Configuration Guide

This guide covers all aspects of configuring Lobster AI, from basic API key setup to advanced model customization and cloud integration.

Quick Start

The easiest way to configure Lobster AI is using the interactive wizard:

# Workspace-specific configuration (default)
lobster init

# Global configuration for all workspaces (v0.4+)
lobster init --global

# Test your configuration
lobster config test

# View your configuration (secrets masked)
lobster config show

What's New in v0.4: External Workspaces

You can now work with data in any directory without per-directory setup:

# Set global defaults once
lobster init --global

# Use any workspace - just works!
lobster chat --workspace ~/Documents/project1
lobster chat --workspace ~/Desktop/quick_analysis
lobster query "cluster cells" --workspace /tmp/test_data

Before v0.4: Each workspace needed its own .env file After v0.4: Global config (~/.config/lobster/providers.json) provides defaults

For advanced configuration options, continue reading below.

Quick Start
Environment Variables
API Key Management
Model Profiles
Supervisor Configuration
Cloud vs Local Configuration
Other Settings
Configuration Management
Security Best Practices
Troubleshooting Configuration

Environment Variables

Lobster AI uses environment variables for configuration. These can be set in a .env file in your project root directory, or as system environment variables.

Required Variables

You must configure at least one Large Language Model (LLM) provider:

Cloud Providers (require API keys):

ANTHROPIC_API_KEY: For using Claude models via Anthropic Direct API
AWS_BEDROCK_ACCESS_KEY and AWS_BEDROCK_SECRET_ACCESS_KEY: For using models via AWS Bedrock
GOOGLE_API_KEY: For using Gemini models via Google AI Studio
OPENAI_API_KEY: For using GPT-4o, o1/o3 reasoning models via OpenAI API
AZURE_AI_ENDPOINT and AZURE_AI_CREDENTIAL: For using Azure AI Foundry models

Local Provider (no API keys needed):

LOBSTER_LLM_PROVIDER=ollama: For using local models via Ollama (requires Ollama installation)

See the API Key Management section for detailed setup instructions.

Optional Variables

Most other settings are controlled via environment variables that follow these patterns:

LOBSTER_*: For core application and model configuration.
SUPERVISOR_*: For controlling the behavior of the supervisor agent.

Details on these variables are provided in the sections below.

API Key Management

Lobster AI supports six LLM providers: five cloud-based and one local. Choose the provider that best fits your needs:

Ollama (Local) - NEW! 🏠

Best for: Privacy, zero API costs, offline work, development without cloud dependencies.

Requirements: 8-48GB RAM depending on model size.

Setup:

# 1. Install Ollama (one-time)
curl -fsSL https://ollama.com/install.sh | sh

# 2. Pull a model (one-time)
ollama pull gpt-oss:20b

# 3. Configure Lobster
lobster init  # Select option 3 (Ollama)
# Or manually:
export LOBSTER_LLM_PROVIDER=ollama

Configuration:

LOBSTER_LLM_PROVIDER=ollama
OLLAMA_BASE_URL=http://localhost:11434  # Optional: default
OLLAMA_DEFAULT_MODEL=gpt-oss:20b  # Optional: default

Model Recommendations:

gpt-oss:20b - Recommended for Lobster (supports tools, 16GB RAM)
mixtral:8x7b-instruct - Better quality (26GB RAM)
llama3:70b-instruct - Maximum quality (48GB VRAM, requires GPU)

Note: llama3:8b models do NOT support tool calling and will fail with Lobster. Use gpt-oss:20b or larger models.

Claude API (Cloud)

Best for: Quick testing, simple setup, best quality.

Configuration:

ANTHROPIC_API_KEY=sk-ant-api03-xxxxx

AWS Bedrock (Cloud)

Best for: Production use, enterprise compliance, higher rate limits.

Configuration:

AWS_BEDROCK_ACCESS_KEY=AKIA...
AWS_BEDROCK_SECRET_ACCESS_KEY=abc123...
AWS_REGION=us-east-1  # Optional: defaults to us-east-1

Google Gemini (Cloud) ✨

Best for: Long context windows, multimodal capabilities, free tier available.

Configuration:

GOOGLE_API_KEY=your-key-here
LOBSTER_LLM_PROVIDER=gemini

Get your API key: https://aistudio.google.com/apikey

Available Models:

gemini-3-pro-preview - Best balance ($2.00 input / $12.00 output per million tokens)
gemini-3-flash-preview - Fastest, free tier available ($0.50 input / $3.00 output)

Note: Gemini 3.0+ models require temperature=1.0 (lower values can cause issues).

