Upgrade Gradio to fix Pydantic 2 conflict

.pytest_cache/.gitignore

@@ -0,0 +1,2 @@
+# Created by pytest automatically.
+*

.pytest_cache/CACHEDIR.TAG

@@ -0,0 +1,4 @@
+Signature: 8a477f597d28d172789f06886806bc55
+# This file is a cache directory tag created by pytest.
+# For information about cache directory tags, see:
+#	https://bford.info/cachedir/spec.html

.pytest_cache/README.md

@@ -0,0 +1,8 @@
+# pytest cache directory #
+
+This directory contains data from the pytest's cache plugin,
+which provides the `--lf` and `--ff` options, as well as the `cache` fixture.
+
+**Do not** commit this to version control.
+
+See [the docs](https://docs.pytest.org/en/stable/how-to/cache.html) for more information.

.pytest_cache/v/cache/lastfailed

@@ -0,0 +1 @@
+{}

.pytest_cache/v/cache/nodeids

@@ -0,0 +1,13 @@
+[
+  "tests/test_patient_sim.py::test_cardiac_population",
+  "tests/test_patient_sim.py::test_cohort_stress_test_warfarin",
+  "tests/test_patient_sim.py::test_generate_cohort_basic",
+  "tests/test_patient_sim.py::test_patient_structure",
+  "tests/test_protocol_rag.py::test_age_violation",
+  "tests/test_protocol_rag.py::test_amendment_structure",
+  "tests/test_protocol_rag.py::test_check_patient_against_criteria",
+  "tests/test_protocol_rag.py::test_check_patient_logic",
+  "tests/test_protocol_rag.py::test_extract_criteria_mock",
+  "tests/test_protocol_rag.py::test_patient_passes_criteria",
+  "tests/test_protocol_rag.py::test_patient_passes_criteria_logic"
+]

README_HF.md

@@ -10,31 +10,4 @@ pinned: false
 license: mit
 ---
 
-# TrialAURA 🔬
-
-**Autonomous Trial Safety & Feasibility Agent for Clinical Trials**
-
-Built for the MCP 1st Birthday Hackathon, TrialAURA uses three Model Context Protocol (MCP) servers to provide comprehensive clinical trial safety analysis:
-
-## Features
-
-- 📄 **Protocol Parsing** (LlamaIndex + Gemini): Extract eligibility criteria from trial protocols
-- 👥 **Synthetic Cohorts** (Faker): Generate realistic patient populations for stress-testing
-- ⚠️ **Safety Analysis**: Detect eligibility violations and safety risks
-- 📝 **Amendment Drafting** (Gemini): Produce regulatory-style protocol amendments
-- 🔄 **Recurring Scans** (Blaxel): Schedule automated safety monitoring
-
-## Architecture
-
-Three MCP servers working together:
-1. **Protocol RAG MCP** - Document parsing and criteria extraction
-2. **Patient Sim MCP** - Synthetic cohort generation
-3. **Safety Ops MCP** - Workflow orchestration and monitoring
-
-## Safety Notice
-
-⚠️ All patients are **synthetic** and used purely for safety simulation. This agent operates in a simulation context only and never provides medical advice to real patients.
-
----
-
-**Built with**: Gemini API · LlamaIndex · Gradio · MCP
+Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference

app.py

@@ -12,4 +12,4 @@ sys.path.append(str(Path(__file__).parent / "backend"))
 from backend.gradio_app import app
 
 if __name__ == "__main__":
-    app.queue().launch(server_name="0.0.0.0", server_port=7860)
+    app.launch(server_name="0.0.0.0", server_port=7860)

backend/gradio_app.py

@@ -279,8 +279,7 @@ with app:
             gr.Markdown("### Artifacts")
             
             artifact_viewer = gr.JSON(
-                label="Current Artifact",
-                value={}
+                label="Current Artifact"
             )
     
     # Event handler

requirements.txt

@@ -1,21 +1,21 @@
 # Core - HF Spaces compatible
-gradio==4.44.0
-huggingface-hub==0.24.0
-
-# MCP and pydantic - compatible versions
-mcp>=0.9.0
+gradio>=5.0.0
+huggingface-hub>=0.25.0
 pydantic>=2.0.0,<3.0.0
+mcp>=0.9.0
+python-dotenv>=1.0.0
 
-# Google Gemini
+# Protocol RAG - LlamaIndex with Google GenAI
+llama-index-core>=0.13.0
+llama-index-llms-google-genai
+llama-index-embeddings-google-genai
 google-generativeai>=0.3.0
+pypdf2>=3.0.0
 
-# Patient simulation  
+# Patient simulation
 faker>=20.0.0
-pandas>=2.0.0
+pandas>=2.0.0,<3.0.0
 numpy>=1.24.0,<2.0.0
 
-# PDF parsing
-pypdf2>=3.0.0
-
-# Utils
-python-dotenv>=1.0.0
+# Optional
+modal>=0.63.0