Version 0.1.0

Author: t-neumann

README.md

@@ -401,7 +401,7 @@ See **[Testing Guide](docs/TESTING.md)** for detailed information.
 
 ```bash
 # Build image
-docker build -t perpendicularity:0.1.0 .
+docker buildx build --platform linux/amd64 -t perpendicularity:0.1.0 .
 
 # Run with custom config
 docker run -d \
@@ -430,7 +430,7 @@ git clone https://github.com/t-neumann/perpendicularity.git
 cd perpendicularity
 
 # 4. Build Docker image
-docker build -t perpendicularity:0.1.0 .
+docker buildx build --platform linux/amd64 -t perpendicularity:0.1.0 .
 
 # 5. Run with host network (allows access to Ollama at localhost:11434)
 docker run -d --name perpendicularity --network host \

cli/main.py

@@ -512,6 +512,7 @@ async def _list_tools(config_path, plain):
 # LIST-MODELS COMMAND
 # ============================================================================
 
+
 @cli.command()
 @click.option(
     "--config",
@@ -541,10 +542,12 @@ def list_models(config, plain):
         formatter.print_error(str(e))
         sys.exit(1)
 
+
 # ============================================================================
 # LIST-PROMPTS COMMAND
 # ============================================================================
 
+
 @cli.command()
 @click.option(
     "--config",
@@ -562,20 +565,21 @@ def list_prompts(config, plain):
     try:
         agent_config = AgentConfig(config)
         default_prompt = agent_config.config.get("agent", {}).get("system_prompt", "default")
-        
+
         # Get all prompts from prompts.yaml
         prompts = agent_config.prompts
-        
+
         if not prompts:
             formatter.print_error("No prompts found in prompts.yaml")
             return
-        
+
         formatter.print_prompt_list(prompts, default_prompt)
 
     except Exception as e:
         formatter.print_error(str(e))
         sys.exit(1)
 
+
 # ============================================================================
 # INFO COMMAND
 # ============================================================================

cli/output.py

@@ -189,43 +189,43 @@ def print_model_list(self, models: dict, default_model: str):
 
     def print_prompt_list(self, prompts: dict, default_prompt: str):
         """Print list of available prompts."""
-        
+
         def extract_description(prompt_text: str, max_length: int = 60) -> str:
             """Extract first line or sentence from prompt as description."""
             if not prompt_text:
                 return "No description"
-            
+
             # Get first line or first sentence
-            lines = prompt_text.strip().split('\n')
+            lines = prompt_text.strip().split("\n")
             first_line = lines[0].strip()
-            
+
             # If first line is too long, take first sentence
             if len(first_line) > max_length:
                 # Try to find first sentence
-                for sep in ['. ', '! ', '? ']:
+                for sep in [". ", "! ", "? "]:
                     if sep in first_line:
-                        first_line = first_line.split(sep)[0] + '.'
+                        first_line = first_line.split(sep)[0] + "."
                         break
-            
+
             # Truncate if still too long
             if len(first_line) > max_length:
-                first_line = first_line[:max_length-3] + "..."
-            
+                first_line = first_line[: max_length - 3] + "..."
+
             return first_line
-        
+
         if self.use_rich:
             from rich.table import Table
-            
+
             table = Table(title="Available System Prompts")
             table.add_column("Prompt Name", style="cyan")
             table.add_column("Description", style="white")
             table.add_column("Default", style="green")
-            
+
             for name in sorted(prompts.keys()):
                 desc = extract_description(prompts[name])
                 default = "✓" if name == default_prompt else ""
                 table.add_row(name, desc, default)
-            
+
             self.console.print()
             self.console.print(table)
             self.console.print()

docs/CHANGELOG.md

@@ -0,0 +1,27 @@
+# Changelog
+
+All notable changes to Perpendicularity will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
+
+## [0.1.0] - 2025-02-23
+
+### Added
+- Initial release of Perpendicularity
+- LangGraph and ReAct agent implementations
+- Support for Gemini, Claude, Ollama, HuggingFace Transformers
+- MCP integration (GenomicOps-MCP, TxGemma-MCP)
+- CLI with interactive and batch modes
+- FastAPI web server with React frontend
+- Docker deployment support
+- Comprehensive documentation (15 guides)
+- Test suite (82% coverage, 427+ tests)
+
+### Features
+- Multi-model support (cloud and local)
+- Real-time SSE streaming
+- Rich terminal output
+- Production-ready deployment options
+- EC2 with Ollama setup guide
+
+[0.1.0]: https://github.com/t-neumann/perpendicularity/releases/tag/v0.1.0

docs/DEPLOYMENT.md

@@ -52,7 +52,7 @@ The Dockerfile uses a **multi-stage build** to optimize image size and support o
 
 ```bash
 # Build image (no local models)
-docker build -t perpendicularity:0.1.0 .
+docker buildx build --platform linux/amd64 -t perpendicularity:0.1.0 .
 
 # Image size: ~1.5GB
 ```
@@ -78,7 +78,7 @@ docker build -t perpendicularity:0.1.0 .
 
 ```bash
 # Build with local models support
-docker build \
+docker buildx build --platform linux/amd64 \
   --build-arg INSTALL_LOCAL_MODELS=true \
   -t perpendicularity:0.1.0-gpu .
 
