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Pull requests list

Document how to check a BabelTest assertion, and stop duplicating the assertion list
#1075 opened Sep 1, 2026 by gaurav Collaborator Loading…
chore(deps-dev): bump ruff from 0.16.3 to 0.16.5 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#1071 opened Aug 30, 2026 by dependabot Bot Loading…
chore(deps-dev): bump rumdl from 0.2.55 to 0.2.62 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#1070 opened Aug 30, 2026 by dependabot Bot Loading…
chore(deps): bump snakemake from 9.25.1 to 9.26.0 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#1069 opened Aug 30, 2026 by dependabot Bot Loading…
Build the Publication compendium from the pubmed2db NDJSON export instead of parsing PubMed XML
#1050 opened Aug 21, 2026 by gaurav Collaborator Loading…
7 tasks
Verify #948 against a real build, and record what that clique diff cost
#1030 opened Aug 17, 2026 by gaurav Collaborator Loading… Babel v1.19
Update setuptools requirement from >=83.0.0 to >=84.0.0 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#1025 opened Aug 16, 2026 by dependabot Bot Loading…
Time a failed job from when it died, not from when the run gave up
#1020 opened Aug 13, 2026 by gaurav Collaborator • Draft
Document the long-term archiving strategy for past runs
#1001 opened Jul 31, 2026 by gaurav Collaborator • Draft
1
Stop redoing per-call setup work, and hand the untyped compendium over as JSONL
#992 opened Jul 30, 2026 by gaurav Collaborator • Draft Babel v1.19
Read concord files through one shared function
#986 opened Jul 30, 2026 by gaurav Collaborator • Draft Babel v1.19
Stop conflate_synonyms computing output it then discards
#985 opened Jul 30, 2026 by gaurav Collaborator • Draft Babel v1.19
Parse PubMed with iterparse and release each article as it is written
#984 opened Jul 30, 2026 by gaurav Collaborator • Draft Babel v1.19
Detect encoding damage in labels and synonyms
#953 opened Jul 21, 2026 by gaurav Collaborator Loading…
Distribute compendia as .txt.gz
#947 opened Jul 20, 2026 by gaurav Collaborator Loading…
Type foods from their NCIt classification, beyond DrugBank (#935)
#936 opened Jul 13, 2026 by gaurav Collaborator • Draft
clique-diff: report the incoming side of cross-compendium moves
#915 opened Jul 10, 2026 by gaurav Collaborator Loading…
Write UberGraph concords in a deterministic order
#901 opened Jul 9, 2026 by gaurav Collaborator • Draft
5 tasks
Babel v1.19
1
Document what Ubergraph's SPARQL results actually contain
#899 opened Jul 9, 2026 by gaurav Collaborator Loading…
Activate glom's MONDO close-match guard, with concord-reader symmetry tests
#888 opened Jul 2, 2026 by gaurav Collaborator Loading… Not urgent
1
drugchemical: record dropped conflation pairs to a retained exclusion report (#754)
#874 opened Jun 24, 2026 by gaurav Collaborator • Draft
fixed issue #827 with DRUGBANK:DB10626 preferred name
#872 opened Jun 23, 2026 by hyi Contributor Loading… Babel v1.19
1
Estimate drugprotein
#848 opened Jun 9, 2026 by gaurav Collaborator • Draft
Add protein/chemical overlap report
#830 opened Jun 4, 2026 by gaurav Collaborator • Draft
docs: add temporary plan for centralizing MeSH tree-number partitioning
#812 opened May 29, 2026 by gaurav Collaborator • Draft
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