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Merge staging into main #587

Merged
merged 30 commits into from
Jan 3, 2025
Merged

Merge staging into main #587

merged 30 commits into from
Jan 3, 2025

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korikuzma
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@korikuzma korikuzma added the priority:high High priority label Jan 2, 2025
@korikuzma korikuzma self-assigned this Jan 2, 2025
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All PRs have been previously approved. Merging

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Pull request cannot be merged via rebase because it has a rebase conflict.

rip. I'll try resolving tomorrow

jsstevenson and others added 26 commits January 3, 2025 08:04
@jsstevenson @korikuzma
chore: update license (#547)
8230ff7
@jsstevenson @korikuzma
cicd: require priority label on PRs (#546)
3c14b70
@jsstevenson @korikuzma
cicd: test install on 3.12 (#544)
c6053cf
@jsstevenson @korikuzma
docs: readme glow-up (#548)
45f2564
@jsstevenson @korikuzma
cicd: update precommit (#558)
528b88b
@jsstevenson @korikuzma
cicd: update workflows/templates from template repo (#556)
60f5abc
@jsstevenson @korikuzma
feat: enable more precise logging configuration (#559)
2e835d5
@jsstevenson @korikuzma
cicd: update precommit dependency in pipfile (#560)
f8531e4
@jsstevenson @korikuzma
style: update ruff (#557)
c18d6bd
@korikuzma
build!: update ga4gh.vrs, cool-seq-tool, + gene-normalizer (#561)
2764cb3
@jsstevenson @korikuzma
build: update requirements and build system (#555)
409ab0c
@korikuzma
docs: update seqrepo version to 2024-02-20 (#562)
8f1b251
@korikuzma
fix(cicd): add reference to stalebot (#563)
aa9cd0b 
Resolves `invalid value workflow reference: no version specified`
@korikuzma
fix: __version__ imports (#565)
4763001
@korikuzma
chore: remove unused files (#568)
a2a5a62 
A working dockerfile will be added back in #553
@korikuzma
style: ruff format (#567)
76bf5cb
@korikuzma
fix: TypeError for params that accept union of enums (#566)
e2da4e3 
* Methods now raise ValueError if incorrect enum value passed
@korikuzma
chore: update ebextensions for downloading latest seqrepo instance (#564
f32b3d6 
)

close #538
@jsstevenson @korikuzma
cicd: allow missing credentials in aws creds detection (#569)
414087a
@korikuzma
feat!: add sequence to SequenceLocation (#570)
3ab2fa7 
close #552

* Remove `vrs_ref_allele_seq` from `GnomadVcfToProteinService` model.
Instead, this is now stored in `variation.locaation.sequence`
@korikuzma
fix: update ga4gh.vrs + add back response_model configs for FastAPI (#…
f681efe 
…571)

close #543
@korikuzma
docs: update vrs versioning (#572)
6128a73
@korikuzma
build: pin cool-seq-tool~=0.6.0 (#575)
d8a6130
@korikuzma
feat: return MANE gene(s) in normalize endpoint for genomic queries (#…
f75d30d 
…576)

initial work for #551
@jsstevenson @korikuzma
cicd: check if PR to main is coming from staging (#580)
a4e60cc 
hell yeah
@korikuzma
chore!: rename optional dependency (#583)
af71533 
* `test` -> `tests`
@korikuzma
feat!: update models to vrs 2.0.0 community review ballot (#582)
b6900a5 
close #581 

* Update modules to vrs
[2.0.0-ballot.2024-11.3](https://github.com/ga4gh/vrs/tree/2.0.0-ballot.2024-11.3)
tag
  * `CopyNumberChange` has `mappings` for EFO code
@korikuzma
build!: require python >= 3.11 (#586)
1657756 
I am hoping this is the last PR before making a new release
@korikuzma
docs: update readme with vrs versioning (#585)
a0424b2
@korikuzma
fix(build): update dependency versions in Pipfile (#584)
dc26a7c 
* Forgot to do this in #582, so Elastic Beanstalk build was failing
@korikuzma korikuzma requested a review from jsstevenson January 3, 2025 13:23
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@jsstevenson I had to rebase staging onto main and forced push these changes, so figure I'd add you as a reviewer.

@korikuzma korikuzma merged commit 71d0f0c into main Jan 3, 2025
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