linkcell 0.3.2__tar.gz → 0.3.4__tar.gz

linkcell-0.3.4/.github/scripts/setup-msvc.ps1

@@ -0,0 +1,31 @@
+Set-StrictMode -Version Latest
+$ErrorActionPreference = "Stop"
+
+$environmentBefore = @{}
+Get-ChildItem Env: | ForEach-Object {
+    $environmentBefore[$_.Name] = $_.Value
+}
+
+$vswhere = Join-Path ${env:ProgramFiles(x86)} `
+    "Microsoft Visual Studio\Installer\vswhere.exe"
+$installationPath = & $vswhere -latest -products * `
+    -requires Microsoft.VisualStudio.Component.VC.Tools.x86.x64 `
+    -property installationPath
+$installationPath = [string]($installationPath | Select-Object -First 1)
+if ([string]::IsNullOrWhiteSpace($installationPath)) {
+    throw "Visual Studio C++ tools not found"
+}
+
+$developerShell = Join-Path $installationPath `
+    "Common7\Tools\Launch-VsDevShell.ps1"
+& $developerShell -Arch amd64 -HostArch amd64 -SkipAutomaticLocation
+
+Get-ChildItem Env: | Where-Object {
+    -not $environmentBefore.ContainsKey($_.Name) -or
+    $environmentBefore[$_.Name] -ne $_.Value
+} | ForEach-Object {
+    $delimiter = "DSEAMS_$([guid]::NewGuid().ToString('N'))"
+    Add-Content -Path $env:GITHUB_ENV -Value "$($_.Name)<<$delimiter"
+    Add-Content -Path $env:GITHUB_ENV -Value $_.Value
+    Add-Content -Path $env:GITHUB_ENV -Value $delimiter
+}

