proteus-python 2026.7.0__tar.gz

proteus_python-2026.7.0/.clang-format

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+BasedOnStyle: LLVM

proteus_python-2026.7.0/.clang-tidy

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+Checks: '-*,clang-diagnostic-*,llvm-*,misc-*,-misc-const-correctness,-misc-unused-parameters,-misc-non-private-member-variables-in-classes,-misc-no-recursion,-misc-use-anonymous-namespace,readability-identifier-naming,-misc-include-cleaner,-llvm-header-guard'
+CheckOptions:
+  - key:             readability-identifier-naming.ClassCase
+    value:           CamelCase
+  - key:             readability-identifier-naming.EnumCase
+    value:           CamelCase
+  - key:             readability-identifier-naming.FunctionCase
+    value:           camelBack
+  # Exclude from scanning as this is an exported symbol used for fuzzing
+  # throughout the code base.
+  - key:             readability-identifier-naming.FunctionIgnoredRegexp
+    value:           "LLVMFuzzerTestOneInput"
+  - key:             readability-identifier-naming.MemberCase
+    value:           CamelCase
+  - key:             readability-identifier-naming.ParameterCase
+    value:           CamelCase
+  - key:             readability-identifier-naming.UnionCase
+    value:           CamelCase
+  - key:             readability-identifier-naming.VariableCase
+    value:           CamelCase
+  - key:             readability-identifier-naming.IgnoreMainLikeFunctions
+    value:           1
+  - key:             readability-redundant-member-init.IgnoreBaseInCopyConstructors
+    value:           1
+  - key:             modernize-use-default-member-init.UseAssignment
+    value:           1

proteus_python-2026.7.0/.github/workflows/check-headers.yml

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+name: Check Header Includes
+
+on:
+  pull_request:
+    paths:
+      - 'include/**/*.h'
+      - 'src/include/**/*.h'
+      - 'scripts/checks/check-headers.py'
+      - '.github/workflows/check-headers.yml'
+
+jobs:
+  check-headers:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      - name: Check public headers
+        run: |
+          python scripts/checks/check-headers.py
+          echo "✅ No internal headers found in public API"

