# Contributing to dnoise
Thanks for your interest in `dnoise`. It is a Rust CLI and library that denoises
Bruker timsTOF `.d` folders with an iterative vertical ion-mobility feature
filter. Contributions of all kinds are welcome, from bug reports and
documentation fixes to new features.
## Reporting bugs and requesting features
Please use [GitHub issues](https://github.com/pgarrett-scripps/dnoise/issues).
- For bugs, include what you ran, what you expected, what happened, and enough
detail to reproduce (OS, Rust version, a minimal `.d` sample or its
characteristics if you can share them).
- For feature requests, describe the use case and the outcome you want.
Search existing issues first to avoid duplicates.
## Development setup
```sh
git clone https://github.com/pgarrett-scripps/dnoise.git
cd dnoise
cargo build --locked
cargo test --workspace --locked
```
The CLI/library require Rust **1.85+**; the GUI requires **1.95+**. Both use
**edition 2024**. `rust-toolchain.toml` pins the development compiler. Check the
core minimum explicitly with `cargo +1.85.0 check --all-targets --locked`.
## Code style
Before submitting, run:
```sh
cargo fmt --all
cargo clippy --workspace --all-targets -- -D warnings
```
CI enforces both. Formatting must match `cargo fmt`, and Clippy runs with
warnings treated as errors, so any warning will fail the build. Please fix or
explicitly address every lint rather than allowing it away without reason.
## Adding tests
- Put unit tests inline in the module they cover, inside a `#[cfg(test)]`
module.
- Put integration tests in the top-level `tests/` directory.
New behavior should come with tests. Bug fixes should ideally include a test
that fails before the fix and passes after.
Synthetic DDA/DIA fixtures are generated by `tests/common`. Before releasing a
writer change, also check real acquisitions against the paper baseline and use
`examples/validate_sdk.py` with a locally installed Bruker SDK; see the
[validation record](docs/implementation-validation-2026-09-09.md).
## Pull request process
1. Branch from `main`.
2. Keep commits focused and the history readable. One logical change per commit
where practical.
3. Make sure `cargo build`, `cargo test --workspace`, `cargo fmt --all --check`,
and `cargo clippy --workspace --all-targets -- -D warnings` all pass locally.
4. Open the PR against `main` and make sure CI is green.
5. Reference any related issue in the PR description.
## Algorithm reference
For the specification of the denoising algorithm itself, see
[ALGORITHM.md](ALGORITHM.md).
## License and Code of Conduct
By contributing, you agree that your contributions will be licensed under the
[MIT License](LICENSE), and that you will follow the
[Code of Conduct](CODE_OF_CONDUCT.md).