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Summary of Changes

Hello @noamteyssier, I'm Gemini Code Assist1! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request finalizes the transition of the VBQ file format to exclusively use embedded indexes. By removing all legacy code and documentation associated with external .vqi index files, the codebase is significantly simplified, and the file format gains improved portability. The changes ensure that the index is an integral part of the VBQ file, streamlining its management and access.

Highlights

  • External Index Code Removal: All code, functions, and error types related to managing external .vqi index files have been systematically removed, including save_to_path, from_path, is_index_mismatch, MissingUpstreamFile, and ByteSizeMismatch.
  • Documentation Updates: Extensive updates have been made across src/lib.rs, src/vbq/index.rs, src/vbq/mod.rs, and src/vbq/reader.rs to reflect the exclusive use of embedded indexes and remove all mentions of separate .vqi files or their migration.
  • MmapReader Simplification: The MmapReader struct no longer stores a PathBuf for the file path and the index_path() method has been removed, as external index files are no longer relevant.
  • Embedded Index Writing Validation: New tests have been added to src/vbq/writer.rs to ensure that the embedded index is always correctly written upon calling finish() and that this operation is idempotent, preventing duplicate index writes.

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Code Review

This pull request is a great simplification of the VBQ format handling by removing all code related to external .vqi index files. The changes are thorough, touching everything from error handling and API surfaces to documentation and examples. The removal of legacy code paths for external indexes makes the library cleaner and easier to maintain.

I'm particularly impressed with the new tests added in src/vbq/writer.rs. The test_index_always_written_on_finish and test_finish_idempotent tests are excellent additions that ensure the correctness and robustness of the embedded index writing logic, which is critical now that it's the only indexing mechanism. The code is clean, the documentation updates are comprehensive, and the overall change is a solid improvement. I have no concerns and recommend merging this.

@noamteyssier noamteyssier merged commit cdc5b7a into binseq-0.9.0 Jan 23, 2026
28 checks passed
@noamteyssier noamteyssier deleted the remove-vbq-external-index-code branch January 23, 2026 23:52
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