OpenAI (Cloud)

Best for: GPT-4o performance, reasoning models (o1/o3), widely-used API, flexible pricing.

Configuration:

OPENAI_API_KEY=sk-proj-xxxxx
LOBSTER_LLM_PROVIDER=openai

Get your API key: https://platform.openai.com/api-keys

Available Models:

gpt-4o - Default model, best balance ($2.50 input / $10.00 output per million tokens)
gpt-4o-mini - Fast and affordable ($0.15 input / $0.60 output per million tokens)
o1 - Advanced reasoning model ($15.00 input / $60.00 output per million tokens)
o1-mini - Smaller reasoning model ($3.00 input / $12.00 output per million tokens)
o3-mini - Latest reasoning model ($1.10 input / $4.40 output per million tokens)

Key Features:

GPT-4o provides excellent performance for multi-agent workflows
Reasoning models (o1/o3) excel at complex scientific analysis
Widely adopted API with extensive ecosystem support
Flexible pricing across model tiers

Note: Reasoning models (o1/o3) automatically adjust parameters - temperature and max_tokens are not applicable.

Azure AI (Cloud) 🔷

Best for: Enterprise customers with existing Azure infrastructure, Azure compliance requirements, multi-model access.

Configuration:

AZURE_AI_ENDPOINT=https://your-project.inference.ai.azure.com/
AZURE_AI_CREDENTIAL=your-api-key
AZURE_AI_API_VERSION=2024-05-01-preview  # Optional
LOBSTER_LLM_PROVIDER=azure

Get your credentials: https://ai.azure.com/

Create/open an Azure AI Foundry project
Deploy a model (GPT-4o, DeepSeek R1, Cohere, Phi, Mistral)
Copy endpoint URL and API key from deployment details

Available Models:

gpt-4o - OpenAI GPT-4o (recommended default) ($5.00 input / $15.00 output per million tokens)
deepseek-r1 - DeepSeek R1 reasoning model ($0.55 input / $2.19 output)
gpt-4-turbo - OpenAI GPT-4 Turbo ($10.00 input / $30.00 output)
cohere-command-r-plus - Cohere Command R+ ($3.00 input / $15.00 output)
phi-4 - Microsoft Phi-4 small model ($0.07 input / $0.14 output)
mistral-large - Mistral Large ($4.00 input / $12.00 output)

Key Features:

Access to multiple model providers through single Azure account
Enterprise compliance (HIPAA, SOC2, ISO 27001)
Data stays within your Azure tenant
Supports custom model deployments

Legacy Environment Variables (backward compatibility):

AZURE_OPENAI_ENDPOINT=https://your-resource.openai.azure.com/
AZURE_OPENAI_API_KEY=your-api-key

Configuration Resolution Priority (v0.4+)

Lobster AI uses a 5-layer priority hierarchy for provider configuration:

Runtime CLI flags: --provider (highest priority, overrides everything)
Workspace config: .lobster_workspace/provider_config.json (project-specific)
Global user config: ~/.config/lobster/providers.json (user-wide defaults)
Environment variable: LOBSTER_LLM_PROVIDER (temporary override)
FAIL: Requires explicit configuration (no auto-detection)

Force a specific provider:

# Runtime override (highest priority)
lobster chat --provider anthropic

# Global defaults (applies to all workspaces)
lobster init --global

# Environment variable (temporary override)
export LOBSTER_LLM_PROVIDER=ollama

# Workspace-specific (project defaults)
lobster init  # Creates .env + provider_config.json

Model resolution follows the same hierarchy plus provider defaults.

Running Multiple Sessions with Different Providers

You can run multiple Lobster sessions simultaneously, each using a different LLM provider. This is useful for:

A/B Testing: Compare analysis quality between providers
Development vs Production: Use local for dev, cloud for production
Cost Optimization: Use local for exploratory work, cloud for final analyses
Privacy Control: Use local for sensitive data, cloud for general analyses

Method 1: Different Terminal Sessions (Current)

Each terminal maintains its own environment variables:

# Terminal 1: Local development with Ollama
export LOBSTER_LLM_PROVIDER=ollama
cd ~/project-dev
lobster chat

# Terminal 2: Production with Claude (simultaneously)
export LOBSTER_LLM_PROVIDER=anthropic
cd ~/project-prod
lobster chat

# Terminal 3: Enterprise with Bedrock
export LOBSTER_LLM_PROVIDER=bedrock
cd ~/project-enterprise
lobster chat

How it works:

Environment variables are process-specific (don't interfere between terminals)
Each session is completely independent
Can run unlimited simultaneous sessions

