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Shanghua Gao b4d9354b8d Merge main into codex/sufianta-batch-review, reconciling two independent weekly-healthcheck reliability designs 
Both branches solved the same problem (a lost CI runner discarding the
whole weekly tool sweep) independently: main shipped sharded matrix jobs
with per-shard log parsing (scripts/summarize_health_sweep.py, already in
production), while this branch restores an unsharded checkpoint/resume
system (--json-output/--resume, atomic JSON checkpointing).

Resolution:
- .github/workflows/weekly-tool-healthcheck.yml and the run_all_patterns()
  call site: took main's sharded design, since it's already shipped and
  replacing it would reintroduce the exact failure mode it was built to
  fix. The checkpoint/resume machinery itself stays -- it's still useful
  standalone for a developer resuming an interrupted local sweep.
- Fixed a real interaction bug this merge would otherwise have introduced:
  checkpoint_complete compared `results` against the full `expected_patterns`
  universe, which is never true for a single shard's `selected` subset, so
  every successful sharded CI run would have incorrectly exited 1. Now
  compared against `selected` -- identical to `expected_patterns` when
  --shard isn't used, correctly scoped when it is. Verified with a manual
  shard simulation.
- Removed test_weekly_workflow_consumes_the_checkpoint_contract: it
  asserted the workflow YAML wires up --json-output and executes an inline
  job-summary heredoc, both part of the design main's sharding replaced.
  Its premise no longer holds under the shipped design.
2026-08-25 07:51:17 -04:00
..
remote
Validate documentation examples recursively
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admetai_tools.rst
release tooluniverse version 1
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adverse_event_tools.rst
release tooluniverse version 1
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agentic_tools.rst
update mcpb
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alphafold_tools.rst
update mcpb
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arxiv_tools.rst
update a lot of paper search tools
2025-10-07 21:42:06 -04:00
bioinformatics_core_tools.rst
update docs for adding tools to toolunivrese
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biomodels_tools.rst
update mcpb
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biorxiv_tools.rst
update docs for adding tools to toolunivrese
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blast_tools.rst
update mcpb
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boltz_mcp_loader_tools.rst
update tests
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boltz_tools.rst
update docs for adding tools to toolunivrese
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cbioportal_tools.rst
update mcpb
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cdc_tools.rst
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cellosaurus_tools.rst
docs: expand redirect map (15 more paper-cited legacy paths) (#211)
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chembl_tools.rst
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cheminformatics_tools.rst
update docs for adding tools to toolunivrese
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clinical_trials_tools.rst
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clinicaltrials_gov_tools.rst
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clinvar_tools.rst
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compact_mode_tools.rst
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compose_tools.rst
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core_tools.rst
update docs for adding tools to toolunivrese
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crossref_tools.rst
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dailymed_tools.rst
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dataset_tools.rst
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dblp_tools.rst
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dbpedia_tools.rst
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dbsnp_tools.rst
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depmap_tools.rst
update docs for adding tools to toolunivrese
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disease_target_score_tools.rst
update docs for adding tools to toolunivrese
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doaj_tools.rst
update a lot of paper search tools
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drug_discovery_agents.rst
update docs for adding tools to toolunivrese
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earth_sciences_tools.rst
release tooluniverse version 1
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efo_tools.rst
release tooluniverse version 1
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embedding_tools.rst
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emdb_tools.rst
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encode_tools.rst
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enrichr_tools.rst
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ensembl_tools.rst
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euhealth_tools.rst
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europe_pmc_tools.rst
release tooluniverse version 1
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expert_feedback_tools.rst
update docs for adding tools to toolunivrese
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fatcat_tools.rst
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fda_drug_adverse_event_detail_tools.rst
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fda_drug_adverse_event_tools.rst
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fda_drug_labeling_tools.rst
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file_download_tools.rst
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finder_tools.rst
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gbif_tools.rst
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gdc_tools.rst
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gene_ontology_tools.rst
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genomics_tools.rst
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geo_tools.rst
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gnomad_tools.rst
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gtex_tools.rst
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gtopdb_tools.rst
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gwas_tools.rst
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hal_tools.rst
update docs for adding tools to toolunivrese
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hca_tools.rst
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health_disparities_tools.rst
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hpa_tools.rst
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humanbase_tools.rst
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idmap_tools.rst
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iedb_tools.rst
