gpflash 0.2.0__tar.gz

gpflash-0.2.0/.clang-format

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+---
+Language:        Cpp
+BasedOnStyle:  Google
+ColumnLimit:     120
+IndentWidth:     4
+BinPackArguments: false
+BinPackParameters: false
+ConstructorInitializerIndentWidth: 8
+ContinuationIndentWidth: 8
+AlignAfterOpenBracket: AlwaysBreak
+AlignOperands: false
+BreakBeforeBinaryOperators: NonAssignment
+IncludeBlocks: Preserve

gpflash-0.2.0/.github/workflows/ci.yml

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+# Builds the C++ library and runs its tests (ctest) on Linux and macOS, after every push to main.
+#
+# Linux installs everything the tests can use, so it runs the full suite: the formatting check with clang-format 15
+# and the MPI optimizer test with MPICH. macOS runs the rest, with Apple clang and Homebrew's libraries, as the README's
+# macOS build does. A manual run (workflow_dispatch) tests any branch on request.
+name: CI
+
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  build_and_test:
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: Linux (GCC)
+            os: ubuntu-24.04
+          - name: macOS (Apple clang)
+            os: macos-15
+    steps:
+      - uses: actions/checkout@v7.0.1
+
+      - name: Install dependencies (Linux)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y cmake g++ libarmadillo-dev libopenblas-dev libhdf5-dev libnlopt-cxx-dev \
+              clang-format-15 mpich libmpich-dev
+
+      - name: Install dependencies (macOS)
+        if: runner.os == 'macOS'
+        run: brew install armadillo libomp hdf5 nlopt
+
+      - name: Configure (Linux)
+        if: runner.os == 'Linux'
+        run: cmake -S . -B build -DCMAKE_BUILD_TYPE=Release
+
+      # The MPI test runs on Linux only: the macOS runner has too few cores for its 4 processes.
+      - name: Configure (macOS)
+        if: runner.os == 'macOS'
+        run: cmake -S . -B build -DCMAKE_BUILD_TYPE=Release -DOpenMP_ROOT="$(brew --prefix libomp)" -DGPFLASH_BUILD_MPI_TEST=OFF
+
+      - name: Build
+        run: cmake --build build --parallel
+
+      - name: Test
+        run: ctest --test-dir build --output-on-failure

