readcon-chemfiles 0.13.0__tar.gz

readcon_chemfiles-0.13.0/.cargo/config.toml

@@ -0,0 +1,6 @@
+# chemfiles-sys vendors an older CMakeLists that still declares
+# cmake_minimum_required(< 3.5). Modern CMake rejects that unless
+# CMAKE_POLICY_VERSION_MINIMUM is set; export it for all cargo builds
+# that pull the optional `chemfiles` feature.
+[env]
+CMAKE_POLICY_VERSION_MINIMUM = "3.5"

readcon_chemfiles-0.13.0/.github/workflows/build_test.yml

@@ -0,0 +1,55 @@
+name: Basic tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+concurrency:
+  group: btest_rust-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
+
+jobs:
+  btest_rust:
+    runs-on: ubuntu-22.04
+    name: Run basic tests and build
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Install Rust toolchain
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Setup sccache
+        uses: mozilla-actions/sccache-action@v0.0.9
+        with:
+          version: "v0.10.0"
+
+      - name: Setup sccache environment
+        run: |
+          echo "SCCACHE_GHA_ENABLED=true" >> $GITHUB_ENV
+          echo "RUSTC_WRAPPER=sccache" >> $GITHUB_ENV
+
+      - name: Install dependencies
+        run: |
+          python -m pip install meson ninja
+          cargo install cbindgen
+          sudo snap install valgrind --classic
+          sudo apt-get update && sudo apt-get install -y libc6-dbg --fix-missing
+
+      - name: Verify shipped C header matches cbindgen output
+        run: scripts/regen-capi-headers.sh --check
+
+      - name: Run Rust tests
+        run: cargo test
+
+      - name: Build and test FFI bindings
+        id: btest_rust
+        run: |
+          meson setup bbdir \
+          -Dwith_tests=False \
+          -Dwith_cpp=True \
+          -Dwith_examples=True \
+          --buildtype=release
+          meson test -C bbdir \
+          --wrap="valgrind --leak-check=full --show-leak-kinds=definite,indirect,possible --track-origins=yes --error-exitcode=1 --suppressions=$GITHUB_WORKSPACE/valgrind.supp --gen-suppressions=all"

readcon_chemfiles-0.13.0/.github/workflows/ci_bench_commenter.yml

@@ -0,0 +1,38 @@
+name: Comment benchmark results
+
+on:
+  workflow_run:
+    workflows: ["Benchmark PR"]
+    types: [completed]
+
+jobs:
+  comment:
+    if: >-
+      github.event.workflow_run.event == 'pull_request' &&
+      github.event.workflow_run.conclusion == 'success'
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
+      issues: write
+      actions: read
+
+    steps:
+      - name: Download benchmark results
+        uses: actions/download-artifact@v4
+        with:
+          name: benchmark-results
+          path: results/
+          run-id: ${{ github.event.workflow_run.id }}
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Post benchmark comment
+        uses: HaoZeke/asv-perch@v1
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          comparison-text-file: results/comparison.txt
+          metadata-file: results/metadata.txt
+          regression-threshold: '10'
+          auto-draft-on-regression: 'true'
+          label-before: main
+          label-after: pr
+          runner-info: ubuntu-22.04

readcon_chemfiles-0.13.0/.github/workflows/ci_benchmark.yml

@@ -0,0 +1,105 @@
+name: Benchmark PR
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+on:
+  pull_request:
+    branches: [main]
+
+env:
+  SCCACHE_GHA_ENABLED: "true"
+
+jobs:
+  benchmark:
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - label: main
+            sha: ${{ github.event.pull_request.base.sha }}
+          - label: pr
+            sha: ${{ github.event.pull_request.head.sha }}
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Checkout target commit
+        run: |
+          mkdir -p /tmp/_bench_preserve
+          cp -r benches/ /tmp/_bench_preserve/
+          git checkout -f ${{ matrix.sha }}
+          git clean -fd
+          cp -r /tmp/_bench_preserve/benches/ benches/
+
+      - name: Install Rust toolchain
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Configure sccache
+        uses: mozilla-actions/sccache-action@v0.0.9
+        with:
+          version: "v0.10.0"
+
+      - name: Setup sccache environment
+        run: |
+          echo "RUSTC_WRAPPER=sccache" >> $GITHUB_ENV
+
+      - name: Run benchmarks
+        run: |
+          cargo bench --bench iterator_bench -- --save-baseline ${{ matrix.label }}
+
+      - name: Export Criterion results
+        run: |
+          tar czf criterion-${{ matrix.label }}.tar.gz -C target criterion/
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: criterion-${{ matrix.label }}
+          path: criterion-${{ matrix.label }}.tar.gz
+          retention-days: 7
+
+  compare:
+    needs: benchmark
+    runs-on: ubuntu-latest
+    steps:
+      - name: Install Rust toolchain
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Install critcmp
+        run: cargo install critcmp
+
+      - name: Download main results
+        uses: actions/download-artifact@v4
+        with:
+          name: criterion-main
+          path: .
+
+      - name: Download PR results
+        uses: actions/download-artifact@v4
+        with:
+          name: criterion-pr
+          path: .
+
+      - name: Extract and compare
+        run: |
+          mkdir -p target
+          tar xzf criterion-main.tar.gz -C target/
+          tar xzf criterion-pr.tar.gz -C target/
+          mkdir -p results
+          critcmp main pr --threshold 5 > results/comparison.txt || true
+          if [ ! -s results/comparison.txt ]; then
+            echo "No benchmark comparison output" > results/comparison.txt
+          fi
+          cat results/comparison.txt
+
+      - name: Write metadata
+        run: |
+          echo "main_sha=${{ github.event.pull_request.base.sha }}" > results/metadata.txt
+          echo "pr_sha=${{ github.event.pull_request.head.sha }}" >> results/metadata.txt
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: benchmark-results
+          path: results/
+          retention-days: 7

