Change Log

All notable changes to this project will be documented in this CHANGELOG.md file. The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Unreleased Changes

  • None.

[0.9.0] - 2024-10-21

Added

  • Initial package release.

[0.9.1] - 2024-10-30

Added

  • Better error message for read_ensembl_gtf() function that now points user to vignette for help when trying to read unsuported file types.

  • Added kaleido as a dependency to allow users to images as multiple formats without having to install new packages.

  • Improved code documentation, corrected spelling errors on vignettes, added two new vignettes.

[0.9.2] - 2024-11-04

Added

  • Increased efficiency of to_intron().

[0.9.3] - 2024-11-07

Added

  • Nothing… Just needed a new release to sync with Zotero for administrative reasons

[0.9.4] - 2024-11-12

Added

  • Changed intron coordinates to be consistent with GTF format (1-index based, inclusive on both sides)

  • Changed make traces function to make sure introns and exon/CDS “touch” in the plot even though their GTF coordinates do not touch.

[0.9.5] - 2024-11-19

Removed

  • Kaleido dependency. Kaleido now requires chrome/chromium to be installed which could complicate the installation.

[1.0.1] - 2025-02-10

Added

  • Changed make_traces() function to avoid transparent dots on the legend.

  • Improved documentation for read_ensembl_gtf() function.

  • Improved documentation for read_expression_matrix() function.

  • Improved formatting on the vignettes.

  • Improved README.md file.

[1.0.2] - 2025-02-27

Added

  • Increase infer_schema_length when reading counts matrix to avoid type errors.

[1.1.0] - 2025-03-12

Added

  • to_intron now automatically calculates exon number if it is not already present.

  • shorten_gaps now automatically calculates exon_number if it is not already present.

  • Adressed issue reported on https://github.com/UK-SBCoA-EbbertLab/RNApysoforms/issues/6#issuecomment-2719061461, improving generalizability of the shorten gaps function

  • Improved documentation for read_ensembl_gtf()

[1.2.7] - 2025-03-27

Added

  • Correction to make the legend for expression match the order of the expression boxes.

[1.2.8] - 2025-04-10

Added

  • Correction to the annotation legend to make it match the annotation order.

[1.2.9] - 2025-04-23

Added

  • Removed debugging print statements

[1.2.10] - 2025-04-24

Added

  • Further removed debugging print statements

[1.2.11] - 2025-09-02

Added

  • Updated dependencies

[1.2.12] - 2025-09-02

Added

  • Fixed tests

[1.3.1] - 2025-10-29

Added

  • Added process_expression_matrix() function to perform wrangling when df is already loaded.

  • Added process_ensembl_gtf() function to perform wrangling when df is already loaded.