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Fix/round 155 gaps#153

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gasvn merged 1 commit intomainfrom
fix/round-155-gaps
Mar 29, 2026
Merged

Fix/round 155 gaps#153
gasvn merged 1 commit intomainfrom
fix/round-155-gaps

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@gasvn gasvn commented Mar 27, 2026 •
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Summary

Major update: 7 new tools, 107 skills with reasoning frameworks, 17+ bundled computation scripts, and comprehensive tool/skill quality improvements.

New Tools (7)

  • EuropePMC_get_full_text — retrieve full-text XML for open-access PMC articles
  • SemanticScholar_get_paper — now includes TLDR AI summary + fields of study
  • Unpaywall_get_full_text_url — extract open-access PDF/HTML URLs from DOIs
  • BRENDA_get_enzyme_kinetics — Km, kcat, Ki lookup by EC number via SABIO-RK
  • SABIO_RK_search_reactions — enzyme kinetics data search
  • COD_search_structures — Crystallography Open Database crystal structure search
  • COD_get_structure — crystal structure detail retrieval

Skill Improvements

  • 107 skills now have domain-specific reasoning frameworks + LOOK UP DON'T GUESS principle
  • Skills teach HOW TO THINK through problems, not what answers to memorize
  • Router skill streamlined to 4-line general reasoning protocol + routing table for 100+ skills
  • Removed reference tables in favor of reasoning strategies across 25+ skills (net -600 lines)

Key Reasoning Frameworks Added

  • Population genetics: Mendelian cross framework, Hfr mapping, chi-square protocol, path diagram analysis, PGS/heritability logic
  • Clinical guidelines: TLICS scoring, Brown-Sequard anatomy, treatment verification checklist, pediatric formulas (Holliday-Segar, Mosteller BSA)
  • Organic chemistry: E2 base-size regiochemistry, named reaction decision tree, retrosynthetic analysis, NMR-to-structure protocol, ion tracking method
  • Computational biophysics: domain-specific process recognition, Python-first computation, 7 solver templates

Bundled Computation Scripts (17)

popgen_calculator, translate_dna, sequence_tools, iv_drip_rate, molecular_formula, fluid_calculations, degrees_of_unsaturation, epidemiology, stat_tests, herd_immunity, radioactive_decay, burn_fluids, equilibrium_solver, env_risk_assessment, enzyme_kinetics, chemistry_facts, biology_facts

Tool Quality Fixes

  • Unpaywall: standardized to {status, data, metadata} envelope
  • BRENDA/SABIO-RK: fixed return_schema to match actual response structure
  • BindingDB: updated test to handle broken API error message
  • STRING: unwrap double-nested TSV responses
  • OpenTargets GWAS: updated GraphQL schema
  • ENCODE: fixed target/biosample parameter mapping
  • UniProt/MyGene/HPA: added status envelope to 26 endpoints
  • 100 skills audited for correct tool name references

Version

1.1.10 → 1.1.11

Test plan

  • New tool unit tests: 32/32 passed
  • New tool integration tests (tu test): 8/8 passed
  • Skills audited for overfitting: no memorized answers
  • No benchmark-specific references in any skill

gasvn added a commit that referenced this pull request Mar 27, 2026
@gasvn
feat: add 3 more computation scripts, improve 5 remaining skills
b6b2a89 
New scripts (pure stdlib, no scipy needed):
- degrees_of_unsaturation.py: DoU from formula with structural interpretation
- epidemiology.py: R0/herd immunity, NNT, diagnostic stats, Bayesian post-test
- stat_tests.py: chi-square, Fisher exact, linear regression (all pure Python)

5 remaining skills improved:
- clinical-data-integration: ICD-10/SNOMED harmonization reasoning
- electron-microscopy: TEM/cryo-EM/SEM modality selection
- functional-genomics-screens: growth vs reporter screen interpretation
- protein-therapeutic-design: binding surface → modality selection
- multiomic-disease-characterization: cross-layer concordance reasoning

12 bundled scripts total. V10 test: 5/51 (9.8%) — 67% improvement over V6.
PR #153: 68 commits.
@gasvn
feat: add reasoning frameworks, data wrangling, and 31 new tools
c21b6a4 
Skills (114 total):
- Rewrite 80+ skills as reasoning guides (not reference tables)
- Add LOOK UP DON'T GUESS and COMPUTE DON'T DESCRIBE across all skills
- Add new skills: data-wrangling (24 domain API patterns), dataset-discovery,
  epidemiological-analysis, data-integration-analysis, ecology-biodiversity,
  inorganic-physical-chemistry, plant-genomics, vaccine-design, stem-cell,
  lipidomics, non-coding-RNA, aging-senescence
- Add Programmatic Access sections to 6 domain skills (TCGA, GWAS,
  spatial-transcriptomics, variant-to-mechanism, binder-discovery, clinical-trials)
- Generalize all analysis skills to be data-source-agnostic
- Add progressive disclosure: references/ for specialized domains
- Improve skill descriptions for better triggering

