Changelog

Version 0.5.0 - 0.5.1

  • Switch to LTLA/nclist-cpp for overlap and intersection operations.

  • Update Github template and setup.py to support editable builds.

Version 0.4.2

  • Fixes edge cases for overlap and search methods.

  • Add tile and sliding window operations.

  • Updates tests to capture most scenarios.

  • Update docstrings and edit tutorials.

Version 0.4.0 - 0.4.1

This is a major rewrite of the package partly driven by performance and for better consistency with the IRanges R/Bioconductor package.

  • Using pybind11, reimplement inter-range methods to a cpp implementation using code derived from the R package.

  • Better Start/End/Width resolver that is similar to the R implementation.

  • Overhaul of many of the find overlaps and search methods to better align with R’s expectations of how these methods work.

  • Update docstrings, more tests.

Version 0.3.0

  • chore: Remove Python 3.8 (EOL)

  • precommit: Replace docformatter with ruff’s formatter

Version 0.2.10 - 0.2.12

  • Added a numpy vectorized version of finding gaps (tldr: not fast compared to the traditional version). May be needs a better implementation

  • Added NCLS based intersection operation (based on what pyranges does in their internals)

  • Added tests for intersection operations.

  • Fixed and issue when coercing IRanges containing mcols.

Version 0.2.8 - 0.2.9

Optimizing a couple of methods in IRanges:

  • Update gaps and reduce to slightly faster NumPy based operations.

  • Switch np.array to np.asarray

Version 0.2.7

Changes to be compatible with NumPy’s 2.0 release:

If using np.array(obj, copy=False) replace it with np.asarray(obj) to allow a copy when needed (no behavior change in NumPy 1.x). For more details, see https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword.

Version 0.2.4

  • Support coercion from IRanges to Polars and vice-versa

  • Setting up myst_nb to execute snippets in tutorial/documentation markdown files

Version 0.2.3

  • Feature complete implementation of IRanges from Bioconductor