Changelog

Version 0.7.0 - 0.7.2

• Classes extend BiocObject from biocutils.
• validate param in the constructor is renamed to _validate.

Version 0.6.0

• Implement CompressedIRangesList extending the base compressed-lists class

Version 0.5.4

• Switch to the nearest implementation from LTLA/nclist-cpp (v0.3.0).
• Improved worksharing across threads for find_overlaps_groups and nearest_groups. The idea is to ensure that all threads are occupied, even when the groups are of different sizes. This is done with some more fine-grained parallelization during both index building and overlap identification.

Version 0.5.0 - 0.5.3

• Switch to LTLA/nclist-cpp for overlap and intersection operations.
• Update Github template and setup.py to support editable builds.
• Improving performance of search operations - nearest, follow and precede.
• Method to delete cached nclist index, automatically remove as needed when properties are modified (starts, widths).
• Add a method to get exclusive end positions.

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