Native structure and bound structs (PR-5)

.github/workflows/ci.yml

@@ -204,7 +204,7 @@ jobs:
           path: wheelhouse
           key: >-
             native-wheel-v1-${{ matrix.id }}-${{ hashFiles('native/**', '!native/tests/**',
-            '!native/benchmarks/**', '!native/**/*.md') }}
+            '!native/**/*.md') }}
       - if: steps.cache.outputs.cache-hit != 'true' && runner.os == 'Linux'
         name: Install the native toolchain
         run: |
@@ -563,7 +563,7 @@ jobs:
       - name: Install the native toolchain
         run: |
           sudo apt-get update
-          sudo apt-get install --yes clang-tidy cmake g++-14 libfftw3-dev ninja-build pkg-config
+          sudo apt-get install --yes cmake g++-14 libfftw3-dev ninja-build pkg-config
       - run: uv python install 3.14
       - run: uv sync --locked --no-install-package solprop-native
       - run: uv run poe check-native
@@ -608,7 +608,6 @@ jobs:
           cmake --preset cuda \
             -DCMAKE_C_COMPILER=gcc-14 -DCMAKE_CXX_COMPILER=g++-14 -DCMAKE_CUDA_HOST_COMPILER=g++-14 \
             -DCUDA_ROOT=/usr/local/cuda-12.8 \
-            -DSOLPROP_NATIVE_BUILD_BENCHMARKS=OFF \
             -DPython_EXECUTABLE="$GITHUB_WORKSPACE/.venv/bin/python"
       - name: Compile, tests included
         working-directory: native
@@ -656,7 +655,6 @@ jobs:
           cmake --preset hip \
             -DCMAKE_CXX_COMPILER="$ROCM_PATH/bin/hipcc" -DCMAKE_PREFIX_PATH="$ROCM_PATH" \
             -DCMAKE_CXX_SCAN_FOR_MODULES=OFF -DKokkos_ENABLE_ROCTHRUST=OFF \
-            -DSOLPROP_NATIVE_BUILD_BENCHMARKS=OFF \
             -DPython_EXECUTABLE="$GITHUB_WORKSPACE/.venv/bin/python"
       - name: Compile, tests included
         working-directory: native

.github/workflows/cuda.yml

@@ -5,7 +5,8 @@
 name: NVIDIA CUDA validation
 
 # Manual workflow for a self-hosted Linux runner labelled nvidia-gpu, with an NVIDIA
-# GPU, the CUDA Toolkit (nvcc, cuFFT, cuBLAS, Compute Sanitizer) and GCC 13 or newer.
+# GPU, the CUDA Toolkit 12.8 or newer (nvcc, cuFFT, cuBLAS, Compute Sanitizer) and GCC 14
+# or newer (CMakeLists.txt refuses an older host compiler).
 # Set the repository variable SOLPROP_NATIVE_CUDA_ARCH to the runner's Kokkos
 # architecture (for example AMPERE80, ADA89 or HOPPER90); HOPPER90 is used when unset.
 # The repository is public: keep this workflow dispatch-only and never let the
@@ -58,3 +59,5 @@ jobs:
         run: |
           compute-sanitizer --tool memcheck --error-exitcode 1 ../.venv/bin/pytest tests/test_numerics.py
           compute-sanitizer --tool racecheck --error-exitcode 1 ../.venv/bin/pytest tests/test_numerics.py
+          compute-sanitizer --tool initcheck --error-exitcode 1 ../.venv/bin/pytest tests/test_numerics.py
+          compute-sanitizer --tool synccheck --error-exitcode 1 ../.venv/bin/pytest tests/test_numerics.py