linkcell-0.3.4/.github/workflows/ci.yml

@@ -0,0 +1,230 @@
+name: ci
+
+on:
+  push:
+    branches: [main]
+    tags: ['v*']
+  pull_request:
+
+jobs:
+  fmt:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      - uses: dtolnay/rust-toolchain@4360b52568e2003a75bf9bc1d59f33a8e3fc893c # stable
+        with:
+          components: rustfmt
+      - run: cargo fmt --check
+
+  header-check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      - uses: dtolnay/rust-toolchain@4360b52568e2003a75bf9bc1d59f33a8e3fc893c # stable
+      # Pin matches the version comment cbindgen writes into include/linkcell.h.
+      - run: cargo install cbindgen --version 0.29.4
+      - run: scripts/regen-capi-headers.sh --check
+
+  python:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      - uses: dtolnay/rust-toolchain@4360b52568e2003a75bf9bc1d59f33a8e3fc893c # stable
+      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
+        with:
+          python-version: '3.12'
+      - uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
+        with:
+          path: |
+            ~/.cargo/registry
+            ~/.cargo/git
+          key: ${{ runner.os }}-py-${{ hashFiles('Cargo.lock', 'python/Cargo.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-py-
+      - name: Install Python test deps
+        run: |
+          python -m venv .venv
+          . .venv/bin/activate
+          python -m pip install --upgrade pip
+          pip install maturin pytest numpy
+          pip install torch --index-url https://download.pytorch.org/whl/cpu
+      - name: maturin develop
+        run: |
+          . .venv/bin/activate
+          maturin develop
+      - name: pytest
+        run: |
+          . .venv/bin/activate
+          pytest tests/python -q
+
+  cargo:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        crate:
+          - name: default
+            flags: ""
+          - name: serial
+            flags: --no-default-features --features capi
+    name: cargo (${{ matrix.os }}, ${{ matrix.crate.name }})
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      - uses: dtolnay/rust-toolchain@4360b52568e2003a75bf9bc1d59f33a8e3fc893c # stable
+        with:
+          components: clippy
+      - uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
+        with:
+          path: |
+            ~/.cargo/registry
+            ~/.cargo/git
+          key: ${{ runner.os }}-cargo-${{ hashFiles('Cargo.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-cargo-
+      - run: cargo test --locked ${{ matrix.crate.flags }}
+      - run: cargo clippy --locked --all-targets ${{ matrix.crate.flags }} -- -D warnings
+
+  meson:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+    name: meson (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      - uses: dtolnay/rust-toolchain@4360b52568e2003a75bf9bc1d59f33a8e3fc893c # stable
+      - name: Configure MSVC
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: .github/scripts/setup-msvc.ps1
+      - uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
+        with:
+          path: |
+            ~/.cargo/registry
+            ~/.cargo/git
+          key: ${{ runner.os }}-cargo-${{ hashFiles('Cargo.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-cargo-
+      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
+        with:
+          python-version: '3.12'
+      - run: pip install meson ninja
+      - name: Meson setup
+        if: runner.os != 'Windows'
+        run: meson setup build --prefix "$PWD/prefix" --libdir lib
+        shell: bash
+      - name: Meson setup
+        if: runner.os == 'Windows'
+        run: meson setup build --prefix "$env:GITHUB_WORKSPACE/prefix" --libdir lib
+        shell: pwsh
+      - run: meson compile -C build
+      - run: meson test -C build --print-errorlogs
+      - run: meson install -C build
+      - name: Installed headers and libraries
+        shell: bash
+        run: |
+          prefix="$PWD/prefix"
+          test -f "$prefix/include/linkcell.h"
+          test -f "$prefix/include/linkcell.hpp"
+          test -f "$prefix/include/linkcell_gpu.h"
