NEXCISION v0.1.1 synchronizes the public source with the implementation used in the formal NEXCISION validation and strengthens several safety behaviours.
Changes
- Rejects removal of every matrix row by default;
--allow-emptypermits this only when explicitly requested. - Stages all requested outputs before committing them and rolls back partial writes if a multi-output operation fails.
- Handles invalid UTF-8 NEXUS and region files with controlled errors.
- Records the
allow_emptysetting in the deterministic JSON provenance report. - Adds permanent regression tests for these safety behaviours.
- Retains zero runtime dependencies and support for Python 3.10 or newer.
Validation
NEXCISION has been independently and adversarially validated using published matrices, fixed edge cases, malformed inputs, generated property tests, 304,000 synthetic site rows, and deliberately faulted implementations.
The complete validation and benchmarking materials are available at:
Preprint
White RT. NEXCISION: exact, validated, and scalable excision of genomic regions from phylogenomic NEXUS matrices. bioRxiv. 2026.