proteus_python-2026.7.0/.github/workflows/ci-build-test.yml

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+name: CI
+
+on:
+  pull_request:
+    paths:
+      - ".github/workflows/ci-build-test.yml"
+      - "CMakeLists.txt"
+      - "bindings/python/**"
+      - "cmake/**"
+      - "include/**"
+      - "src/**"
+      - "tests/**"
+  push:
+    branches:
+      - main
+    paths:
+      - ".github/workflows/ci-build-test.yml"
+      - "CMakeLists.txt"
+      - "bindings/python/**"
+      - "cmake/**"
+      - "include/**"
+      - "src/**"
+      - "tests/**"
+
+jobs:
+  prepare-conda:
+    name: prepare conda ${{ matrix.os }} LLVM ${{ matrix.llvm }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        llvm: [19.1.7, 20.1.8, 22.1.0]
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - name: Setup conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-version: latest
+          conda-remove-defaults: true
+      # Build the toolchain env once per LLVM version, then hand it to build jobs.
+      - name: Create environment
+        run: |
+          conda create -y -n llvm-env -c conda-forge \
+            conda-pack \
+            python=3.12 \
+            pybind11 \
+            clang=${{ matrix.llvm }} \
+            clangxx=${{ matrix.llvm }} \
+            clangdev=${{ matrix.llvm }} \
+            llvmdev=${{ matrix.llvm }} \
+            lit=${{ matrix.llvm }} \
+            mlir=${{ matrix.llvm }} \
+            zlib zstd
+      - name: Pack environment
+        run: |
+          mkdir -p "$RUNNER_TEMP/conda-artifacts"
+          conda run -n llvm-env conda-pack -n llvm-env \
+            -o "$RUNNER_TEMP/conda-artifacts/llvm-env-${{ matrix.llvm }}.tar.gz"
+      - name: Upload environment
+        uses: actions/upload-artifact@v7
+        with:
+          name: llvm-conda-${{ matrix.llvm }}
+          path: ${{ runner.temp }}/conda-artifacts/llvm-env-${{ matrix.llvm }}.tar.gz
+          compression-level: 0
+          retention-days: 1
+
+  build-and-test:
+    name: proteus ${{ matrix.os }} LLVM ${{ matrix.llvm }} shared ${{ matrix.build_shared }} MLIR ${{ matrix.mlir }}
+    runs-on: ${{ matrix.os }}
+    needs: prepare-conda
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        llvm: [19.1.7, 20.1.8, 22.1.0]
+        build_shared: [on, off]
+        mlir: [on, off]
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Download environment
+        uses: actions/download-artifact@v8
+        with:
+          name: llvm-conda-${{ matrix.llvm }}
+          path: ${{ runner.temp }}/conda-artifacts
+      - name: Unpack environment
+        run: |
+          env_dir="$RUNNER_TEMP/llvm-env-${{ matrix.llvm }}"
+          mkdir -p "$env_dir"
+          tar -xzf "$RUNNER_TEMP/conda-artifacts/llvm-env-${{ matrix.llvm }}.tar.gz" -C "$env_dir"
+          "$env_dir/bin/conda-unpack"
+          echo "CONDA_PREFIX=$env_dir" >> "$GITHUB_ENV"
+          echo "$env_dir/bin" >> "$GITHUB_PATH"
+      - name: Build build_shared=${{ matrix.build_shared }}
+        run: |
+          mkdir -p build
+          pushd build
+          set -o pipefail
+          cmake .. \
+            -DCMAKE_PREFIX_PATH="$CONDA_PREFIX;$CONDA_PREFIX/lib/cmake" \
+            -DCMAKE_C_COMPILER=clang \
+            -DCMAKE_CXX_COMPILER=clang++ \
+            -DENABLE_DEVELOPER_COMPILER_FLAGS=on \
+            -DENABLE_TESTS=on \
+            -DLLVM_INSTALL_DIR=$(llvm-config --prefix) \
+            -DPROTEUS_ENABLE_MLIR=${{ matrix.mlir }} \
+            -DPROTEUS_ENABLE_PYTHON=on \
+            -DBUILD_SHARED=${{ matrix.build_shared }} |& tee cmake_output.log
+          if grep -q "Manually-specified variables were not used by the project:" cmake_output.log; then
+            echo "Error: Unused variables detected"
+            exit 1
+          fi
+          make -j
+          popd
+      - name: Test
+        run: |
+          pushd build
+          ctest -j8 -T test --output-on-failure
+          popd
+
+  build-and-test-macos:
+    name: proteus macos LLVM ${{ matrix.llvm }} shared ${{ matrix.build_shared }} MLIR ${{ matrix.mlir }}
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        llvm: [19, 20, 22]
+        build_shared: [on, off]
+        mlir: [on, off]
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install LLVM
+        run: |
+          brew install llvm@${{ matrix.llvm }}
+      - name: Install lit
+        run: |
+          brew install lit
+      - name: Install Python bindings dependencies
+        run: |
+          brew install python pybind11
+      - name: Configure LLVM environment
+        run: |
+          LLVM_PREFIX="$(brew --prefix llvm@${{ matrix.llvm }})"
+          PYTHON_PREFIX="$(brew --prefix python)"
+          PYBIND11_PREFIX="$(brew --prefix pybind11)"
+          echo "LLVM_PREFIX=$LLVM_PREFIX" >> "$GITHUB_ENV"
+          echo "PYTHON_PREFIX=$PYTHON_PREFIX" >> "$GITHUB_ENV"
+          echo "PYBIND11_PREFIX=$PYBIND11_PREFIX" >> "$GITHUB_ENV"
+          echo "CC=$LLVM_PREFIX/bin/clang" >> "$GITHUB_ENV"
+          echo "CXX=$LLVM_PREFIX/bin/clang++" >> "$GITHUB_ENV"
+          echo "$LLVM_PREFIX/bin" >> "$GITHUB_PATH"
+          echo "$PYTHON_PREFIX/bin" >> "$GITHUB_PATH"
+      - name: Build build_shared=${{ matrix.build_shared }}
+        run: |
+          mkdir -p build
+          pushd build
+          set -o pipefail
+          cmake .. \
+            -DCMAKE_PREFIX_PATH="$LLVM_PREFIX;$PYTHON_PREFIX;$PYBIND11_PREFIX" \
+            -DCMAKE_C_COMPILER="$CC" \
+            -DCMAKE_CXX_COMPILER="$CXX" \
+            -DCMAKE_OSX_SYSROOT="$(xcrun --sdk macosx --show-sdk-path)" \
+            -DENABLE_DEVELOPER_COMPILER_FLAGS=on \
+            -DENABLE_TESTS=on \
+            -DLLVM_INSTALL_DIR="$LLVM_PREFIX" \
+            -DPROTEUS_ENABLE_MLIR=${{ matrix.mlir }} \
+            -DPROTEUS_ENABLE_PYTHON=on \
+            -DBUILD_SHARED=${{ matrix.build_shared }} 2>&1 | tee cmake_output.log
+          if grep -q "Manually-specified variables were not used by the project:" cmake_output.log; then
+            echo "Error: Unused variables detected"
+            exit 1
+          fi
+          make -j
+          popd
+      - name: Test
+        run: |
+          pushd build
+          ctest -j8 -T test --output-on-failure
+          popd