+          test -f "$prefix/include/linkcell_gpu.hpp"
+          case "$RUNNER_OS" in
+            Windows)
+              test -f "$prefix/bin/linkcell.dll"
+              test -f "$prefix/lib/linkcell.dll.lib"
+              test -f "$prefix/lib/linkcell.lib"
+              test -f "$prefix/lib/linkcell_gpu.lib"
+              ;;
+            macOS)
+              test -f "$prefix/lib/liblinkcell.dylib"
+              test -f "$prefix/lib/liblinkcell.a"
+              test -f "$prefix/lib/liblinkcell_gpu.a"
+              ;;
+            Linux)
+              test -f "$prefix/lib/liblinkcell.so"
+              test -f "$prefix/lib/liblinkcell.a"
+              test -f "$prefix/lib/liblinkcell_gpu.a"
+              ;;
+          esac
+      - name: pkg-config after meson install
+        if: runner.os != 'Windows'
+        run: |
+          prefix="$PWD/prefix"
+          export PKG_CONFIG_PATH="$prefix/lib/pkgconfig"
+          pkg-config --exists --print-errors linkcell
+          pkg-config --modversion linkcell
+          pkg-config --cflags --libs linkcell
+          pkg-config --exists --print-errors linkcell-gpu
+          pkg-config --modversion linkcell-gpu
+          c++ -std=c++17 tests/cmake-consumer/gpu.cpp \
+            $(pkg-config --cflags --libs linkcell-gpu) \
+            -o build/installed-gpu-consumer
+
+  cmake:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+    name: cmake (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      - uses: dtolnay/rust-toolchain@4360b52568e2003a75bf9bc1d59f33a8e3fc893c # stable
+      - name: Configure MSVC
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: .github/scripts/setup-msvc.ps1
+      - uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
+        with:
+          path: |
+            ~/.cargo/registry
+            ~/.cargo/git
+          key: ${{ runner.os }}-cargo-${{ hashFiles('Cargo.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-cargo-
+      - run: cmake -S . -B build -DCMAKE_INSTALL_PREFIX="$PWD/prefix"
+        shell: bash
+      - run: cmake --build build --config Release
+      - run: ctest --test-dir build -C Release --output-on-failure
+      - run: cmake --install build --config Release
+      - name: find_package after cmake install
+        shell: bash
+        run: |
+          test -f prefix/include/linkcell.h
+          test -f prefix/lib/cmake/linkcell/linkcellConfig.cmake
+          if [[ "$RUNNER_OS" == "Windows" ]]; then
+            test -f prefix/bin/linkcell.dll
+            test -f prefix/lib/linkcell.dll.lib
+            test -f prefix/lib/linkcell.lib
+            test -f prefix/lib/linkcell_gpu.lib
+          elif [[ "$RUNNER_OS" == "macOS" ]]; then
+            test -f prefix/lib/liblinkcell.dylib
+            test -f prefix/lib/liblinkcell.a
+            test -f prefix/lib/liblinkcell_gpu.a
+          else
+            test -f prefix/lib/liblinkcell.so
+            test -f prefix/lib/liblinkcell.a
+            test -f prefix/lib/liblinkcell_gpu.a
+          fi
+          cmake -S tests/cmake-consumer -B find-build \
+            -DCMAKE_PREFIX_PATH="$PWD/prefix" \
+            -DLINKCELL_C_EXAMPLE="$PWD/examples/two_points.c" \
+            -DLINKCELL_CPP_EXAMPLE="$PWD/examples/two_points.cpp"
+          cmake --build find-build --config Release
+          if [[ "$RUNNER_OS" == "Windows" ]]; then
+            export PATH="$PWD/prefix/bin:$PATH"
+          elif [[ "$RUNNER_OS" == "macOS" ]]; then
+            export DYLD_LIBRARY_PATH="$PWD/prefix/lib${DYLD_LIBRARY_PATH:+:$DYLD_LIBRARY_PATH}"
+          else
+            export LD_LIBRARY_PATH="$PWD/prefix/lib${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}"
+          fi
+          ctest --test-dir find-build -C Release --output-on-failure
+      - name: pkg-config after cmake install
+        if: runner.os != 'Windows'
+        run: |
+          test -f prefix/lib/pkgconfig/linkcell.pc
+          export PKG_CONFIG_PATH="$PWD/prefix/lib/pkgconfig"
+          pkg-config --exists --print-errors linkcell
+          pkg-config --modversion linkcell

