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molprint v0.1.0
High-performance molecular fingerprint computation and similarity search in Rust. - SMILES parser (lexer → MolGraph, ring closure, branches, bracket atoms) - Ring perception via SSSR (Horton BFS algorithm) - Aromaticity perception - SMARTS engine with VF2 subgraph isomorphism - Morgan/ECFP fingerprints (configurable radius, 512–4096 bit, deterministic) - MACCS-166 structural keys (100% RDKit-accurate on ChEMBL 10k) - Tanimoto, Dice, Cosine similarity via POPCNT on u64 word arrays - Parallel threshold and top-k screening via Rayon - FPS (chemfp-compatible), SDF V2000 (+ gzip), SMILES file I/O - CLI: fp and search subcommands - mdBook documentation site
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‎.github/rdkit-env.yml‎

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name: rdkit-env
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channels:
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- conda-forge
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- defaults
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dependencies:
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- python=3.11
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- rdkit>=2023.09

‎.github/workflows/ci.yml‎

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name: CI
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on:
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push:
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branches: [main]
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pull_request:
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schedule:
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# Weekly run every Monday at 03:00 UTC (for fuzz + RDKit validation jobs)
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- cron: "0 3 * * 1"
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env:
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CARGO_TERM_COLOR: always
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jobs:
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# ── Core checks ─────────────────────────────────────────────────────────────
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test:
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name: Test
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: dtolnay/rust-toolchain@stable
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- uses: Swatinem/rust-cache@v2
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- run: cargo test --workspace
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clippy:
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name: Clippy
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: dtolnay/rust-toolchain@stable
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with:
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components: clippy
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- uses: Swatinem/rust-cache@v2
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- run: cargo clippy --workspace -- -D warnings
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fmt:
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name: Format
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: dtolnay/rust-toolchain@stable
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with:
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components: rustfmt
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- run: cargo fmt --check
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doc:
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name: Docs
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: dtolnay/rust-toolchain@stable
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- uses: Swatinem/rust-cache@v2
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- run: cargo doc --no-deps --workspace
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# ── MSRV check ───────────────────────────────────────────────────────────────
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msrv:
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name: MSRV (1.75)
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: dtolnay/rust-toolchain@1.75
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- uses: Swatinem/rust-cache@v2
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- run: cargo check --workspace
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# ── Dependency audit ─────────────────────────────────────────────────────────
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audit:
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name: Security Audit
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: dtolnay/rust-toolchain@stable
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- uses: Swatinem/rust-cache@v2
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- run: cargo install cargo-audit --quiet
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- run: cargo audit
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# ── Fuzz (short CI run) ──────────────────────────────────────────────────────
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fuzz:
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name: Fuzz SMILES (60s)
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runs-on: ubuntu-latest
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# Only run on schedule or when parser code changes
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if: >
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github.event_name == 'schedule' ||
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contains(github.event.head_commit.message, '[fuzz]')
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steps:
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- uses: actions/checkout@v4
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- uses: dtolnay/rust-toolchain@nightly
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- uses: Swatinem/rust-cache@v2
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- run: cargo install cargo-fuzz --quiet
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- run: cargo +nightly fuzz run fuzz_smiles -- -max_total_time=60
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working-directory: fuzz
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# ── RDKit validation (weekly / fingerprint changes) ──────────────────────────
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rdkit-validate:
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name: RDKit MACCS Validation
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runs-on: ubuntu-latest
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if: >
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github.event_name == 'schedule' ||
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contains(github.event.head_commit.modified, 'crates/molprint-fp') ||
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contains(github.event.head_commit.modified, 'crates/molprint-core')
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steps:
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- uses: actions/checkout@v4
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- uses: dtolnay/rust-toolchain@stable
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- uses: Swatinem/rust-cache@v2
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- name: Install conda (Miniforge)
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uses: conda-incubator/setup-miniconda@v3
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with:
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miniforge-version: latest
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activate-environment: rdkit-env
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environment-file: .github/rdkit-env.yml
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- name: Build release binary
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run: cargo build --release
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- name: Generate RDKit reference data
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shell: bash -el {0}
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run: python scripts/generate_reference.py
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- name: Run MACCS validation test
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run: cargo test -p molprint-fp validate_maccs_against_rdkit -- --nocapture

