builder code changes for Nov-2025 LTS
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