Feature/iterative deep research workflows

.env.example

@@ -7,9 +7,9 @@ LLM_PROVIDER=openai
 OPENAI_API_KEY=sk-your-key-here
 ANTHROPIC_API_KEY=sk-ant-your-key-here
 
-# Model names (optional - sensible defaults)
-ANTHROPIC_MODEL=claude-3-5-sonnet-20240620
-OPENAI_MODEL=gpt-4-turbo
+# Model names (optional - sensible defaults set in config.py)
+# ANTHROPIC_MODEL=claude-sonnet-4-5-20250929
+# OPENAI_MODEL=gpt-5.1
 
 # ============== EMBEDDINGS ==============
 

.github/README.md

@@ -0,0 +1,203 @@
+---
+title: DeepCritical
+emoji: 🧬
+colorFrom: blue
+colorTo: purple
+sdk: gradio
+sdk_version: "6.0.1"
+python_version: "3.11"
+app_file: src/app.py
+pinned: false
+license: mit
+tags:
+  - mcp-in-action-track-enterprise
+  - mcp-hackathon
+  - drug-repurposing
+  - biomedical-ai
+  - pydantic-ai
+  - llamaindex
+  - modal
+---
+
+# DeepCritical
+
+## Intro
+
+## Features
+
+- **Multi-Source Search**: PubMed, ClinicalTrials.gov, bioRxiv/medRxiv
+- **MCP Integration**: Use our tools from Claude Desktop or any MCP client
+- **Modal Sandbox**: Secure execution of AI-generated statistical code
+- **LlamaIndex RAG**: Semantic search and evidence synthesis
+- **HuggingfaceInference**: 
+- **HuggingfaceMCP Custom Config To Use Community Tools**:
+- **Strongly Typed Composable Graphs**:
+- **Specialized Research Teams of Agents**: 
+
+## Quick Start
+
+### 1. Environment Setup
+
+```bash
+# Install uv if you haven't already
+pip install uv
+
+# Sync dependencies
+uv sync
+```
+
+### 2. Run the UI
+
+```bash
+# Start the Gradio app
+uv run gradio run src/app.py
+```
+
+Open your browser to `http://localhost:7860`.
+
+### 3. Connect via MCP
+
+This application exposes a Model Context Protocol (MCP) server, allowing you to use its search tools directly from Claude Desktop or other MCP clients.
+
+**MCP Server URL**: `http://localhost:7860/gradio_api/mcp/`
+
+**Claude Desktop Configuration**:
+Add this to your `claude_desktop_config.json`:
+```json
+{
+  "mcpServers": {
+    "deepcritical": {
+      "url": "http://localhost:7860/gradio_api/mcp/"
+    }
+  }
+}
+```
+
+**Available Tools**:
+- `search_pubmed`: Search peer-reviewed biomedical literature.
+- `search_clinical_trials`: Search ClinicalTrials.gov.
+- `search_biorxiv`: Search bioRxiv/medRxiv preprints.
+- `search_all`: Search all sources simultaneously.
+- `analyze_hypothesis`: Secure statistical analysis using Modal sandboxes.
+
+
+## Deep Research Flows 
+
+- iterativeResearch
+- deepResearch
+- researchTeam
+
+### Iterative Research
+
+sequenceDiagram
+    participant IterativeFlow
+    participant ThinkingAgent
+    participant KnowledgeGapAgent
+    participant ToolSelector
+    participant ToolExecutor
+    participant JudgeHandler
+    participant WriterAgent
+
+    IterativeFlow->>IterativeFlow: run(query)
+
+    loop Until complete or max_iterations
+        IterativeFlow->>ThinkingAgent: generate_observations()
+        ThinkingAgent-->>IterativeFlow: observations
+
+        IterativeFlow->>KnowledgeGapAgent: evaluate_gaps()
+        KnowledgeGapAgent-->>IterativeFlow: KnowledgeGapOutput
+
+        alt Research complete
+            IterativeFlow->>WriterAgent: create_final_report()
+            WriterAgent-->>IterativeFlow: final_report
+        else Gaps remain
+            IterativeFlow->>ToolSelector: select_agents(gap)
