v0.3.2

• chore: bump version to 0.3.2
• fix: suppress pandas FutureWarning for fillna downcasting
• refactor: remove obsolete reclustering check log message
• refactor: quality-aware resolution selection and improved refinement
• fix: use hashlib for deterministic fragment generation
• tune: adjust learning rate, coverage threshold, and refinement rounds
• refactor: remove unused tqdm import from output module
• refactor: replace transformers tokenizer with standalone implementation
• refactor: remove transformers dependency from core requirements
• feat: add version number to params.json output
• fix: correct BUSCO gene family parsing and lower quality thresholds
• perf: add deterministic fragments, k-NN caching, and simplified logging
• refactor: improve resolution testing and fix refinement without -k
• perf: cache k-NN graph in adaptive resolution + improve metrics
• fix: remove logic that assigns unembedded contigs to largest cluster
• perf: cache k-NN graph during refinement + extend resolution range + find most conservative solution
• fix: remove minimum resolution threshold in refinement
• refactor: simplify refinement with fixed resolution steps
• refactor: fix k-neighbors and threshold during refinement
• refactor: count only single-copy genes for completeness metric
• refactor: round resolution value in Leiden log message
• refactor: fix clustering parameters during resolution testing
• refactor: widen auto-resolution testing range
• refactor: increase refinement resolution steps for faster convergence
• chore: increase default minimum bin size to 300kb
• chore: change default base learning rate to 0.001
• refactor: remove redundant resolution log message
• refactor: improve auto-resolution metrics and refinement
• fix: add --save-filtered-contigs to Filtering & Processing section
• refactor: simplify CLI by removing parameter range restrictions
• refactor: remove experimental SCG loss functionality
• chore: remove unused dependencies (psutil, biopython, joblib)
• refactor: remove 3 redundant refinement log messages
• refactor: merge graph info messages into one
• refactor: round resolution values in Leiden clustering message
• refactor: remove 'Adaptive resolution determination' message
• refactor: remove duplicate message and increase batch size
• perf: optimize miniprot execution with caching
• refactor: move SCG feature matrix message to debug
• refactor: remove redundant filtered FASTA message
• refactor: clean up output logging
• refactor: move fragment augmentation message to debug
• refactor: move SCG gene mappings message to debug
• refactor: simplify miniprot logging message
• refactor: clean up BAM processing progress display
• refactor: improve BAM processing logging and progress display
• feat: improve logging and add save-filtered-contigs option
• feat: update HyenaDNA classifier to use improved model
• refactor: improve CLI UX with positional args and optional output
• refactor: move calculate_raw_coverage.py to scripts directory
• feat: add SCG-aware contrastive learning with consolidated miniprot execution
• fix: add run_exports to bioconda recipe template
  Full Changelog: v0.3.1...v0.3.2

Full Changelog: v0.3.1...v0.3.2