Release 2025.2.0#455

Merged

bencap merged 178 commits intomainfrom

release-2025.2.0

Jun 13, 2025

Commits on Mar 29, 2025

Commits on Apr 3, 2025

Show the variants that have problem in error message.
EstelleDa
committed

Commits on Apr 8, 2025

Commits on Apr 9, 2025

wip: clingen submission and linkage scripts
bencap
committed

Commits on Apr 18, 2025

Flesh out retry logic for linking clingen allele ids
bencap
committed

Commits on Apr 23, 2025

Tests for VRS Variation Extraction Utilities
bencap
committed

Commits on May 5, 2025

Commits on May 6, 2025

The Ubuntu 20.04 Actions runner image will begin deprecation on 2025-02-01 and will be fully unsupported by 2025-04-15. Workflows using the ubuntu-20.04 image label should be updated to ubuntu-late…
EstelleDa
committed
Merge pull request #388 from VariantEffect/jstone-dev/variant-search
jstone-dev
authored
Fix Docker Casing Warnings

bencap
authored and
jstone-dev
committed
Refactor Dataframe Validation Logic

bencap
authored and
jstone-dev
committed
Refactor Tests to Better Identify Dependency Separation Issues

bencap
authored and
jstone-dev
committed
Bump Dependencies

bencap
authored and
jstone-dev
committed
Check for Nonetype Target Sequences to Silence MyPy Error

bencap
authored and
jstone-dev
committed
Replace DataSet Columns Setter in Worker Variant Mocker

bencap
authored and
jstone-dev
committed
Add Base Editor Column to Target Accessions Table

bencap
authored and
jstone-dev
committed
Validation logic and test cases for base editor data

bencap
authored and
jstone-dev
committed
Add isBaseEditor Flag to Remaining Accession Tests

bencap
authored and
jstone-dev
committed
Add GUIDE_SEQUENCE_COLUMN constant to mave lib

bencap
authored and
jstone-dev
committed
Use existing boolean flag for transgenic marker in prefix validation

bencap
authored and
jstone-dev
committed
Clarify error message for accession based variants with accessions missing from targets list

bencap
authored and
jstone-dev
committed
Move guide sequence column to the end of the standard columns sorted list

bencap
authored and
jstone-dev
committed
Add additional column validation tests

bencap
authored and
jstone-dev
committed
Fix sort order of dataframe test case columns

bencap
authored and
jstone-dev
committed
Use equality comparison over is operator for column name comparison

bencap
authored and
jstone-dev
committed
Allow the Unix Domain Socket during test runs

bencap
authored and
jstone-dev
committed
Add Multi-Variant Support for Accession Based Targets

bencap
authored and
jstone-dev
committed
Multi-Variant Genomic Validation Tests

bencap
authored and
jstone-dev
committed
Logical names for git action checks

bencap
authored and
jstone-dev
committed
Bump SeqRepo Version, Add Volume to Dev Containers

bencap
authored and
jstone-dev
committed
Add SeqRepo based seqfetcher to data provider

bencap
authored and
jstone-dev
committed
Add SeqFetcher MyPy type stub

bencap
authored and
jstone-dev
committed
Refactor fixes

bencap
authored and
jstone-dev
committed
Use MaveHGVS to determine if variant is a multi-variant

bencap
authored and
jstone-dev
committed
Fix tests for MaveHGVS parsing

bencap
authored and
jstone-dev
committed
Rebase fixes (could fixup)

bencap
authored and
jstone-dev
committed
wip: Use new MaveHGVS methods for allelic validation

bencap
authored and
jstone-dev
committed
Fixed rebasing error.
jstone-dev
committed
Updated MaveHGVS to version 0.7.0.
jstone-dev
committed
Fixed: MaveHGVS parsing error handling
jstone-dev
committed
Fixed rebasing error.
jstone-dev
committed
Fixed rebasing error.
jstone-dev
committed

Commits on May 7, 2025

Commits on May 13, 2025

Commits on May 15, 2025

Merge branch 'release-2025.2.0' into improve/estelle/350/surfaceValidationErrors
EstelleDa
authored

Commits on May 19, 2025

Commits on May 21, 2025

Commits on May 22, 2025

Support mapper update for multi-target score sets
sallybg
committed

Commits on May 23, 2025

Merge pull request #435 from VariantEffect/jstone-dev/clingen-linkage
bencap
authored

Commits on May 24, 2025

Add OddsPath Property to ScoreRange Data Model
bencap
committed

Commits on Jun 1, 2025

Try again. Add an importorskip.
EstelleDa
committed

Commits on Jun 4, 2025

Commits on Jun 5, 2025

Merge pull request #447 from VariantEffect/bugfix/estelle/61/numScoreSetsAndExperiments
EstelleDa
authored

Commits on Jun 9, 2025

Update VRSMap class and script for multi-target mapper changes
sallybg
committed

Commits on Jun 10, 2025

Create accession-based score set in db before mapping tests
sallybg
committed