linkcell-0.3.4/.github/workflows/publish.yml

@@ -0,0 +1,25 @@
+name: publish
+
+on:
+  push:
+    tags: ["v*"]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      id-token: write
+    steps:
+      - uses: actions/checkout@v6
+      - uses: dtolnay/rust-toolchain@stable
+      - uses: rust-lang/crates-io-auth-action@v1.0.5
+        id: auth
+      - name: Publish linkcell
+        env:
+          CARGO_REGISTRY_TOKEN: ${{ steps.auth.outputs.token }}
+        run: cargo publish --no-verify -p linkcell

{linkcell-0.3.2 → linkcell-0.3.4}/.github/workflows/wheels.yml

@@ -2,6 +2,7 @@ name: wheels
 
 on:
   push:
+    branches: [main]
     tags: ["v*"]
   pull_request:
     paths:
@@ -37,14 +38,18 @@ jobs:
           - name: macos-arm64
             os: macos-latest
             arch: arm64
+          - name: windows-x86_64
+            os: windows-latest
+            arch: AMD64
     steps:
-      - uses: actions/checkout@v4
-      - uses: dtolnay/rust-toolchain@stable
-      - uses: astral-sh/setup-uv@v5
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      - uses: dtolnay/rust-toolchain@4360b52568e2003a75bf9bc1d59f33a8e3fc893c # stable
+      - uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
         with:
           python-version: "3.12"
+          cache-suffix: abi3-${{ matrix.arch }}
       - name: Build abi3 wheel
-        run: uvx --from 'cibuildwheel>=3.2,<4' cibuildwheel --output-dir wheelhouse
+        run: uvx --from 'cibuildwheel>=4,<5' cibuildwheel --output-dir wheelhouse
         env:
           CIBW_BUILD: "cp312-*"
           CIBW_SKIP: "*musllinux* *i686* cp3??t-*"
@@ -52,14 +57,16 @@ jobs:
           CIBW_ENVIRONMENT: MATURIN_PEP517_ARGS="--features abi3"
           CIBW_TEST_REQUIRES: pytest numpy
           CIBW_TEST_COMMAND: pytest {project}/tests/python -q
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
         with:
           name: wheels-abi3-${{ matrix.name }}
           path: ./wheelhouse/*.whl
 
