Release 2.1

[AntonPetrov]

This pull request includes several updates and improvements across multiple files. The primary changes involve updating version numbers, modifying Docker-related configurations, and adding new biological data sequences.

Version Updates:

• Dockerfile: Updated BASE_IMAGE_VERSION from v2.0.1 to v2.1.
• Readme.md: Updated version from 2.0 (2024) to 2.1 (2025).

Docker Configuration:

• .github/workflows/base-image.yml: Removed the workflow for building and pushing the base Docker image.
• .dockerignore: Added 2.0/ to the ignore list.

tmRNA templates:

• data/tmrna/cm/all.fa: Added multiple tmRNA sequences and their respective annotations.
• data/tmrna/cm/all.fa.njs: Added metadata for the all.fa nucleotide database.
• data/tmrna/cm/modelinfo.txt: Added model information for various tmRNA sequences.
• data/tmrna/fasta/tmRNA.fasta, data/tmrna/fasta/tmRNA_alpha.fasta, data/tmrna/fasta/tmRNA_beta.fasta, data/tmrna/fasta/tmRNA_cyano.fasta, data/tmrna/fasta/tmRNA_intron.fasta, data/tmrna/fasta/tmRNA_mito.fasta: Added tmRNA sequences with secondary structure annotations. [1] [2] [3] [4] [5] [6]
• data/tmrna/metadata.tsv: Added metadata for tmRNA models including species, taxid, and RNA type.
• data/tmrna/sto/tmRNA_beta.sto: Added Stockholm format alignment for tmRNA_beta.
• Lowercase sequences are preserved in the final diagrams.

Base Image:

• base_image/Dockerfile: Updated traveler_COMMIT to a new commit hash to use the fixed version of Infernal-to-Traveler mapping.

nmt-tRNAs

The correct anticodon is now selected using the information in the note field of tRNAScan output that is produced with the --detail option.

[github-actions]

Docker image tag(s) pushed:

rnacentral/r2dt:pr-178

Labels added to images:

org.opencontainers.image.created=2025-02-02T17:39:10.275Z
org.opencontainers.image.description=Visualise RNA secondary structure in consistent, reproducible and recognisable layouts
org.opencontainers.image.licenses=Apache-2.0
org.opencontainers.image.revision=2a97e380c26f2411f3ecb780ff7e21d3965c22f0
org.opencontainers.image.source=https://github.com/r2dt-bio/R2DT
org.opencontainers.image.title=R2DT
org.opencontainers.image.url=https://github.com/r2dt-bio/R2DT
org.opencontainers.image.version=pr-178