# alphadia-search-rs
High-performance alphaDIA backend.
## Notes for users
This repository contains the high-performance backend for alphaDIA. This
code should to used as part of [alphaDIA](https://github.com/MannLabs/alphadia).
## Development Setup
---
**📌 Versioning Policy**
This repository strictly follows [**Semantic Versioning 2.0.0**](https://semver.org/). Given a version number `MAJOR.MINOR.PATCH`:
- **MAJOR** version for incompatible API changes
- **MINOR** version for backwards-compatible functionality additions
- **PATCH** version for backwards-compatible bug fixes
---
### Prerequisites
- **Rust 1.88.0**
- **Python 3.11+**
### Quick Start
1. **Clone and enter the repository:**
```bash
git clone <repository-url>
cd alphadia-search-rs
```
2. **Set up pre-commit hooks (recommended):**
```bash
# Install pre-commit
pip install pre-commit
# or: conda install -c conda-forge pre-commit
# or: brew install pre-commit
# Install the git hook scripts
pre-commit install
```
3. **Install Python dependencies:**
```bash
conda activate alphadia-search-rs # or create environment if it doesn't exist
pip install maturin
```
4. **Build the Rust extension:**
```bash
maturin develop --release
```
Omit the `--release` extension for a developer build.
5. **Run tests:**
```bash
cargo test # Rust tests
python ./scripts/test_search.py # Python integration test
```
## Testing
### Integration Test
The `scripts/test_search.py` script provides a comprehensive integration test.
```bash
# Run the integration test
python ./scripts/test_search.py --path ./test_data
```
The script will automatically:
1. Use existing test data in `./test_data` if available (using a temporary directory if `--path` not specified).
2. Otherwise download required files:
- `spectrum_df.parquet` - Mass spectrometry spectra data
- `peak_df.parquet` - Peak detection results
- `precursor_df.parquet` - Precursor ion information
- `fragment_df.parquet` - Fragment ion data
**Expected output:**
- Processing speed: ~200k+ precursors per second
- Results: ~11M candidates found
## Scripts
The `scripts/` directory contains analysis pipelines for processing DIA-MS data:
### Key Scripts
1. **Candidate Selection**: Takes a calibrated speclib as an input and an AlphaRaw hdf. Performs candidate selection and saves the candidates.
```bash
python scripts/candidate_selection.py --ms_data_path data.hdf --spec_lib_path lib.hdf --output_folder ./output
```
2. **Candidate Scoring**: Performs scoring following selection. Takes input from previous step and save precursor at 1% FDR.
```bash
python scripts/candidate_scoring.py --ms_data_path data.hdf --spec_lib_path lib.hdf --candidates_path candidates.parquet --fdr --quantify
```
- option to perform quantification with `--quantify`
- option to perform FDR adn filter @1% with `--fdr`
- option to add diagnosis plot for all features with `--diagnosis`
## CLI Benchmarking
### Score Benchmark Tool
The `score-benchmark` CLI tool benchmarks multiple implementations of `axis_log_dot_product` to compare performance and verify numerical accuracy.
```bash
# Run the benchmark
cargo run --bin score-benchmark
```
### Troubleshooting
**Library Loading Error on macOS:**
If you encounter the error `dyld[xxxxx]: Library not loaded: @rpath/libpython3.11.dylib` when running `cargo test`, set the library path:
Mac:
```bash
export DYLD_LIBRARY_PATH=$(realpath $(which python)/../../lib)
cargo test
```
Linux:
```bash
export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH
cargo test
```
## Development Workflow
### Code Quality Standards
This project enforces strict code quality standards via automated tooling:
- **Formatting**: All code must be formatted with `rustfmt`
- **Linting**: All code must pass `clippy` with no warnings
- **Consistency**: Same toolchain used locally and in CI (Rust 1.88.0)
### Pre-Commit Hooks
We use the [pre-commit](https://pre-commit.com/) framework for automated code quality checks:
```bash
# Install pre-commit (one-time setup)
pip install pre-commit
# Install hooks (one-time setup)
pre-commit install
```
### Manual Code Quality Checks
You can run the same checks manually:
```bash
# Format code
cargo fmt
# Check formatting (without modifying files)
cargo fmt --all -- --check
# Run linting
cargo clippy -- -D warnings
# Run all pre-commit hooks manually
pre-commit run --all-files
```
