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Merge pull request #2 from OpenMS/wrap-more
feat: Sage API parity — frames, converters, config
2 parents 1d139f4 + 3ec0c71 commit 4f31019

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‎.github/workflows/test.yml‎

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name: Tests
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on:
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push:
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branches: [master]
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pull_request:
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workflow_dispatch:
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jobs:
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stub-tests:
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name: Stub Tests (no dataset)
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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 Rust
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uses: dtolnay/rust-toolchain@stable
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- name: Cargo test (stub mode)
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run: cargo test -- --nocapture
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- name: Build library (debug)
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run: cargo build
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- name: Fetch Catch2
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run: tests_cpp/fetch_catch2.sh
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- name: C++ ABI tests
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run: |
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cd tests_cpp
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make test LIBDIR=../target/debug
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integration-tests:
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name: Integration Tests (real data)
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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 Rust
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uses: dtolnay/rust-toolchain@stable
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- name: Cache test datasets
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id: cache-testdata
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uses: actions/cache@v4
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with:
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path: testdata
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key: test-data-v1
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- name: Download test datasets
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if: steps.cache-testdata.outputs.cache-hit != 'true'
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env:
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GH_TOKEN: ${{ github.token }}
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run: |
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mkdir -p testdata
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gh release download test-data-v1 -D testdata
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unzip testdata/DDA_HeLa_50ng_5_6min.d.zip -d testdata
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unzip testdata/DIA_HeLa_50ng_5_6min.d.zip -d testdata
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rm testdata/*.d.zip
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- name: Build library (release, with timsrust)
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run: cargo build --features with_timsrust --release
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- name: Rust integration tests
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env:
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TIMSRUST_TEST_DATA_DDA: testdata/20210510_TIMS03_EVO03_PaSk_MA_HeLa_50ng_5_6min_DDA_S1-B1_1_25185.d
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TIMSRUST_TEST_DATA_DIA: testdata/20210510_TIMS03_EVO03_PaSk_SA_HeLa_50ng_5_6min_DIA_high_speed_S1-B2_1_25186.d
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run: cargo test --features with_timsrust -- --nocapture
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- name: Fetch Catch2
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run: tests_cpp/fetch_catch2.sh
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- name: C++ smoke tests
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run: |
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cd tests_cpp
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make test LIBDIR=../target/release \
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DDA=../testdata/20210510_TIMS03_EVO03_PaSk_MA_HeLa_50ng_5_6min_DDA_S1-B1_1_25185.d \
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DIA=../testdata/20210510_TIMS03_EVO03_PaSk_SA_HeLa_50ng_5_6min_DIA_high_speed_S1-B2_1_25186.d

‎.gitignore‎

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# Build artifacts
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target/
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# Catch2 amalgamated files (download via tests_cpp/fetch_catch2.sh)
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tests_cpp/catch2/
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# Compiled test objects and binary
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tests_cpp/*.o
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tests_cpp/run_tests

‎Cargo.toml‎

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[lib]
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# We want something C/C++ can link against
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crate-type = ["cdylib", "staticlib"]
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crate-type = ["cdylib", "staticlib", "lib"]
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[dependencies]
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# timsrust is optional for environments where the native crate is available.
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# only if you want auto header generation
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cbindgen = "0.27"
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[dev-dependencies]
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libc = "0.2"
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‎README.md‎

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}
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```
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## Testing
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The project uses a two-tier testing strategy: **stub tests** (no data needed) and **integration tests** (real Bruker datasets).
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### Stub Tests
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Run the FFI contract tests against the lightweight stub build (no `timsrust` dependency, no datasets):
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```bash
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cargo test
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```
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C++ ABI layout tests (requires Catch2, fetched automatically):
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```bash
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cargo build
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tests_cpp/fetch_catch2.sh
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cd tests_cpp && make test LIBDIR=../target/debug
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```
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### Integration Tests (Real Data)
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Integration tests require real Bruker timsTOF Pro `.d` datasets. Test data is available as [GitHub release artifacts](https://github.com/OpenMS/timsrust_cpp_bridge/releases/tag/test-data-v1) (HeLa 50ng, 5.6-min gradient, from [PRIDE PXD027359](https://www.ebi.ac.uk/pride/archive/projects/PXD027359)).
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Download and extract the datasets, then point the env vars at them:
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```bash
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# Download and extract
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gh release download test-data-v1 -D testdata
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unzip testdata/DDA_HeLa_50ng_5_6min.d.zip -d testdata
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unzip testdata/DIA_HeLa_50ng_5_6min.d.zip -d testdata
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# Run Rust integration tests
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TIMSRUST_TEST_DATA_DDA=testdata/20210510_TIMS03_EVO03_PaSk_MA_HeLa_50ng_5_6min_DDA_S1-B1_1_25185.d \
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TIMSRUST_TEST_DATA_DIA=testdata/20210510_TIMS03_EVO03_PaSk_SA_HeLa_50ng_5_6min_DIA_high_speed_S1-B2_1_25186.d \
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cargo test --features with_timsrust -- --nocapture
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# Run C++ smoke tests (after building with --features with_timsrust --release)
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cd tests_cpp && make test LIBDIR=../target/release \
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DDA=../testdata/20210510_TIMS03_EVO03_PaSk_MA_HeLa_50ng_5_6min_DDA_S1-B1_1_25185.d \
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DIA=../testdata/20210510_TIMS03_EVO03_PaSk_SA_HeLa_50ng_5_6min_DIA_high_speed_S1-B2_1_25186.d
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```
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Tests gracefully skip if the env vars are unset.
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### CI
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Both test tiers run on every push and PR via GitHub Actions. Integration test datasets are cached to avoid repeated downloads.
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## Notes and Caveats
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- For DIA-PASEF datasets, `tims_num_spectra` reflects expanded MS2 spectra, while `tims_num_frames` reflects raw LC frames (including MS1).

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