inchi-sys 0.1.3

Low-level FFI bindings to the vendored IUPAC InChI 1.07 reference C library
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# Vendored IUPAC InChI source

This directory contains a verbatim subset of the official IUPAC International Chemical Identifier (InChI) reference implementation, vendored so that `inchi-sys` builds with **no network access** and **no system InChI install**.

| Field    | Value                                      |
| -------- | ------------------------------------------ |
| Project  | InChI                                      |
| Upstream | <https://github.com/IUPAC-InChI/InChI>     |
| Version  | 1.07.5                                     |
| Git tag  | `v1.07.5`                                  |
| Commit   | `11a87982bb518f57ac013f0b258c283655e1ea1d` |
| License  | MIT (see [`inchi/LICENSE`](inchi/LICENSE)) |

## What is included

Only the files required to build the InChI shared library (the "InChI API") are vendored, mirroring the upstream `INCHI_API/libinchi/gcc/makefile` build:

```
inchi/INCHI_BASE/src/             core algorithm + classic API header (inchi_api.h)
inchi/INCHI_API/libinchi/src/     DLL/API entry points (GetINCHI, FreeINCHI, ...)
inchi/INCHI_API/libinchi/src/ixa/ InChI eXtensible API (IXA)
```

The command-line front-end (`INCHI_EXE`), the GUI helper (`inchi_gui.c`), prebuilt binaries (`INCHI-1-BIN`), tests, and documentation from the upstream repository are intentionally **not** vendored.

## Updating

1. Download the desired release tarball from the upstream releases page.
2. Replace the three `src` trees above with the new versions.
3. Update the version/commit metadata in this file.
4. Run `cargo test -p inchi-sys` and `cargo test -p inchi` to confirm the build still links and the reference InChI/InChIKey test vectors still pass.
5. If the public C API changed, regenerate the bindings: `cargo build -p inchi-sys --features regenerate-bindings` and copy `target/.../out/bindings.rs` over `crates/inchi-sys/src/bindings.rs`.
6. Re-apply the patch listed below if the affected file changed upstream.

## Local patches

The vendored C sources are otherwise verbatim, with a single memory-safety fix. Each patched site is marked with an `inchi-rs patch:` comment so it can be located and re-applied after an upstream update.

| File | Function | Fix |
| ---- | -------- | --- |
| `inchi/INCHI_API/libinchi/src/inchi_dll.c` | `SetInChIExtInputByExtOrigAtData` | Fixes a use-after-free: 1.07.5 frees the polymer unit allocations that the caller still holds via `*iip`, replacing them with a `memcpy` approach that silently no-ops when `*iip` is NULL (the normal case at the call site). The patch restores direct pointer ownership and removes the premature frees. Does **not** change any computed InChI string. |

This patch was reported upstream; remove it once a fixed release is vendored.