- Add .DEFAULT_GOAL := all to Makefile for consistent default target
- Document -j/--jobs option in README.md to allow parallel compilation
- Add JOBS variable and -j/--jobs argument to install script (default: 1)
- Replace fragile mkdir/cp commands with robust error handling and clear diagnostics
- Add build directory preservation on copy failure for manual recovery
- Pass -j option to make during compilation to enable parallel builds
- Add colored terminal output support (GREEN, YELLOW, BLUE, NC)
- Introduce `help` target to document all Makefile targets
- Enhance `bump-version` to accept VERSION env var for manual version setting
- Refactor jjpush: split into modular targets (jjpush-notes, jjpush-push, jjpush-tag)
- Replace orla with aichat for AI-powered release notes generation
- Add robust JSON parsing using Python for release notes extraction
- Use stakk for PR submission (replacing raw `jj git push`)
- Generate and store release notes in temp files for tag creation
- Add installation instructions to release tags
- Update .PHONY with new targets
4.4.20: Rope-based parsing, improved release tooling, and bug fixes
### Enhancements
- **Rope-based parsing**: Added direct rope parsing for FASTA, EMBL, and FASTQ formats via `FastaChunkParserRope`, `EmblChunkParserRope`, and `FastqChunkRope` functions, eliminating unnecessary memory allocation via Pack(). Sequence extraction now supports U→T conversion and improved line ending detection.
- **Rope scanner refactoring**: Unified rope scanning logic under a new `ropeScanner`, improving maintainability and consistency across parsers.
- **Sequence handling**: Added `TakeQualities()` method to BioSequence for more efficient quality data handling.
### Bug Fixes
- **Compression behavior**: Fixed CompressStream to correctly use the `compressed` variable instead of a hardcoded boolean.
- **String splitting**: Replaced ambiguous `SplitInTwo` calls with precise `LeftSplitInTwo` or `RightSplitInTwo`, and added dedicated right-split utility.
### Tooling & Workflow Improvements
- **Makefile enhancements**: Added colored terminal output, a `help` target for documenting all targets, and improved release workflow automation.
- **Release process**: Refactored `jjpush` into modular targets (`jjpush-notes`, `jjpush-push`, `jjpush-tag`), replaced `orla` with `aichat` for AI-assisted release notes, and introduced robust JSON parsing using Python. Release notes are now generated and stored in temp files for tag creation.
- **Versioning**: `bump-version` now supports the VERSION environment variable for manual version setting.
- **Submission**: Switched from raw `jj git push` to `stakk` for PR submission.
### Internal Notes
- Installation instructions are now included in release tags.
- Fixed-size carry buffer replaced with dynamic slice for arbitrarily long line support without extra allocations.
Split the jjpush target into multiple sub-targets (jjpush-describe, jjpush-bump, jjpush-push, jjpush-tag) for better modularity and control.
Enhance release notes generation by:
- Using git log with full commit messages instead of GitHub API for pre-release mode
- Adding robust JSON parsing with fallbacks for release notes
- Including detailed installation instructions in release notes
- Supporting both pre-release and published release modes
Update release_notes.sh to handle pre-release mode, improve commit message fetching, and add installation section to release notes.
Add .PHONY declarations for new sub-targets.
Update version from 4.4.11 to 4.4.12
- Bump version in version.go
- Enhance release note generation in Makefile to use JSON output from orla and fallback to raw output if JSON parsing fails
- Improve test script to verify minimum super k-mer length is >= k (default k=31)
Mise à jour du Makefile pour améliorer le processus de version bump et de création de tag.
- Utilisation de variables pour stocker les versions précédente et actuelle
- Ajout de la génération automatique des notes de version à partir des commits entre les tags
- Intégration d'une logique de fallback si orla n'est pas disponible
- Amélioration de la documentation des étapes du processus de release
- Mise à jour de la commande de création du tag avec le message généré
This commit introduces a new GitHub Actions workflow to automatically create releases when tags matching the pattern 'Release_*' are pushed. It also updates the Makefile to use the new tag format 'Release_<version>' for tagging commits, ensuring consistency with the new release automation.
Add Jaccard distance and similarity computations for KmerSet and KmerSetGroup
This commit introduces Jaccard distance and similarity methods for KmerSet and KmerSetGroup.
For KmerSet:
- Added JaccardDistance method to compute the Jaccard distance between two KmerSets
- Added JaccardSimilarity method to compute the Jaccard similarity between two KmerSets
For KmerSetGroup:
- Added JaccardDistanceMatrix method to compute a pairwise Jaccard distance matrix
- Added JaccardSimilarityMatrix method to compute a pairwise Jaccard similarity matrix
Also includes:
- New DistMatrix implementation in pkg/obidist for storing and computing distance/similarity matrices
- Updated version handling with bump-version target in Makefile
- Added tests for all new methods
