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Release 2.0 #148

Merged
merged 159 commits into from
Sep 28, 2024
Merged

Release 2.0 #148

merged 159 commits into from
Sep 28, 2024

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AntonPetrov
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AntonPetrov and others added 30 commits October 13, 2023 13:31
@AntonPetrov @anayden
Fix file extension
4fe80b6
@AntonPetrov @anayden
Prevent crashes if CM does not exist
d661ffe
@AntonPetrov @anayden
Fix tRNAscan model path
d437ae9
@AntonPetrov @anayden
Handle NNN anticodon for mito-vert tRNAs
dfc7793
@AntonPetrov @anayden
Clean up .ssi files after tests
ca24928 
This prevents errors if sequences are added to existing fasta files.
@AntonPetrov @anayden
Add tag to justfile
0d0baef
@AntonPetrov @anayden
Avoid spawning a new process and use python api
e351aa3
@AntonPetrov @anayden
Improve based on code review
a57f5bd
@dependabot @anayden
Bump pillow from 10.0.0 to 10.0.1
336f56d 
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]>
@anayden
Allow full local build for arbitrary platforms
d9e15ba
@anayden
Remove docker_build.py
a53eb68
@anayden
Parallel build for base image
cc00985
@anayden
Update workflow name
16b1823
@anayden
Fix docker driver
7d754a4
@anayden
Update parallel build
dd58eb1
@anayden
Remove setup step
a7e6743
@anayden
Fix final build
e201b46
@anayden
Fix final build tags
03852e1
@anayden
Test BuildJet
0d7b3f8
@anayden
Use registry cache
b063786
@anayden
Add missing Dockerhub credentials
4a9d72e
@anayden
Fix cache usage
119cb12
@anayden
Experiments with caching
bd9a925
@anayden
Update docs and justfile
b597dc2
@anayden
Build custom image tags when building with custom base tag
dede99d
@AntonPetrov
Typo fix
d7f3016
@AntonPetrov
Merge pull request #119 from RNAcentral/local-docker-build-full
18bb845 
Allow full local build for arbitrary platforms
@AntonPetrov
Merge pull request #120 from RNAcentral/parallel-base-build
b6ce5e7 
Experiment: run base image builds in parallel
@AntonPetrov
Detect templatefree mode automatically
893aee1
@AntonPetrov
Overwrite results if they exist
f68aee6
AntonPetrov and others added 25 commits August 18, 2024 17:31
@AntonPetrov
Add a utility for scaling up templates
c8638a3
@AntonPetrov
Ignore RF00005 hits below Min GA cutoff
b8f99fa
@AntonPetrov
Prevent crashes for python traveler utilities
131c4db
@AntonPetrov
Change error color to red
ab514b5
@AntonPetrov
Merge pull request #142 from RNAcentral/r2dt-blast
561db40 
Use Blast for template selection
@AntonPetrov
Scale template-free templates 3x, update tests
f4d3191
@AntonPetrov
Scale up GtRNAdb templates, update tests
e41ba16
@AntonPetrov
Scale up Rfam R2R templates on generation
6b28c0e
@AntonPetrov
Scale up precomputed Rfam R2R templates
8f03aba
@AntonPetrov
Update tests
2db0f85
@AntonPetrov
Delete leftover print statement
564530f
@AntonPetrov
Add a command to create new precomputed library
501285d
@AntonPetrov
Update version number to 2.0
68b401c
@AntonPetrov
Do not require just for installation
f88632a
@AntonPetrov
Update hit acceptance criteria
7e1320e
@AntonPetrov
Update tests
d930be6
@AntonPetrov
Scale up SRP RNArtist template
2db1f35
@AntonPetrov
Adjust font sizes
e056271
@AntonPetrov
Merge pull request #144 from RNAcentral/scale-templates
77c9c3f 
Scale up templates, update version number, update precomputed library
@AntonPetrov
Add draft 2.0 announcement
0ce7c24
@AntonPetrov
Update Docker base image version
538c8f5
@AntonPetrov
Merge branch 'main' into develop
2d35c53
@AntonPetrov
Update GitHub urls after repo transfer
494f2c4
@anayden
Update versions of used GH Actions
dc31ca5
@anayden
explicitly grant write permissions to a github token
74f4f5a
@github-actions GitHub Actions
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github-actions bot commented Aug 27, 2024 •
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Docker image tag(s) pushed:

rnacentral/r2dt:pr-148

Labels added to images:

org.opencontainers.image.created=2024-09-18T09:27:18.845Z
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=ca426f25764646e8fdb9100219696469e3276178
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-148

@AntonPetrov
Skip tRNA hits on the reverse strand
ecb5cd7 
Fix #149
@AntonPetrov
Include precomputed Blast databases
fa8e650 
Singularity has permission issues and does not allow writing in the folder where the Blast files are expected
@AntonPetrov
Fix a bug in template-free detection
5b5eec9
@AntonPetrov AntonPetrov merged commit bf0dce4 into main Sep 28, 2024
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@AntonPetrov @anayden