theo-exp#6011

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theosanderson wants to merge 19 commits intomainfrom

seq-exp

Commits on Feb 27, 2026

feat(deployment): add sequlus CI + Kubernetes deployment with useSequlus toggle

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refactor: rename lapis-rs to sequlus

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Enable useSequlus in values.yaml
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fix: fix sequlus deployment - Dockerfile runtime libs, startup probe, CI image wait

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fix: add /health endpoint and fix probe configuration

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Increase sequlus image wait timeout to 20min, add build caching

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Use /health for readiness probe instead of /info

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Add initContainer to wait for backend before starting sequlus

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Set sequlus refresh interval to 10 seconds

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Add stub lineageDefinition endpoint to sequlus

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Fix system field filtering and response in sequlus

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Fix accession arrays, FASTA downloads, dataUseTerms filter, and lineage definitions

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Use DuckDB for details metadata, handle form-urlencoded POST bodies

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Add debug logging to details endpoint for annotation test investigation

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Fix submissionId as system field and enable regex on system fields

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Start serving immediately, run ETL in background

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fix: use config-processor to resolve reference genome URLs in sequlus deployment

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feat: add compression, custom FASTA headers, and headerless CSV/TSV support

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Commits on Feb 28, 2026

fix: add referenceGenome endpoint, fix FASTA charset, fix downloadAsFile boolean handling

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theo-exp#6011

theo-exp#6011
theosanderson wants to merge 19 commits intomainfrom
seq-exp

Commits on Feb 27, 2026

feat(deployment): add sequlus CI + Kubernetes deployment with useSequlus toggle

refactor: rename lapis-rs to sequlus

Enable useSequlus in values.yaml

fix: fix sequlus deployment - Dockerfile runtime libs, startup probe, CI image wait

fix: add /health endpoint and fix probe configuration

Increase sequlus image wait timeout to 20min, add build caching

Use /health for readiness probe instead of /info

Add initContainer to wait for backend before starting sequlus

Set sequlus refresh interval to 10 seconds

Add stub lineageDefinition endpoint to sequlus

Fix system field filtering and response in sequlus

Fix accession arrays, FASTA downloads, dataUseTerms filter, and lineage definitions

Use DuckDB for details metadata, handle form-urlencoded POST bodies

Add debug logging to details endpoint for annotation test investigation

Fix submissionId as system field and enable regex on system fields

Start serving immediately, run ETL in background

fix: use config-processor to resolve reference genome URLs in sequlus deployment

feat: add compression, custom FASTA headers, and headerless CSV/TSV support

Commits on Feb 28, 2026

fix: add referenceGenome endpoint, fix FASTA charset, fix downloadAsFile boolean handling