gpflash-0.2.0/.github/workflows/wheels.yml

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+# Builds the Python wheels and sdist and tests each wheel, after every push to main, and publishes to PyPI when a
+# GitHub release is published. A manual run (workflow_dispatch) tests any branch, and can publish to TestPyPI to try a
+# release first. Pull requests do not run it: a run takes several hundred billed minutes on a private repository.
+#
+# Publishing uses PyPI trusted publishing: no token is stored. Before the first release, add this repository and
+# workflow (wheels.yml, environment "pypi") as a trusted publisher on the PyPI project, and likewise on TestPyPI with
+# environment "testpypi". Publishing runs only in the public repository, where the trusted publishers point.
+name: Wheels
+
+on:
+  push:
+    branches: [main]
+  release:
+    types: [published]
+  workflow_dispatch:
+    inputs:
+      platforms:
+        description: "Which platforms to build wheels for"
+        type: choice
+        options: [all, linux, macos, windows]
+        default: all
+      publish_to_testpypi:
+        description: "Publish the built distributions to TestPyPI (needs every platform)"
+        type: boolean
+        default: false
+
+permissions:
+  contents: read
+
+jobs:
+  # The runners, one per wheel platform: Linux x86_64 and aarch64 (native), macOS arm64 and x86_64, Windows x64. A
+  # manual run can keep one platform, so a fix for it costs one runner rather than five.
+  plan:
+    name: Choose platforms
+    runs-on: ubuntu-24.04
+    outputs:
+      include: ${{ steps.pick.outputs.include }}
+    steps:
+      - id: pick
+        env:
+          PLATFORMS: ${{ inputs.platforms || 'all' }}
+        run: |
+          runners='[
+            {"platform": "linux",   "os": "ubuntu-24.04"},
+            {"platform": "linux",   "os": "ubuntu-24.04-arm"},
+            {"platform": "macos",   "os": "macos-15",       "macos_deployment_target": "15.0"},
+            {"platform": "macos",   "os": "macos-15-intel", "macos_deployment_target": "15.0"},
+            {"platform": "windows", "os": "windows-2025"}
+          ]'
+          include=$(jq -c --arg p "$PLATFORMS" '[.[] | select($p == "all" or .platform == $p)]' <<< "$runners")
+          echo "include=$include" >> "$GITHUB_OUTPUT"
+
+  build_wheels:
+    name: Wheels on ${{ matrix.os }}
+    needs: plan
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include: ${{ fromJSON(needs.plan.outputs.include) }}
+    steps:
+      - uses: actions/checkout@v7.0.1
+      # Windows builds its libraries from source, OpenBLAS alone taking almost two hours, so they are cached, keyed on
+      # the script that builds them. The script reuses a restored install, and only a complete one is saved.
+      - name: Restore Windows libraries
+        id: windows_deps
+        if: runner.os == 'Windows'
+        uses: actions/cache/restore@v6.1.0
+        with:
+          path: C:\gpflash_deps
+          key: windows-deps-${{ hashFiles('python/ci/install_deps_windows.ps1') }}
+      - uses: pypa/cibuildwheel@v4.2.1
+        env:
+          # The oldest macOS the wheel runs on. It must not be older than the Homebrew libraries delocate bundles,
+          # which are built for the runner's own macOS.
+          MACOSX_DEPLOYMENT_TARGET: ${{ matrix.macos_deployment_target }}
+      - name: Check Windows libraries
+        id: windows_deps_check
+        if: always() && runner.os == 'Windows' && steps.windows_deps.outputs.cache-hit != 'true'
+        shell: pwsh
+        run: if (Test-Path C:\gpflash_deps\gpflash_deps_complete) { "complete=true" >> $env:GITHUB_OUTPUT }
+      - name: Save Windows libraries
+        if: always() && steps.windows_deps_check.outputs.complete == 'true'
+        uses: actions/cache/save@v6.1.0
+        with:
+          path: C:\gpflash_deps
+          key: windows-deps-${{ hashFiles('python/ci/install_deps_windows.ps1') }}
+      - uses: actions/upload-artifact@v7.0.1
+        with:
+          name: wheels-${{ matrix.os }}
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Source distribution
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v7.0.1
+      - uses: actions/setup-python@v7.0.0
+        with:
+          python-version: "3.13"
+      - run: python -m pip install build
+      - run: python -m build --sdist
+      - uses: actions/upload-artifact@v7.0.1
+        with:
+          name: sdist
+          path: dist/*.tar.gz
+
+  publish_pypi:
+    name: Publish to PyPI
+    needs: [build_wheels, build_sdist]
+    if: github.repository == 'marchildon/gpflash' && github.event_name == 'release' && github.event.action == 'published'
+    runs-on: ubuntu-24.04
+    environment:
+      name: pypi
+      url: https://pypi.org/p/gpflash
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v8.0.1
+        with:
+          path: dist
+          merge-multiple: true
+      - uses: pypa/gh-action-pypi-publish@v1.14.2
+        with:
+          skip-existing: true  # a rerun after a partial upload skips what is already there
+
+  publish_testpypi:
+    name: Publish to TestPyPI
+    needs: [build_wheels, build_sdist]
+    if: github.repository == 'marchildon/gpflash' && github.event_name == 'workflow_dispatch' && inputs.publish_to_testpypi && inputs.platforms == 'all'
+    runs-on: ubuntu-24.04
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/gpflash
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v8.0.1
+        with:
+          path: dist
+          merge-multiple: true
+      - uses: pypa/gh-action-pypi-publish@v1.14.2
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          skip-existing: true

