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Changelog

This changelog tracks the notable changes for downstream users in each version of Honeybee. Everything in Honeybee is rolling release / unversioned except for the Honeybee Biology Library/Container, which are released in lockstep for compatability and reproducibility.

Older versions

[0.7.0] - 2026-05-14

This release should be stable for the first Honeybee workshop at the CZ Biohub San Francisco!

Added

  • We now create official .tar.gz images for Standard Bio Docker image
  • In patch 166b97e: Add download link for notebook launcher
  • In patch a2a9a50: Updated editor styles (thank you Brian Hempel for the honeycomb idea!)

Changed

  • Improvements to Standard Bio library and Docker image. Pipelines for RNA-seq, ATAC-seq, and LEMONmethyl-seq should all be quite usable now!

Fixed

  • Fixed scroll bug where "Next CHOICE" button did not go high enough
  • Fixed bug where "Start navigating" button was clickable too early
  • In patch 166b97e: Fixed bug where code in cells would get cut off when too long

[0.6.1] - 2026-05-01

Changed

  • Minor improvements to Standard Bio library and Docker image

[0.6.0] - 2026-04-29

Added

  • Added erasure of static information
  • Added Honeybee Standard Bio Docker image (still WIP, but has a lot of functionality)
  • Added basic EM-seq support

Changed

  • Paths are now statically embedded in the output program instead of dynamically via Dir.make()
  • std-bio now has static erasure enabled
  • Added a lot of polish (changes) to std-bio library

[0.5.0] - 2026-02-23

Added

  • Add additional UI + information to help fill out information in the first phase of Honeybee (#109)
  • Add "use hints" that allow for quick comparison between tools (#101)
  • Add /unstable route for accessing latest pushed unreleased version
  • Add hover text for complex concepts
  • Add "Undo" button to frontend
  • Add Honeybee citation to output script
  • Add citation backreferences via Google Scholar
  • Add tool search via Google and DuckDuckGo
  • Add reference to PubMed entry (PMID) for each tool (#102)
  • Add GoatCounter private analytics
  • Add website (https://honeybee-lang.org), including video demo
  • Add link to Zulip chat

Changed

  • Emit Jupyter Notebooks instead of Python files (#115)
  • Overhaul glue annotations into the Honey language, resulting in much more ergnomic definitions for building blocks, better codegen, and a smoother editor experience, including auto-selecting the "functions" that declare the user's workflow (#95)
  • Move "Next CHOICE" button (and new "Undo" button) to bottom of screen
  • Make variable names in generated code nicer (e.g. TRANSCRIPT_MATRICES, not TRANSCRIPTMATRICES)
  • Make "Go to download" button simply a "Download" button
  • Make code preview nicer (shows holes as circles) (#107)
  • Made the menu bar sticky (#103, #108)