Unvendor boost eigen

.github/workflows/pypi.yml

@@ -0,0 +1,147 @@
+name: Build Status 
+
+on: [push, pull_request]
+
+env:
+  BOOST_VERSION: 1.84.0
+  EIGEN_VERSION: 3.4.0
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        # macos-13 is an intel runner, macos-14 is apple silicon
+        python: [38, 39, 310, 311, 312]
+        cfg:
+          - { os: ubuntu-latest, cibw_id: manylinux_x86_64, cc: gcc, cxx: g++,  platform: x64, root_install_dir: '/home/runner/work'}
+          - { os: ubuntu-latest, cibw_id: musllinux_x86_64, cc: gcc, cxx: g++, platform: x64, root_install_dir: '/home/runner/work'}
+          - { os: macos-13, cibw_id: macosx_x86_64, cc: clang, cxx: clang++, platform: x64, root_install_dir: '/Users/runner/work'} # intel runner
+          - { os: macos-14, cibw_id: macosx_arm64, cc: clang, cxx: clang++, platform: arm64, root_install_dir: '/Users/runner/work'} # apple silicon runner
+          - { os: windows-latest, cibw_id: win_amd64, cc: cl, cxx: cl, platform: x64, root_install_dir: 'D:\'}
+    env:
+      PYTHON_VENV_ROOT: ${{github.workspace}}/src/python-venv
+
+
+    name: Build and test on ${{ matrix.cfg.os }} for cp${{ matrix.python }}-${{ matrix.cfg.cibw_id }}
+    runs-on: ${{ matrix.cfg.os }}
+
+    steps:
+    - name: Checkout project 
+      uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - name: Get history and tags for SCM versioning to work
+      run: |
+        git fetch --prune --unshallow
+        # git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+    - name: Install dependencies
+      id: install-dependencies
+      uses: vinecopulib/vinecopulib/.github/actions/install-dependencies@better-actions
+      with:
+          os: ${{ matrix.cfg.os }}
+          platform: ${{ matrix.cfg.platform }}
+          boost_install_dir: ${{ matrix.cfg.root_install_dir }}
+          eigen_install_dir: ${{ matrix.cfg.root_install_dir }}
+          boost_version: ${{ env.BOOST_VERSION }}
+          eigen_version: ${{ env.EIGEN_VERSION }}
+          wdm: 'false'
+    - name: Lint with flake8
+      if: matrix.cfg.os != 'windows-latest'
+      run: |
+        python3 -m venv ${PYTHON_VENV_ROOT}
+        source ${PYTHON_VENV_ROOT}/bin/activate
+        pip3 install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude=lib
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --exclude=lib
+    - name: Build and test wheels
+      uses: pypa/cibuildwheel@v2.20.0
+      env:
+        CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.cfg.cibw_id }}
+        CIBW_ENVIRONMENT_WINDOWS: Boost_INCLUDE_DIR='${{steps.install-dependencies.outputs.BOOST_ROOT}}\include' EIGEN3_INCLUDE_DIR='C:\ProgramData\chocolatey\lib\eigen\include'
+        CIBW_ENVIRONMENT_MACOS: "Boost_INCLUDE_DIR=${{steps.install-dependencies.outputs.BOOST_ROOT}}/include EIGEN3_INCLUDE_DIR=${{matrix.cfg.root_install_dir}}/include/eigen3"
+        CIBW_ENVIRONMENT_LINUX: "Boost_INCLUDE_DIR=/host${{steps.install-dependencies.outputs.BOOST_ROOT}}/include EIGEN3_INCLUDE_DIR=/host${{matrix.cfg.root_install_dir}}/include/eigen3"
+        CIBW_ENVIRONMENT_PASS_LINUX: "Boost_INCLUDE_DIR EIGEN3_INCLUDE_DIR"
+    - name: Upload binaries
+      uses: actions/upload-artifact@v4
+      with:
+        name: cibw-wheels-${{ matrix.cfg.os }}-${{ matrix.python }}-${{ matrix.cfg.cibw_id }}
+        path: ./wheelhouse/*.whl
+
+  build_sdist:
+    runs-on: ubuntu-latest
+    # needs: build
+    steps:
+    - name: Checkout project 
+      uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - name: Get history and tags for SCM versioning to work
+      run: |
+        git fetch --prune --unshallow
+        git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+    - name: Install dependencies
+      id: install-dependencies
+      uses: vinecopulib/vinecopulib/.github/actions/install-dependencies@better-actions
+      with:
+          os: 'ubuntu-latest'
+          boost_install_dir: '/home/runner/work'
+          eigen_install_dir: '/home/runner/work'
+          boost_version: ${{ env.BOOST_VERSION }}
+          eigen_version: ${{ env.EIGEN_VERSION }}
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.8
+    - name: Upgrade pip and install build dependency
+      run: |
+        echo "Boost_INCLUDE_DIR=${{steps.install-dependencies.outputs.BOOST_ROOT}}/include" >> $GITHUB_ENV
+        echo "EIGEN3_INCLUDE_DIR=/home/runner/work/include/eigen3" >> $GITHUB_ENV
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Create source distribution 
+      run: |
+        export Boost_INCLUDE_DIR=$Boost_INCLUDE_DIR
+        export EIGEN3_INCLUDE_DIR=$EIGEN3_INCLUDE_DIR
+        pipx run build --sdist
+    - name: Upload binaries
+      uses: actions/upload-artifact@v4
+      with:
+        name: cibw-sdist
+        path: dist/*.tar.gz
+
+  upload_to_pypi:
+    needs: build
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - name: Download cibw artifacts
+        uses: actions/download-artifact@v4
+        with:
+          # unpacks all CIBW artifacts into dist/
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+      - name: Publish distribution Test PyPI
+        if: |
+          job.status == 'success' 
+            && github.base_ref == 'main' 
+            && github.head_ref == 'dev'
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.test_pypi_password }}
+          repository_url: https://test.pypi.org/legacy/
+      - name: Publish distribution to PyPI
+        if: |
+          job.status == 'success' 
+            && github.event_name == 'push' 
+            && startsWith(github.event.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.pypi_password }}

