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Release 1.5 #112

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Commits on Oct 13, 2023

  1. Fix file extension

    @AntonPetrov @anayden
    AntonPetrov authored and anayden committed Oct 13, 2023
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  2. Prevent crashes if CM does not exist

    @AntonPetrov @anayden
    AntonPetrov authored and anayden committed Oct 13, 2023
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  3. Fix tRNAscan model path

    @AntonPetrov @anayden
    AntonPetrov authored and anayden committed Oct 13, 2023
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  4. Handle NNN anticodon for mito-vert tRNAs

    @AntonPetrov @anayden
    AntonPetrov authored and anayden committed Oct 13, 2023
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  5. Clean up .ssi files after tests 

    This prevents errors if sequences are added to existing fasta files.
    @AntonPetrov @anayden
    AntonPetrov authored and anayden committed Oct 13, 2023
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  6. Add tag to justfile

    @AntonPetrov @anayden
    AntonPetrov authored and anayden committed Oct 13, 2023
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  7. Avoid spawning a new process and use python api

    @AntonPetrov @anayden
    AntonPetrov authored and anayden committed Oct 13, 2023
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  8. Improve based on code review

    @AntonPetrov @anayden
    AntonPetrov authored and anayden committed Oct 13, 2023
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  9. Bump pillow from 10.0.0 to 10.0.1 

    Bumps [pillow](https://github.com/python-pillow/Pillow) from 10.0.0 to 10.0.1.
- [Release notes](https://github.com/python-pillow/Pillow/releases)
- [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst)
- [Commits](python-pillow/Pillow@10.0.0...10.0.1)

---
updated-dependencies:
- dependency-name: pillow
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
    @dependabot @anayden
    dependabot[bot] authored and anayden committed Oct 13, 2023
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  10. Allow full local build for arbitrary platforms

    @anayden
    anayden committed Oct 13, 2023
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  11. Remove docker_build.py

    @anayden
    anayden committed Oct 13, 2023
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  12. Parallel build for base image

    @anayden
    anayden committed Oct 13, 2023
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  13. Update workflow name

    @anayden
    anayden committed Oct 13, 2023
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  14. Fix docker driver

    @anayden
    anayden committed Oct 13, 2023
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  15. Update parallel build

    @anayden
    anayden committed Oct 13, 2023
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  16. Remove setup step

    @anayden
    anayden committed Oct 13, 2023
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  17. Fix final build

    @anayden
    anayden committed Oct 13, 2023
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  18. Fix final build tags

    @anayden
    anayden committed Oct 13, 2023
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  19. Test BuildJet

    @anayden
    anayden committed Oct 13, 2023
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  20. Use registry cache

    @anayden
    anayden committed Oct 13, 2023
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  21. Add missing Dockerhub credentials

    @anayden
    anayden committed Oct 13, 2023
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  22. Fix cache usage

    @anayden
    anayden committed Oct 13, 2023
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  23. Experiments with caching

    @anayden
    anayden committed Oct 13, 2023
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Commits on Oct 17, 2023

  1. Update docs and justfile

    @anayden
    anayden committed Oct 17, 2023
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Commits on Oct 18, 2023

  1. Build custom image tags when building with custom base tag

    @anayden
    anayden committed Oct 18, 2023
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Commits on Oct 19, 2023

  1. Typo fix

    @AntonPetrov
    AntonPetrov committed Oct 19, 2023
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  2. Merge pull request #119 from RNAcentral/local-docker-build-full 

    Allow full local build for arbitrary platforms
    @AntonPetrov
    AntonPetrov committed Oct 19, 2023
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  3. Merge pull request #120 from RNAcentral/parallel-base-build 

    Experiment: run base image builds in parallel
    @AntonPetrov
    AntonPetrov committed Oct 19, 2023
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Commits on Nov 9, 2023

  1. Detect templatefree mode automatically

    @AntonPetrov
    AntonPetrov committed Nov 9, 2023
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  2. Overwrite results if they exist

    @AntonPetrov
    AntonPetrov committed Nov 9, 2023
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Commits on Nov 22, 2023

  1. Add auto-walrus pre-commit hook

    @anayden
    anayden committed Nov 22, 2023
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  2. Fix indentation

    @anayden
    anayden committed Nov 22, 2023
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Commits on Nov 23, 2023

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

    Add auto-walrus pre-commit hook
    @AntonPetrov
    AntonPetrov committed Nov 23, 2023
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Commits on Nov 24, 2023

  1. Setup devcontainer

    @anayden
    anayden committed Nov 24, 2023
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  2. Add explicit image

    @anayden
    anayden committed Nov 24, 2023
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  3. Migrate to Docker image

    @anayden
    anayden committed Nov 24, 2023
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  4. Fix dockerfile path

    @anayden
    anayden committed Nov 24, 2023
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  5. Add VSCode extensions for Python and Docker

    @anayden
    anayden committed Nov 24, 2023
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  6. Add chafa dependencies

    @anayden
    anayden committed Nov 24, 2023
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Commits on Dec 4, 2023

  1. Update overview slides

    @AntonPetrov
    AntonPetrov committed Dec 4, 2023
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  2. Fix off by one error when generating templates 

