Changelog

All notable changes to CRISPRzip will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[1.2.0] - 2025-07-08

Fixed

  • Major bugfix: R-loop cost is now properly converted to units kBT (at room temperature, 20 Celsius). In all previous versions, R-loop cost was reported in units kcal/mol, being a factor ~1.7 too small.

  • End-to-end test no longer passes automatically. Test values are updated according to new R-loop costs.

Added

  • Inclusion of Nearest-Neighbor values from Banerjee et al. (2020) for RNA/DNA hybrids at physiological salt conditions (100 mM NaCl). Support for these values is quite limited; they are only available for matching hybrid basepairs, and no similar salt correction can yet be made for the dsDNA base pairs.

  • A set of sequence parameters for a smooth protein landscape. However, these values will be replaced soon (see Notes below).

Notes

  • With the R-loop cost being corrected, new sequence-dependent energy landscapes should be generated and included with this package. This makes version 1.2.0 a temporary version, and the more stable 1.2.1 will follow very soon.

[1.1.1] - 2025-04-08

Fixed

  • More robust approach to checking sequence input. Any sequence (protospacer/off-target) can now be offered in a 20/23/24 nt format.

[1.1.0] - 2025-02-18

Added

  • Function load_landscape in crisprzip.kinetics for robust parameter loading

  • Cross-platform testing: MacOS, Ubuntu, Windows for Python 3.10, 3.11, 3.12

Fixed

  • Parameters for nucleic acid stability and landscape definitions are now included as package data which avoids relative path issues.

[1.0.0] - 2025-02-04

Added

  • Initial release of the package.

  • Comprehensive documentation for setup and usage, hosted on GitHub-pages.

  • Implemented end-to-end testing.

Notes

  • This version marks the first stable release of CRISPRzip.

  • Feedback and contributions are welcome to improve the project.