ITADN

builder code changes for Nov-2025 LTS

#1435Pull Requestmlin 创建于 2025-11-03
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mlincommented
This diff to main should effect all builder code changes needed for the upcoming LTS (Nov-2025). It includes #1420 and #1427, previously reviewed when merging into this intermediate branch; and furthermore (#1433, not yet reviewed): - updates to CxG schema 7 - revises assay lists as specified in #1432 - updates COG version Previously-reviewed changes: - Advance `CENSUS_SCHEMA_VERSION` to 2.4.0 - Replace spatial assay `EFO:0010961` with `EFO:0022857` - Source `organism` and `organism_ontology_term_id` from `uns` instead of `obs` in the h5ad inputs - incidental: rewire summary stats calculations - Add organisms/experiments callithrix_jacchus, macaca_mulatta, and pan_troglodytes - incidental: download h5ad's only for the organisms to be included (helped with testing the new ones) - incidental: revise census_summary reports to more clearly break down by organism - strike number_donors_* from the summary table (#1373) - update to numpy 2, alleviating some dependency problems (#1418) - Perf optimizations for TileDB and AWS CLI NOTE: doc/notebook updates will be in a separate PR. It will be easier to work on the notebooks once this code is on main and we make a (non-LTS) build in the public production bucket.
合并状态:未合并 关闭于 2025-11-03 6 条评论