Method 2: Shell Aliases (Convenience)

Create aliases for quick provider switching:

# Add to ~/.bashrc or ~/.zshrc
alias lobster-ollama='LOBSTER_LLM_PROVIDER=ollama lobster'
alias lobster-cloud='LOBSTER_LLM_PROVIDER=anthropic lobster'
alias lobster-bedrock='LOBSTER_LLM_PROVIDER=bedrock lobster'
alias lobster-gemini='LOBSTER_LLM_PROVIDER=gemini lobster'
alias lobster-openai='LOBSTER_LLM_PROVIDER=openai lobster'

# Usage
lobster-ollama chat    # Always uses Ollama (local)
lobster-cloud query "analyze data"  # Always uses Claude
lobster-bedrock chat   # Always uses Bedrock
lobster-gemini chat    # Always uses Gemini
lobster-openai chat    # Always uses OpenAI

Method 3: Per-Command Inline (Quick Tests)

# One-off command with specific provider
LOBSTER_LLM_PROVIDER=ollama lobster query "cluster my data"
LOBSTER_LLM_PROVIDER=anthropic lobster query "cluster my data"

# Compare results side-by-side

Method 4: CLI Flag (Coming Soon)

Future enhancement - provider flag per command:

lobster chat --provider ollama
lobster query --provider anthropic "analyze data"

Method 5: Workspace-Specific Config (Coming Soon)

Future enhancement - each workspace remembers its provider:

# project1/.lobster_workspace/config.json
{"llm_provider": "ollama"}

# project2/.lobster_workspace/config.json
{"llm_provider": "anthropic"}

cd project1 && lobster chat  # Auto-uses Ollama
cd project2 && lobster chat  # Auto-uses Claude

Provider Selection Priority

When multiple configurations exist, Lobster uses this resolution order:

1. Runtime CLI flag (--provider)                           [✅ v0.4+]
2. Workspace config (.lobster_workspace/provider_config.json)  [✅ Current]
3. Global user config (~/.config/lobster/providers.json)      [✅ v0.4+]
4. Environment variable (LOBSTER_LLM_PROVIDER)                [✅ Current]
5. FAIL with diagnostic message                               [✅ v0.4+]

Key improvements in v0.4:

Added global user config for user-wide defaults
External workspaces now inherit from global config
Better error diagnostics showing what was checked

Practical Example: Development Workflow

# Setup: Configure both providers once
cat > ~/.env << EOF
ANTHROPIC_API_KEY=sk-ant-xxx
LOBSTER_LLM_PROVIDER=anthropic  # Default to cloud
EOF

# Day-to-day usage:
# Quick local test (Terminal 1)
LOBSTER_LLM_PROVIDER=ollama lobster chat

# Production analysis (Terminal 2, simultaneously)
lobster chat  # Uses default (anthropic)

# Both sessions run independently!

NCBI API Key (Optional)

Benefits: Enhanced literature search with higher rate limits.

Configuration:

NCBI_API_KEY=your-ncbi-api-key-here

Deployment Patterns

Lobster supports flexible deployment configurations combining execution environments, LLM providers, and data sources. Choose a pattern based on your privacy, quality, and scale requirements.

Pattern 1: Local + Ollama (Zero-Cost Stack)

Best for: Individual researchers, privacy-sensitive data, unlimited usage, offline work

Setup:

# 1. Install Ollama (one-time)
curl -fsSL https://ollama.com/install.sh | sh

# 2. Pull model
ollama pull gpt-oss:20b

# 3. Install Lobster
uv pip install lobster-ai

# 4. Run
lobster chat
# Ollama auto-detected, no API keys needed

Characteristics:

✅ Zero cost: No API charges
✅ Full privacy: All data stays on your machine
✅ Offline capable: Works without internet
✅ Unlimited usage: No rate limits
✅ Tool support: gpt-oss:20b supports multi-agent tool calling
⚠️ Hardware dependent: Requires 16-48GB RAM depending on model
⚠️ Quality varies: Model-dependent (gpt-oss:20b < mixtral < llama3:70b)

Configuration:

LOBSTER_LLM_PROVIDER=ollama
OLLAMA_BASE_URL=http://localhost:11434  # Optional: default
OLLAMA_DEFAULT_MODEL=gpt-oss:20b  # Optional: default

Pattern 2: Local + Anthropic (Quality-First)

Best for: High-quality analysis, quick start, flexible execution, development

Setup:

# 1. Get API key from console.anthropic.com

# 2. Install Lobster
uv pip install lobster-ai

# 3. Configure
export ANTHROPIC_API_KEY=sk-ant-api03-...

# 4. Run
lobster chat

Characteristics:

