Release notes

Release notes#

Release notes summarize intended changes. For reproducible analysis, also record the exact Git commit, model files, quality-control database, and dependency environment.

Unreleased#

Installation changes#

  • Reworked the mainland-China installer to prefer micromamba, support TUNA, BFSU, USTC, upstream, and institutional channels, and keep mirror settings out of global user configuration.

  • Added dry-run, cached/offline, update, local model archive, custom model URL, and explicit manager/path options.

  • Made the official PKU-EMBL/BASALT_WEIGHT Hugging Face repository the first automatic model source, with Figshare and Baidu Netdisk fallbacks.

  • Removed the obsolete esteinig and defaults channel requirements and separated legacy CheckM from the maintained Python 3.12 environment.

  • Removed the duplicate uv/pip scientific-stack transaction from basalt_environment.yml; the base runtime is now solved once through Conda, while VAMB and LorBin remain explicitly optional adapters.

  • Added shallow-clone installation guidance and a validated, persistent ~/.bashrc configuration for BASALT_WEIGHT.

  • Added a bounded Hugging Face reachability check, a release-pinned model revision, and matching mainland-installer controls so model installation remains auditable on blocked or mirrored routes.

  • Documented VAMB as an isolated optional environment because its pinned PyTorch stack conflicts with the validated BASALT model runtime.

  • Documented PKU-EMBL/LorBin-BASALT-Extrabinner as the maintained -e l integration target, including pinned-source installation, dependency validation, warning-only failure semantics, and fork-commit reporting.

BASALT 1.2.1#

Tagged 15 May 2026.

Changes#

  • Updated the VAMB adapter for the VAMB 5 command family.

  • Added VAMB 5 to the Python 3.12 environment definition.

  • Added warning-based failure handling for optional binners so other candidate generators can continue.

Compatibility boundaries#

  • Optional-adapter success must be verified from logs and output FASTA files.

  • VAMB, PyTorch, CUDA, and driver versions remain part of the analysis provenance.

  • The Conda edition does not implement BASALT --version; record the Git tag and commit directly.

BASALT 1.2.0#

Released 16 December 2025.

Changes#

  • Updated the documented environment to Python 3.12.

  • Added a LorBin adapter under -e l.

  • Selected CheckM2 as the default quality-control backend.

  • Added accelerator-compatible dependency paths for SemiBin 2 and model inference.

  • Made the model directory configurable through BASALT_WEIGHT.

  • Renamed the historical --autopara option to --sensitive.

Compatibility boundaries#

  • The Conda edition does not implement BASALT --version or BASALT --check-deps.

  • Optional binner adapters require independent installation and validation.

  • Resuming checkpoints created with earlier code or database versions is not recommended.

BASALT 1.1.0#

Released 12 June 2024.

  • Revised installation workflows.

  • Added China-mainland mirror support.

  • Added a Singularity distribution route.

  • Included maintenance and stability changes.

BASALT 1.0.0#

Released 18 August 2023.

  • Introduced multi-assembly candidate generation and bin selection.

  • Introduced model-based contig screening and read-supported retrieval.

  • Added bin-level reassembly and OLC stages.

  • Added external-bin data feeding.

  • Added CheckM-based quality assessment and textual checkpoints.

Publication#

Qiu, Z., Yuan, L., Lian, C.-A. et al. BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis. Nature Communications 15, 2179 (2024). https://doi.org/10.1038/s41467-024-46539-7

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