readcon_chemfiles-0.13.0/.github/workflows/ci_doc_commenter.yml

@@ -0,0 +1,23 @@
+name: Comment on pull request
+
+on:
+  workflow_run:
+    workflows: ["Documentation"]
+    types: [completed]
+
+jobs:
+  pr_comment:
+    if: github.event.workflow_run.event == 'pull_request' && github.event.workflow_run.conclusion == 'success'
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
+      issues: write
+      actions: read
+
+    steps:
+      - uses: HaoZeke/doc-previewer@0e1094735b4f7ee9a2c60a18a34d7a7e5bc6bb63
+        with:
+          workflow_run_id: ${{ github.event.workflow_run.id }}
+          head_sha: ${{ github.event.workflow_run.head_sha }}
+          artifact_name: github-pages
+          comment_header: "### readcon-core Documentation Preview"

readcon_chemfiles-0.13.0/.github/workflows/ci_docs.yml

@@ -0,0 +1,55 @@
+name: Documentation
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - uses: prefix-dev/setup-pixi@v0.9.4
+        with:
+          cache: true
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
+          environments: docs
+
+      - name: Add cargo bin to PATH
+        run: echo "${{ runner.temp }}/.cargo/bin" >> "$GITHUB_PATH"
+
+      - name: Build documentation
+        run: pixi r -e docs docbld
+        env:
+          CARGO_HOME: ${{ runner.temp }}/.cargo
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v4
+        with:
+          path: docs/build
+
+  deploy:
+    if: github.ref == 'refs/heads/main'
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

readcon_chemfiles-0.13.0/.github/workflows/coverage.yml

@@ -0,0 +1,76 @@
+name: Coverage
+# Adapted from https://github.com/metatensor/metatensor/pull/939
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+concurrency:
+  group: coverage-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
+
+jobs:
+  coverage:
+    runs-on: ubuntu-22.04
+    name: collect code coverage
+    # Adapted from https://www.scivision.dev/github-actions-latest-llvm-clang-flang/
+    strategy:
+      matrix:
+        llvm-version: [20]
+    env:
+      CMAKE_C_COMPILER: clang-${{ matrix.llvm-version }}
+      CMAKE_CXX_COMPILER: clang++-${{ matrix.llvm-version }}
+      CC: clang-${{ matrix.llvm-version }}
+      CXX: clang++-${{ matrix.llvm-version }}
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Setup LLVM
+        run: |
+            wget https://apt.llvm.org/llvm.sh
+            chmod +x llvm.sh
+            sudo ./llvm.sh ${{ matrix.llvm-version }}
+            sudo apt-get update
+            sudo apt-get install --no-install-recommends -y clang-${{ matrix.llvm-version }}
+
+      - name: Install Rust toolchain
+        uses: dtolnay/rust-toolchain@stable
+        with:
+          components: llvm-tools-preview
+
+      - name: Install cargo-llvm-cov
+        uses: taiki-e/install-action@cargo-llvm-cov
+
+      - uses: prefix-dev/setup-pixi@v0.9.4
+        with:
+          cache: true
+          environments: default
+
+      - name: Setup sccache
+        uses: mozilla-actions/sccache-action@v0.0.9
+        with:
+          version: "v0.10.0"
+
+      - name: Setup sccache environment
+        run: |
+          echo "SCCACHE_GHA_ENABLED=true" >> $GITHUB_ENV
+          echo "RUSTC_WRAPPER=sccache" >> $GITHUB_ENV
+
+      - name: Generate rust code coverage
+        id: coverage
+        run: |
+          PIXI_PYTHON="$(pixi r -e default which python)"
+          PYO3_PYTHON="$PIXI_PYTHON" pixi r -e default \
+            cargo llvm-cov --features rpc,python --workspace \
+            --no-fail-fast --codecov \
+            --include-ffi \
+            --output-path rust_codecov.json
+
+      # - name: Upload to codecov.io
+      #   uses: codecov/codecov-action@v5
+      #   with:
+      #     fail_ci_if_error: true
+      #     files: rust_codecov.json
+      #     token: ${{ secrets.CODECOV_TOKEN }}