✅ Best quality: Claude Sonnet 4.5, highest accuracy
✅ Quick setup: Just API key, no infrastructure
✅ Local execution: Your hardware, your control
✅ Flexible: Switch to other providers anytime
⚠️ API costs: ~$0.50/analysis
⚠️ Rate limits: ~50 requests/min for new accounts
⚠️ Requires internet: Online-only

Configuration:

ANTHROPIC_API_KEY=sk-ant-api03-xxxxx
LOBSTER_LLM_PROVIDER=anthropic  # Optional: auto-detected

Pattern 3: Cloud + Bedrock (Enterprise Scale)

Best for: Team collaboration, production workloads, compliance requirements, high throughput

Setup:

# 1. Configure AWS Bedrock access
export LOBSTER_CLOUD_KEY=your-cloud-key
export AWS_BEDROCK_ACCESS_KEY=AKIA...
export AWS_BEDROCK_SECRET_ACCESS_KEY=...

# 2. Install Lobster
uv pip install lobster-ai

# 3. Run
lobster chat
# Cloud mode + Bedrock auto-configured

Characteristics:

✅ Enterprise SLA: Production-grade reliability
✅ High rate limits: No throttling for production use
✅ Team collaboration: Shared cloud infrastructure
✅ Compliance ready: HIPAA, SOC2, GDPR support
✅ Scalable: Handles large datasets automatically
⚠️ Cost: $6K-$30K/year (volume-based)
⚠️ Setup complexity: Requires AWS configuration

Configuration:

# Cloud execution
LOBSTER_CLOUD_KEY=your-cloud-api-key
LOBSTER_ENDPOINT=https://api.lobster.omics-os.com  # Optional

# AWS Bedrock LLM
AWS_BEDROCK_ACCESS_KEY=AKIA...
AWS_BEDROCK_SECRET_ACCESS_KEY=...
AWS_REGION=us-east-1  # Optional: default
LOBSTER_LLM_PROVIDER=bedrock  # Optional: auto-detected

Comparison Matrix

Aspect	Pattern 1 (Ollama)	Pattern 2 (Anthropic)	Pattern 3 (Bedrock)
Cost	Free	~$0.50/analysis	$6K-$30K/year
Setup	Ollama install	API key	AWS + Cloud key
Quality	Model-dependent	Highest (Claude 4.5)	Highest (Claude 4.5)
Privacy	100% local	Cloud LLM, local data	Cloud execution
Rate Limits	None	50 req/min	Enterprise (high)
Offline	✅ Yes	❌ No	❌ No
Scalability	Hardware-limited	Hardware-limited	Cloud-managed
Best For	Privacy, learning	Quality, development	Production, teams

Switching Between Patterns

You can switch patterns anytime or run multiple sessions with different patterns simultaneously:

# Terminal 1: Privacy-focused with Ollama
export LOBSTER_LLM_PROVIDER=ollama
cd ~/private-project
lobster chat

# Terminal 2: Quality-focused with Anthropic (simultaneously)
export LOBSTER_LLM_PROVIDER=anthropic
export ANTHROPIC_API_KEY=sk-ant-xxx
cd ~/research-project
lobster chat

# Terminal 3: Production with Bedrock
export LOBSTER_CLOUD_KEY=xxx
export LOBSTER_LLM_PROVIDER=bedrock
cd ~/production-project
lobster chat

Each session is completely independent with its own workspace, configuration, and execution environment.

Model Profiles

Lobster AI uses a profile-based system to manage agent and model configurations. You can set the active profile using the LOBSTER_PROFILE environment variable.

Available Profiles

production (Default): Supervisor uses Claude 4.5 Sonnet, expert agents use Claude 4 Sonnet, assistant uses Claude 3.7 Sonnet. Recommended for production deployments with optimal coordination and balanced analysis.
development: Supervisor and expert agents use Claude 4 Sonnet, assistant uses Claude 3.7 Sonnet. Ideal for development and testing with consistent expert-tier performance.
godmode: All agents (supervisor, experts, and assistant) use Claude 4.5 Sonnet. Maximum performance and capability for demanding analyses.

Set the profile in your .env file:

LOBSTER_PROFILE=production    # Default
LOBSTER_PROFILE=development   # Development/testing
LOBSTER_PROFILE=godmode       # Maximum performance

Available Models

The following models are available in Lobster AI:

claude-3-7-sonnet: Claude 3.7 Sonnet - Development and worker tier model
claude-4-sonnet: Claude 4 Sonnet - Production tier model (balanced performance)
claude-4-5-sonnet: Claude 4.5 Sonnet - Highest performance model for demanding tasks

Custom Model Configuration

You can override the model for all agents or for specific agents using environment variables.

