJECT_NAME "_${PROJECT_NAME}")

option(USE_WARNINGS "${PROJECT_NAME}: Build with runtime warnings" ON)
option(USE_XSIMD "${PROJECT_NAME}: Build with hardware optimization" OFF)

if (DEFINED ENV{SETUPTOOLS_SCM_PRETEND_VERSION})
set(PROJECT_VERSION $ENV{SETUPTOOLS_SCM_PRETEND_VERSION})
message(STATUS "Building ${PROJECT_NAME} ${PROJECT_VERSION} (read from SETUPTOOLS_SCM_PRETEND_VERSION)")
else()
execute_process(
COMMAND python -c "from setuptools_scm import get_version; print(get_version(root='..'))"
WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
OUTPUT_VARIABLE PROJECT_VERSION
OUTPUT_STRIP_TRAILING_WHITESPACE)

message(STATUS "Building ${PROJECT_NAME} ${PROJECT_VERSION}")
endif()

if(NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE Release)
endif()

find_package(xtensor REQUIRED)
find_package(pybind11 REQUIRED CONFIG)

if (SKBUILD)
find_package(NumPy REQUIRED)
else()
find_package(Python REQUIRED COMPONENTS Interpreter Development NumPy)
endif()

pybind11_add_module(${PYPROJECT_NAME} module/main.cpp)

target_compile_definitions(${PYPROJECT_NAME} PUBLIC VERSION_INFO=${PROJECT_VERSION})
target_link_libraries(${PYPROJECT_NAME} PUBLIC xtensor)
target_include_directories(${PYPROJECT_NAME} PUBLIC "../include")

if (SKBUILD)
target_include_directories(${PYPROJECT_NAME} PUBLIC ${NumPy_INCLUDE_DIRS})
else()
target_link_libraries(${PYPROJECT_NAME} PUBLIC pybind11::module Python::NumPy)
endif()

if (USE_SIMD)
find_package(xsimd REQUIRED)
target_link_libraries(${PYPROJECT_NAME} PUBLIC xtensor::optimize xtensor::use_xsimd)
message(STATUS "Compiling ${PROJECT_NAME}-Python with hardware optimization")
endif()

if (SKBUILD)
if(APPLE)
set_target_properties(${PYPROJECT_NAME} PROPERTIES INSTALL_RPATH "@loader_path/${CMAKE_INSTALL_LIBDIR}")
else()
set_target_properties(${PYPROJECT_NAME} PROPERTIES INSTALL_RPATH "$ORIGIN/${CMAKE_INSTALL_LIBDIR}")
endif()
install(TARGETS ${PYPROJECT_NAME} DESTINATION .)
endif()
60 changes: 60 additions & 0 deletionspython-module/module/main.cpp
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/**
* @file
* @copyright Copyright 2020. Tom de Geus. All rights reserved.
* @license This project is released under the GNU Public License (MIT).
*/

#include <pybind11/pybind11.h>
#include <pybind11/stl.h>

#define FORCE_IMPORT_ARRAY
#include <xtensor-python/pyarray.hpp>
#include <xtensor-python/pytensor.hpp>
#include <xtensor.hpp>

namespace py = pybind11;

/**
* Overrides the `__name__` of a module.
* Classes defined by pybind11 use the `__name__` of the module as of the time they are defined,
* which affects the `__repr__` of the class type objects.
*/
class ScopedModuleNameOverride {
public:
explicit ScopedModuleNameOverride(py::module m, std::string name) : module_(std::move(m))
{
original_name_ = module_.attr("__name__");
module_.attr("__name__") = name;
}
~ScopedModuleNameOverride()
{
module_.attr("__name__") = original_name_;
}

private:
py::module module_;
py::object original_name_;
};