.github/workflows/native-deep.yml

@@ -0,0 +1,204 @@
+# SPDX-FileCopyrightText: 2026 John C. Travers and contributors
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+name: Native deep checks
+
+# Weekly, by hand, and on a pull request that changes this file: the native checks too
+# slow for every pull request. Each job reports (an artifact and the job summary) and
+# gates nothing.
+#
+# - coverage: Clang source coverage of the native code over the GoogleTest suite and
+#   the native pytest suite (SOLPROP_NATIVE_ENABLE_COVERAGE). Its uncovered lines are
+#   where to look for dead code.
+# - extension-asan: the extension itself built with ASan and UBSan and run under the
+#   native pytest suite, which exercises the nanobind bindings the gate's sanitizer
+#   stage (GoogleTest only) never reaches.
+# - include-cleaner: clang-tidy's misc-include-cleaner over the sources, as a report of
+#   missing and unused includes.
+
+on:
+  schedule:
+    - cron: "17 3 * * 1"
+  workflow_dispatch:
+  # A pull request that changes this workflow runs it, so that a change is seen to work
+  # before the next weekly run (dispatch needs the workflow on the default branch).
+  pull_request:
+    paths:
+      - .github/workflows/native-deep.yml
+
+permissions:
+  contents: read
+
+concurrency:
+  group: native-deep-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  coverage:
+    runs-on: ubuntu-24.04
+    timeout-minutes: 240
+    env:
+      CC: clang-18
+      CXX: clang++-18
+      OMP_PROC_BIND: "false"
+      SOLPROP_NATIVE_THREADS: "2"
+      UV_NO_SYNC: "1"
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          fetch-depth: 0
+      - uses: astral-sh/setup-uv@68559e99cc807c1eb7e9238fd43a15bba460eec2 # v10.3.3
+        with:
+          enable-cache: true
+      - name: Install Clang, its OpenMP runtime and FFTW
+        run: |
+          sudo apt-get update
+          sudo apt-get install --yes clang-18 llvm-18 libomp-18-dev cmake libfftw3-dev ninja-build pkg-config
+      - run: uv python install 3.14
+      - run: uv sync --locked --no-install-package solprop-native
+      - name: Build the instrumented extension and native tests
+        # FFTW's pthreads library: Ubuntu's OpenMP FFTW links GNU OpenMP, and Clang's
+        # build runs LLVM's. No vendor BLAS (the reference profile).
+        # Report-only: a warning from this job's compiler, which no pull-request lane
+        # builds with, does not stop the report.
+        env:
+          CMAKE_ARGS: >-
+            -DSOLPROP_NATIVE_WARNINGS_AS_ERRORS=OFF
+            -DSOLPROP_NATIVE_ENABLE_COVERAGE=ON
+            -DSOLPROP_NATIVE_PROFILE=REFERENCE
+            -DSOLPROP_NATIVE_FFTW_THREADING=PTHREADS
+            -DBUILD_TESTING=ON
+        run: |
+          uv pip install --no-deps --no-build-isolation -e native \
+            --config-settings build-dir=build/coverage
+      - name: GoogleTest suite
+        continue-on-error: true
+        env:
+          LLVM_PROFILE_FILE: ${{ github.workspace }}/profiles/gtest-%p-%m.profraw
+        run: native/build/coverage/solprop_native_tests
+      - name: Native pytest suite
+        continue-on-error: true
+        working-directory: native
+        env:
+          LLVM_PROFILE_FILE: ${{ github.workspace }}/profiles/pytest-%p-%m.profraw
+        run: uv run pytest -n 2 -p no:cacheprovider
+      - name: Report
+        if: always()
+        run: |
+          extension=$(uv run python -c "import solprop_native._core as m; print(m.__file__)")
+          llvm-profdata-18 merge -sparse profiles/*.profraw -o coverage.profdata
+          objects=("$extension" -object native/build/coverage/solprop_native_tests)
+          sources=(native/src native/include/solprop_native)
+          mkdir -p native-coverage
+          llvm-cov-18 report "${objects[@]}" -instr-profile coverage.profdata "${sources[@]}" \
+            | tee native-coverage/report.txt
+          llvm-cov-18 show "${objects[@]}" -instr-profile coverage.profdata "${sources[@]}" \
+            -format=html -show-line-counts-or-regions -output-dir native-coverage/html
+          { echo '## Native source coverage'; echo '```'; tail -n 40 native-coverage/report.txt; echo '```'; } >> "$GITHUB_STEP_SUMMARY"
+      - uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
+        if: always()
+        with:
+          name: native-coverage
+          path: native-coverage
+          retention-days: 30
+
+  extension-asan:
+    runs-on: ubuntu-24.04
+    timeout-minutes: 240
+    env:
+      CXX: g++-14
+      OMP_PROC_BIND: "false"
+      SOLPROP_NATIVE_THREADS: "2"
+      UV_NO_SYNC: "1"
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          fetch-depth: 0
+      - uses: astral-sh/setup-uv@68559e99cc807c1eb7e9238fd43a15bba460eec2 # v10.3.3
+        with:
+          enable-cache: true
+      - name: Install the native toolchain
+        run: |
+          sudo apt-get update
+          sudo apt-get install --yes cmake g++-14 libfftw3-dev ninja-build pkg-config
+      - run: uv python install 3.14
+      - run: uv sync --locked --no-install-package solprop-native
+      - name: Build the extension with ASan, UBSan and Kokkos bounds checks
+        env:
+          CMAKE_ARGS: >-
+            -DSOLPROP_NATIVE_WARNINGS_AS_ERRORS=OFF
+            -DSOLPROP_NATIVE_ENABLE_SANITIZERS=ON
+            -DSOLPROP_NATIVE_PROFILE=REFERENCE
+            -DKokkos_ENABLE_DEBUG_BOUNDS_CHECK=ON
+        run: |
+          uv pip install --no-deps --no-build-isolation -e native \
+            --config-settings build-dir=build/asan \
+            --config-settings cmake.build-type=RelWithDebInfo
+      - name: Native pytest suite under the sanitizers
+        working-directory: native
+        # Python is not instrumented, so the ASan runtime is preloaded, with libstdc++
+        # beside it: ASan resolves __cxa_throw when it starts, and Python loads no C++
+        # runtime of its own, so without it every C++ exception aborts. CPython's own
+        # allocations at exit are not leaks of this package. setarch -R: Ubuntu's
+        # high-entropy ASLR can map a library inside ASan's shadow range. Report-only:
+        # the summary records the outcome and the log is the artifact.
+        run: |
+          set -o pipefail
+          export LD_PRELOAD="$(g++-14 -print-file-name=libasan.so):$(g++-14 -print-file-name=libstdc++.so)"
+          export ASAN_OPTIONS=detect_leaks=0:abort_on_error=1
+          export UBSAN_OPTIONS=print_stacktrace=1:halt_on_error=1
+          status=0
+          setarch "$(uname -m)" -R uv run pytest -n 2 -p no:cacheprovider 2>&1 | tee ../asan.log || status=$?
+          { echo '## Native pytest under ASan and UBSan'; echo "exit status ${status}"; echo '```'
+            grep -E 'ERROR: AddressSanitizer|runtime error|^FAILED|passed|failed' ../asan.log | tail -n 40
+            echo '```'; } >> "$GITHUB_STEP_SUMMARY"
+      - uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
+        if: always()
+        with:
+          name: native-extension-asan
+          path: asan.log
+          retention-days: 30
+
+  include-cleaner:
+    runs-on: ubuntu-24.04
+    timeout-minutes: 90
+    env:
+      CXX: g++-14
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          fetch-depth: 0
+      - uses: astral-sh/setup-uv@68559e99cc807c1eb7e9238fd43a15bba460eec2 # v10.3.3
+        with:
+          enable-cache: true
+      - name: Install the native toolchain
+        run: |
+          sudo apt-get update
+          sudo apt-get install --yes cmake g++-14 libfftw3-dev ninja-build pkg-config
+      - run: uv python install 3.14
+      - run: uv sync --locked --no-install-package solprop-native
+      - name: Configure the cpu-tidy preset (compile commands and generated headers)
+        working-directory: native
+        run: |
+          cmake --preset cpu-tidy -DCMAKE_CXX_COMPILER="$(command -v g++-14)" \
+            -DPython_EXECUTABLE="$GITHUB_WORKSPACE/.venv/bin/python"
+          # SLEEF's header comes from its own build.
+          cmake --build --preset cpu-tidy --target solprop_native_sleef_build
+      - name: misc-include-cleaner
+        run: |
+          build=native/build/presets/cpu-tidy
+          # The pinned clang-tidy and the arguments the build gives it.
+          mapfile -t tidy < "$build/clang_tidy_command.txt"
+          git ls-files -z -- 'native/src/*.cpp' 'native/tests/native/*.cpp' |
+            xargs -0 -n 1 -P "$(nproc)" "${tidy[@]}" --quiet -p "$build" \
+              --checks='-*,misc-include-cleaner' --warnings-as-errors='' \
+              > include-cleaner.txt 2>&1 || true
+          findings=$(grep -c 'misc-include-cleaner' include-cleaner.txt || true)
+          echo "## misc-include-cleaner: ${findings} findings" >> "$GITHUB_STEP_SUMMARY"
+      - uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
+        if: always()
+        with:
+          name: native-include-cleaner
+          path: include-cleaner.txt
+          retention-days: 30

