Adopt ecoli-sources data bundle as the ParCa input source - #426

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cplong90 wants to merge 24 commits into

CovertLab:masterfrom

vivarium-collective:data-bundle-migration

Commits on May 4, 2026

Commits on May 5, 2026

Drop deprecated rnaseq CLI plumbing now that bundle is the source of truth
cplong90
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ad2b91a
Remove wholecell.io.data_qc: upstream-data QC moves out of vEcoli
cplong90
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1d03116
Rewrite data ingestion docs around the bundle pattern
cplong90
committed
2088519

Commits on May 6, 2026

Commits on May 21, 2026

Fail-fast on misplaced parca_options keys at config top level

cplong90
and
claude
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354bf23
Merge upstream/master (CovertLab/vEcoli) into data-bundle-migration

cplong90
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claude
committed
9ea8285
Switch ecoli-sources pin from SSH to HTTPS

cplong90
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claude
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1a2c721
parameters: drop now-unused os + ROOT_PATH imports

cplong90
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claude
committed
9615b9e
Surface cistron_id_to_monomer_ids on sim_data; fix get_TU_ID

cplong90
and
claude
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d26592d
Dockerfile: install git for uv to fetch git-pinned ecoli-sources

cplong90
and
claude
committed
f2734dc

Commits on May 28, 2026

Commits on Jun 8, 2026

Singularity: install git for uv to fetch git-pinned ecoli-sources

cplong90
and
claude
committed
b3bb993