-  # Free-threaded set: one wheel per CPython t ABI (no limited API).
-  freethreaded:
-    name: freethreaded ${{ matrix.name }}
+  # One abi3t wheel per platform (CPython 3.15+ GIL and free-threaded).
+  # abi3audit --strict still treats PEP 793 PyModExport / PyType_FromSlots
+  # as non-abi3, so the audit step is off for this job only.
+  abi3t:
+    name: abi3t ${{ matrix.name }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -74,37 +81,50 @@ jobs:
           - name: macos-arm64
             os: macos-latest
             arch: arm64
+          - name: windows-x86_64
+            os: windows-latest
+            arch: AMD64
     steps:
-      - uses: actions/checkout@v4
-      - uses: dtolnay/rust-toolchain@stable
-      - uses: astral-sh/setup-uv@v5
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      - uses: dtolnay/rust-toolchain@4360b52568e2003a75bf9bc1d59f33a8e3fc893c # stable
+      - uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
         with:
-          python-version: "3.13"
-      - name: Build free-threaded wheels
-        run: uvx --from 'cibuildwheel>=3.2,<4' cibuildwheel --output-dir wheelhouse
+          python-version: "3.15"
+          cache-suffix: abi3t-${{ matrix.arch }}
+      - name: Build abi3t wheel
+        run: uvx --from 'cibuildwheel>=4,<5' cibuildwheel --output-dir wheelhouse
         env:
-          CIBW_BUILD: "cp314t-*"
-          CIBW_SKIP: "*musllinux* *i686*"
+          CIBW_BUILD: "cp315-*"
+          CIBW_SKIP: "*musllinux* *i686* cp3??t-*"
           CIBW_ARCHS: ${{ matrix.arch }}
+          CIBW_ENVIRONMENT: MATURIN_PEP517_ARGS="--features abi3t"
+          CIBW_AUDIT_COMMAND: ""
           CIBW_TEST_REQUIRES: pytest numpy
           CIBW_TEST_COMMAND: pytest {project}/tests/python -q
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
         with:
-          name: wheels-freethreaded-${{ matrix.name }}
+          name: wheels-abi3t-${{ matrix.name }}
           path: ./wheelhouse/*.whl
 
   sdist:
     name: Source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      - uses: dtolnay/rust-toolchain@stable
-      - uses: astral-sh/setup-uv@v5
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+      - uses: dtolnay/rust-toolchain@4360b52568e2003a75bf9bc1d59f33a8e3fc893c # stable
+      - uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
         with:
           python-version: "3.12"
+          cache-suffix: sdist
       - name: Build sdist
         run: uvx maturin sdist --out dist
-      - uses: actions/upload-artifact@v4
+      - name: Test installed sdist
+        run: |
+          uv venv --clear .sdist-venv
+          uv pip install --python .sdist-venv/bin/python dist/*.tar.gz pytest numpy
+          .sdist-venv/bin/python -I -c "import linkcell; print(linkcell.__file__)"
+          .sdist-venv/bin/python -I -m pytest --import-mode=importlib "$PWD/tests/python" -q
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
         with:
           name: sdist
           path: dist/*.tar.gz
@@ -114,7 +134,7 @@ jobs:
   # on this job.
   publish:
     name: Publish to PyPI
-    needs: [abi3, freethreaded, sdist]
+    needs: [abi3, abi3t, sdist]
     runs-on: ubuntu-latest
     if: >-
       github.repository == 'd-SEAMS/linkcell' &&
@@ -124,7 +144,7 @@ jobs:
       id-token: write
       contents: read
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
         with:
           path: dist
           merge-multiple: true