proteus_python-2026.7.0/.github/workflows/ci-pr-pages.yml

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+name: pages
+
+on:
+  pull_request:
+    paths:
+      - "docs/**"
+      - "include/**"
+      - "mkdocs.yml"
+      - "src/**"
+      - "scripts/generate_simple_wheel_index.py"
+      - ".github/workflows/ci-pr-pages.yml"
+      - ".github/workflows/deploy-pages-main.yml"
+      - ".github/workflows/deploy-pages-release.yml"
+      - ".github/workflows/gh-pages-docs.yml"
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-24.04
+    env:
+      PROTEUS_HOST_BACKEND_PACKAGE: "proteus-python-backend-host-llvm22"
+      PROTEUS_CUDA_BACKEND_PACKAGE: "proteus-python-backend-cuda12-llvm22"
+      PROTEUS_ROCM_BACKEND_PACKAGE: "proteus-python-backend-rocm72"
+    steps:
+      - name: Checkout
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+
+      - name: Set up Python
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        with:
+          python-version: "3.12"
+
+      - name: Build docs
+        run: |
+          set -euo pipefail
+          sudo apt-get update
+          sudo apt-get install -y graphviz doxygen
+          python -m pip install --upgrade pip
+          python -m pip install mike mkdocs-material
+          pushd docs
+          doxygen
+          popd
+          mkdocs build --strict
+
+      - name: Smoke test mike publishing
+        run: |
+          set -euo pipefail
+
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+
+          git tag -f v0.0.0-smoke
+          git tag -f v0.0.0rc1-smoke
+          git branch -f gh-pages-smoke HEAD
+
+          cleanup() {
+            local worktree_dir="${1:-}"
+            if [[ -n "${worktree_dir}" && -d "${worktree_dir}" ]]; then
+              git worktree remove --force "${worktree_dir}" || true
+            fi
+            git branch -D gh-pages-smoke || true
+            git tag -d v0.0.0-smoke || true
+            git tag -d v0.0.0rc1-smoke || true
+          }
+
+          smoke_dir="$(mktemp -d)"
+          trap 'cleanup "${smoke_dir}"' EXIT
+
+          mike deploy --branch gh-pages-smoke --update-aliases --title Development main
+          mike deploy \
+            --branch gh-pages-smoke \
+            --update-aliases \
+            --title v0.0.0-smoke \
+            v0.0.0-smoke \
+            latest
+          mike deploy \
+            --branch gh-pages-smoke \
+            --update-aliases \
+            --title v0.0.0rc1-smoke \
+            v0.0.0rc1-smoke \
+            prerelease
+          mike set-default --branch gh-pages-smoke latest
+
+          git worktree add --force "${smoke_dir}" gh-pages-smoke
+          test -f "${smoke_dir}/index.html"
+          test -f "${smoke_dir}/versions.json"
+          test -f "${smoke_dir}/main/index.html"
+          test -f "${smoke_dir}/v0.0.0-smoke/index.html"
+          test -f "${smoke_dir}/v0.0.0rc1-smoke/index.html"
+          test -f "${smoke_dir}/latest/index.html"
+          test -f "${smoke_dir}/prerelease/index.html"
+
+          python scripts/remove_prerelease_mike_docs.py --site-dir "${smoke_dir}"
+
+          test -f "${smoke_dir}/main/index.html"
+          test -f "${smoke_dir}/v0.0.0-smoke/index.html"
+          test -f "${smoke_dir}/latest/index.html"
+          test ! -e "${smoke_dir}/v0.0.0rc1-smoke"
+          test ! -e "${smoke_dir}/prerelease"
+          python -c 'import json, sys; from scripts.remove_prerelease_mike_docs import is_prerelease_version; versions = json.load(open(sys.argv[1], encoding="utf-8")); assert all(not is_prerelease_version(entry["version"]) for entry in versions); assert all("prerelease" not in entry.get("aliases", []) for entry in versions)' "${smoke_dir}/versions.json"
+
+      - name: Smoke test wheel index generation
+        run: |
+          set -euo pipefail
+
+          releases_json="$(mktemp)"
+          wheel_dir="$(mktemp -d)"
+
+          cat > "${releases_json}" <<'JSON'
+          [
+            {
+              "tag_name": "v0.2.0",
+              "draft": false,
+              "prerelease": false,