‎.github/workflows/docs.yml‎

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name: Docs
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on:
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push:
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branches: [main]
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workflow_dispatch:
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permissions:
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contents: read
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pages: write
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id-token: write
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concurrency:
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group: pages
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cancel-in-progress: true
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Install mdBook
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run: |
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curl -sSL https://github.com/rust-lang/mdBook/releases/download/v0.4.40/mdbook-v0.4.40-x86_64-unknown-linux-gnu.tar.gz \
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| tar -xz --directory /usr/local/bin
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- name: Build book
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run: mdbook build docs
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- name: Upload Pages artifact
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uses: actions/upload-pages-artifact@v3
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with:
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path: docs/book
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deploy:
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needs: build
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runs-on: ubuntu-latest
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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steps:
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v4

‎.github/workflows/release.yml‎

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name: Release
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on:
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push:
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tags:
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- "v*"
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permissions:
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contents: write
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jobs:
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build:
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name: Build ${{ matrix.target }}
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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include:
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- target: x86_64-unknown-linux-musl
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os: ubuntu-latest
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archive: tar.gz
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- target: aarch64-unknown-linux-musl
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os: ubuntu-latest
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archive: tar.gz
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- target: x86_64-apple-darwin
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os: macos-latest
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archive: tar.gz
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- target: aarch64-apple-darwin
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os: macos-latest
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archive: tar.gz
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- target: x86_64-pc-windows-msvc
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os: windows-latest
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archive: zip
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steps:
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- uses: actions/checkout@v4
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- uses: dtolnay/rust-toolchain@stable
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with:
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targets: ${{ matrix.target }}
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- name: Install musl tools (Linux)
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if: contains(matrix.target, 'musl')
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run: sudo apt-get install -y musl-tools
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- name: Install cross-compiler (aarch64 Linux)
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if: matrix.target == 'aarch64-unknown-linux-musl'
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run: |
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sudo apt-get install -y gcc-aarch64-linux-gnu
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echo "CARGO_TARGET_AARCH64_UNKNOWN_LINUX_MUSL_LINKER=aarch64-linux-gnu-gcc" >> $GITHUB_ENV
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- uses: Swatinem/rust-cache@v2
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with:
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key: ${{ matrix.target }}
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- name: Build
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run: cargo build --release --target ${{ matrix.target }} -p molprint-cli
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- name: Package (Unix)
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if: matrix.archive == 'tar.gz'
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shell: bash
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run: |
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BIN=molprint
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STAGING="molprint-${{ github.ref_name }}-${{ matrix.target }}"
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mkdir "$STAGING"
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cp "target/${{ matrix.target }}/release/$BIN" "$STAGING/"
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cp README.md "$STAGING/"
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tar -czf "$STAGING.tar.gz" "$STAGING"
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echo "ASSET=$STAGING.tar.gz" >> $GITHUB_ENV
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- name: Package (Windows)
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if: matrix.archive == 'zip'
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shell: pwsh
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run: |
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$STAGING = "molprint-${{ github.ref_name }}-${{ matrix.target }}"
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New-Item -ItemType Directory -Path $STAGING
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Copy-Item "target\${{ matrix.target }}\release\molprint.exe" "$STAGING\"
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Copy-Item "README.md" "$STAGING\"
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Compress-Archive -Path "$STAGING\*" -DestinationPath "$STAGING.zip"
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echo "ASSET=$STAGING.zip" | Out-File -Append -FilePath $env:GITHUB_ENV
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- name: Upload artifact
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uses: actions/upload-artifact@v4
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with:
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name: ${{ matrix.target }}
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path: ${{ env.ASSET }}
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release:
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name: Create release
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needs: build
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Download all artifacts
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uses: actions/download-artifact@v4
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with:
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path: artifacts
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merge-multiple: true
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- name: Create GitHub release
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uses: softprops/action-gh-release@v2
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with:
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files: artifacts/*
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generate_release_notes: true
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make_latest: true

‎.gitignore‎

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/target/
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.claude/
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.venv/

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