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by Tonic - opened Nov 29, 2025

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initial commit5affb13e

adds scaffolding6fbbcdac

adds scaffolding1465eefe

add initial documentation for DeepCritical project, including architecture overview, design patterns, and user guidesf2b4e490

refine design patterns documentation by adjusting formatting for improved clarity and consistency0c3cb270

refine formatting in design patterns documentation for better readabilitya496d9d2

docs: add alternative frameworks analysis and stretch goalsc7584c17

docs: update guides and add testing strategy documentationb4aa4adf

docs: add reference repos, orchestration patterns, and 100% ironclad specs18838b91

docs: add implementation specifications for phases 1 to 47c07ade4

docs: expand Phase 3 Judge implementation specificationse35d6b16

docs: enhance implementation documentation for Phase 4 Orchestrator and UI20ba79bd

docs: reorganize and update implementation documentation for phases 1 and 2dde5c6f7

docs: finalize implementation documentation for Phase 4 Orchestrator and UI62d32abd

docs: update implementation documentation for Phases 2, 3, and 47ecca955

docs: enhance implementation documentation for Phase 2 search tools19808474

docs: expand Phase 3 Judge implementation with new models and promptsb1310d37

docs: enhance Phase 4 documentation with detailed implementation and deployment instructionsd0b14c08

docs: enhance Phase 4 UI and Orchestrator documentation5c8b0309

docs: update implementation documentation for Phases 1-477627ff7

docs: finalize Phase 4 implementation with Orchestrator and Gradio UI33b0f43c

docs: update Phase 1 documentation with new directory structure and configuration detailsd33aedd1

fix: add bash language identifier to code block (CodeRabbit)481bdd70

fix: markdown lint warnings in roadmap.md953b850e

feat(phase1): Foundation & Tooling complete069f0a0a

feat(phase1): add Makefile for developer experience32fcf601

feat(phase2): implement search slice (PubMed, Web, Orchestrator) (#4)499170be

fix: resolve mypy divergence between make check and pre-commitcace02fa

feat(phase2): add sample_evidence fixture to conftest.py2457ae0f

ci: add GitHub Actions workflow for CI/CD572b5691

fix(phase2): address CodeRabbit review feedback + add examples32e3b61a

feat(phase3): implement judge slice (LLM Judge, Prompts, Models)d7e5abb8

fix(tests): resolve mypy divergence and test failures95d2e294

fix: add type ignore comment for Agent instantiation in JudgeHandler9760706d

feat(phase4): Orchestrator and UI complete25c3a8b6

refactor(phase4): address CodeRabbit review36983aef

Merge pull request #7 from The-Obstacle-Is-The-Way/feat/phase435ebd091

fix: pydantic-ai v1 compatibility and Anthropic model update47326678

fix: pass API keys explicitly to pydantic-ai providers1f967353

fix: linting and types for phase 51922dbde

chore: vendor agent-framework for deployment (fix pre-commit)7057335f

fix(phase5): align configs and add agent tests15459e9e

fix(ci): skip agent tests when agent-framework not installed5a821714

fix(ci): add E402/RUF100 to ignore for cross-env compatibilityecbc47b1

feat(phase6): implement embeddings for semantic search and deduplication53bf3951

feat(phase8): implement Report Agent for structured scientific report generation27636723

feat(architecture): update system design and roadmap for Phases 1-82dc022a1

docs: comprehensive Phase 6-8 spec revisions (Senior Architect audit)ec3d7dc0

Merge main: Phase 5 + Phase 6-8 doc revisions24a58782

feat(phase6): Embeddings & Semantic Search implementation3bacbf80

fix(phase6): critical fixes from senior audit59afc842

fix: address CodeRabbit Phase 5 review feedbackd247864f

fix: address CodeRabbit Phase 6 review feedback506a9c04

Merge pull request #10 from The-Obstacle-Is-The-Way/feat/phase6-embeddingsb25ffdba