# Override the model for ALL agents
LOBSTER_GLOBAL_MODEL=claude-4-5-sonnet

# Override the model for a specific agent
LOBSTER_SINGLECELL_EXPERT_AGENT_MODEL=claude-4-sonnet

# Override the temperature for a specific agent (0.0 to 1.0)
LOBSTER_SUPERVISOR_TEMPERATURE=0.3

"Thinking" Configuration

For models that support it, you can enable a "thinking" feature, which allows the model to perform a chain-of-thought before answering.

# Set a global thinking preset for all agents (light, standard, extended, deep)
LOBSTER_GLOBAL_THINKING=standard

# Enable or disable thinking for a specific agent
LOBSTER_SUPERVISOR_THINKING_ENABLED=true

# Set the token budget for thinking
LOBSTER_SUPERVISOR_THINKING_BUDGET=2000

Supervisor Configuration

The supervisor agent's behavior can be fine-tuned using SUPERVISOR_* environment variables.

# Interaction Settings
SUPERVISOR_ASK_QUESTIONS=true               # Ask clarification questions (default: true)
SUPERVISOR_MAX_QUESTIONS=2                  # Max clarification questions (default: 2)
SUPERVISOR_REQUIRE_CONFIRMATION=true        # Require download confirmation (default: true)
SUPERVISOR_REQUIRE_PREVIEW=true             # Preview metadata before download (default: true)

# Response Settings
SUPERVISOR_AUTO_SUGGEST=true               # Suggest next steps (default: true)
SUPERVISOR_VERBOSE=true                    # Verbose delegation explanations (default: true)
SUPERVISOR_INCLUDE_EXPERT_OUTPUT=true      # Include full expert output (default: true)
SUPERVISOR_SUMMARIZE_OUTPUT=false          # Summarize expert output (default: false)

# Context Settings
SUPERVISOR_INCLUDE_DATA=true              # Include data context (default: true)
SUPERVISOR_INCLUDE_WORKSPACE=true         # Include workspace status (default: true)
SUPERVISOR_INCLUDE_SYSTEM=false           # Include system info (default: false)
SUPERVISOR_INCLUDE_MEMORY=false           # Include memory stats (default: false)

# Workflow Guidance
SUPERVISOR_WORKFLOW_GUIDANCE=detailed      # minimal, standard, detailed (default: detailed)
SUPERVISOR_DELEGATION_STRATEGY=auto        # auto, conservative, aggressive (default: auto)
SUPERVISOR_ERROR_HANDLING=informative      # silent, informative, verbose (default: informative)

# Agent Discovery
SUPERVISOR_AUTO_DISCOVER=true             # Auto-discover agents (default: true)
SUPERVISOR_INCLUDE_AGENT_TOOLS=true       # List agent tools (default: true)
SUPERVISOR_MAX_TOOLS_PER_AGENT=20         # Tools shown per agent (default: 20)

Cloud vs Local Configuration

Lobster AI can run in local mode (default) or cloud mode.

Local Mode (Default)

Trigger: No LOBSTER_CLOUD_KEY is set.
Processing: Runs entirely on your local machine.
Requires: Local compute resources and API keys.

Cloud Mode

Trigger: LOBSTER_CLOUD_KEY is set.
Processing: Occurs on the Omics-OS Cloud infrastructure.
Requires: A valid LOBSTER_CLOUD_KEY.

# Cloud API key enables cloud mode
LOBSTER_CLOUD_KEY=your-cloud-api-key-here

# Optional: custom endpoint for development or enterprise
LOBSTER_ENDPOINT=https://api.lobster.omics-os.com

Other Settings

These variables control other aspects of the application.

# --- Data Processing ---
# Maximum file size for uploads in MB
LOBSTER_MAX_FILE_SIZE_MB=500
# Default resolution for clustering algorithms
LOBSTER_CLUSTER_RESOLUTION=0.5
# Directory for caching data
LOBSTER_CACHE_DIR=./lobster/data/cache

# --- Web Server ---
# Port for the Streamlit web interface
PORT=8501
# Host address for the web interface
HOST=0.0.0.0
# Enable or disable debug mode
DEBUG=False

# --- SSL/HTTPS ---
# Verify SSL certificates for outgoing requests
LOBSTER_SSL_VERIFY=true
# Path to a custom SSL certificate bundle
LOBSTER_SSL_CERT_PATH=