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"description": "# alphadia-search-rs\n\nHigh-performance alphaDIA backend.\n\n## Notes for users\nThis repository contains the high-performance backend for alphaDIA. This\ncode should to used as part of [alphaDIA](https://github.com/MannLabs/alphadia).\n\n\n## Development Setup\n\n---\n\n**\ud83d\udccc Versioning Policy**\n\nThis repository strictly follows [**Semantic Versioning 2.0.0**](https://semver.org/). Given a version number `MAJOR.MINOR.PATCH`:\n- **MAJOR** version for incompatible API changes\n- **MINOR** version for backwards-compatible functionality additions\n- **PATCH** version for backwards-compatible bug fixes\n\n---\n\n### Prerequisites\n\n- **Rust 1.88.0**\n- **Python 3.11+**\n\n### Quick Start\n\n1. **Clone and enter the repository:**\n ```bash\n git clone <repository-url>\n cd alphadia-search-rs\n ```\n\n2. **Set up pre-commit hooks (recommended):**\n ```bash\n # Install pre-commit\n pip install pre-commit\n # or: conda install -c conda-forge pre-commit\n # or: brew install pre-commit\n\n # Install the git hook scripts\n pre-commit install\n ```\n\n3. **Install Python dependencies:**\n ```bash\n conda activate alphadia-search-rs # or create environment if it doesn't exist\n pip install maturin\n ```\n\n4. **Build the Rust extension:**\n ```bash\n maturin develop --release\n ```\nOmit the `--release` extension for a developer build.\n\n5. **Run tests:**\n ```bash\n cargo test # Rust tests\n python ./scripts/test_search.py # Python integration test\n ```\n\n## Testing\n\n### Integration Test\n\nThe `scripts/test_search.py` script provides a comprehensive integration test.\n```bash\n# Run the integration test\npython ./scripts/test_search.py --path ./test_data\n```\n\nThe script will automatically:\n1. Use existing test data in `./test_data` if available (using a temporary directory if `--path` not specified).\n2. Otherwise download required files:\n - `spectrum_df.parquet` - Mass spectrometry spectra data\n - `peak_df.parquet` - Peak detection results\n - `precursor_df.parquet` - Precursor ion information\n - `fragment_df.parquet` - Fragment ion data\n\n**Expected output:**\n- Processing speed: ~200k+ precursors per second\n- Results: ~11M candidates found\n\n## Scripts\n\nThe `scripts/` directory contains analysis pipelines for processing DIA-MS data:\n\n\n### Key Scripts\n\n\n1. **Candidate Selection**: Takes a calibrated speclib as an input and an AlphaRaw hdf. Performs candidate selection and saves the candidates.\n ```bash\n python scripts/candidate_selection.py --ms_data_path data.hdf --spec_lib_path lib.hdf --output_folder ./output\n ```\n\n2. **Candidate Scoring**: Performs scoring following selection. Takes input from previous step and save precursor at 1% FDR.\n ```bash\n python scripts/candidate_scoring.py --ms_data_path data.hdf --spec_lib_path lib.hdf --candidates_path candidates.parquet --fdr --quantify\n ```\n - option to perform quantification with `--quantify`\n - option to perform FDR adn filter @1% with `--fdr`\n - option to add diagnosis plot for all features with `--diagnosis`\n\n\n## CLI Benchmarking\n\n### Score Benchmark Tool\n\nThe `score-benchmark` CLI tool benchmarks multiple implementations of `axis_log_dot_product` to compare performance and verify numerical accuracy.\n\n```bash\n# Run the benchmark\ncargo run --bin score-benchmark\n```\n\n### Troubleshooting\n\n**Library Loading Error on macOS:**\nIf you encounter the error `dyld[xxxxx]: Library not loaded: @rpath/libpython3.11.dylib` when running `cargo test`, set the library path:\n\nMac:\n```bash\nexport DYLD_LIBRARY_PATH=$(realpath $(which python)/../../lib)\ncargo test\n```\n\nLinux:\n```bash\nexport LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH\ncargo test\n```\n\n## Development Workflow\n\n### Code Quality Standards\n\nThis project enforces strict code quality standards via automated tooling:\n\n- **Formatting**: All code must be formatted with `rustfmt`\n- **Linting**: All code must pass `clippy` with no warnings\n- **Consistency**: Same toolchain used locally and in CI (Rust 1.88.0)\n\n### Pre-Commit Hooks\n\nWe use the [pre-commit](https://pre-commit.com/) framework for automated code quality checks:\n\n```bash\n# Install pre-commit (one-time setup)\npip install pre-commit\n\n# Install hooks (one-time setup)\npre-commit install\n```\n\n### Manual Code Quality Checks\n\nYou can run the same checks manually:\n\n```bash\n# Format code\ncargo fmt\n\n# Check formatting (without modifying files)\ncargo fmt --all -- --check\n\n# Run linting\ncargo clippy -- -D warnings\n\n# Run all pre-commit hooks manually\npre-commit run --all-files\n```\n\n",
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