feat(phase7): implement Hypothesis Agent for mechanistic reasoningc690006b

fix: address CodeRabbit Phase 7 review feedbackbc745311

fix: address CodeRabbit Phase 7 nitpicksa6398e46

fix: mock get_model in tests to avoid API key requirement in CIebc6429d

Merge pull request #11 from The-Obstacle-Is-The-Way/feat/phase7-hypothesis-agente993253c

fix: apply lazy init pattern and pydantic-ai fixes to ReportAgent (#12)3139749e

fix: address all CodeRabbit Phase 8 review feedbackf1e4e5b6

feat(examples): add Phase 6-8 demos for full stack demonstration0efdc2f0

refactor(examples): purge all mocks - real API calls onlycfb473dc

refactor(examples): apply CodeRabbit feedback (validations, complexity, formatting)cd11dad9

fix(report): add explicit JSON structure guidance in promptd01e70da

Merge pull request #13 from The-Obstacle-Is-The-Way/dev388cd058

feat(docs): update implementation roadmap and add specs for Phases 9-113fcd8e76

feat: Complete Phase 9 Source Cleanup (Remove WebTool) (#14)cd004e16

feat: Implement Phase 10 (ClinicalTrials.gov) with requests4e2ccbfe

chore: Update httpx dependency and remove unused extras in pyproject.toml and uv.lock1efef063

refactor: address CodeRabbit nitpicks for Phase 101bc9785b

Merge pull request #15 from The-Obstacle-Is-The-Way/feat/phase10-clinicaltrials17bd211d

feat: Integrate Mario's Modal code execution + LlamaIndex RAG3aa91e9f

fix(rag): apply lazy imports and use centralized config055a3a71

fix(rag): use get_content() for BaseNode compatibility3f90da87

refactor: address CodeRabbit review feedback for Mario integrationcbd94a4a

fix(rag): address remaining CodeRabbit feedback2f0030be

refactor: address final CodeRabbit feedbackb50fffd8

refactor: centralize embedding configuration in Settings20c7bada

Merge pull request #16 from The-Obstacle-Is-The-Way/feat/mario-integration31809fa7

feat: Phase 11 bioRxiv Preprint Integration (#19)e67c99ff

docs: update demos to use all 3 search sources8625dedb

docs: add comprehensive hackathon documentation and integration plans7b20f5d0

docs: add Phase 12 MCP Server Integration specificationdd587c93

docs: add Phase 14 Demo Video & Hackathon Submission specificatione16b9e68

docs: enhance Phase 13 Modal integration documentation0d84878d

chore: update Gradio dependency to include MCP extras and version bumpf5b2917f

feat: add MCP tool wrappers for biomedical search toolsc1146505

feat: enhance Gradio UI with MCP server support and new tool interfaces10e234ce

docs: update MCP server integration documentation and statuscde8f480

docs: address CodeRabbit feedback for Phase 12 PRf9cb2b7b

Merge pull request #20 from The-Obstacle-Is-The-Way/feat/phase12-mcp-server5264b253

feat: implement phase 13 modal pipeline integration7cc8b69f

fix: wire analyze_hypothesis MCP tool into Gradio app521d97d3

docs: add AI agent context files for team collaborationacdce611

docs: add AI agent context files for team collaboration5e7604a3

fix: address CodeRabbit review feedback for Phase 13f32a2ca9

refactor: address CodeRabbit nitpick suggestions901acc3d

docs: sync AI agent context files and fix final nitpicks8bac7505

Merge branch 'main' into feat/phase13-modal-integration71665e50

Merge pull request #21 from The-Obstacle-Is-The-Way/feat/phase13-modal-integrationde588e7b

docs: update README for Phase 14 submission27616320

docs: add Josephrp to team contributors8f92b9fd

Merge pull request #22 from The-Obstacle-Is-The-Way/feat/phase14-demo-submission13be9d7d