+              "published_at": "2026-06-30T12:00:00Z",
+              "html_url": "https://github.com/Olympus-HPC/proteus/releases/tag/v0.2.0",
+              "assets": [
+                {
+                  "name": "proteus_python_backend_host_llvm22-0.2.0-cp312-cp312-manylinux_2_28_x86_64.whl",
+                  "browser_download_url": "https://github.com/Olympus-HPC/proteus/releases/download/v0.2.0/proteus_python_backend_host_llvm22-0.2.0-cp312-cp312-manylinux_2_28_x86_64.whl"
+                },
+                {
+                  "name": "proteus_python_backend_cuda12_llvm22-0.2.0-cp312-cp312-manylinux_2_28_x86_64.whl",
+                  "browser_download_url": "https://github.com/Olympus-HPC/proteus/releases/download/v0.2.0/proteus_python_backend_cuda12_llvm22-0.2.0-cp312-cp312-manylinux_2_28_x86_64.whl"
+                },
+                {
+                  "name": "proteus_python_backend_rocm72-0.2.0-cp312-cp312-manylinux_2_28_x86_64.whl",
+                  "browser_download_url": "https://github.com/Olympus-HPC/proteus/releases/download/v0.2.0/proteus_python_backend_rocm72-0.2.0-cp312-cp312-manylinux_2_28_x86_64.whl"
+                }
+              ]
+            },
+            {
+              "tag_name": "v0.3.0rc1",
+              "draft": false,
+              "prerelease": true,
+              "published_at": "2026-06-29T12:00:00Z",
+              "html_url": "https://github.com/Olympus-HPC/proteus/releases/tag/v0.3.0rc1",
+              "assets": [
+                {
+                  "name": "proteus_python_backend_host_llvm22-0.3.0rc1-cp312-cp312-manylinux_2_28_x86_64.whl",
+                  "browser_download_url": "https://github.com/Olympus-HPC/proteus/releases/download/v0.3.0rc1/proteus_python_backend_host_llvm22-0.3.0rc1-cp312-cp312-manylinux_2_28_x86_64.whl"
+                }
+              ]
+            }
+          ]
+          JSON
+
+          python scripts/generate_simple_wheel_index.py \
+            --releases-json "${releases_json}" \
+            --output-dir "${wheel_dir}" \
+            --project "${PROTEUS_HOST_BACKEND_PACKAGE}" \
+            --project "${PROTEUS_CUDA_BACKEND_PACKAGE}" \
+            --project "${PROTEUS_ROCM_BACKEND_PACKAGE}"
+
+          test -f "${wheel_dir}/simple/index.html"
+          test -f "${wheel_dir}/test/index.html"
+          test -f "${wheel_dir}/simple/proteus-python-backend-host-llvm22/index.html"
+          test -f "${wheel_dir}/simple/proteus-python-backend-cuda12-llvm22/index.html"
+          test -f "${wheel_dir}/simple/proteus-python-backend-rocm72/index.html"
+          test -f "${wheel_dir}/test/proteus-python-backend-host-llvm22/index.html"
+
+          grep -n "<h1>Proteus wheel index: simple</h1>" "${wheel_dir}/simple/index.html"
+          grep -n "<h1>Proteus wheel index: test</h1>" "${wheel_dir}/test/index.html"
+          grep -n '<ul class="link-list">' "${wheel_dir}/simple/index.html"
+          grep -n '<li><a href="proteus-python-backend-host-llvm22/">' "${wheel_dir}/simple/index.html"
+          grep -n "<h1>proteus-python-backend-host-llvm22</h1>" "${wheel_dir}/simple/proteus-python-backend-host-llvm22/index.html"
+          grep -n "&larr; Back to simple index" "${wheel_dir}/simple/proteus-python-backend-host-llvm22/index.html"
+          grep -n "proteus_python_backend_host_llvm22-0.2.0" "${wheel_dir}/simple/proteus-python-backend-host-llvm22/index.html"
+          grep -n "proteus_python_backend_host_llvm22-0.3.0rc1" "${wheel_dir}/test/proteus-python-backend-host-llvm22/index.html"
+          if grep -q "proteus_python_backend_host_llvm22-0.3.0rc1" "${wheel_dir}/simple/proteus-python-backend-host-llvm22/index.html"; then
+            echo "prerelease wheel unexpectedly appeared in simple channel" >&2
+            exit 1
+          fi
+          if grep -q "proteus_python_backend_host_llvm22-0.2.0" "${wheel_dir}/test/proteus-python-backend-host-llvm22/index.html"; then
+            echo "stable wheel unexpectedly appeared in test channel" >&2
+            exit 1
+          fi