@@ -245,15 +245,15 @@ docker exec perpendicularity nvidia-smi
 
 ```bash
 # Use BuildKit for faster builds
-DOCKER_BUILDKIT=1 docker build -t perpendicularity:0.1.0 .
+DOCKER_BUILDKIT=1 docker buildx build --platform linux/amd64 -t perpendicularity:0.1.0 .
 
 # Multi-platform build (for deployment on different architectures)
 docker buildx build \
   --platform linux/amd64,linux/arm64 \
   -t perpendicularity:0.1.0 .
 
 # Build with specific Python version
-docker build \
+docker buildx build --platform linux/amd64 \
   --build-arg PYTHON_VERSION=3.11 \
   -t perpendicularity:0.1.0 .
 ```
@@ -264,10 +264,10 @@ docker build \
 
 ```bash
 # Build with no cache
-docker build --no-cache -t perpendicularity:0.1.0 .
+docker buildx build --platform linux/amd64 --no-cache -t perpendicularity:0.1.0 .
 
 # Use BuildKit cache
-docker build \
+docker buildx build --platform linux/amd64 \
   --cache-from perpendicularity:latest \
   -t perpendicularity:0.1.0 .
 ```
@@ -326,7 +326,7 @@ ollama pull qwen2.5:14b-instruct
 # 3. Deploy Perpendicularity
 git clone https://github.com/t-neumann/perpendicularity.git
 cd perpendicularity
-docker build -t perpendicularity:0.1.0 .
+docker buildx build --platform linux/amd64 -t perpendicularity:0.1.0 .
 docker run -d --network host \
   -v $(pwd)/config/agent_config.yaml:/app/config/agent_config.yaml:ro \
   perpendicularity:0.1.0
@@ -534,7 +534,7 @@ perpendicularity api --reload
 
 ```bash
 # Build and run in Docker
-docker build -t perpendicularity:0.1.0 .
+docker buildx build --platform linux/amd64 -t perpendicularity:0.1.0 .
 docker run -d \
   --name perpendicularity \
   --restart unless-stopped \
@@ -554,7 +554,7 @@ ollama pull qwen2.5:14b-instruct
 
 git clone https://github.com/t-neumann/perpendicularity.git
 cd perpendicularity
-docker build -t perpendicularity:0.1.0 .
+docker buildx build --platform linux/amd64 -t perpendicularity:0.1.0 .
 docker run -d --network host perpendicularity:0.1.0
 ```
 

docs/EC2_SETUP.md

@@ -88,7 +88,7 @@ cd perpendicularity
 nano config/agent_config.yaml
 
 # 8. Build and run
-docker build -t perpendicularity:0.1.0 .
+docker buildx build --platform linux/amd64 -t perpendicularity:0.1.0 .
 docker run -d --name perpendicularity --network host \
   -v $(pwd)/config/agent_config.yaml:/app/config/agent_config.yaml:ro \
   perpendicularity:0.1.0 \
@@ -540,7 +540,7 @@ cd perpendicularity
 git pull
 
 # Rebuild Docker image
-docker build -t perpendicularity:0.1.0 .
+docker buildx build --platform linux/amd64 -t perpendicularity:0.1.0 .
 
 # Stop old container
 docker stop perpendicularity

docs/GETTING_STARTED.md

@@ -67,7 +67,7 @@ git clone https://github.com/t-neumann/perpendicularity.git
 cd perpendicularity
 
 # Build Docker image
-docker build -t perpendicularity:0.1.0 .
+docker buildx build --platform linux/amd64 -t perpendicularity:0.1.0 .
 
 # Run (see Deployment section for full options)
 docker run -p 8000:8000 perpendicularity:0.1.0

docs/TROUBLESHOOTING.md

@@ -532,14 +532,14 @@ ls Dockerfile
 # Docker Desktop → Settings → Resources → Memory → 8GB+
 
 # 3. Build with verbose output
-docker build -t perpendicularity:0.1.0 . --progress=plain
+docker buildx build --platform linux/amd64 -t perpendicularity:0.1.0 . --progress=plain
 
 # 4. Clear Docker cache
 docker builder prune -a
 
 # 5. Build stages separately
-docker build --target frontend-builder -t perp-frontend .
-docker build -t perpendicularity:0.1.0 .
+docker buildx build --platform linux/amd64 --target frontend-builder -t perp-frontend .
+docker buildx build --platform linux/amd64 -t perpendicularity:0.1.0 .
 ```
 
 ---

frontend/package.json

@@ -1,7 +1,7 @@
 {
   "name": "perpendicularity-frontend",
   "private": true,
-  "version": "0.3.0",
+  "version": "0.1.0",
   "type": "module",
   "scripts": {
     "predev": "mkdir -p public && cp ../assets/logo.png public/logo.png",

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "Perpendicularity"
-version = "0.3.0"  # Updated to match CLI version
+version = "0.1.0" 
 description = "Perpendicularity therapeutics drug discovery agent to unite the realms of genomics and therapeutics using AI synthesis"
 readme = "README.md"
 requires-python = ">=3.11"