gpflash-0.2.0/.gitignore

@@ -0,0 +1,15 @@
+# No trailing slash, so it also matches a `build` symlink; `build/` matches directories only.
+/build
+
+# Every other build directory, at any depth, such as tst/build or a builds/ tree.
+**/build*/
+
+# macOS Finder metadata.
+.DS_Store
+
+# Python: bytecode, test caches, and the sdist and wheels python -m build writes. build_python/, where pip builds
+# the module, matches the build-directory rule above.
+__pycache__/
+.pytest_cache/
+/dist/
+*.egg-info/

gpflash-0.2.0/CHANGELOG.md

@@ -0,0 +1,35 @@
+# Changelog
+
+Every release of GpFlash and what it changed. Version numbers follow
+[semantic versioning](https://semver.org); before 1.0, a minor release may change the interface.
+
+## 0.2.0 (2026-10-17)
+
+### Added
+
+- **Python package**, `pip install gpflash`, with wheels for Linux (x86_64, aarch64), macOS
+  (arm64, x86_64) and Windows (x64) on Python 3.11 to 3.14, every dependency included. It offers
+  a NumPy-style `GaussianProcess` (`fit`, `predict`, `predict_gradient`, `save`, `load`) and the
+  C++ interface under its C++ names. See [`python/README.md`](python/README.md).
+- CMake option `GPFLASH_BUILD_PYTHON`, off by default, to build the Python module.
+- Citation information for the GpFlash paper, [arXiv:2610.16861](https://arxiv.org/abs/2610.16861):
+  `CITATION.cff`, which gives the repository a "Cite this repository" button, and a BibTeX
+  entry in [`python/README.md`](python/README.md).
+- Continuous integration: the C++ tests on Linux and macOS, and the Python wheels on every
+  platform, after each push to `main`.
+
+### Fixed
+
+- A cache save that fails part way, as on a full disk, no longer leaves its file open in HDF5. HDF5 1.10
+  cannot close it, and the process may crash as it exits.
+
+### Changed
+
+- The version is set in one place, `include/gpflash/Version.hpp`; CMake and the Python package
+  read it from there.
+
+## 0.1.0 (2026-10-12)
+
+First release: a header-only C++14 library for exact Gaussian process regression, with the
+marginal log likelihood and its analytic hyperparameter gradients, hyperparameter fitting
+through NLopt, posterior mean and variance with their gradients, and an HDF5 posterior cache.

gpflash-0.2.0/CITATION.cff

@@ -0,0 +1,33 @@
+cff-version: 1.2.0
+message: "If you use GpFlash, please cite the paper below."
+type: software
+title: GpFlash
+abstract: >-
+  Header-only C++ library for exact, dense Gaussian process regression: the marginal log
+  likelihood with analytic hyperparameter gradients, hyperparameter fitting, and posterior
+  mean and variance, with Python bindings.
+authors:
+  - family-names: Marchildon
+    given-names: André
+repository-code: "https://github.com/marchildon/gpflash"
+license: Apache-2.0
+keywords:
+  - gaussian-process
+  - kriging
+  - surrogate-model
+  - cpp
+  - python
+preferred-citation:
+  type: article
+  title: "GpFlash: Maximizing Speed and Minimizing Memory for Gaussian Process Training and Prediction"
+  authors:
+    - family-names: Marchildon
+      given-names: André
+  year: 2026
+  month: 10
+  url: "https://arxiv.org/abs/2610.16861"
+  doi: 10.48550/arXiv.2610.16861
+  identifiers:
+    - type: other
+      value: "arXiv:2610.16861"
+      description: The arXiv preprint