proteus_python-2026.7.0/.github/workflows/ci-test-spack.yml

@@ -0,0 +1,49 @@
+name: spack CI
+
+on:
+  pull_request:
+    paths:
+      - ".github/workflows/ci-test-spack.yml"
+      - "CMakeLists.txt"
+      - "cmake/**"
+      - "include/**"
+      - "packaging/spack/**"
+      - "src/**"
+
+jobs:
+  build-and-test:
+    name: spack ${{ matrix.os }} LLVM ${{ matrix.llvm }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        llvm: [18, 19, 20]
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - uses: actions/checkout@v4
+      # Install Clang/LLVM using system packages for Spack external package detection.
+      - name: Install LLVM ${{ matrix.llvm }}
+        run: |
+          sudo apt-get update
+          # Remove existing LLVM/Clang packages to avoid conflics with spack external package configuration.
+          sudo apt-get remove -y clang-[0-9]* llvm-[0-9]*-dev libclang-[0-9]*-dev 2>/dev/null || true
+          sudo apt-get install -y llvm-${{ matrix.llvm }}-dev libclang-${{ matrix.llvm }}-dev clang-${{ matrix.llvm }}
+      - name: Run spack test
+        run: |
+          # Install spack
+          export SPACK_DISABLE_LOCAL_CONFIG=true
+          export SPACK_USER_CACHE_PATH=/tmp/spack/user_cache
+          git clone --quiet --depth=2 --branch v1.1.1 https://github.com/spack/spack.git /tmp/spack
+          source /tmp/spack/share/spack/setup-env.sh
+          # Create spack environment
+          spack env create -d /tmp/proteus-spack-env
+          spack env activate /tmp/proteus-spack-env
+          # Find external dependencies
+          spack external find
+          # Add proteus package and install
+          spack repo add ${GITHUB_WORKSPACE}/packaging/spack
+          spack add proteus@git.${{ github.event.pull_request.head.sha }} ^llvm@${{ matrix.llvm }}
+          spack concretize -f
+          spack install -v