Version 2.3.0

This release bundles a large number of bug fixes (several of which fix silent
correctness issues in training and clustering), removes the deprecated
SemiBin1 command, and includes many documentation improvements.

User-visible changes

• Remove SemiBin1. Only SemiBin2 is shipped now; if you have old scripts that still call SemiBin1, they will need to be updated.
• Accept hybrid as a synonym for long_read in --sequencing-type (#216)
• Remove --environment parameter when learning a new model (#218)
• check_install: now also looks for samtools and reports it (in verbose mode) when missing. This is a soft check: missing samtools does not cause check_install to fail, since samtools is only required for CRAM input.
• --allow-missing-mmseqs2 is now marked as deprecated in the help text (the option is already a no-op since mmseqs2 is no longer required by check_install).
• Data-generation log message now distinguishes between generating training data and generating features for inference with a pretrained model (#219)
• Add Python 3.14 to the supported/tested Python versions (SemiBin now runs on Python 3.8–3.14)
• Add the missing COPYING.MIT license file (#214)

Bug fixes

• single_easy_bin: fix AttributeError: 'Namespace' object has no attribute 'training_type' when running with abundance files (-a) instead of BAM files. set_training_type() was only invoked on the BAM path, so the abundance-based single-sample workflow crashed before doing any work.
• Semi-supervised training: fix wrong input in the unlabeled contrastive-learning branch. The second argument to model.forward() was unlabeled_train_input1 instead of unlabeled_train_input2, meaning both branches received identical data and the unlabeled-pair contrastive signal was being silently discarded.
• Long-read clustering: clip zero depth values before np.log. Zero depth (no reads mapped) was producing -inf values, silently corrupting the embedding used for DBSCAN clustering.
• Multi-sample binning: fix split_data matching sample names that are prefixes of others (e.g., S1 matching S10:contig). Now uses str.startswith() rather than str.contains().
• Marker calling: validate the cached markers.hmmout against an input fingerprint (FASTA size/mtime, binned_length, ORF finder) before reusing it. Previously, reruns into an existing output directory could silently reuse stale marker calls from a different input or different parameters. On mismatch a warning is logged and markers are recomputed.
• Long-read binning: remove stale output bins from previous runs before writing new results (previously, rerunning into the same output directory with fewer bins left old FASTA files behind).
• Empty FASTA inputs now fail cleanly with Input file ... is empty. Please check inputs. instead of crashing with ZeroDivisionError (single-sample paths) or ValueError: attempt to get argmax of an empty sequence (multi-sample paths).
• ORF finding: fix prodigal errors being silently ignored.
• model_load: raise a clear ValueError for unknown model names instead of an UnboundLocalError.
• check_install: fix incorrect logic when checking for prodigal.
• Several minor error-message and validation improvements in utils.py and main.py.

Documentation fixes

• Fix outdated output descriptions in docs/output.md (default model type, missing bins_info.tsv/contig_bins.tsv, clarify output_bins is the final output)
• Fix wrong split_contigs output filename in README strobealign-aemb example (split.fa → split_contigs.fna.gz)
• Fix docs/aemb.md description of split_contigs.fna.gz contents (only split halves, not originals) and an undefined variable in the helper script
• Remove references to --mode and --training-type flags no longer accepted by SemiBin2 in docs/subcommands.md
• Update docs/semibin2.md and docs/index.md to reflect that only SemiBin2 is installed since v2.2
• Clarify -b/-a are alternatives (not both required) in docs/subcommands.md for single_easy_bin, generate_sequence_features_single, and generate_sequence_features_multi
• Fix docs/generate.md path from scripts/ to script/
• Clarify Prodigal is optional in docs/install.md; add samtools to the source-install dependency list
• Fix step numbering in docs/usage.md (steps went 1, 3, 4 → now 1, 2, 3)
• Make it more prominent in the FAQ and usage docs how to handle hybrid (long+short) data
• Fix Python version ranges in README and install docs
• Fix truncated help text for --random-seed
• Fix wrong DOI for SemiBin2 in CITATION.md
• Remove incorrect --depth-metabat2 mention from generate_sequence_features_single docs
• Remove duplicate HMMER entry and fix malformed Bedtools URL in README
• Many other smaller documentation corrections (typos, grammar, broken links, incorrect option names)

Internal improvements

• Self-supervised training reads each input CSV once instead of every epoch.
• Fix unclosed file handle in run_prodigal.
• Remove unused pyyaml dependency.
• Avoid naked except: clauses (better error reporting and easier debugging).
• Write validation errors to the log file (not just to stderr).
• Various small refactors and additional type annotations.