Changelog

Version 0.7.0 - 0.7.3

  • Changes to switch to LTLA/nclist-cpp in the iranges package for overlap and search operations.

  • Improve performance of search operations, bump version of iranges to 0.5.4.

  • Optimize group by operations that GenomicRanges uses internally for the inter-range operations.

  • Reset cached indexes when ranges were modified.

Version 0.6.2 - 0.6.3

  • Implement biocutil’s extract_row_names generic.

  • Fix when SeqInfo’s attributes contain lists with numpy elements.

Version 0.6.0 - 0.6.1

An rewrite of the package to use the new and improve IRanges packages (>= 0.4.2)

  • More consistent results across all methods compared to R/Bioconductor implementations.

  • Similar to IRanges, search and overlap operations may return a hits like object.

  • Nearest returns slightly different matches but since the select=“arbitrary”, its probably ok.

  • More robust testing of the combination of inputs and parameter choices.

  • Updated the tests, docstrings

Version 0.5.2

  • Restrict IRanges to the last compatible version before the migration.

Version 0.5.1

  • Fixed an issue with numpy arrays as slice arguments. Code now uses Biocutils’s subset functions to perform these operations.

  • Rename GitHub actions for consistency with the rest of the packages.

Version 0.5.0

  • chore: Remove Python 3.8 (EOL)

  • precommit: Replace docformatter with ruff’s formatter

Version 0.4.32 - 0.4.33

  • Bump IRanges package version to fix coercion issues to pandas.

  • Remove reverse mapping in iranges in reduce operation.

  • Fixes issue with combine merging sequence names without properly using the accessor methods.

Version 0.4.27 - 0.4.31

  • Implement subtract method, add tests.

  • Use accessor methods to access properties especially get_seqnames()

  • Modify search and overlap methods for strand-awareness.

  • Choose appropriate NumPy dtype for sequences.

  • Update tests and documentation.

Version 0.4.26

  • Expose the generic_accessor method used internally by GenomicRangesList to call functions from the underlying GenomicRanges for each element.

  • Add class method to initialize GenomicRangesList from dictionary.

  • Update tests

Version 0.4.25

  • Method to split GenomicRanges by a list of groups.

  • Coerce GenomicRangesList to GenomicRanges.

  • Add tests and documentation.

Version 0.4.21 - 0.4.24

  • Optimize intersect operation on large number of genomic regions

  • Add a fast_combine_granges method that only concatenates seqnames and intervals.

  • Use np.asarray as much as possible for conversion

  • Update tests and documentation

Version 0.4.20

Updated dependencies (especially IRanges), to be compatible with NumPy’s 2.0 release.

Version 0.4.19

  • Fix an issue related to combining GenomicRanges or GenomicRangesList objects containing different metadata columns. This switches the operation from combine_rows to relaxed_combine_rows.

  • Set NumPy to <2.0.0 before the migration to 2.0 release.

  • Updated tests

Version 0.4.17

Initialize GenomicRanges from a polars DataFrame. Also coerce a GRanges object to polars.

Version 0.4.9 - 0.4.16

Bring SeqInfo upto speed with the rest of the class implementations. Added subset and pretty print functionality.

Fix minor bugs and update documentation.

Version 0.4.0 to 0.4.8

This is a complete rewrite of both these classes following the functional paradigm from our developer notes.

GenomicRanges is now closer to Bioconductor’s GenomicRanges class both in the design and implementation.

The package does not rely on pandas anymore. While we try to provide backwards compatibility to construct a GenomicRanges object from a pandas dataframe using the from_pandas method, please note that the default constructor to genomic ranges does not accept a pandas data frame anymore!

Most range based methods have been reimplemented and the heavy lifting is done in the IRanges package for interval operations. The package depends on nclist-cpp data structure to perform search and overlap operations.

Tests, documentation and readme has been updated to reflect these changes.

Version 0.3.0

This release migrates the package to a more palatable Google’s Python style guide. A major modification to the package is with casing, all camelCase methods, functions and parameters are now snake_case.

In addition, docstrings and documentation has been updated to use sphinx’s features of linking objects to their types. Sphinx now also documents private and special dunder methods (e.g. __getitem__, __copy__ etc). Intersphinx has been updated to link to references from dependent packages.

Configuration for flake8, ruff and black has been added to pyproject.toml and setup.cfg to be less annoying.

Finally, pyscaffold has been updated to use “myst-parser” as the markdown compiler instead of recommonmark. As part of the pyscaffold setup, one may use pre-commits to run some of the routine tasks of linting and formatting before every commit. While this is sometimes annoying and can be ignored with --no-verify, it brings some consistency to the code base.

Version 0.2

  • Now uses BiocFrame as the underlying class

  • Implement interval based operations

  • update documentation, readme

  • comprehensive tests

Version 0.1

  • Create base class for GenomicRanges

  • Import into GenomicRanges from pandas/GTF/UCSC

  • tests

  • documentation