gpflash-0.2.0/CMakeLists.txt

@@ -0,0 +1,131 @@
+# The package's one build: standalone, from a parent project's add_subdirectory, or by a build system that puts the
+# dependencies on CMAKE_PREFIX_PATH.
+
+cmake_minimum_required(VERSION 3.22)
+
+# The version is set once, in include/gpflash/Version.hpp; CMake and pyproject.toml both read it from there.
+file(READ ${CMAKE_CURRENT_SOURCE_DIR}/include/gpflash/Version.hpp _gpflash_version_hpp)
+string(REGEX MATCH "MAJOR ([0-9]+)\n#define GPFLASH_VERSION_MINOR ([0-9]+)\n#define GPFLASH_VERSION_PATCH ([0-9]+)"
+       _ "${_gpflash_version_hpp}")
+project(GpFlash VERSION ${CMAKE_MATCH_1}.${CMAKE_MATCH_2}.${CMAKE_MATCH_3} LANGUAGES CXX)
+
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+# The package's own targets, the tests, compile as ISO C++14 (-std=c++14, not the compiler's gnu++14 default), so a
+# GNU extension in a header fails here. Not exported: a consumer only inherits the cxx_std_14 floor below.
+set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+set(GPFLASH_ROOT ${CMAKE_CURRENT_SOURCE_DIR})
+
+# Only 64-bit targets have been built and tested. A 32-bit one should compile, ARMA_64BIT_WORD below keeping the
+# element counts 64-bit, and run out of address space at roughly 10,000 training points.
+if(NOT CMAKE_SIZEOF_VOID_P EQUAL 8)
+    message(WARNING "GpFlash is tested on 64-bit targets only; this one has ${CMAKE_SIZEOF_VOID_P}-byte pointers.")
+endif()
+
+include(GNUInstallDirs)
+include(CMakePackageConfigHelpers)
+
+# The vendor as FindBLAS spells it (OpenBLAS, Apple for Accelerate, Intel10_64lp for MKL, ...). The caller's
+# BLA_VENDOR wins; otherwise Accelerate on Apple, which every Mac has, and OpenBLAS elsewhere.
+if(DEFINED BLA_VENDOR)
+    set(GPFLASH_BLA_VENDOR "${BLA_VENDOR}")
+elseif(DEFINED ENV{BLA_VENDOR})
+    set(GPFLASH_BLA_VENDOR "$ENV{BLA_VENDOR}")
+elseif(APPLE)
+    set(GPFLASH_BLA_VENDOR Apple)
+else()
+    set(GPFLASH_BLA_VENDOR OpenBLAS)
+endif()
+
+# ARMA_DONT_USE_WRAPPER binds BlasLapack.hpp's extern "C" prototypes straight to the linked library.
+# ARMA_USE_BLAS and ARMA_USE_LAPACK let Armadillo's own operations call the same library.
+# ARMA_DONT_USE_FORTRAN_HIDDEN_ARGS stays off: BlasLapack.hpp follows Armadillo's hidden-length setting, and a
+# gfortran-built LAPACK needs the lengths (GCC bug 90329).
+# ARMA_NO_DEBUG drops Armadillo's bounds checks; the library's own checks guard what reaches its loops.
+# ARMA_USE_HDF5 selects the save path posterior_cache/ needs; a consumer compiling without it would get a different
+# one that does not work.
+# ARMA_64BIT_WORD is Armadillo's default on a 64-bit target, stated because an n_train by n_train buffer passes 2^31
+# elements at n_train ~ 46,000. BlasLapack.hpp static_asserts it for a consumer compiling without these defines.
+# The target's INTERFACE definitions below hand every one to consumers.
+set(GPFLASH_ARMA_DEFS
+    ARMA_DONT_USE_WRAPPER
+    ARMA_NO_DEBUG
+    ARMA_USE_BLAS
+    ARMA_USE_LAPACK
+    ARMA_USE_HDF5
+    ARMA_64BIT_WORD)
+
+# Platform.hpp's probe, decided here where the vendor is known; "All" leaves it to the header. Apple and NAS are
+# FindBLAS's names for Accelerate.
+if(GPFLASH_BLA_VENDOR MATCHES "^(Apple|NAS)$")
+    set(GPFLASH_PLATFORM_DEFS GPFLASH_BLAS_SKINNY_GEMV_IS_SLOW=1)
+elseif(GPFLASH_BLA_VENDOR STREQUAL "All")