Configuration Management

Interactive Setup

The recommended way to configure Lobster AI:

# Workspace-specific configuration (default)
lobster init

# Global configuration for all workspaces (v0.4+)
lobster init --global

# The wizard will:
# 1. Prompt you to choose LLM provider:
#    - Option 1: Claude API (Anthropic)
#    - Option 2: AWS Bedrock
#    - Option 3: Ollama (Local)
#    - Option 4: Google Gemini
#    - Option 5: Azure AI
#    - Option 6: OpenAI - GPT-4o, o1 reasoning models
# 2. Guide you through provider-specific setup:
#    - Cloud: Securely collect API keys (input is masked)
#    - Ollama: Check installation, list available models
#    - Gemini: Collect Google API key, select model (Pro/Flash)
#    - OpenAI: Collect OpenAI API key from platform.openai.com
# 3. Optionally configure NCBI API key
# 4. Save configuration:
#    - Workspace mode: .env + .lobster_workspace/provider_config.json
#    - Global mode: ~/.config/lobster/providers.json

When to use --global:

Set user-wide defaults that apply to all workspaces
Enable seamless use of external workspaces without per-workspace setup
Ideal for users who want consistent settings across projects

Global config location (platform-specific):

Linux/macOS: ~/.config/lobster/providers.json (CLI convention)
Windows: %APPDATA%\lobster\providers.json (e.g., C:\Users\Name\AppData\Roaming\lobster\providers.json)

External Workspaces (v0.4+)

External workspaces allow you to work with data in any directory without per-directory configuration:

# Step 1: Set global defaults (one-time)
lobster init --global

# Step 2: Use any workspace seamlessly
lobster chat --workspace ~/Documents/project1
lobster chat --workspace ~/Desktop/analysis
lobster query "analyze data" --workspace /tmp/quick_test

# All workspaces inherit from your global config!

How it works:

You run lobster init --global to set user-wide provider defaults
When you use --workspace with a directory that has no config:
- Lobster checks .lobster_workspace/provider_config.json (not found)
- Falls back to global config (platform-specific location)
- Uses your defaults seamlessly

Global config locations:

Linux/macOS: ~/.config/lobster/providers.json
Windows: %APPDATA%\lobster\providers.json

Override for specific workspace:

cd ~/special_project
lobster init  # Creates workspace-specific config
lobster chat  # Uses workspace config (overrides global)

Best practices:

Use global config for your typical setup (e.g., Ollama for privacy)
Use workspace config only when a project needs different settings
Store API keys in environment variables (not in config files)

Configuration Commands

Use the lobster config commands to manage and verify your configuration:

# Test API connectivity and validate configuration
lobster config test

# Display current configuration with masked secrets (simple view)
lobster config show

# Display detailed runtime configuration (shows per-agent models)
lobster config show-config

# List available providers
lobster config provider

# View available models for current provider
lobster config model

New in v0.4.0: The lobster config show-config command now displays actual runtime configuration using ConfigResolver and ProviderRegistry, showing:

Active provider and configuration source
Per-agent model assignments (see which model each agent uses)
Profile information
Configuration files status
License tier and available agents

Testing Your Configuration

The lobster config test command validates your LLM provider connectivity:

# Auto-detect and test current provider
lobster config test

# Test specific configuration profile
lobster config test --profile production

# Test specific agent in a profile
lobster config test --profile production --agent transcriptomics_expert

Auto-detection behavior (when no --profile is specified):

Detects your currently configured provider from:
- LOBSTER_LLM_PROVIDER environment variable, or
- Auto-detection (Ollama → Anthropic → Bedrock → Gemini)
Tests basic connectivity with a simple API call
Displays clear success/failure message with provider name

Profile-based testing (when --profile is specified):

Tests all agents configured in that profile
Validates model configurations and API access
Useful for testing custom profile setups

Advanced Options

# Reconfigure (creates timestamped backup of existing .env)
lobster init --force
lobster init --global --force

# Non-interactive mode for CI/CD and automation

# Option 1: Claude API (workspace)
lobster init --non-interactive \
  --anthropic-key=sk-ant-xxx

# Option 1b: Claude API (global defaults)
lobster init --global --non-interactive \
  --anthropic-key=sk-ant-xxx

# Option 2: AWS Bedrock
lobster init --non-interactive \
  --bedrock-access-key=AKIA... \
  --bedrock-secret-key=xxx

# Option 3: Ollama (Local) - Global
lobster init --global --non-interactive \
  --use-ollama

# Ollama with custom model
lobster init --non-interactive \
  --use-ollama \
  --ollama-model=mixtral:8x7b-instruct

# Option 4: Google Gemini - Global
lobster init --global --non-interactive \
  --gemini-key=your-google-api-key

# Gemini with specific model
lobster init --non-interactive \
  --gemini-key=your-google-api-key \
  --gemini-model=gemini-3-flash-preview

