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Change Log

All notable changes to the ribotools package will be documented in this file.

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

[Unreleased] - started 2025-11

[2.0.0] 2025-11-20

Changed

  • Requires rpbp >= 4.0.1
  • Environment (R=4.4.3, argparser)
  • Option --stranded to --rna-stranded
  • Scripts
  • Documentation

Added

  • Support for Python 3.11, 3.12, and 3.13
  • Regression testing and CI
  • Option to create ORF profiles for QC
  • Slurm option for get_gtf_from_predictions.py

Fixed

  • 'coef' should specify same coefficient as in results 'res'
  • Allow both 'samples' and 'sample_name_map' in scripts

Removed

  • Support for Python 3.7, 3.8 (EOL), 3.9 and 3.10

[1.0.3]

Added

  • TEA/DEA scripts
  • PyPI deploy
  • Documentation (RTD)

Fixed

  • Discouraged "script-files" (wrapped as module for packaging)
  • Import

[1.0.0]

Changed

  • API to conform to Rp-Bp v3

Removed

  • Track-related scripts (moved to trackhub-utils)
  • pep_bed6_to_bed12.py
  • match_appris_scores.py, get_psite_count_table.py, get_all_seq_filtering_counts.py, etc. (draft scripts)
  • create_rna_profiles.py, extract_rna_profiles.py, etc.
  • Notebooks

[0.1.0]

Restructure package, add to GitHub. Previous changes not documented.