+    set(GPFLASH_PLATFORM_DEFS "")
+else()
+    set(GPFLASH_PLATFORM_DEFS GPFLASH_BLAS_SKINNY_GEMV_IS_SLOW=0)
+endif()
+
+macro(gpflash_find_dependency)
+    find_package(${ARGV} REQUIRED)
+endmacro()
+include(cmake/GpFlashDependencies.cmake)
+
+# Header-only, so an INTERFACE target: a consumer compiles every loop itself, with its own flags. The README's
+# "Compiling the headers" section is the contract this target meets; a build not using it follows that section.
+add_library(GpFlash INTERFACE)
+# The installed name, so a parent project's add_subdirectory links the same target a find_package user does.
+add_library(GpFlash::GpFlash ALIAS GpFlash)
+target_include_directories(GpFlash INTERFACE
+    $<BUILD_INTERFACE:${GPFLASH_ROOT}/include>
+    $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>)
+target_compile_definitions(GpFlash INTERFACE ${GPFLASH_ARMA_DEFS} ${GPFLASH_PLATFORM_DEFS})
+
+# A floor, not a pin.
+target_compile_features(GpFlash INTERFACE cxx_std_14)
+
+target_link_libraries(GpFlash INTERFACE
+    GpFlash::Armadillo
+    OpenMP::OpenMP_CXX
+    LAPACK::LAPACK
+    BLAS::BLAS
+    GpFlash::HDF5
+    GpFlash::NLopt)
+
+install(DIRECTORY include/ DESTINATION ${CMAKE_INSTALL_INCLUDEDIR} FILES_MATCHING PATTERN "*.hpp")
+install(FILES LICENSE NOTICE THIRD-PARTY-NOTICES DESTINATION ${CMAKE_INSTALL_DOCDIR})
+
+# A consumer calls find_package(GpFlash) and links GpFlash::GpFlash. The package config finds the dependencies,
+# then includes the targets file.
+set(GPFLASH_INSTALL_CMAKEDIR ${CMAKE_INSTALL_LIBDIR}/cmake/GpFlash)
+install(TARGETS GpFlash EXPORT GpFlash-export)
+install(EXPORT GpFlash-export
+        NAMESPACE GpFlash::
+        DESTINATION ${GPFLASH_INSTALL_CMAKEDIR}
+        FILE GpFlashTargets.cmake)
+configure_file(cmake/GpFlashConfig.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/GpFlashConfig.cmake @ONLY)
+# Before 1.0 a minor release may break the interface, so a request for 0.Y accepts only 0.Y.x.
+write_basic_package_version_file(${CMAKE_CURRENT_BINARY_DIR}/GpFlashConfigVersion.cmake
+                                 COMPATIBILITY SameMinorVersion
+                                 ARCH_INDEPENDENT)
+install(FILES
+        ${CMAKE_CURRENT_BINARY_DIR}/GpFlashConfig.cmake
+        ${CMAKE_CURRENT_BINARY_DIR}/GpFlashConfigVersion.cmake
+        cmake/GpFlashDependencies.cmake
+        DESTINATION ${GPFLASH_INSTALL_CMAKEDIR})
+
+# The Python module gpflash._core: built when pip drives this file through scikit-build-core (pyproject.toml), which
+# defines SKBUILD, or on request. A C++ consumer never needs Python.
+option(GPFLASH_BUILD_PYTHON "Build the Python module gpflash._core" OFF)
+if(GPFLASH_BUILD_PYTHON OR DEFINED SKBUILD)
+    add_subdirectory(python)
+endif()
+
+# Only for this project's own build: a parent project's add_subdirectory builds none of the tests.
+if(PROJECT_IS_TOP_LEVEL)
+    include(CTest)
+    if(BUILD_TESTING)
+        add_subdirectory(tst)
+    endif()
+endif()

gpflash-0.2.0/LICENSE

@@ -0,0 +1,202 @@
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
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+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
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+
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gpflash-0.2.0/NOTICE

@@ -0,0 +1,2 @@
+GpFlash
+Copyright 2026 André Marchildon