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Release 2.0#148

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AntonPetrov merged 159 commits intomainr2dt-bio/R2DT:mainfrom developr2dt-bio/R2DT:developCopy head branch name to clipboardSep 28, 2024

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Commits on Oct 13, 2023

• Fix file extension

  

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• Prevent crashes if CM does not exist

  

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• Fix tRNAscan model path

  

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• Handle NNN anticodon for mito-vert tRNAs

  

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• Clean up .ssi files after tests

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• Add tag to justfile

  

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• Avoid spawning a new process and use python api

  

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• Improve based on code review

  

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• Bump pillow from 10.0.0 to 10.0.1

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• Allow full local build for arbitrary platforms

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• Remove docker_build.py

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• Parallel build for base image

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• Update workflow name

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• Fix docker driver

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• Update parallel build

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• Remove setup step

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• Fix final build

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• Fix final build tags

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• Test BuildJet

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• Use registry cache

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• Add missing Dockerhub credentials

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• Fix cache usage

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• Experiments with caching

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Commits on Oct 17, 2023

• Update docs and justfile

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Commits on Oct 18, 2023

• Build custom image tags when building with custom base tag

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Commits on Oct 19, 2023

• Typo fix

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• Merge pull request #119 from RNAcentral/local-docker-build-full

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• Merge pull request #120 from RNAcentral/parallel-base-build

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Commits on Nov 9, 2023

• Detect templatefree mode automatically

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• Overwrite results if they exist

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Commits on Nov 22, 2023

• Add auto-walrus pre-commit hook

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• Fix indentation

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Commits on Nov 23, 2023

• Merge pull request #126 from RNAcentral/auto-walrusize-r2dt

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Commits on Nov 24, 2023

• Setup devcontainer

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• Add explicit image

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• Migrate to Docker image

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• Fix dockerfile path

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• Add VSCode extensions for Python and Docker

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• Add chafa dependencies

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Commits on Dec 4, 2023

• Update overview slides

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• Fix off by one error when generating templates

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• Suppress output when copying evalues

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• Use /tmp instead of temp for example CM

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Commits on Dec 6, 2023

• Start docs server inside the container

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• Enable admonitions in docs (note, warning etc)

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Commits on Dec 7, 2023

• Enable creating and using private templates

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• Test creating new template and using it locally

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• Add examples for new test

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• Document using private templates locally

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• Fix post prob not showing after insertion removal

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• Use --quiet throughout to reduce console output

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• Remove obsolete config options

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• Remove all temporary files

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• Remove leftover print statement

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• Quiet down a leftover print statement

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• Fix broken structure when 5'/3' labels are present

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• Add Codespaces Badge/Button

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Commits on Dec 8, 2023

• Merge pull request #127 from RNAcentral/codespace

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• Merge pull request #129 from RNAcentral/custom-template-improvements

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• Switch to http instead of ftp

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Commits on Dec 12, 2023

• Update Rfam id list for release 14.10

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• Update R-scape to latest version

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• Update clean up script to remove helixcov files

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• Update Rfam files for release 14.10

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• Do not generate thumbnails for enriched SVGs

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• Move rfam setup code out of r2dt.py

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Commits on Jan 11, 2024

• Install RNArtist

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Commits on Feb 28, 2024

• Update R-scape to stop R2R issues

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• Ignore lancaster annotations and 5' labels

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• Minor improvements

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• Use cm suffix

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• Update regex to account for characters in 5' label

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• Switch to new method of managing Rfam seeds

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• Delete temporary r2r_meta files

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• Update Rfam templates to release 14.10

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• Fix broken test

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• Replace / in seq_id with underscore

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• Fix font size in enriched diagrams too

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• Fix conflict

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• Merge pull request #132 from RNAcentral/rfam-updates

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Commits on Aug 11, 2024

• Add RNArtist class

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• Pin numpy version to prevent crashes

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• Install tqdm

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• Setup RNArtist and generate prefer_rnartist.txt

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• Use tempfile instead of headers.txt

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• Add --rscape and --rnartist options to rfam draw

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• Add setup_rnartist method

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• Add TestRnartist test

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• Minor fix

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• Add WUSS to SS_cons characters

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• Update BioEasel

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• Add RNArtist traveler template files

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• Remove --rscape option as it is the default

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• Document --rnartist option

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Commits on Aug 12, 2024

• Remove --rscape option

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• Test RNArtist template generation

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• Restore --rscape option

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• Document --rscape option

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• Add RNArtist tests

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• Add a list of families where RNArtist is preferred

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• Add Ribovision to the docs

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• Make destination optional argument

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• Update RNArtist prefer list

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• Add --rnartist option for setup-rfam

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• Set default Rfam template to "auto"

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• Update example file to ensure tests pass

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• Document animate.py usage

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• Test animation

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• Minor fixes in animate.py

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• Merge pull request #140 from RNAcentral/rnartist

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• Merge pull request #141 from RNAcentral/animate-docs

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• Exclude ps files from GH language stats

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Commits on Aug 13, 2024

• Docker linting fixes

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• Ignore local virtual environment if present

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• Install Ribovore rt-blast branch and NCBI blast

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• Ignore blast database files

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• Add --1blast option to ribovore

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• Add CRW model blacklist

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• Close files when generating test html reports

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• Update tests for ribotyper --1blast option

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• Update library compression script

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Commits on Aug 18, 2024

• Add Ribovore class for parsing results

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• Add RfamThreshold for getting curated cutoffs

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• Use new Ribovore class for getting results

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• Update tests

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• Run blast methods first

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• List models by type

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• Add RNArtist template free mode

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• Test template free RNArtist mode

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• Document RNArtist template free mode

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• Add bridge RNA example fasta file for tests

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• Add a utility for scaling up templates

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• Ignore RF00005 hits below Min GA cutoff

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• Prevent crashes for python traveler utilities

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• Change error color to red

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Commits on Aug 19, 2024

• Merge pull request #142 from RNAcentral/r2dt-blast

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• Scale template-free templates 3x, update tests

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• Scale up GtRNAdb templates, update tests

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• Scale up Rfam R2R templates on generation

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• Scale up precomputed Rfam R2R templates

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• Update tests

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Commits on Aug 22, 2024

• Delete leftover print statement

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Commits on Aug 23, 2024

• Add a command to create new precomputed library

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• Update version number to 2.0

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• Do not require just for installation

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• Update hit acceptance criteria

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• Update tests

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• Scale up SRP RNArtist template

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• Adjust font sizes

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• Merge pull request #144 from RNAcentral/scale-templates

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• Add draft 2.0 announcement

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• Update Docker base image version

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• Merge branch 'main' into develop

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Commits on Aug 26, 2024

• Update GitHub urls after repo transfer

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Commits on Aug 27, 2024

• Update versions of used GH Actions

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• explicitly grant write permissions to a github token

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Commits on Sep 4, 2024

• Skip tRNA hits on the reverse strand

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Commits on Sep 9, 2024

• Include precomputed Blast databases

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Commits on Sep 18, 2024

• Fix a bug in template-free detection

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