Rust backend for Peptonizer2000#4
Open
SimonVandeVyver wants to merge 87 commits into
Open
Conversation
…ng on execution directory
pverscha
requested changes
May 22, 2026
Contributor
pverscha
left a comment
There was a problem hiding this comment.
I have reviewed and tested the changes in this PR. Overall very nice work, thank you!
I do have some remarks that you should take a look at before we can continue and merge this PR:
- The tests for Rust do not succeed. This is the error that is generated when running
cargo testin thepeptonizer_rustdirectory:
error[E0425]: cannot find function `parse_taxon_scores` in this scope
--> src/zero_lookahead_belief_propagation.rs:55:20
|
55 | let json = parse_taxon_scores(csv_content);
| ^^^^^^^^^^^^^^^^^^ not found in this scope
- Continueing with the tests, I think it would be good if we could also implement a GitHub Action workflow that automatically runs the Rust tests on push to the repo.
I have also left some comments directly onto the code, please take a look at those as well.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
This PR adds a complete Rust backend for Peptonizer2000 and wires it into the full package ecosystem.
peptonizer_rust/, with native and WASM build targetspeptonizer_tscan consume the compiled WebAssembly buildpeptonizer_rustusingpyo3andmaturinpeptonizer_rustwheel artifacts