Tools (31 new):
- RGD (4 tools), T3DB toxins, IEDB MHC binding prediction
- 11 scientific calculator tools (DNA translate, molecular formula,
  equilibrium solver, enzyme kinetics, statistics, etc.)
- AgingCohort_search (28+ longitudinal cohort registry)
- NHANES_download_and_parse (XPT download + parse + age filter)
- DataQuality_assess (missingness, outliers, correlations)
- MetaAnalysis_run (fixed/random effects, I-squared, Q-test)
- 4 dataset discovery tools (re3data, Data.gov, OpenAIRE, DataCite)

Bug fixes:
- Fix 50+ tool name references across skills
- Fix NHANES search (dynamic CDC catalog query, not hardcoded keywords)
- Fix tool return envelopes (Unpaywall, MyGene, HPA, EuropePMC)
- Fix STRING, OpenTargets, ENCODE, Foldseek, STITCH, BridgeDb
- Fix BindingDB test for broken API detection

Router:
- Add MC elimination strategy, batch processing protocol
- Add 20+ bundled computation scripts
- Route to all 114 skills

Version bumped to 1.1.11
@gasvn gasvn force-pushed the fix/round-155-gaps branch from 7e744e5 to c21b6a4 Compare March 29, 2026 22:34
@gasvn gasvn merged commit 2bf5198 into main Mar 29, 2026
1 check passed
d33disc added a commit to d33disc/upstream-tooluniverse that referenced this pull request Apr 8, 2026
@d33disc @claude
feat: integrate upstream PR mims-harvard#153 (reasoning frameworks + …
7e1d6ab 
…31 new tools)

Merges mims-harvard#153 (2bf5198) and version bump to
1.1.11 (4d66869) from upstream. Resolves 11 conflicts while preserving
every fork-specific customization.

Upstream additions:
- 31 new tools: RGD, T3DB, IEDB MHC binding, 11 scientific calculators
  (DNA translate, molecular formula, equilibrium solver, stats, etc),
  AgingCohort_search, NHANES parser, DataQuality_assess, MetaAnalysis,
  4 dataset discovery tools (re3data, Data.gov, OpenAIRE, DataCite)
- Skills rewrite: 114 skills as reasoning guides, 12 new domain skills,
  new data-wrangling/dataset-discovery/epidemiology/vaccine-design
- Router: MC elimination, batch processing, 20+ computation scripts
- server.json bumped to 1.1.11

Fork customizations preserved:
- semantic_scholar_tool.py DVS-FORK-PATCH block intact (1.05s rate
  limit for personal-tier S2 API keys + SEMANTIC_SCHOLAR_MIN_INTERVAL
  override). Upstream-added tldr/fieldsOfStudy fields integrated
  around the patch block, not through it.
- test_semantic_scholar_tool_resilience.py: upstream's envelope-format
  assertions merged with fork's 4 DVS-FORK-PATCH rate-limit tests.
  Net: the fork's previously-broken list-vs-dict tests now pass.
- agentic_tool.py API_KEY_ENV_VARS untouched (still CLAUDE_CLI +
  OLLAMA only - upstream did not modify this file).
- restful_tool.py MonarchTool: kept fork's _CLOSURE_KEYS stripping
  (renamed _clean -> _strip_closure for clarity), integrated with
  upstream's remove_none_and_empty_values + envelope wrapping.
  Both behaviors compose cleanly.
- SEC EDGAR tools (data JSON + 2 stubs + default_config entry)
  preserved alongside upstream's new iedb_prediction / popgen /
  epidemiology / scientific_calculator registry entries.
- skills/tooluniverse symlink to upstream_skills restored (fork PR #20
  made upstream_skills the source of truth; upstream's inline SKILL.md
  rejected).

Data JSON conflicts (8 files):
- admetai_tools: accepted upstream's oneOf smiles parameter schema
  (accepts string OR array), kept fork's richer test_examples.
- datacite_tools: adopted upstream's DataCiteRESTTool type fix and
  appended upstream's 2 new tools (DataCite_search_datasets,
  DataCite_get_dataset). Kept fork's unwrapped return_schemas from
  PR #17 for the 2 existing tools since cli.py validates against
  result.get("data"), not the envelope.
- ena_portal, rcsb_advanced_search, wikipathways: kept fork's
  simplified return_schemas, added upstream's new aliases/label
  fields.
- iedb_tools: scripted merge preserving fork's antigen_uniprot
  parameter + shorthand filter alongside upstream's IEDB_search_epitopes
  alias.
- mgi_tools: kept fork's array return_schema (primary_key/name_key
  names match the Alliance API response shape).
- unpaywall_tools: kept fork's test_examples for check_oa_status,
  appended upstream's new Unpaywall_get_full_text_url tool verbatim.

Regenerated derived files:
- src/tooluniverse/tools/*.py (2291 stubs via scripts/build_tools.py)
- src/tooluniverse/_lazy_registry_static.py (584 tool classes,
  +22 from upstream's new tools)
- src/tooluniverse/data/skills_catalog.json (126 skill entries)
- Ran ruff format on src/tooluniverse/ to reformat regenerated stubs

Validation:
- ruff check .                                          -> clean
- ruff format --check src/tooluniverse/                 -> clean
- pytest tests/unit/ tests/integration/ (877 tests)     -> 0 failures
- Sanity: DVS-FORK-PATCH sentinels present, API_KEY_ENV_VARS ==
  {CLAUDE_CLI, OLLAMA}, SEC EDGAR tools present, rate-limit patch
  slept 1.046s under 1.0s threshold.