.gitignore

@@ -85,3 +85,16 @@ Temporary Items
 .apdisk
 # boost
 lib/boost
+
+CMakeLists.txt.user
+CMakeCache.txt
+CMakeFiles
+CMakeScripts
+Testing
+Makefile
+cmake_install.cmake
+install_manifest.txt
+compile_commands.json
+CTestTestfile.cmake
+_deps
+CMakeUserPresets.json

.gitmodules

@@ -1,6 +1,3 @@
-[submodule "lib/eigen"]
-	path = lib/eigen
-	url = https://github.com/eigenteam/eigen-git-mirror
 [submodule "lib/kde1d"]
 	path = lib/kde1d
 	url = https://github.com/vinecopulib/kde1d-cpp

LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright © 2019 Thomas Nagler and Thibault Vatter
+Copyright © 2024 Thomas Nagler and Thibault Vatter
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the “Software”), to deal in

MANIFEST.in

@@ -1,6 +1,3 @@
 include README.md LICENSE requirements.txt
 recursive-include src *
-recursive-include lib/boost *.hpp *.h
-recursive-include lib/eigen/Eigen *
-recursive-include lib/eigen/unsupported/Eigen *
-recursive-include lib/kde1d-cpp/include *.hpp
+recursive-include lib/kde1d/include *.hpp

README.md

@@ -4,3 +4,45 @@
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/3c0056d3ca5244a5ba6a2b32f87be4cf)](https://www.codacy.com/gh/vinecopulib/pykde1d?utm_source=github.com&utm_medium=referral&utm_content=vinecopulib/pykde1d&utm_campaign=Badge_Grade)
 [![Documentation](https://img.shields.io/website/http/vinecopulib.github.io/pykde1d.svg)](https://vinecopulib.github.io/pykde1d/)
+
+### Summary
+
+This library provides a fast and flexible univariate kernel density estimator for Python:
+
+- It implements a univariate kernel density estimator that can handle
+bounded and discrete data,
+- It provides classical kernel density as well as log-linear and log-quadratic methods,
+- It is highly efficient due to the Fast Fourier Transform, spline interpolation,
+  and a C++ backend.
+
+For details, see the
+[API documentation](https://tnagler.github.io/kde1d/).
+
+### Prerequisites
+
+- numpy (>=1.14)
+- To install from source:
+    - pybind11 (>=2.4)
+    - setuptools (>=30.3.0)
+    - setuptools_scm (>=2.0.0)
+    - a compiler with C++11 support (Linux, OS X) or Visual Studio 2015 (required for all Python versions, see notes below)
+    - Eigen (the environment variable `EIGEN3_INCLUDE_DIR` must be set to the directory containing the Eigen headers)
+    - boost (the environment variable `Boost_INCLUDE_DIR` must be set to the directory containing the boost headers)
+
+### Installation
+
+The easiest way to install the latest release is to use `pip`:
+
+```
+pip install pykde1d
+```
+
+To install from source, just clone this repository and do `pip install`.
+Note the `--recursive` option which is needed for the `vinecopulib` and `wdm` submodules:
+
+```bash
+git clone --recursive https://github.com/vinecopulib/pykde1d.git
+pip install ./pykde1d
+```
+
+Note that Eigen and Boost need to be available on your system for the build to succeed, using the environment variables `EIGEN3_INCLUDE_DIR` and `Boost_INCLUDE_DIR` respectively.

pyproject.toml

@@ -0,0 +1,50 @@
+[build-system]
+requires = ["setuptools>=64.0.0", "setuptools_scm>=8.0.0", "pybind11>=2.10.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pykde1d"
+dynamic = ["version"]
+authors = [
+  { name="Thibault Vatter", email="info@vinecopulib.com" },
+  { name="Thomas Nagler", email="info@vinecopulib.com" },
+]
+description = "A python interface to kde1d"
+readme = "README.md"
+license = {file = "LICENSE"}
+requires-python = ">=3.8"
+keywords = ['kernel density estimation', 'nonparametric statistics']
+classifiers = [
+        'Development Status :: 3 - Alpha',
+        'Topic :: Scientific/Engineering',
+        'Topic :: Scientific/Engineering :: Mathematics',
+        'Programming Language :: C++',
+        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
+        'License :: OSI Approved :: MIT License'
+]
+dependencies = [
+  'numpy>=1.14'
+]
+
+[tool.setuptools_scm]
+version_scheme = "python-simplified-semver"
+local_scheme = "no-local-version"
+
+[project.urls]
+Homepage = "https://github.com/vinecopulib/pykde1d/"
+Documentation = "https://vinecopulib.github.io/pykde1d"
+Repository = "https://github.com/vinecopulib/pykde1d.git"
+Issues = "https://github.com/vinecopulib/pykde1d/issues"
+
+[tool.pytest.ini_options]
+pythonpath = [
+  "src"
+]
+
+[tool.cibuildwheel]
+test-requires = "pytest"
+test-command = "pytest {project}/tests -r a"