readcon_chemfiles-0.13.0/.github/workflows/crates_publish.yml

@@ -0,0 +1,69 @@
+# Publish readcon-core to crates.io on version tags.
+# Secret: CARGO_REGISTRY_TOKEN (crates.io API token for the publish owner).
+# cargo-dist's Release workflow handles binary archives + GitHub Release only.
+name: Publish to crates.io
+
+on:
+  push:
+    tags:
+      - 'v*'
+  workflow_dispatch:
+    inputs:
+      tag:
+        description: 'Tag to publish (e.g. v0.13.0); defaults to ref'
+        required: false
+        type: string
+
+permissions:
+  contents: read
+
+jobs:
+  publish-crates-io:
+    name: Publish to crates.io
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          ref: ${{ inputs.tag || github.ref }}
+
+      - name: Install Rust toolchain
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Resolve crate version
+        id: check
+        run: |
+          # Prefer Cargo.toml so workflow_dispatch on `main` still targets the
+          # package version. On a v* tag, ref name must match Cargo.toml.
+          version="$(sed -n 's/^version = "\([^"]*\)"/\1/p' Cargo.toml | head -1)"
+          ref_name="${GITHUB_REF_NAME:-}"
+          if [ -n "${{ inputs.tag }}" ]; then
+            ref_name="${{ inputs.tag }}"
+          fi
+          if [[ "$ref_name" == v* ]]; then
+            tag_ver="${ref_name#v}"
+            if [ "$tag_ver" != "$version" ]; then
+              echo "tag ${ref_name} does not match Cargo.toml version ${version}" >&2
+              exit 1
+            fi
+          fi
+          echo "version=${version}" >> "$GITHUB_OUTPUT"
+          if curl -sfL \
+              -H "User-Agent: readcon-core-release-check (lode-org)" \
+              "https://crates.io/api/v1/crates/readcon-core/${version}" \
+              -o /dev/null; then
+              echo "already_published=true" >> "$GITHUB_OUTPUT"
+              echo "readcon-core ${version} is already published; skipping."
+          else
+              echo "already_published=false" >> "$GITHUB_OUTPUT"
+          fi
+
+      - name: cargo publish
+        if: steps.check.outputs.already_published != 'true'
+        env:
+          CARGO_REGISTRY_TOKEN: ${{ secrets.CARGO_REGISTRY_TOKEN }}
+        run: |
+          if [ -z "${CARGO_REGISTRY_TOKEN:-}" ]; then
+            echo "CARGO_REGISTRY_TOKEN secret is empty; set it on the repo." >&2
+            exit 1
+          fi
+          cargo publish --locked

readcon_chemfiles-0.13.0/.github/workflows/lint.yml

@@ -0,0 +1,21 @@
+name: Lint
+
+on:
+  pull_request:
+    branches: [main]
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v6
+      with:
+        fetch-depth: 0
+
+    - name: Conventional commits check
+      uses: cocogitto/cocogitto-action@v3
+
+    - name: Audit for large files
+      uses: HaoZeke/large-file-auditor@v0.1.0
+      with:
+        file-size-threshold: "1M"

