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4.4.21: Parallel builds, robust installation, and rope-based parsing enhancements

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This release introduces significant improvements to build reliability and performance, alongside key parsing enhancements for sequence data.

### Build & Installation Improvements
- Added support for parallel compilation via `-j/--jobs` option in both the Makefile and install script, enabling faster builds on multi-core systems. The default remains single-threaded for safety.
- Enhanced Makefile with `.DEFAULT_GOAL := all` for consistent behavior and a documented `help` target.
- Replaced fragile file operations with robust error handling, clear diagnostics, and automatic preservation of the build directory on copy failures to aid recovery.

### Rope-Based Parsing Enhancements (from 4.4.20)
- Introduced direct rope-based parsers for FASTA, EMBL, and FASTQ formats, improving memory efficiency for large files.
- Added U→T conversion support during sequence extraction and more reliable line ending detection.
- Unified rope scanning logic under a new `ropeScanner` for better maintainability.
- Added `TakeQualities()` method to BioSequence for more efficient handling of quality data.

### Bug Fixes (from 4.4.20)
- Fixed `CompressStream` to correctly respect the `compressed` variable.
- Replaced ambiguous string splitting utilities with precise left/right split variants (`LeftSplitInTwo`, `RightSplitInTwo`).

### Release Tooling (from 4.4.20)
- Streamlined release process with modular targets (`jjpush-notes`, `jjpush-push`, `jjpush-tag`) and AI-assisted note generation via `aichat`.
- Improved versioning support via the `VERSION` environment variable in `bump-version`.
- Switched PR submission from raw `jj git push` to `stakk` for consistency and reliability.

Note: This release incorporates key enhancements from 4.4.20 that impact end users, while focusing on build robustness and performance gains.
This commit is contained in:
Eric Coissac
2026-03-13 11:59:32 +01:00
parent 82a9972be7
commit cdc72c5346
2 changed files with 2 additions and 2 deletions
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2
pkg/obioptions/version.go
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@@ -3,7 +3,7 @@ package obioptions
// Version is automatically updated by the Makefile from version.txt
// The patch number (third digit) is incremented on each push to the repository
var _Version = "Release 4.4.20"
var _Version = "Release 4.4.21"
// Version returns the version of the obitools package.
//

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version.txt
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@@ -1 +1 @@
4.4.20
4.4.21