v0.4.0

• release: bump version to 0.4.0
• style: apply formatting-only updates across modules and tests
• remove automated bioconda PR, generate recipe as artifact only; fix recipe (Python >=3.9, add scipy)
• clean up duplicate imports, stale comments, and misplaced import re
• remove unused imports and stale comments in hyenadna files
• remove dead variables and unused import in clustering.py
• fix: --filter-only flag was silently ignored (missing from args Namespace)
• remove dead _leiden_clustering_on_graph() function
• remove dead PathManager class from utils.py
• docs: update README to match current pipeline and fix cli OPTION_GROUPS ghost reference
• remove dead greedy_min_score parameter (F1 scores are always >= 0)
• Revert "fix: tighten greedy clustering contamination cap to 5%"
• fix: tighten greedy clustering contamination cap to 5%
• fix: block rescue merges above 10% duplication
• feat: expose rescue duplication limits in CLI and enforce max total duplication
• Revert "refactor: update encoder architecture to be dynamic and balanced"
• refactor: update encoder architecture to be dynamic and balanced
• fix: rate limit unconditional fusion debug logs
• fix: rate limit debug logging for gating weights
• fix: switch debug prints to logger.debug
• feat: add debug prints for gating weights
• Revert to state after 'feat: add short-reads/sr mode' (77f1ea5)
• Update rescue threshold: 0.9 for single sample, 0.7 for coassemblies
• Add 0.05 to default Leiden resolutions for larger clusters
• Fix indentation bug in rescue loop causing duplicate merges
• Update rescue strategy: use global SCG count for contamination and enforce 10% ceiling
• feat: add short-reads/sr mode to enforce 1000bp min contig length
• feat: add contamination filter to greedy clustering
• tune: implement F1-score based bin quality metric inspired by SemiBin2
• tune: add 0.1 to greedy clustering resolutions
• tune: score bins by total core genes (unique families) - 5*dups
• tune: set miniprot query coverage 0.6 identity 0.4, revert global -N/-p
• fix: use query coverage instead of target coverage for miniprot filtering
• Revert "Increase contamination penalty from 5 to 7 in bin quality scoring"
• Revert "Remove Singleton Rescue step"
• Revert "Increase contamination penalty from 7 to 10"
• Revert "Add 0.1 to default greedy clustering resolutions"
• Revert "tune: tighten miniprot thresholds"
• Revert "chore: remove agents instructions"
• Revert "tune: lower contamination penalty"
• Revert "tune: score bins by total core genes"
• Revert "tune: relax miniprot filters"
• Revert "tune: restore miniprot outs"
• tune: restore miniprot outs
• tune: relax miniprot filters
• tune: score bins by total core genes
• tune: lower contamination penalty
• chore: remove agents instructions
• tune: tighten miniprot thresholds
• Add 0.1 to default greedy clustering resolutions
• Increase contamination penalty from 7 to 10
• Remove Singleton Rescue step
• Increase contamination penalty from 5 to 7 in bin quality scoring
• Add debug logging for singleton rescue
• Restore exact logging format
• Revert greedy clustering parallelization
• Replace joblib with concurrent.futures
• Parallelize greedy clustering resolution search
• Reduce rescue duplication tolerance to 3%
• Implement Singleton Rescue step
• Remove refinement step and related CLI options
• Restore missing _leiden_clustering_on_graph function
• Replace adaptive resolution with greedy Leiden clustering
• fix: handle duplicate alignment filenames by using parent directory for disambiguation
• Fix: Remove unexpected 'use_header_cache' argument from check_core_gene_duplications calls
• feat: Log command line arguments for reproducibility
• test: add reproduction test for issue verification
• feat: implement bin rescue strategy
• chore: update .gitignore
• test: Add tests for CLI default parameters
• fix(tests): Resolve existing test suite failures
• feat: Update coassembly defaults for learning rate and lambda
• Remove standalone directory
• Tune coassembly resolution
• chore: remove AGENTS documentation
  Full Changelog: v0.3.4...v0.4.0

Full Changelog: v0.3.4...v0.4.0