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image_processing_tools.rst
release tooluniverse version 1
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immune_compass_tools.rst
update docs for adding tools to toolunivrese
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interpro_tools.rst
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jaspar_tools.rst
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kegg_tools.rst
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literature_search_tools.rst
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machine_learning_tools.rst
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markitdown_tools.rst
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mcp_client_tools_example.rst
update docs for adding tools to toolunivrese
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medlineplus_tools.rst
update docs for adding tools to toolunivrese
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medrxiv_tools.rst
update docs for adding tools to toolunivrese
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mgnify_tools.rst
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molecule_2d_tools.rst
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molecule_3d_tools.rst
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monarch_tools.rst
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mpd_tools.rst
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neuroscience_tools.rst
release tooluniverse version 1
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nhanes_tools.rst
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obis_tools.rst
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odphp_tools.rst
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ols_tools.rst
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openaire_tools.rst
update docs for adding tools to toolunivrese
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openalex_tools.rst
release tooluniverse version 1
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opentarget_tools.rst
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optimizer_tools.rst
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osf_preprints_tools.rst
update docs for adding tools to toolunivrese
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output_summarization_tools.rst
release tooluniverse version 1
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package_discovery_tools.rst
update mcpb
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paleobiology_tools.rst
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pathway_commons_tools.rst
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physics_astronomy_tools.rst
release tooluniverse version 1
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pinnacle_tools.rst
update docs for adding tools to toolunivrese
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pmc_tools.rst
update docs for adding tools to toolunivrese
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ppi_tools.rst
update docs for adding tools to toolunivrese
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pride_tools.rst
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protein_structure_3d_tools.rst
update docs for adding tools to toolunivrese
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pubchem_tools.rst
update docs for adding tools to toolunivrese
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pubmed_tools.rst
update a lot of paper search tools
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pubtator_tools.rst
update docs for adding tools to toolunivrese
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pypi_package_inspector_tools.rst
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python_executor_tools.rst
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rcsb_pdb_tools.rst
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rcsb_search_tools.rst
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reactome_tools.rst
release tooluniverse version 1
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regulomedb_tools.rst
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remap_tools.rst
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remote_tools.rst
release tooluniverse version 1
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rnacentral_tools.rst
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rxnorm_tools.rst
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scientific_computing_tools.rst
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screen_tools.rst
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semantic_scholar_tools.rst
update docs for adding tools to toolunivrese
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simbad_tools.rst
feat: add SIMBAD astronomical database tools (#62)
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single_cell_tools.rst
update docs for adding tools to toolunivrese
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smolagent_tools.rst
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special_tools.rst
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structural_biology_tools.rst
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tool_composition_tools.rst
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tool_discovery_agents.rst
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tools_config_index.rst
docs: expand redirect map (15 more paper-cited legacy paths) (#211)
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transcriptformer_tools.rst
release tooluniverse version 1
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txagent_client_tools.rst
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umls_tools.rst
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unified_guideline_tools.rst
update docs for adding tools to toolunivrese
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uniprot_tools.rst
Fix Round 30: UniProt returned no protein for a species-level bacterial taxid
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unpaywall_tools.rst
update a lot of paper search tools
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url_fetch_tools.rst
update docs for adding tools to toolunivrese
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uspto_downloader_tools.rst
release tooluniverse version 1
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uspto_tools.rst
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visualization_tools.rst
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web_search_tools.rst
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who_gho_tools.rst
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wikidata_sparql_tools.rst
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wikipathways_tools.rst
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wikipedia_tools.rst
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worms_tools.rst
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xml_tools.rst
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zenodo_tools.rst
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