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Compress module#1

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alnfedorov merged 7 commits into
devfrom
compress
Dec 28, 2025
Merged

Compress module#1
alnfedorov merged 7 commits into
devfrom
compress

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This pull request introduces a new compress crate to the workspace, providing a modular framework for compression and decompression algorithms. The implementation includes an adapter-based design for supporting multiple formats (identity, deflate, gzip, bgzf and biobit serialization support.

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Pull request overview

This pull request introduces a new compress crate to the workspace, providing a modular compression/decompression framework with an adapter-based design. The implementation supports multiple formats including identity (no compression), deflate, gzip, and bgzf. Additionally, it includes minor refactoring changes to the existing multilock crate.

Key Changes:

  • New compress crate with trait-based encoder/decoder architecture supporting multiple compression formats via feature flags
  • Adapter pattern implementation allowing flexible type erasure and constraint handling
  • Minor code improvements in multilock (closure simplification and documentation formatting)

Reviewed changes

Copilot reviewed 24 out of 24 changed files in this pull request and generated 30 comments.

Show a summary per file
File Description
Cargo.toml Adds compress workspace member and compression-related dependencies (flate2, noodles-bgzf, bitcode)
workspace/compress/Cargo.toml Defines the new compress crate with feature flags for selective format support
workspace/compress/src/lib.rs Provides crate-level documentation with a comprehensive roundtrip usage example
workspace/compress/src/format.rs Implements format detection from file extensions and factory methods for encoders/decoders
workspace/compress/src/encode/*.rs Defines encoding traits, adapters, and implementations for each compression format
workspace/compress/src/decode/*.rs Defines decoding traits, adapters, and implementations for each compression format
workspace/compress/src/adapter/boxed_sync.rs Provides BoxedSync adapter for type-erased trait objects with Send + Sync bounds
workspace/multilock/src/multi_guard.rs Simplifies closure to use constructor shorthand syntax
workspace/multilock/src/lock.rs Removes trailing colon from Safety doc comment header

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Comment thread workspace/compress/src/encode/bgzf.rs Outdated
Comment thread workspace/compress/src/encode/adapter.rs Outdated
Comment thread workspace/compress/src/lib.rs Outdated
Comment thread workspace/compress/src/encode/encoder.rs
Comment thread workspace/compress/src/format.rs Outdated
Comment thread workspace/compress/src/adapter/boxed_sync.rs
alnfedorov and others added 3 commits December 28, 2025 11:27
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
@biomancy biomancy deleted a comment from Copilot AI Dec 28, 2025
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@alnfedorov alnfedorov merged commit 2c6af51 into dev Dec 28, 2025
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@alnfedorov alnfedorov deleted the compress branch December 28, 2025 11:45
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2 participants