The pre-existing environmental failure test_compose_tool::test_external
_file_tools (nested Claude CLI unavailable) and 3 test_mcp_protocol
tests (require .venv/bin on PATH) both fail identically on origin/main
and are unrelated to this merge.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
@d33disc d33disc mentioned this pull request Apr 8, 2026
Merged
4 tasks
d33disc added a commit to d33disc/upstream-tooluniverse that referenced this pull request Apr 8, 2026
@d33disc @claude
feat: integrate upstream PR mims-harvard#153 (reasoning frameworks + …
26bb9d1 
…31 new tools) (#28)

Merges mims-harvard#153 (2bf5198) and version bump to
1.1.11 (4d66869) from upstream. Resolves 11 conflicts while preserving
every fork-specific customization.

Upstream additions:
- 31 new tools: RGD, T3DB, IEDB MHC binding, 11 scientific calculators
  (DNA translate, molecular formula, equilibrium solver, stats, etc),
  AgingCohort_search, NHANES parser, DataQuality_assess, MetaAnalysis,
  4 dataset discovery tools (re3data, Data.gov, OpenAIRE, DataCite)
- Skills rewrite: 114 skills as reasoning guides, 12 new domain skills,
  new data-wrangling/dataset-discovery/epidemiology/vaccine-design
- Router: MC elimination, batch processing, 20+ computation scripts
- server.json bumped to 1.1.11

Fork customizations preserved:
- semantic_scholar_tool.py DVS-FORK-PATCH block intact (1.05s rate
  limit for personal-tier S2 API keys + SEMANTIC_SCHOLAR_MIN_INTERVAL
  override). Upstream-added tldr/fieldsOfStudy fields integrated
  around the patch block, not through it.
- test_semantic_scholar_tool_resilience.py: upstream's envelope-format
  assertions merged with fork's 4 DVS-FORK-PATCH rate-limit tests.
  Net: the fork's previously-broken list-vs-dict tests now pass.
- agentic_tool.py API_KEY_ENV_VARS untouched (still CLAUDE_CLI +
  OLLAMA only - upstream did not modify this file).
- restful_tool.py MonarchTool: kept fork's _CLOSURE_KEYS stripping
  (renamed _clean -> _strip_closure for clarity), integrated with
  upstream's remove_none_and_empty_values + envelope wrapping.
  Both behaviors compose cleanly.
- SEC EDGAR tools (data JSON + 2 stubs + default_config entry)
  preserved alongside upstream's new iedb_prediction / popgen /
  epidemiology / scientific_calculator registry entries.
- skills/tooluniverse symlink to upstream_skills restored (fork PR #20
  made upstream_skills the source of truth; upstream's inline SKILL.md
  rejected).

Data JSON conflicts (8 files):
- admetai_tools: accepted upstream's oneOf smiles parameter schema
  (accepts string OR array), kept fork's richer test_examples.
- datacite_tools: adopted upstream's DataCiteRESTTool type fix and
  appended upstream's 2 new tools (DataCite_search_datasets,
  DataCite_get_dataset). Kept fork's unwrapped return_schemas from
  PR #17 for the 2 existing tools since cli.py validates against
  result.get("data"), not the envelope.
- ena_portal, rcsb_advanced_search, wikipathways: kept fork's
  simplified return_schemas, added upstream's new aliases/label
  fields.
- iedb_tools: scripted merge preserving fork's antigen_uniprot
  parameter + shorthand filter alongside upstream's IEDB_search_epitopes
  alias.
- mgi_tools: kept fork's array return_schema (primary_key/name_key
  names match the Alliance API response shape).
- unpaywall_tools: kept fork's test_examples for check_oa_status,
  appended upstream's new Unpaywall_get_full_text_url tool verbatim.

Regenerated derived files:
- src/tooluniverse/tools/*.py (2291 stubs via scripts/build_tools.py)
- src/tooluniverse/_lazy_registry_static.py (584 tool classes,
  +22 from upstream's new tools)
- src/tooluniverse/data/skills_catalog.json (126 skill entries)
- Ran ruff format on src/tooluniverse/ to reformat regenerated stubs

Validation:
- ruff check .                                          -> clean
- ruff format --check src/tooluniverse/                 -> clean
- pytest tests/unit/ tests/integration/ (877 tests)     -> 0 failures
- Sanity: DVS-FORK-PATCH sentinels present, API_KEY_ENV_VARS ==
  {CLAUDE_CLI, OLLAMA}, SEC EDGAR tools present, rate-limit patch
  slept 1.046s under 1.0s threshold.

The pre-existing environmental failure test_compose_tool::test_external
_file_tools (nested Claude CLI unavailable) and 3 test_mcp_protocol
tests (require .venv/bin on PATH) both fail identically on origin/main
and are unrelated to this merge.

Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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@gasvn