{linkcell-0.3.2 → linkcell-0.3.4}/.gitignore

@@ -30,6 +30,8 @@ rustc-ice-*.txt
 
 # Prerequisites
 *.d
+!changelog.d/
+!changelog.d/**
 
 # Compiled Object files
 *.slo

linkcell-0.3.4/CHANGELOG.md

@@ -0,0 +1,121 @@
+# Changelog
+
+All notable changes to this project are documented in this file.
+
+The format is [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+Unreleased notes live in [`changelog.d/`](changelog.d/) and are assembled
+by [towncrier](https://towncrier.readthedocs.io/).
+
+<!-- towncrier release notes start -->
+
+## [0.3.4] - 2026-09-27
+
+### Added
+
+- `pairs_within` returns every atom-image pair inside a cutoff with integer cell shift `S`. `knearest` still unique-indexes. Image stencils above 2^24 fail closed.
+
+### Changed
+
+- `knearest_brute` ranks with `Cell::dist2_euclidean` (Smith then Minkowski 27-image).
+- The crate depends on minimage 0.1.2 from crates.io.
+- CHANGELOG.md follows Keep a Changelog. Unreleased notes are changelog.d fragments assembled by towncrier.
+
+### Fixed
+
+- The MSVC build defines `NOMINMAX` before `windows.h` and calls `(std::min)` / `(std::max)`, so those names are not macros. The header includes `<cassert>` and `<optional>` itself. MSVC does not provide those through the other standard headers.
+
+## [0.3.3] - 2026-08-17
+
+### Changed
+
+- Two wheels: `abi3-py312` (GIL, CPython 3.12+) and `abi3t-py315` (PEP 803, CPython 3.15 GIL and free-threaded). cibuildwheel 4.x builds 3.15.0rc1 by default. PyO3 0.29 `abi3t-py315`; maturin 1.14+ tags the `abi3t` ABI. The 0.3.2 `cp314t` set is gone. cibuildwheel's abi3audit step is off for the abi3t job: current abi3audit flags PEP 793 `PyModExport` and `PyType_FromSlots`.
+
+## [0.3.2] - 2026-08-17
+
+### Changed
+
+- Python `linkcell` module (maturin / PyO3). Arrays are DLPack via dlpk: any `__dlpack__()` object in, `(indices, dist2)` out. `xyz` may be `(n, 3)` or `(n_frames, n, 3)`. `cell` is a DLPack tensor on any device. A CUDA cell is inverted on device; the host reads only the four launch ints. Two wheels: CPython 3.12 limited ABI, and a free-threaded `cp314t` set. Both compile the gpulite device walk. CUDA `__dlpack__` tensors (`torch`) go to `lc_gpu_*` by device pointer; the result is a pair of CUDA DLPack capsules. `lc_knearest_d2` and `lc_knearest_many` write squared distances and a frame-major batch. `lc_gpu_*` is the C waist for the device `Workspace`. A `v*` tag on d-SEAMS/linkcell publishes the two wheel kinds and the sdist to PyPI (trusted publisher, no Actions environment).
+
+## [0.3.1] - 2026-08-16
+
+### Changed
+
+- Device `Workspace` folds with `Hinv` and shifts with `na a + nb b + nc c`. Sheared cells use the host walk. `k <= 16`.
+
+## [0.3.0] - 2026-08-16
+
+### Changed
+
+- Optional gpulite device path: `linkcell::gpu::Workspace::knearest_into` writes the same packed `n * k` indices as the host walk (fold, bin, Chebyshev shells). The device walk uses a tiled exclusive scan, a precomputed Chebyshev stencil, cell-major coordinates with an O(1) home slot, and `knearest_into_many` for a frame batch. Occupancy defaults to threads-per-particle 8 (HOOMD/vesin), overridable by `LINKCELL_TPP` and `LINKCELL_BLOCK`. Setup copies ride the workspace stream. Orthorhombic cells, `k <= 16`. Meson feature `with_gpulite`.
+
+## [0.2.4] - 2026-08-15
+
+### Changed
+
+- A wrap consumer always links the static archive. The parent `default_library` does not change this option, so a shared default left `pydseams.yoda` needing `liblinkcell.so` at import time.
+
+## [0.2.3] - 2026-08-15
+
+### Changed
+
+- A static `libyodaLib.a` no longer passes `liblinkcell.so` to `ar`. The Meson dependency attaches a generated header as the build-order edge, not both cargo outputs.
+
+## [0.2.2] - 2026-08-15
+
+### Changed
+
+- The crate is `d-SEAMS/linkcell`. `HaoZeke/linkcell` redirects.
+
+## [0.2.1] - 2026-08-15
+
+### Changed
+
+- `Error::MaskLen` when `mask` is `Some` and `mask.len() != n`.
+- `Error::Overflow` when `n * k` does not fit a slice. `BufferSize`
+- remains a caller `out` whose length is not `n * k`.
+- `lc_last_error` is written only by `lc_knearest`. `lc_version` does
+- not clear the slot. An interior NUL in a message no longer drops the string to `NULL`.
+- C++ `Neighbours` owns the packed `n * k` buffer. `knearest_into`
+- takes `out_len`. There is no 5-argument `knearest(..., int *out)`.
+- CI checks `include/linkcell.h` against cbindgen 0.29.4.
+- Branding: sheared linked cells, k=4 neighbours, periodic wrap
+- (`assets/branding/`).
+
+## [0.2.0] - 2026-08-15
+
+### Changed
+
+- ABI break. Existing 0.1.x C and C++ callers must rebuild.
+- `lc_knearest` takes `size_t n` and `size_t k`. The 0.1.x `int` counts
+- overflowed on large frames.
+- `lc_last_error` is thread-local. Concurrent searches no longer share
+- one process-wide slot. `lc_version` stays process-static.
+- C++ `linkcell::knearest` writes a packed `n * k` index buffer (unused
+- slots `-1`) and returns a `Neighbours` view. It no longer returns `std::vector<std::vector<int>>`. Failure throws `linkcell::Error`.
+- Rust `Error::Empty` is an empty point list only. A wrong-length
+- `knearest_into` buffer is `Error::BufferSize`. An overflowing linked-cell mesh is `Error::TooManyCells`.
+- The per-source k-set keeps one image of each neighbour (the
+- nearest). The same particle visited through two wraps does not occupy two slots.
+- `knearest_brute` on a sheared cell takes the 27-image minimum.
+- The single parallelepiped wrap is not the Wigner-Seitz cell of a 60-degree hex prism.
+
+## [0.1.2] - 2026-08-15
+
+### Changed
+
+- Fold once, then Cartesian pair distances plus a lattice shift (the vesin / LAMMPS ghost trick). Sources run in parallel. The C ABI writes indices into the caller buffer.
+
+## [0.1.1] - 2026-08-15
+
+### Changed
+
+- Orthorhombic boxes use the three-wrap minimum image, not two 3x3 matvecs. The C ABI reads packed xyz in place. The k-heap for k <= 16 stays on the stack.
+
+## [0.1.0] - 2026-08-15
+
+### Changed
+
+- Periodic linked-cell k-nearest neighbour search. Rust crate, C ABI (`lc_*`), C++ header. The cell is a general parallelepiped; orthorhombic boxes are `Cell::ortho` / `lc_cell_ortho`.
+- Installable from Meson (`linkcell_dep`, `pkg.generate`), CMake (`find_package(linkcell)`, `linkcell::linkcell`), and pkg-config (`linkcell.pc`).