    Fix #121
    @AntonPetrov
    AntonPetrov committed Dec 4, 2023
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  3. Suppress output when copying evalues

    @AntonPetrov
    AntonPetrov committed Dec 4, 2023
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  4. Use /tmp instead of temp for example CM

    @AntonPetrov
    AntonPetrov committed Dec 4, 2023
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Commits on Dec 6, 2023

  1. Start docs server inside the container

    @AntonPetrov
    AntonPetrov committed Dec 6, 2023
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  2. Enable admonitions in docs (note, warning etc)

    @AntonPetrov
    AntonPetrov committed Dec 6, 2023
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Commits on Dec 7, 2023

  1. Enable creating and using private templates

    @AntonPetrov
    AntonPetrov committed Dec 7, 2023
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  2. Test creating new template and using it locally

    @AntonPetrov
    AntonPetrov committed Dec 7, 2023
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  3. Add examples for new test

    @AntonPetrov
    AntonPetrov committed Dec 7, 2023
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  4. Document using private templates locally

    @AntonPetrov
    AntonPetrov committed Dec 7, 2023
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  5. Fix post prob not showing after insertion removal 

    This fixes a bug in TestCrw
    @AntonPetrov
    AntonPetrov committed Dec 7, 2023
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  6. Use --quiet throughout to reduce console output

    @AntonPetrov
    AntonPetrov committed Dec 7, 2023
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  7. Remove obsolete config options

    @AntonPetrov
    AntonPetrov committed Dec 7, 2023
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  8. Remove all temporary files

    @AntonPetrov
    AntonPetrov committed Dec 7, 2023
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  9. Remove leftover print statement

    @AntonPetrov
    AntonPetrov committed Dec 7, 2023
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  10. Quiet down a leftover print statement

    @AntonPetrov
    AntonPetrov committed Dec 7, 2023
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  11. Fix broken structure when 5'/3' labels are present

    @AntonPetrov
    AntonPetrov committed Dec 7, 2023
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  12. Add Codespaces Badge/Button

    @anayden
    anayden committed Dec 7, 2023
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Commits on Dec 8, 2023

  1. Merge pull request #127 from RNAcentral/codespace 

    Add required tools to the codespace image
    @AntonPetrov
    AntonPetrov committed Dec 8, 2023
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  2. Merge pull request #129 from RNAcentral/custom-template-improvements 

    Custom template improvements
    @AntonPetrov
    AntonPetrov committed Dec 8, 2023
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  3. Switch to http instead of ftp

    @AntonPetrov
    AntonPetrov committed Dec 8, 2023
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Commits on Dec 12, 2023

  1. Update Rfam id list for release 14.10

    @AntonPetrov
    AntonPetrov committed Dec 12, 2023
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  2. Update R-scape to latest version

    @AntonPetrov
    AntonPetrov committed Dec 12, 2023
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  3. Update clean up script to remove helixcov files

    @AntonPetrov
    AntonPetrov committed Dec 12, 2023
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  4. Update Rfam files for release 14.10

    @AntonPetrov
    AntonPetrov committed Dec 12, 2023
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  5. Do not generate thumbnails for enriched SVGs

    @AntonPetrov
    AntonPetrov committed Dec 12, 2023
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  6. Move rfam setup code out of r2dt.py

    @AntonPetrov
    AntonPetrov committed Dec 12, 2023
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Commits on Jan 11, 2024

  1. Install RNArtist

    @AntonPetrov
    AntonPetrov committed Jan 11, 2024
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Commits on Feb 28, 2024

  1. Update R-scape to stop R2R issues

    @AntonPetrov
    AntonPetrov committed Feb 28, 2024
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  2. Ignore lancaster annotations and 5' labels

    @AntonPetrov
    AntonPetrov committed Feb 28, 2024
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  3. Minor improvements

    @AntonPetrov
    AntonPetrov committed Feb 28, 2024
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  4. Use cm suffix

    @AntonPetrov
    AntonPetrov committed Feb 28, 2024
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  5. Update regex to account for characters in 5' label

    @AntonPetrov
    AntonPetrov committed Feb 28, 2024
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  6. Switch to new method of managing Rfam seeds 

    Fix #124
    @AntonPetrov
    AntonPetrov committed Feb 28, 2024
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  7. Delete temporary r2r_meta files

    @AntonPetrov
    AntonPetrov committed Feb 28, 2024
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  8. Update Rfam templates to release 14.10 

    Also delete templates without consensus secondary structure
    @AntonPetrov
    AntonPetrov committed Feb 28, 2024
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  9. Fix broken test

    @AntonPetrov
    AntonPetrov committed Feb 28, 2024
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  10. Replace / in seq_id with underscore

    @AntonPetrov
    AntonPetrov committed Feb 28, 2024
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  11. Fix font size in enriched diagrams too

    @AntonPetrov
    AntonPetrov committed Feb 28, 2024
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  12. Fix conflict

    @AntonPetrov
    AntonPetrov committed Feb 28, 2024
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  13. Merge pull request #132 from RNAcentral/rfam-updates 

    Rfam updates
    @AntonPetrov
    AntonPetrov committed Feb 28, 2024
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