R2DT

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Bumps [pillow](https://github.com/python-pillow/Pillow) from 10.0.0 to 10.3.0. Release notes Sourced from pillow's releases. 10.3.0 https://pillow.readthedocs.io/en/stable/releasenotes/10.3.0.html Changes CVE-2024-28219: Use strncpy to avoid buffer overflow #7928 [@​hugovk] Use functools.lru_cache for hopper() #7912 [@​hugovk]...

dependabot[bot]

Release 1.5

1

- Streamline using custom templates (#129) - GitHub Codespaces integration (#127) - Consistent use of `--quiet` (#129) - Bug fixes and docs improvements (fix #121) - Rfam version 14.10 (https://github.com/RNAcentral/R2DT/pull/132)...

AntonPetrov

Switch to relative coordinates

6

The [RNA 2D JSON Schema](https://github.com/LDWLab/RNA2D-data-schema) is switching from absolute to relative coordinates. This means that the code that uses R2DT JSON output needs to be updated or the SVG images...

AntonPetrov

Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.2 to 3.1.3. Release notes Sourced from jinja2's releases. 3.1.3 This is a fix release for the 3.1.x feature branch. Fix for GHSA-h5c8-rqwp-cp95. You are affected if...

dependabot[bot]

Use RNArtist instead of R2R to avoid overlaps in Rfam templates

4

The idea is to run [RNArtist](https://github.com/fjossinet/RNArtistCore) on Rfam families, get [JSON output](https://raw.githubusercontent.com/fjossinet/RNArtist/master/RNArtist/samples/projects/1u6b.json), convert it into R2DT templates and then anytime anyone tries to visualise a sequence from that Rfam family,...

AntonPetrov

[Typer](https://typer.tiangolo.com) and [rich](https://rich.readthedocs.io/en/stable/) can help improve R2DT CLI interface and console output.

AntonPetrov

The [code that generates thumbnail images](https://github.com/RNAcentral/R2DT/blob/cd77ed21e75d27263be0a99072b1bcbe7e49825c/utils/shared.py#L421) works well but the images sometimes have jagged edges and the lines are not very smooth ([example](https://rnacentral.org/api/v1/rna/URS0000162127/2d/svg/)). It is desirable to improve the images...

AntonPetrov

A new version of traveler (https://github.com/cusbg/traveler/commit/b0d69bc64f507fecb7da05b9cf747eb962e97f58) fixes an issue in R2DT where data layers did not work for residues with a label like `NaN`.

AntonPetrov

Some sequences should not be filtered out based on the presence of the `MultipleHits` warning generated by ribotyper. I am investigating using bit scores as an additional signal to use...

AntonPetrov

Bundle Rfam seeds into cms tarball?

2

As part of the RNAcentral pipeline, we run R2DT in a nextflow process that makes use of a singularity container converted from the docker container built in this repo. We...

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