Codex CLI Best Practice

codex-cli-best-practice

Skill by ara.so — Codex Skills collection.

A comprehensive guide and reference implementation for Codex CLI best practices, covering the journey from vibe coding to agentic engineering. This skill teaches you how to leverage Codex CLI's advanced features: subagents, skills, MCP servers, workflows, and configuration patterns.

What This Project Provides

codex-cli-best-practice is a reference repository that demonstrates:

• Subagents: Custom TOML-configured agents for parallel orchestration
• Skills: Reusable instruction packages with progressive disclosure
• MCP Integration: Model Context Protocol servers for external tool access
• Workflows: End-to-end patterns (Agent → Skill → Output)
• Configuration: Layered TOML config system with profiles and approval policies
• Hooks: Shell scripts that inject into the agentic loop
• Memories: Cross-session memory pipeline for context retention

Installation

Prerequisites

1. Install Codex CLI (requires Codex Pro subscription):

   # macOS
   brew install --cask codex-cli
   
   # Or download from https://developers.openai.com/codex/cli
   

2. Clone this repository:

   git clone https://github.com/shanraisshan/codex-cli-best-practice.git
   cd codex-cli-best-practice
   

3. Initialize Codex in your project:

   codex init
   

Key Concepts & Configuration

1. Subagents (.codex/agents/<name>.toml)

Subagents are custom agents with dedicated role configs. Example weather agent:

# .codex/agents/weather-agent.toml
[agents.weather-agent]
model = "gpt-5.4"
instructions = """
You are a weather data specialist. When asked:
1. Extract location and units from user request
2. Fetch current weather from Open-Meteo API
3. Return structured data for downstream skills
"""
temperature = 0.7
max_tokens = 2000

Invoke with:

codex
> @weather-agent Get Dubai weather in Celsius

Global agent settings in .codex/config.toml:

[agents]
max_threads = 4
max_depth = 3
job_max_runtime_seconds = 300

2. Skills (.agents/skills/<name>/SKILL.md)

Skills are reusable instruction packages. Required structure:

.agents/skills/weather-svg-creator/
├── SKILL.md              # Core instructions with YAML frontmatter
├── scripts/              # Helper scripts
│   └── create_svg.py
├── references/           # Documentation
│   └── svg-spec.md
└── assets/              # Templates, images
    └── template.svg

Example SKILL.md:

---
name: weather-svg-creator
description: Creates SVG weather cards from structured weather data
---

# Weather SVG Creator

You create beautiful SVG weather cards. When invoked:

1. Accept weather data (location, temp, condition, humidity)
2. Use scripts/create_svg.py to generate SVG
3. Output to specified path

## Usage Pattern

```python
# scripts/create_svg.py will be called with:
python scripts/create_svg.py \
  --location "Dubai" \
  --temp "32" \
  --condition "Sunny" \
  --output "weather.svg"

Invoke skills:
```bash
# Explicit
codex
> Use $weather-svg-creator to make a card for Dubai, 32°C, Sunny

# Implicit (by description match)
> Create an SVG weather card

3. MCP Servers (.codex/config.toml)

Connect external tools via Model Context Protocol:

# .codex/config.toml
[mcp_servers.filesystem]
command = "npx"
args = ["-y", "@modelcontextprotocol/server-filesystem", "/Users/shan/projects"]
supports_parallel_tool_calls = true

[mcp_servers.github]
command = "npx"
args = ["-y", "@modelcontextprotocol/server-github"]
env = { GITHUB_PERSONAL_ACCESS_TOKEN = "${GITHUB_TOKEN}" }

[mcp_servers.weather]
command = "python"
args = ["-m", "mcp_server_weather"]
working_directory = ".codex/mcp-servers/weather"

Manage MCP servers:

# List available servers
codex mcp list

# Add new server
codex mcp add weather

# Test server
codex mcp get weather

# OAuth login (for supported servers)
codex mcp login github

4. Orchestration Workflow (Agent → Skill)

The canonical pattern from this repo:

codex
> Fetch the current weather for Dubai in Celsius and create the SVG weather card output using the repo.