{linkcell-0.3.2 → linkcell-0.3.4}/CITATION.cff

@@ -7,7 +7,7 @@ authors:
     given-names: Rohit
     orcid: https://orcid.org/0000-0002-2393-8056
 license: MIT
-version: 0.3.2
+version: 0.3.3
 date-released: "2026-08-17"
 repository-code: "https://github.com/d-SEAMS/linkcell"
 url: "https://github.com/d-SEAMS/linkcell"

{linkcell-0.3.2 → linkcell-0.3.4}/CMakeLists.txt

@@ -27,6 +27,7 @@ find_program(CARGO_EXECUTABLE cargo REQUIRED)
 
 option(LINKCELL_BUILD_EXAMPLES "Build C and C++ example programs" ON)
 option(LINKCELL_INSTALL "Install headers, libraries, pkg-config, and CMake package" ON)
+option(LINKCELL_WITH_GPULITE "Build the device k-nearest C and C++ APIs" ON)
 
 if(WIN32)
   set(LINKCELL_SHARED_NAME linkcell.dll)
@@ -36,6 +37,8 @@ else()
   set(LINKCELL_SHARED_NAME "${CMAKE_SHARED_LIBRARY_PREFIX}linkcell${CMAKE_SHARED_LIBRARY_SUFFIX}")
   set(LINKCELL_STATIC_NAME "${CMAKE_STATIC_LIBRARY_PREFIX}linkcell${CMAKE_STATIC_LIBRARY_SUFFIX}")
 endif()
+set(LINKCELL_GPU_STATIC_NAME
+  "${CMAKE_STATIC_LIBRARY_PREFIX}linkcell_gpu${CMAKE_STATIC_LIBRARY_SUFFIX}")
 
 set(LINKCELL_CARGO_DIR "${CMAKE_CURRENT_BINARY_DIR}/cargo-target")
 string(TOLOWER "${CMAKE_BUILD_TYPE}" _linkcell_build_type)
@@ -128,12 +131,43 @@ set_target_properties(linkcell_static PROPERTIES
   INTERFACE_LINK_LIBRARIES "${_linkcell_sys}"
 )
 
+add_library(linkcell_cpp INTERFACE)
+add_library(linkcell::cpp ALIAS linkcell_cpp)
+target_link_libraries(linkcell_cpp INTERFACE linkcell::linkcell)
+target_compile_features(linkcell_cpp INTERFACE cxx_std_17)
+
+set(LINKCELL_GPU_SYSTEM_LIBS Threads::Threads)
+if(CMAKE_DL_LIBS)
+  list(APPEND LINKCELL_GPU_SYSTEM_LIBS ${CMAKE_DL_LIBS})
+endif()
+
+if(LINKCELL_WITH_GPULITE)
+  add_library(linkcell_gpu STATIC
+    src/gpu/knearest.cpp
+    src/gpu/capi.cpp
+  )
+  add_library(linkcell::gpu ALIAS linkcell_gpu)
+  target_include_directories(linkcell_gpu
+    PUBLIC
+      "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
+      "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
+    PRIVATE
+      "${CMAKE_CURRENT_SOURCE_DIR}/third_party/gpulite"
+  )
+  target_compile_definitions(linkcell_gpu PUBLIC LINKCELL_HAS_GPULITE=1)
+  target_compile_features(linkcell_gpu PUBLIC cxx_std_17)
+  target_link_libraries(linkcell_gpu PUBLIC
+    linkcell::linkcell
+    ${LINKCELL_GPU_SYSTEM_LIBS}
+  )
+endif()
+
 if(LINKCELL_BUILD_EXAMPLES)
   add_executable(two_points examples/two_points.c)
   target_link_libraries(two_points PRIVATE linkcell::linkcell)
   set_target_properties(two_points PROPERTIES BUILD_RPATH "${CMAKE_CURRENT_BINARY_DIR}")
   add_executable(two_points_cpp examples/two_points.cpp)
-  target_link_libraries(two_points_cpp PRIVATE linkcell::linkcell)
+  target_link_libraries(two_points_cpp PRIVATE linkcell::cpp)
   set_target_properties(two_points_cpp PROPERTIES BUILD_RPATH "${CMAKE_CURRENT_BINARY_DIR}")
   enable_testing()
   add_test(NAME two-points-c COMMAND two_points)
@@ -150,10 +184,13 @@ endif()
 if(LINKCELL_INSTALL)
   if(UNIX AND NOT APPLE)
     set(LINKCELL_PKG_LIBS_PRIVATE "-ldl -lpthread -lm")
+    set(LINKCELL_GPU_PKG_LIBS "-ldl -lpthread")
   elseif(APPLE)
     set(LINKCELL_PKG_LIBS_PRIVATE "-lpthread -lm")
+    set(LINKCELL_GPU_PKG_LIBS "-lpthread")
   else()
     set(LINKCELL_PKG_LIBS_PRIVATE "")
+    set(LINKCELL_GPU_PKG_LIBS "")
   endif()
 