+            ToolSelector-->>IterativeFlow: AgentSelectionPlan
+
+            IterativeFlow->>ToolExecutor: execute_tool_tasks()
+            ToolExecutor-->>IterativeFlow: ToolAgentOutput[]
+
+            IterativeFlow->>JudgeHandler: assess_evidence()
+            JudgeHandler-->>IterativeFlow: should_continue
+        end
+    end
+
+
+### Deep Research
+
+sequenceDiagram
+    actor User
+    participant GraphOrchestrator
+    participant InputParser
+    participant GraphBuilder
+    participant GraphExecutor
+    participant Agent
+    participant BudgetTracker
+    participant WorkflowState
+
+    User->>GraphOrchestrator: run(query)
+    GraphOrchestrator->>InputParser: detect_research_mode(query)
+    InputParser-->>GraphOrchestrator: mode (iterative/deep)
+    GraphOrchestrator->>GraphBuilder: build_graph(mode)
+    GraphBuilder-->>GraphOrchestrator: ResearchGraph
+    GraphOrchestrator->>WorkflowState: init_workflow_state()
+    GraphOrchestrator->>BudgetTracker: create_budget()
+    GraphOrchestrator->>GraphExecutor: _execute_graph(graph)
+
+    loop For each node in graph
+        GraphExecutor->>Agent: execute_node(agent_node)
+        Agent->>Agent: process_input
+        Agent-->>GraphExecutor: result
+        GraphExecutor->>WorkflowState: update_state(result)
+        GraphExecutor->>BudgetTracker: add_tokens(used)
+        GraphExecutor->>BudgetTracker: check_budget()
+        alt Budget exceeded
+            GraphExecutor->>GraphOrchestrator: emit(error_event)
+        else Continue
+            GraphExecutor->>GraphOrchestrator: emit(progress_event)
+        end
+    end
+
+    GraphOrchestrator->>User: AsyncGenerator[AgentEvent]
+
+### Research Team
+Critical Deep Research Agent
+
+## Development
+
+### Run Tests
+
+```bash
+uv run pytest
+```
+
+### Run Checks
+
+```bash
+make check
+```
+
+## Architecture
+
+DeepCritical uses a Vertical Slice Architecture:
+
+1.  **Search Slice**: Retrieving evidence from PubMed, ClinicalTrials.gov, and bioRxiv.
+2.  **Judge Slice**: Evaluating evidence quality using LLMs.
+3.  **Orchestrator Slice**: Managing the research loop and UI.
+
+Built with:
+- **PydanticAI**: For robust agent interactions.
+- **Gradio**: For the streaming user interface.
+- **PubMed, ClinicalTrials.gov, bioRxiv**: For biomedical data.
+- **MCP**: For universal tool access.
+- **Modal**: For secure code execution.
+
+## Team
+
+- The-Obstacle-Is-The-Way
+- MarioAderman
+- Josephrp
+
+## Links
+
+- [GitHub Repository](https://github.com/The-Obstacle-Is-The-Way/DeepCritical-1)

.github/workflows/ci.yml

@@ -2,33 +2,66 @@ name: CI
 
 on:
   push:
-    branches: [main, dev]
+    branches: [main, develop]
   pull_request:
-    branches: [main, dev]
+    branches: [main, develop]
 
 jobs:
-  check:
+  test:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11"]
 
     steps:
       - uses: actions/checkout@v4
 
-      - name: Install uv
-        uses: astral-sh/setup-uv@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
         with:
-          version: "latest"
-
-      - name: Set up Python 3.11
-        run: uv python install 3.11
+          python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
-        run: uv sync --all-extras
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev]"
 
