v1.7.1

MINOR release. Three new bundled domain packs (theory_math, wet_lab,
engineering) ship using the v1.7.0 plugin infrastructure unchanged.
5 domain packs total now bundled with the core wheel. No breaking
changes; the plugin API, namespace conventions, and stress-runner
contract from v1.7.0 are stable.

Added — theory_math pack (bundled)

• src/research_os_theory_math/ — 8 protocols + 3 tools + domain detector + 8 router entries.
• Protocols: proof/proof_verification_workflow, proof/lemma_library, proof/theorem_dependency_graph, conjecture/conjecture_tracking, formal/lean_integration, formal/coq_integration, output/theory_paper_structure, method/proof_strategy_selection.
• Tools: tool_theory_math_lean_check (runs lean --make + parses errors), tool_theory_math_coq_check (runs coqc + parses errors), tool_theory_math_dep_graph (parses .lean / .v imports + theorems → Mermaid + JSON DAG).
• Domain detector: .lean / .v / .agda / .thy files, LaTeX \begin{proof} / \begin{theorem} envs, Mathlib references, theory terminology.
• Naming note: tools are tool_theory_math_* (matches the tool_<pack>_ namespace rule; the brief's shorthand tool_theory_* would have collided with future packs starting theory_*).

Added — wet_lab pack (bundled)

• src/research_os_wet_lab/ — 8 protocols + 3 tools + domain detector + 8 router entries.
• Protocols: protocol/sop_versioning, protocol/reagent_lot_tracking, protocol/plate_map_provenance, protocol/instrument_run_log, protocol/sample_lineage, method/wet_lab_experiment_design, audit/wet_lab_reproducibility_audit, output/methods_section_wet_lab.
• Tools: tool_wet_lab_plate_map_render (96/384-well layout → PNG + SVG + ASCII fallback), tool_wet_lab_reagent_query (per-supplier portal link + reagent YAML stub; no live API calls), tool_wet_lab_sample_lineage_export (parent → splits → readouts as Mermaid + JSON).
• Domain detector: instrument output files (.fcs / .qpcr / .czi / .raw / .tiff), catalog-number patterns, FACS / qPCR / ELISA / Western terminology, inputs/protocols/ subdirectory.

Added — engineering pack (bundled)

• src/research_os_engineering/ — 7 protocols + 3 tools + domain detector + 7 router entries.
• Protocols: design/design_iteration, design/requirements_traceability, safety/fmea_protocol, safety/fault_tree_analysis, test/test_failure_causation, test/build_test_fix_loop, output/engineering_report_structure.
• Tools: tool_engineering_fmea_render (Failure Mode and Effects Analysis table → CSV + Markdown + optional Excel; auto-computes RPN; flags RPN ≥ 100), tool_engineering_fault_tree_render (AND / OR gates + basic events → Mermaid), tool_engineering_requirements_matrix (bidirectional SRS ↔ SDD ↔ test cases ↔ results → Markdown + optional Excel; flags orphan requirements + orphan tests).
• Domain detector: CAD files (.stp / .iges / .sldprt / .dwg / .dxf), simulation outputs (.odb / .raw), control-system code (.plc / .st), SRS / SDD / REQ / FR / TC IDs, V&V terminology.

Added — stress-matrix fixtures

• 3 new reference projects under tests/fixtures/projects/: theory_math_short_proof (2-page theorem + lemma library + dependency graph), wet_lab_qpcr_run (single qPCR experiment with plate map + reagent tracking + instrument run log), engineering_fmea_simple (5-item FMEA + 3 requirements traced to test cases).
• CI stress matrix updated: 5 → 8 reference projects, each running against the mock model on every PR.
• docs/RELIABILITY.md auto-regenerates with the 3 new fixtures added to the per-project + per-protocol tables.

Added — extras

• pip install research-os[theory_math], [wet_lab], [engineering] reserved as no-op extras (packs ship bundled).
• pip install research-os[all_packs] convenience meta-extra → installs every domain pack.

Added — tests

• 50 new tests under tests/unit/test_v171_three_packs.py: all 5 packs register, 23 new pack protocols load, 9 new pack tools register + dispatch, 3 domain detectors trigger on their signature inputs, 3 reference projects parse + stress-run at 100% success against mock model, preflight checks pass with 5 packs.

Bumped

• version 1.7.0 → 1.7.1 in pyproject.toml, src/research_os/__init__.py, CITATION.cff.
• All 114 core protocol YAMLs bumped 1.7.0 → 1.7.1.
• All 36 bundled-pack protocol YAMLs ship at 1.7.1 (humanities + qualitative pack protocols bumped along with the new theory_math + wet_lab + engineering protocols).
• _router_index.yaml version 12 → 13.
• Embeddings rebuilt (now 150 protocol docs + 189 tool docs).

Counts

• Bundled packs: 2 → 5 (humanities, qualitative, theory_math, wet_lab, engineering).
• Tools surface: 180 → 189 (+9 new pack tools).
• Protocols: 127 → 150 (+8 theory_math, +8 wet_lab, +7 engineering).
• Stress matrix: 5 → 8 reference projects × 1 model = 8 stress jobs per PR.
• Preflight: 19/19 green.
• Pytest: 635 → 685 passes.

Compatibility

No breaking changes. Every v1.6.x and v1.7.0 tool name, protocol name, alias, redirect stub, plugin API surface, and stress-runner contract continues to work. The 5 bundled packs use the v1.7.0 plugin infrastructure unchanged.

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