fix: make ResearchReport.references optional with defaultf8826097

style: add pytest.mark.unit to test_models (CodeRabbit)6af82681

Merge pull request #24 from The-Obstacle-Is-The-Way/fix/research-report-references-default6dccda9f

chore: improve DevEx and clean up obsolete docs (#25)f632ba82

chore: include coverage in make check for better DevEx85d55c28

fix: update requirements.txt for HuggingFace Spaces buildee048f16

chore: update README to specify Python version as 3.11 (#26)5d9e8aab

fix: Gradio examples format for additional_inputsf66a8622

feat: add smoke tests and fix Gradio 6.x compatibility2bd94623

fix: remove duplicate typer dependency per CodeRabbit reviewb001fefd

fix: upgrade Gradio to 5.32.0+ for MCP server support1812a2ac

Merge pull request #28 from The-Obstacle-Is-The-Way/fix/gradio-upgrade-cleanup16742859

feat: add demo mode warnings and BYOK (Bring Your Own Key) support4d87419a

fix: use config settings for model names instead of hardcoded valuesf5747b16

chore: clean up env config and upgrade model defaults9e9bc6b1

fix: address CodeRabbit review feedback923641cd

Merge pull request #29 from The-Obstacle-Is-The-Way/claude/debug-gradio-mock-data-01MDfoUPcbfZ7FLootfhe8zsb455f8a7

Merge pull request #30 from The-Obstacle-Is-The-Way/chore/env-cleanup-model-upgrade6c9bd427

fix: upgrade Gradio SDK to 6.0.1 and add fill_height for HF Spaces UI fixf236de1d

Merge pull request #33 from The-Obstacle-Is-The-Way/fix/gradio-ui-scrolling2ab9ddaf

fix: move title/description into ChatInterface for proper HF Spaces layout998d05db

fix: correct UI layout ordering - title at tope4a11294

fix: require Gradio 6.0+ for css in launch() APIe760d70f

Merge pull request #34 from The-Obstacle-Is-The-Way/devfea6e648

fix: resolve Gradio UI cutoff by removing fill_height=True and restructuring layout87de5ef8

chore: update .env.example and config.py for LLM and agent settings9dd37c60

Merge pull request #35 from The-Obstacle-Is-The-Way/fix/gradio-ui-finald7ef283c

fix: remove header: mini from README to resolve desktop overlay issuesf9c67ed5

chore: trigger HF rebuild39b452a4

docs: add bug report for intermittent gradio loading issuesb9919fb6

fix: disable ssr_mode to resolve intermittent gradio hydration issues420d8ba0

fix: wire EmbeddingService to simple orchestrator + improve search quality2e4a7607

feat: implement HFInferenceJudgeHandler for free-tier AI analysis7fab6d4a

feat: add documentation for Magentic mode bug and implementation specfb7b8d78

feat: implement Magentic ChatAgent pattern with semantic state management645a0511

docs: add P0 blockers documentation for Magentic mode implementationc2f7da26

fix: address CodeRabbit feedback and P0 blockersf9852242

fix: pin agent-framework-core and remove resolved bug doc474538cc

chore: remove resolved bug documentationa941b786

feat: HFInferenceJudgeHandler - Free AI analysis for hackathon judges (#36)b1152292