# Option 6: OpenAI - Global
lobster init --global --non-interactive \
  --openai-key=sk-proj-xxx

# OpenAI with specific model
lobster init --non-interactive \
  --openai-key=sk-proj-xxx \
  --openai-model=gpt-4o-mini

# With NCBI API key
lobster init --non-interactive \
  --anthropic-key=sk-ant-xxx \
  --ncbi-key=your-ncbi-key

Global vs Workspace Configuration:

lobster init (default): Creates .env + workspace config in current directory
lobster init --global: Creates ~/.config/lobster/providers.json for all workspaces
Global config is ideal for users who want consistent settings across all projects
Workspace config overrides global config (project-specific needs)

Manual Configuration

For advanced users, you can manually edit the .env file in your working directory. See the Environment Variables and API Key Management sections for details on available settings.

Configuration Architecture (Advanced)

For developers extending Lobster AI or understanding the configuration system internals, this section documents the architecture patterns used for configuration management.

Single Source of Truth Pattern

As of v0.4.0+, Lobster AI uses a constants module as the single source of truth for valid providers and profiles. This eliminates code duplication and ensures consistency across the codebase.

File: lobster/config/constants.py

from typing import Final, List

# Valid LLM providers (single source of truth)
VALID_PROVIDERS: Final[List[str]] = ["anthropic", "bedrock", "ollama", "gemini", "azure", "openai"]

# Valid model profiles
VALID_PROFILES: Final[List[str]] = ["development", "production", "ultra", "godmode", "hybrid"]

# Provider display names for user interfaces
PROVIDER_DISPLAY_NAMES: Final[dict] = {
    "anthropic": "Anthropic Direct API",
    "bedrock": "AWS Bedrock",
    "ollama": "Ollama (Local)",
    "gemini": "Google Gemini",
    "azure": "Azure AI",
    "openai": "OpenAI",
}

Benefits:

No duplication: Adding a new provider requires updating only constants.py
Type safety: Final[List[str]] ensures immutability
Centralized: All consumers import from same location
Maintainable: Changes propagate automatically to all config classes

Abstract Base Class Pattern

Configuration classes inherit from ProviderConfigBase, which provides shared validation logic and abstract properties.

File: lobster/config/base_config.py

import abc
from pydantic import BaseModel, model_validator
from lobster.config.constants import VALID_PROVIDERS, VALID_PROFILES

class ProviderConfigBase(BaseModel, abc.ABC):
    """Abstract base for WorkspaceProviderConfig and GlobalProviderConfig."""

    @property
    @abc.abstractmethod
    def provider_field_name(self) -> str:
        """Name of the provider field (e.g., 'global_provider', 'default_provider')."""
        pass

    @property
    @abc.abstractmethod
    def model_field_suffix(self) -> str:
        """Suffix for model fields (e.g., '_model', '_default_model')."""
        pass

    @model_validator(mode="before")
    @classmethod
    def validate_providers_and_profiles(cls, data):
        """Shared validation for provider and profile fields."""
        # Validates global_provider, default_provider, profile, per_agent_providers
        # Uses VALID_PROVIDERS and VALID_PROFILES from constants.py
        ...

    def get_model_for_provider(self, provider: str) -> Optional[str]:
        """Get model name for provider (e.g., 'anthropic' -> 'anthropic_model')."""
        field_name = f"{provider}{self.model_field_suffix}"
        return getattr(self, field_name, None)

Benefits:

Shared validation: Pydantic model_validator ensures consistency
Explicit contracts: Abstract properties enforce implementation
DRY principle: ~120 lines of duplicated code removed
Extensible: Adding validation logic applies to all config classes

Configuration Classes

WorkspaceProviderConfig (lobster/config/workspace_config.py):

from lobster.config.base_config import ProviderConfigBase

class WorkspaceProviderConfig(ProviderConfigBase):
    """Workspace-specific provider configuration."""

    @property
    def provider_field_name(self) -> str:
        return "global_provider"

    @property
    def model_field_suffix(self) -> str:
        return "_model"

    # Fields: global_provider, anthropic_model, bedrock_model, ollama_model, gemini_model, etc.

GlobalProviderConfig (lobster/config/global_config.py):

from lobster.config.base_config import ProviderConfigBase

class GlobalProviderConfig(ProviderConfigBase):
    """Global provider configuration."""

