Improve namespace of codebase

[noamteyssier]

No description provided.

[gemini-code-assist]

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 focuses on enhancing the clarity and consistency of the codebase's naming conventions, particularly within the bq and vbq modules. By standardizing header and writer struct names to FileHeader and Writer, the changes aim to improve readability and reduce potential confusion. Additionally, new utility methods have been introduced to streamline the process of creating writer builders from pre-existing header configurations, simplifying API usage for developers.

Highlights

• Namespace Refinement for BQ Module: The BinseqHeader and BinseqHeaderBuilder structs within the bq module have been renamed to FileHeader and FileHeaderBuilder respectively. Similarly, BinseqWriter and BinseqWriterBuilder are now Writer and WriterBuilder.
• Namespace Refinement for VBQ Module: The VBinseqHeader and VBinseqHeaderBuilder structs within the vbq module have been renamed to FileHeader and FileHeaderBuilder respectively. The VBinseqWriter and VBinseqWriterBuilder are now Writer and WriterBuilder.
• Documentation Updates: Extensive updates have been made across the codebase, including examples and module-level documentation, to reflect the new naming conventions and clarify references to 'BQ' and 'VBQ' file formats.
• New Builder Initialization Methods: The BinseqWriterBuilder now includes convenience methods (from_bq_header, from_vbq_header, from_cbq_header) to initialize a builder instance directly from existing BQ, VBQ, or CBQ header configurations.

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[gemini-code-assist]

Code Review

This pull request introduces a significant and well-executed refactoring to improve naming conventions across the codebase. Key structs like BinseqHeader and BinseqWriter have been renamed to the more generic FileHeader and Writer respectively, within both the bq and vbq modules. These changes are consistently applied throughout the code, including documentation and examples, enhancing clarity and maintainability. The addition of from_*_header constructors in src/write.rs is a nice touch for improving interoperability between formats. Overall, this is a high-quality refactoring with no apparent issues.