---
title: "Development and Vendoring"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Development and Vendoring}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
```

Rsassy builds a small Rust crate during package installation. That crate depends
on `sassy` for approximate matching and `needletail` for chunked FASTA/FASTQ
iteration.

```toml
sassy = { version = "0.2.1", default-features = false }
needletail = { version = "0.6.3", default-features = false, features = ["flate2"] }
```

Only needletail's gzip path is enabled by default; bzip2, xz, and zstd support
are intentionally not enabled unless the package chooses to expand compression
support later.

## Vendoring

Rust sources are installed from the vendored bundle. Refresh it after Rust
dependency changes:

```{sh, eval=FALSE}
make vendor-rust
```

This updates:

```text
src/rust/vendor.tar.xz
inst/AUTHORS
inst/LICENCE.note
```

Package installation then runs Cargo in offline mode.

## Development commands

```{sh, eval=FALSE}
make rd       # regenerate NAMESPACE and man/*.Rd
make readme   # regenerate README.md
make install  # local install
make test     # tinytest
make check    # R CMD build + R CMD check
make reports  # render committed benchmark/conformance markdown reports
make clean    # remove build artifacts
```

`make check` uses two Cargo jobs by default. For local builds:

```{sh, eval=FALSE}
make CARGO_JOBS=10 check
```

## R build hooks

- `configure` / `configure.win` generate `src/Makevars` files.
- `src/Makevars.in` / `src/Makevars.win.in` build the Rust libraries.
- `src/install.libs.R` installs backend libraries under `backends/`.
- `cleanup` removes generated files.