       - name: Lint with ruff
-        run: uv run ruff check src tests
+        run: |
+          ruff check . --exclude tests
+          ruff format --check . --exclude tests
 
       - name: Type check with mypy
-        run: uv run mypy src
+        run: |
+          mypy src
+
+      - name: Install embedding dependencies
+        run: |
+          pip install -e ".[embeddings]"
+
+      - name: Run unit tests (excluding OpenAI and embedding providers)
+        env:
+          HF_TOKEN: ${{ secrets.HF_TOKEN }}
+        run: |
+          pytest tests/unit/ -v -m "not openai and not embedding_provider" --tb=short -p no:logfire
+
+      - name: Run local embeddings tests
+        env:
+          HF_TOKEN: ${{ secrets.HF_TOKEN }}
+        run: |
+          pytest tests/ -v -m "local_embeddings" --tb=short -p no:logfire || true
+        continue-on-error: true  # Allow failures if dependencies not available
+
+      - name: Run HuggingFace integration tests
+        env:
+          HF_TOKEN: ${{ secrets.HF_TOKEN }}
+        run: |
+          pytest tests/integration/ -v -m "huggingface and not embedding_provider" --tb=short -p no:logfire || true
+        continue-on-error: true  # Allow failures if HF_TOKEN not set
 
-      - name: Run tests
-        run: uv run pytest tests/unit/ -v
+      - name: Run non-OpenAI integration tests (excluding embedding providers)
+        env:
+          HF_TOKEN: ${{ secrets.HF_TOKEN }}
+        run: |
+          pytest tests/integration/ -v -m "integration and not openai and not embedding_provider" --tb=short -p no:logfire || true
+        continue-on-error: true  # Allow failures if dependencies not available

.gitignore

@@ -1,3 +1,6 @@
+folder/
+.cursor/
+.ruff_cache/
 # Python
 __pycache__/
 *.py[cod]

.pre-commit-config.yaml

@@ -3,19 +3,62 @@ repos:
     rev: v0.4.4
     hooks:
       - id: ruff
-        args: [--fix]
+        args: [--fix, --exclude, tests]
         exclude: ^reference_repos/
       - id: ruff-format
+        args: [--exclude, tests]
         exclude: ^reference_repos/
 
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.10.0
     hooks:
       - id: mypy
         files: ^src/
+        exclude: ^folder
         additional_dependencies:
           - pydantic>=2.7
           - pydantic-settings>=2.2
           - tenacity>=8.2
           - pydantic-ai>=0.0.16
         args: [--ignore-missing-imports]
+
+  - repo: local
+    hooks:
+      - id: pytest-unit
+        name: pytest unit tests (no OpenAI)
+        entry: uv
+        language: system
+        types: [python]
+        args: [
+          "run",
+          "pytest",
+          "tests/unit/",
+          "-v",
+          "-m",
+          "not openai and not embedding_provider",
+          "--tb=short",
+          "-p",
+          "no:logfire",
+        ]
+        pass_filenames: false
+        always_run: true
+        require_serial: false
+      - id: pytest-local-embeddings
+        name: pytest local embeddings tests
+        entry: uv
+        language: system
+        types: [python]
+        args: [
+          "run",
+          "pytest",
+          "tests/",
+          "-v",
+          "-m",
+          "local_embeddings",
+          "--tb=short",
+          "-p",
+          "no:logfire",
+        ]
+        pass_filenames: false
+        always_run: true
+        require_serial: false

.pre-commit-hooks/run_pytest.ps1

@@ -0,0 +1,14 @@
+# PowerShell pytest runner for pre-commit (Windows)
+# Uses uv if available, otherwise falls back to pytest
+
+if (Get-Command uv -ErrorAction SilentlyContinue) {
+    uv run pytest $args
+} else {
+    Write-Warning "uv not found, using system pytest (may have missing dependencies)"
+    pytest $args
+}
+
+
+
+
+