PYBIND11_MODULE(_xt, m)
{
// Ensure members to display as `xt.X` (not `xt._xt.X`)
ScopedModuleNameOverride name_override(m, "xt");

xt::import_numpy();

m.doc() = "Python bindings of xtensor";

m.def("mean", [](const xt::pyarray<double>& a) -> xt::pyarray<double> { return xt::mean(a); });
m.def("average", [](const xt::pyarray<double>& a, const xt::pyarray<double>& w) -> xt::pyarray<double> { return xt::average(a, w); });
m.def("average", [](const xt::pyarray<double>& a, const xt::pyarray<double>& w, const std::vector<ptrdiff_t>& axes) -> xt::pyarray<double> { return xt::average(a, w, axes); });

m.def("flip", [](const xt::pyarray<double>& a, ptrdiff_t axis) -> xt::pyarray<double> { return xt::flip(a, axis); });

m.def("cos", [](const xt::pyarray<double>& a) -> xt::pyarray<double> { return xt::cos(a); });

m.def("isin", [](const xt::pyarray<int>& a, const xt::pyarray<int>& b) -> xt::pyarray<bool> { return xt::isin(a, b); });
m.def("in1d", [](const xt::pyarray<int>& a, const xt::pyarray<int>& b) -> xt::pyarray<bool> { return xt::in1d(a, b); });


}
1 change: 1 addition & 0 deletionspython-module/module/xt/__init__.py
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from ._xt import * # noqa: F401, F403
79 changes: 79 additions & 0 deletionspython-module/profiling/test_a.py
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import unittest
import timeit
import warnings
from prettytable import PrettyTable

import xt
import numpy as np


class test_a(unittest.TestCase):
"""
??
"""

@classmethod
def setUpClass(self):

self.a = np.random.random([103, 102, 101])
self.axis = int(np.random.randint(0, high=3))
self.data = []

@classmethod
def tearDownClass(self):

self.data = sorted(self.data, key=lambda x: x[1])

table = PrettyTable(["function", "xtensor / numpy"])

for row in self.data:
table.add_row(row)

print("")
print(table)
print("")

# code = table.get_html_string()
# with open('profile.html', 'w') as file:
# file.write(code)

def test_mean(self):

n = timeit.timeit(lambda: np.mean(self.a), number=10)
x = timeit.timeit(lambda: xt.mean(self.a), number=10)
self.data.append(("mean", x / n))

def test_flip(self):

n = timeit.timeit(lambda: np.flip(self.a, self.axis), number=10)
x = timeit.timeit(lambda: xt.flip(self.a, self.axis), number=10)
self.data.append(("flip", x / n))

def test_cos(self):

n = timeit.timeit(lambda: np.cos(self.a), number=10)
x = timeit.timeit(lambda: xt.cos(self.a), number=10)
self.data.append(("cos", x / n))

def test_isin(self):

a = (np.random.random([103, 102]) * 1000).astype(np.intc)
b = (np.random.random([103, 102]) * 1000).astype(np.intc)

n = timeit.timeit(lambda: np.isin(a, b), number=10)
x = timeit.timeit(lambda: xt.isin(a, b), number=10)
self.data.append(("isin", x / n))

def test_in1d(self):

a = (np.random.random([1003]) * 1000).astype(np.intc)
b = (np.random.random([1003]) * 1000).astype(np.intc)

n = timeit.timeit(lambda: np.in1d(a, b), number=10)
x = timeit.timeit(lambda: xt.in1d(a, b), number=10)
self.data.append(("in1d", x / n))


if __name__ == "__main__":

unittest.main()
24 changes: 24 additions & 0 deletionspython-module/setup.py
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from pathlib import Path

from setuptools_scm import get_version
from skbuild import setup

project_name = "xt"

this_directory = Path(__file__).parent
long_description = (this_directory / ".." / "README.md").read_text()
license = (this_directory / ".." / "LICENSE").read_text()

setup(
name=project_name,
description="xt - Python bindings of xtensor",
long_description=long_description,
version=get_version(root="..", relative_to=__file__),
license=license,
author="Tom de Geus",
url=f"ttps://github.com/xtensor-stack/{project_name}",
packages=[f"{project_name}"],
package_dir={"": "module"},
cmake_install_dir=f"module/{project_name}",
cmake_minimum_required_version="3.13",
)
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