diff options
| -rw-r--r-- | topics/pangenome/impg/impg-agc-bindings.gmi | 40 |
1 files changed, 37 insertions, 3 deletions
diff --git a/topics/pangenome/impg/impg-agc-bindings.gmi b/topics/pangenome/impg/impg-agc-bindings.gmi index cc11756..5b95685 100644 --- a/topics/pangenome/impg/impg-agc-bindings.gmi +++ b/topics/pangenome/impg/impg-agc-bindings.gmi @@ -25,8 +25,8 @@ One early choice is a separation of concerns. We will try to build the library i # Tasks -* [ ] Fix AGC passing exceptions through C ABI -* [ ] Get guix to compile impg with AGC +* [X] Fix AGC passing exceptions through C ABI +* [X] Get guix to compile impg (here testlibagc) with AGC * [ ] Add optimization * [ ] Make sure spoa build in spoa-rs is optimized * [ ] Create static binary for distribution @@ -136,7 +136,7 @@ For C++ only libraries, the narrative gets a bit harder. If the C++ interface is To support AGC in Rust we need to: -* [ ] Create a Rust binding that uses the AGC C ABI instead of the C++ one, so we can use a statically built AGC lib and don't need the source tree for cargo +* [X] Create a Rust binding that uses the AGC C ABI instead of the C++ one, so we can use a statically built AGC lib and don't need the source tree for cargo We will also write a @@ -210,3 +210,37 @@ To create a rust package for binding libagc it is worth reading: * The library crate should provide declarations for types and functions in libfoo, but not higher-level abstractions. So we should create an agc-rs crate that provides a high-level interface to the upcoming libagc-sys crate. No wonder these crates proliferate. + +# Shifting to a dynamic libagc.so + +I managed to create a crate that binds libagc.so against Rust: + +=> https://github.com/pjotrp/libagc-sys + +See also the included test in lib.rs. It binds against the updated agc: + +=> https://github.com/refresh-bio/agc/compare/main...pjotrp:agc:main + +which contains the fixes that don't allow C++ exceptions to pass through the C ABI. +Also I fixed one function and added a shared lib as output. + +Finally, rather than messing with the impg code tree (which keeps changing), I created a test crate that mirrors impg: + +=> https://github.com/pjotrp/testlibagc + +which can be build and run with + +``` +cargo build --release +target/release/testagc-sys +Number of samples: 4 +``` + +At least we have a reference implementation for binding successfully against a shared C library with a very *light* and standardised interface. It obviously also works in Guix. We can use it to benchmark against the new (impressive) Rust implementation by Erik. It also acts as a template for future bindings. + +Note that we should discourage C++ bindings. Mostly because there is no standard C++ ABI (in contrast to the C one), so avoid the use of the cxx crates - unless you really know what you are doing. + +Potential future work is: + +- [ ] Optimized runtime +- [ ] Static binary for distribution |