    @property
    def provider_field_name(self) -> str:
        return "default_provider"

    @property
    def model_field_suffix(self) -> str:
        return "_default_model"

    # Fields: default_provider, anthropic_default_model, bedrock_default_model, etc.

Configuration Priority System (v0.4+)

Lobster AI uses a 5-layer priority system for configuration resolution:

1. Runtime CLI flags (highest priority)
   ↓  --provider, --model
2. Workspace config
   ↓  .lobster_workspace/provider_config.json
3. Global user config
   ↓  ~/.config/lobster/providers.json
4. Environment variable
   ↓  LOBSTER_LLM_PROVIDER
5. FAIL with diagnostic message (lowest priority)
   ↓  No auto-detection, no silent defaults

Implementation: lobster/core/config_resolver.py

Design Philosophy:

No auto-detection: Prevents unexpected costs from accidental API usage
Explicit configuration: Users must consciously choose a provider
Diagnostic errors: Shows exactly what was checked when config is missing
Multiple layers: Supports workspace overrides and global defaults

Example diagnostic error:

❌ No provider configured.

Checked (in priority order):
  ✗ Runtime flag: --provider not provided
  ✗ Workspace config: .lobster_workspace/provider_config.json (not found)
  ✗ Global config: ~/.config/lobster/providers.json (not found)
  ✗ Environment: LOBSTER_LLM_PROVIDER (not set)

Quick Setup:
  lobster init              # Configure this workspace
  lobster init --global     # Set global defaults for all workspaces

Adding a New Provider (Developer Guide)

To add a new LLM provider (e.g., "cohere"):

Update constants (lobster/config/constants.py):

VALID_PROVIDERS: Final[List[str]] = ["anthropic", "bedrock", "ollama", "gemini", "azure", "openai", "cohere"]
PROVIDER_DISPLAY_NAMES["cohere"] = "Cohere API"

Add provider class (lobster/config/providers/cohere_provider.py):

class CohereProvider(BaseProvider):
    """Cohere provider implementation."""
    ...

Register provider (lobster/config/providers/registry.py):
```
PROVIDER_REGISTRY.register("cohere", CohereProvider)
```
Update config fields:
- workspace_config.py: Add cohere_model: Optional[str] = None
- global_config.py: Add cohere_default_model: Optional[str] = None
- Update reset() and set_model_for_provider() methods
Update CLI (lobster/cli.py):
- Add Cohere option to lobster init wizard
- Add provider setup logic in provider_setup.py

Regenerate allowlist:

python scripts/generate_allowlist.py --write

The constants pattern ensures that provider validation automatically includes the new provider across all configuration classes without additional changes.

Security Best Practices

Never commit .env files to version control.
Use system environment variables or a secrets management tool for production.
Rotate API keys regularly.

Troubleshooting Configuration

Diagnostic Error Messages (v0.4+)

When provider configuration is missing, Lobster now shows exactly what was checked:

❌ No provider configured.

Checked (in priority order):
  ✗ Runtime flag: --provider not provided
  ✗ Workspace config: /path/to/workspace/provider_config.json (not found)
  ✗ Global config: ~/.config/lobster/providers.json (not found)
  ✗ Environment: LOBSTER_LLM_PROVIDER (not set)

Quick Setup:
  lobster init              # Configure this workspace
  lobster init --global     # Set global defaults for all workspaces

Or set environment variable:
  export LOBSTER_LLM_PROVIDER=anthropic

This makes troubleshooting much easier - you can see which configuration sources were checked and why they failed.

Common Issues

Issue: "No provider configured" in external workspace

# Solution: Set global defaults (one-time)
lobster init --global
# Now all external workspaces work automatically

Issue: Wrong provider being used

# Check priority order - workspace overrides global
lobster config show-config  # See which config is active

# Force specific provider for this session
lobster chat --provider anthropic

Issue: Invalid environment variable

# v0.4+ raises explicit error for invalid values
export LOBSTER_LLM_PROVIDER=typo
lobster chat
# Error: Invalid provider 'typo' in LOBSTER_LLM_PROVIDER

Configuration Commands

Use lobster config show to see your current configuration with masked secrets.
Use lobster config show-config to see runtime resolution (provider, models, sources).
Use lobster config test to validate API connectivity and test your configuration.
Use lobster init --force to reconfigure (creates a backup of your existing .env file).
Use lobster init --global to set user-wide defaults for all workspaces.
Run lobster chat --debug for verbose configuration loading information.
If you see "No configuration found" errors, run lobster init to create your .env file.

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