Merge branch 'main' into dev80368172

fix: simplify Gradio UI to fit single viewport8dc3e50d

refactor: enhance Gradio UI for improved user experience291b9e61

fix: exclude reference_repos from mypy and cleanup0a480cb5

refactor(tools): replace BioRxiv with Europe PMC (Phase 01)2f8ae1fa

feat(search): implement PubMed query preprocessing (Phase 02)e502f0d9

feat(search): implement ClinicalTrials.gov filtering (Phase 03)d55440b7

fix(config): increase max iterations to 1072b2667f

refactor(tests): add type annotations and clean up test functions05ffeb4f

fix: update references to Europe PMC in examples and documentation9d21bf8d

fix: update remaining bioRxiv references to Europe PMC in examples1515e72e

docs: replace completed bug docs with new Magentic bug report8a980243

docs: add TDD fix plan for Magentic mode report generation17d34a8e

fix(magentic): defensive text extraction & cleanup biorxiv refs3bfd42c9

docs: update P1 bug report with actual Gradio accordion root causea46131e5

fix: address CodeRabbit feedback and CI failure2ff16a36

fix: mock all agent creation in _build_workflow test7323f55d

Merge pull request #38 from The-Obstacle-Is-The-Way/dev5b5d2ca1

fix: repair Gradio accordion bug and cleanup env varsfcc601a9

fix: address CodeRabbit feedbackbe7e1a20

feat: add roadmap summary and detailed improvement plans for data sources9286db51

feat: implement async-safe rate limiting (Phase 17) (#40)316dc7d0

Merge branch 'dev'b72f9f12

feat: implement dual-mode architecture (Simple + Advanced) (#45)b2929fc3

feat: add hierarchical orchestration with web search (integrates PR #44) (#46)20f762e4

fix: add limits package to requirements.txt for HuggingFace Spaces4fb11a99

fix: add missing packages to requirements.txt for HuggingFace Spaces4e438f3f

Merge pull request #1 from The-Obstacle-Is-The-Way/main898cd378

adds the initial iterative and deep research workflows731a241d

chore: update model names in .env.example and tests58ff8fb5

style: auto-format 4 files (ruff)a8057691

fix: skip Modal integration tests when package not installed4e785f88

Merge branch 'dev' into feature/iterative-deep-research-workflowse6c21427

adds the initial iterative and deep research workflows687a1f1f

Merge branch 'feature/iterative-deep-research-workflows' of https://github.com/Josephrp/DeepCritical-HFSpace into feature/iterative-deep-research-workflows66c7f79c

adds the initial iterative and deep research workflowsf78d2c11

Update tests/unit/agent_factory/test_graph_builder.py1241da62

Update tests/integration/test_research_flows.pyb9de79de

adds tests , integration tests , github readme , and more!96aa0624

Merge branch 'feature/iterative-deep-research-workflows' of https://github.com/Josephrp/DeepCritical-HFSpace into feature/iterative-deep-research-workflows8c8dc90a

trigger workflows310fb902

adds local embeddings and huggingface inference as defaults , adds tests , improves precommit and cicd46aca9

ruff format check solution6811b678

ruff format check solution3ab54ea9

Merge pull request #1 from Josephrp/feature/iterative-deep-research-workflows40aa8de0

Add architecture section to README67341ab2

demo launches53c4c465

demo starts , needs debugging on huggingface spacesc37620ba

demo starts , needs debugging on huggingface spacesca3a4f75

Initial demo testing (#4)ab33e9d8

Merge branch 'main' into devbea30160

adds or improves : interface , tests, docs , ci , precommit , build , and democe644a9a

Tonic

Data Quests for Open Science org Nov 29, 2025

No description provided.

ignores ci , hardens gradio select menus448c6790

Tonic changed pull request status to open Nov 29, 2025

Tonic changed pull request title from solves startup errors to force merge Nov 29, 2025

Tonic changed pull request status to closed Nov 29, 2025

fix interfacecb48bd4b

Merge branch 'dev' into feat/demo-improvements202f9180

fix interface05d4430a

Merge branch 'feat/demo-improvements' of https://github.com/DeepCritical/GradioDemo into feat/demo-improvementsa9547e78

Tonic changed pull request status to open Nov 29, 2025

Tonic changed pull request status to merged Nov 29, 2025

fix interface12522e5f

Tonic

Data Quests for Open Science org Nov 29, 2025

reopen

Tonic pinned discussion Nov 29, 2025

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