What happens:

1. @weather-agent fetches data from Open-Meteo
2. Returns structured JSON: {"location": "Dubai", "temp": 32, "condition": "Clear"}
3. Codex matches $weather-svg-creator skill by description
4. Skill runs scripts/create_svg.py with data
5. SVG output saved and displayed

5. Configuration Layers

# .codex/config.toml
[features]
memories = true           # Cross-session memory
codex_hooks = true       # Enable hooks
fast_mode = false        # 1.5x speed mode

[approval_policy]
edits_outside_cwd = "prompt"
deletions = "prompt"
shell_commands = "auto_approve_safe"

[sandbox]
enabled = true
include_patterns = ["src/**", "tests/**"]
exclude_patterns = ["*.pyc", "__pycache__/**"]

[model]
default = "gpt-5.4"
review_model = "gpt-5.4-large-context"
temperature = 0.7

[memories]
max_tokens = 10000
collection_interval_seconds = 300

# Developer instructions (always included)
developer_instructions = """
Follow repo conventions:
- Use type hints in Python
- Run pytest before committing
- Update AGENTS.md for architectural changes
"""

6. Hooks (.codex/hooks.json)

Inject shell scripts into the agentic loop:

{
  "hooks": {
    "before_edit": {
      "script": ".codex/hooks/lint-check.sh",
      "description": "Run linter before edits"
    },
    "after_shell": {
      "script": ".codex/hooks/log-command.sh",
      "description": "Log all shell commands"
    },
    "before_commit": {
      "script": ".codex/hooks/run-tests.sh",
      "description": "Run test suite"
    }
  }
}

Hook script example:

#!/bin/bash
# .codex/hooks/lint-check.sh

# Codex provides context via env vars:
# CODEX_HOOK_FILES, CODEX_HOOK_CONTEXT

for file in $CODEX_HOOK_FILES; do
  if [[ $file == *.py ]]; then
    ruff check "$file" || exit 1
  fi
done

exit 0

7. Plugins & Marketplace

Install plugin marketplaces:

# Add GitHub marketplace
codex plugin marketplace add github:openai/codex-plugins

# Add local marketplace
codex plugin marketplace add ~/my-plugins

# Browse installed plugins
codex
> /plugins

# Install specific plugin
codex plugin install security-scanner

Create a plugin (.codex-plugin/plugin.json):

{
  "name": "my-workflow-plugin",
  "version": "1.0.0",
  "description": "Custom workflow automation",
  "skills": ["skills/planner", "skills/executor"],
  "mcp_servers": {
    "custom-api": {
      "command": "node",
      "args": ["mcp-server.js"]
    }
  }
}

8. Memories (Cross-Session Context)

Enable in config:

[features]
memories = true

[memories]
max_tokens = 10000
collection_interval_seconds = 300

Control via TUI:

codex
> /memories use      # Enable for this session
> /memories reset    # Clear all memories

Memories are user-scoped, not project-scoped.

Common Workflows

Create a New Subagent

codex
> Create a subagent called @api-designer that specializes in REST API design. 
  It should use gpt-5.4-large-context and follow OpenAPI 3.0 standards.
  Save to .codex/agents/api-designer.toml

Create a New Skill

codex
> Use the $skill-creator to make a new skill called database-migrator.
  It should help write Alembic migrations for SQLAlchemy models.
  Include example migration scripts.