readcon_chemfiles-0.13.0/.github/workflows/python_wheels.yml

@@ -0,0 +1,208 @@
+name: Python wheels
+
+on:
+  push:
+    tags:
+      - 'v*'
+  pull_request:
+    paths:
+      - 'src/**'
+      - 'Cargo.toml'
+      - 'Cargo.lock'
+      - 'pyproject.toml'
+      - 'pyproject.chemfiles.toml'
+      - '.github/workflows/python_wheels.yml'
+  workflow_dispatch:
+
+concurrency:
+  group: python-wheels-${{ github.ref }}
+  cancel-in-progress: ${{ !startsWith(github.ref, 'refs/tags/') }}
+
+permissions:
+  contents: read
+
+env:
+  CARGO_HTTP_MULTIPLEXING: "false"
+  CARGO_NET_RETRY: "10"
+  CARGO_HTTP_TIMEOUT: "120"
+
+jobs:
+  # Lean `readcon` + chemfiles-linked `readcon-chemfiles` (separate PyPI names,
+  # same extension module `readcon`). Matrix is the usual dual-distribution pattern.
+  sdist:
+    name: Build sdist (${{ matrix.variant }})
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - variant: default
+            pyproject: pyproject.toml
+          - variant: chemfiles
+            pyproject: pyproject.chemfiles.toml
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Select pyproject for variant
+        shell: bash
+        run: |
+          if [ "${{ matrix.pyproject }}" != "pyproject.toml" ]; then
+            cp "${{ matrix.pyproject }}" pyproject.toml
+          fi
+          head -15 pyproject.toml
+
+      - name: Build sdist
+        uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out dist
+
+      - name: Validate sdist
+        run: pipx run twine check --strict dist/*
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: sdist-${{ matrix.variant }}
+          path: dist/*.tar.gz
+          if-no-files-found: error
+
+  wheels:
+    name: Wheel ${{ matrix.variant }} (${{ matrix.os }}, ${{ matrix.target }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      # Explicit rows only (no axis × include cartesian product).
+      matrix:
+        include:
+          # --- default (lean): features from pyproject.toml [tool.maturin]
+          - variant: default
+            os: ubuntu-latest
+            target: x86_64
+            pyproject: pyproject.toml
+            features: python
+          - variant: default
+            os: ubuntu-22.04
+            target: aarch64
+            pyproject: pyproject.toml
+            features: python
+          - variant: default
+            os: macos-15
+            target: x86_64
+            pyproject: pyproject.toml
+            features: python
+          - variant: default
+            os: macos-14
+            target: aarch64
+            pyproject: pyproject.toml
+            features: python
+          - variant: default
+            os: windows-latest
+            target: x86_64
+            pyproject: pyproject.toml
+            features: python
+          # --- chemfiles-linked distribution (readcon-chemfiles on PyPI)
+          - variant: chemfiles
+            os: ubuntu-latest
+            target: x86_64
+            pyproject: pyproject.chemfiles.toml
+            features: python,chemfiles
+          - variant: chemfiles
+            os: ubuntu-22.04
+            target: aarch64
+            pyproject: pyproject.chemfiles.toml
+            features: python,chemfiles
+          - variant: chemfiles
+            os: macos-15
+            target: x86_64
+            pyproject: pyproject.chemfiles.toml
+            features: python,chemfiles
+          - variant: chemfiles
+            os: macos-14
+            target: aarch64
+            pyproject: pyproject.chemfiles.toml
+            features: python,chemfiles
+          # Windows + chemfiles-sys/CMake is unreliable on GHA; ship lean
+          # Windows wheels only. Linux/macOS cover full chemfiles matrices.
+          # - variant: chemfiles / windows-latest — omitted on purpose
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Select pyproject for variant
+        shell: bash
+        run: |
+          if [ "${{ matrix.pyproject }}" != "pyproject.toml" ]; then
+            cp "${{ matrix.pyproject }}" pyproject.toml
+          fi
+          echo "Building features=${{ matrix.features }} from:"
+          head -20 pyproject.toml
+
+      - name: Build wheels
+        id: build1
+        continue-on-error: true
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist --features ${{ matrix.features }} --find-interpreter
+          manylinux: auto
+          docker-options: >-
+            -e CARGO_HTTP_MULTIPLEXING=false
+            -e CARGO_NET_RETRY=10
+            -e CARGO_HTTP_TIMEOUT=120
+            -e CMAKE_POLICY_VERSION_MINIMUM=3.5
+
+      - name: Build wheels (retry)
+        if: steps.build1.outcome == 'failure'
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist --features ${{ matrix.features }} --find-interpreter
+          manylinux: auto
+          docker-options: >-
+            -e CARGO_HTTP_MULTIPLEXING=false
+            -e CARGO_NET_RETRY=10
+            -e CARGO_HTTP_TIMEOUT=120
+            -e CMAKE_POLICY_VERSION_MINIMUM=3.5
+
+      - name: Validate wheels
+        if: matrix.target != 'aarch64' || runner.os != 'Linux'
+        run: pipx run twine check --strict dist/*
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.variant }}-${{ matrix.os }}-${{ matrix.target }}
+          path: dist/*.whl
+          if-no-files-found: error
+
+  publish:
+    name: Publish to PyPI
+    needs: [sdist, wheels]
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/v')
+    environment:
+      name: pypi
+      url: https://pypi.org/p/readcon
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: '{sdist-*,wheels-*}'
+          merge-multiple: true
+          path: dist/
+
+      - name: List artifacts
+        run: |
+          ls -la dist/
+          echo "--- expected packages: readcon (lean) and readcon-chemfiles (full) ---"
+          ls dist/*.whl dist/*.tar.gz | sed 's|.*/||' | sort -u
+
+      # Trusted publishers must be configured on PyPI for *both* project names
+      # `readcon` and `readcon-chemfiles` (same workflow + environment `pypi`).
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          skip-existing: true