Release 2.0

R2DT 2.0 is a major new release that brings performance improvements, more legible diagrams, and new layouts powered by RNArtist. Find out more in a corresponding bioRxiv preprint.

Major new features

• Rfam updates by @AntonPetrov in #132
• RNArtist templates by @AntonPetrov in #140
• Use Blast for template selection by @AntonPetrov in #142
• Custom template improvements by @AntonPetrov in #129

Other improvements

• Create workflow for tagging base image in Dockerhub by @anayden in #116
• Update DockerHub tagging by @anayden in #117
• Fix tag workflow typo by @anayden in #118
• Update documentation by @anayden in #109
• Allow full local build for arbitrary platforms by @anayden in #119
• Run base image builds in parallel by @anayden in #120
• Add procps to base image by @afg1 in #123
• Add auto-walrus pre-commit hook by @anayden in #126
• Add required tools to the codespace image by @anayden in #127
• Update docs conf.py to configure canonical URL by @AntonPetrov in #139
• Document animation script by @AntonPetrov in #141
• Scale up templates, update version number, update precomputed library by @AntonPetrov in #144
• Release 2.0 by @AntonPetrov in #148

New Contributors

• @afg1 made their first contribution in #123

Full Changelog: v1.4...v2.0

v2.0-alpha

Usage

# pull the release preview docker image
docker pull rnacentral/r2dt:pr-148

# download the new precomputed library, this will create a 2.0 folder with 2 subfolders: crw and rfam
curl -L -O https://github.com/RNAcentral/R2DT/releases/download/v2.0-alpha/cms.tar.gz
tar -xzf cms.tar.gz

# point to the location of the 2.0 folder
export R2DT_LIBRARY=<full path to the precomputed library>

# run all tests to confirm the installation was successful 
docker run  -v $R2DT_LIBRARY/:/rna/r2dt/data/cms -it --rm rnacentral/r2dt:pr-112 bash -c "./r2dt.py test"
..............................
----------------------------------------------------------------------
Ran 30 tests in 177.144s

OK

Full Changelog: v1.4...v2.0-alpha

Release 1.4

Release announcement

Explore all features in detail

What's Changed

• Add new tRNA templates by @AntonPetrov in #85
• Move documentation to Read the Docs by @AntonPetrov in #90
• Dockerfile improvements by @AntonPetrov in #92
• Black formatting by @AntonPetrov in #94
• Display posterior probabilities by @AntonPetrov in #95
• Documentation improvements by @AntonPetrov in #102
• Initial version of image comparison instead of file comparison by @anayden in #106
• Separate base image build by @anayden in #105
• Release 1.4 by @AntonPetrov in #89

New Contributors

• @anayden made their first contribution in #106

Full Changelog: v1.3...v1.4

Release 1.3

What's Changed

• Major changes @AntonPetrov in #71
• Constrained folding by @hmccann3 in #66
• Add and update templates by @AntonPetrov in #70
• Update Readme.md by @davidhoksza in #57

New Contributors

• @davidhoksza made their first contribution in #57
• @hmccann3 made their first contribution in #66

Full Changelog: v1.2...v1.3

Release 1.2

• Update Rfam to version 14.6
• Add a new template LD_SSU_3D for Leishmania donovani based on 6AZ1
• Include version number and date
• New helpers r2dt.py test and r2dt.py version
• Document updating Rfam templates

v1.1

Add link to generate_cm_library script in Readme

v1.0

This version of R2DT was used in https://www.biorxiv.org/content/10.1101/2020.09.10.290924v1.