   configure_file(
@@ -161,6 +198,13 @@ if(LINKCELL_INSTALL)
     "${CMAKE_CURRENT_BINARY_DIR}/linkcell.pc"
     @ONLY
   )
+  if(LINKCELL_WITH_GPULITE)
+    configure_file(
+      "${CMAKE_CURRENT_SOURCE_DIR}/cmake/linkcell-gpu.pc.in"
+      "${CMAKE_CURRENT_BINARY_DIR}/linkcell-gpu.pc"
+      @ONLY
+    )
+  endif()
   configure_package_config_file(
     "${CMAKE_CURRENT_SOURCE_DIR}/cmake/linkcellConfig.cmake.in"
     "${CMAKE_CURRENT_BINARY_DIR}/linkcellConfig.cmake"
@@ -179,16 +223,29 @@ if(LINKCELL_INSTALL)
     install(FILES "${LINKCELL_SHARED}" DESTINATION "${CMAKE_INSTALL_LIBDIR}")
   endif()
   install(FILES "${LINKCELL_STATIC}" DESTINATION "${CMAKE_INSTALL_LIBDIR}")
+  if(LINKCELL_WITH_GPULITE)
+    install(TARGETS linkcell_gpu ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}")
+  endif()
   install(FILES
     "${CMAKE_CURRENT_SOURCE_DIR}/include/linkcell.h"
     "${CMAKE_CURRENT_SOURCE_DIR}/include/linkcell.hpp"
-    "${CMAKE_CURRENT_SOURCE_DIR}/include/linkcell_gpu.h"
-    "${CMAKE_CURRENT_SOURCE_DIR}/include/linkcell_gpu.hpp"
     DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}"
   )
+  if(LINKCELL_WITH_GPULITE)
+    install(FILES
+      "${CMAKE_CURRENT_SOURCE_DIR}/include/linkcell_gpu.h"
+      "${CMAKE_CURRENT_SOURCE_DIR}/include/linkcell_gpu.hpp"
+      DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}"
+    )
+  endif()
   install(FILES "${CMAKE_CURRENT_BINARY_DIR}/linkcell.pc"
     DESTINATION "${CMAKE_INSTALL_LIBDIR}/pkgconfig"
   )
+  if(LINKCELL_WITH_GPULITE)
+    install(FILES "${CMAKE_CURRENT_BINARY_DIR}/linkcell-gpu.pc"
+      DESTINATION "${CMAKE_INSTALL_LIBDIR}/pkgconfig"
+    )
+  endif()
   install(FILES
     "${CMAKE_CURRENT_BINARY_DIR}/linkcellConfig.cmake"
     "${CMAKE_CURRENT_BINARY_DIR}/linkcellConfigVersion.cmake"