native/benchmarks/size_cliffs.py → benchmarks/size_cliffs.py

@@ -17,7 +17,7 @@
 cheapest, because fixed per-evaluation costs make small grids dearer per sample.
 ``--check`` exits non-zero on one. Run on a quiet machine, with the threads pinned::
 
-    OMP_PLACES=cores OMP_PROC_BIND=close python native/benchmarks/size_cliffs.py --check
+    OMP_PLACES=cores OMP_PROC_BIND=close python -m benchmarks.size_cliffs --check
 """
 
 from __future__ import annotations
@@ -31,6 +31,10 @@
 import warnings
 from typing import Any, cast
 
+from solprop.driver import Simulation
+from solprop.grid import FieldGrid
+from solprop.stepper import RungeKutta
+
 FACTORS = (1.0, 1.125, 1.25, 1.375, 1.5, 1.75, 2.0)
 LENGTH = 1.5
 STEP = LENGTH / 4000
@@ -39,10 +43,6 @@
 
 def simulation(factor: float, fft_size: str, backend: str, steps: int) -> Any:
     """Return the RDW case on one grid, with `steps` capped Runge-Kutta steps."""
-    from solprop.driver import Simulation
-    from solprop.grid import FieldGrid
-    from solprop.stepper import RungeKutta
-
     grid = FieldGrid.from_limits(
         LENGTH, 800e-9, (90e-9, 4e-6), factor * 400e-15, fft_size=fft_size
     )