Set Up MCP Server for Custom Tool

# .codex/mcp-servers/weather/server.py
from mcp.server import Server
from mcp.server.stdio import stdio_server

app = Server("weather-mcp")

@app.tool()
async def get_weather(location: str, units: str = "celsius"):
    """Fetch current weather for a location."""
    # Integration with Open-Meteo API
    import httpx
    async with httpx.AsyncClient() as client:
        response = await client.get(
            "https://api.open-meteo.com/v1/forecast",
            params={
                "latitude": ...,
                "longitude": ...,
                "current_weather": "true",
                "temperature_unit": units
            }
        )
        return response.json()

if __name__ == "__main__":
    stdio_server(app)

Add to config:

[mcp_servers.weather]
command = "python"
args = [".codex/mcp-servers/weather/server.py"]

Implement Agent → Skill Workflow

1. Create the agent:

# .codex/agents/data-fetcher.toml
[agents.data-fetcher]
model = "gpt-5.4"
instructions = "Fetch data from APIs and return structured JSON"

2. Create the skill:

# .agents/skills/data-visualizer/SKILL.md
---
name: data-visualizer
description: Creates charts from JSON data
---

Accept JSON data and create matplotlib/plotly visualizations.

3. Invoke:

codex
> @data-fetcher get GitHub stars for shanraisshan/codex-cli-best-practice, 
  then $data-visualizer create a trend chart

Enable Fast Mode

codex
> /fast on         # Enable 1.5x speed (2x credits)
> /fast status     # Check current mode
> /fast off        # Disable

Or in config:

[model]
service_tier = "fast"  # Always use fast mode

Code Review Workflow

# Review uncommitted changes
codex
> /review

# Review specific branch
> /review main..feature-branch

# Review with custom instructions
> /review --instructions "Focus on security and performance"

Configure review model:

[model]
review_model = "gpt-5.4-large-context"

Slash Commands Reference

Environment Variables

# Required
export OPENAI_API_KEY="sk-..."  # Codex Pro API key

# Optional
export CODEX_HOME="$HOME/.codex"  # Config directory
export GITHUB_TOKEN="ghp_..."     # For GitHub MCP server
export ANTHROPIC_API_KEY="sk-..." # For Claude models (if configured)

Troubleshooting

Subagent Not Found

Issue: @my-agent not recognized

Solution:

# Check agent config exists
ls .codex/agents/my-agent.toml

# Verify TOML syntax
codex config validate

# Restart codex session
codex
> /exit
codex

Skill Not Triggering

Issue: Skill not invoked implicitly

Solution:

• Use explicit invoke: $skill-name
• Check skill description is specific enough
• Verify SKILL.md has valid YAML frontmatter
• Check .agents/skills/ directory structure

MCP Server Connection Failed

Issue: MCP server 'xyz' not responding

Solution:

# Test server directly
codex mcp get xyz

# Check server logs
cat ~/.codex/logs/mcp-xyz.log

# Verify command and args in config.toml
# Ensure env vars are set (use ${VAR} syntax)

# Restart server
codex mcp remove xyz
codex mcp add xyz

Hooks Not Running

Issue: Hooks defined but not executing

Solution:

# Enable in config
[features]
codex_hooks = true

# Make scripts executable
chmod +x .codex/hooks/*.sh

# Test hook directly
.codex/hooks/my-hook.sh

Memory Not Persisting

Issue: Context lost between sessions

Solution:

codex
> /memories use  # Enable for this thread

# Check feature flag
# In .codex/config.toml:
[features]
memories = true

Approval Policy Too Restrictive

Issue: Every action requires approval

Solution:

[approval_policy]
shell_commands = "auto_approve_safe"  # Auto-approve safe commands
edits_outside_cwd = "auto_approve"    # Less restrictive
network_access = "auto_approve"       # For MCP servers

# Or use profiles
[profiles.dev]
approval_policy.shell_commands = "auto_approve_safe"

Best Practices

1. Start with /plan: Let Codex create execution plans for complex tasks
2. Use AGENTS.md: Document project structure and conventions
3. Namespace subagents: Use descriptive names like @api-designer not @api
4. Scope skills narrowly: One skill = one clear responsibility
5. Test MCP servers: Use codex mcp get to verify before adding to workflow
6. Layer configs: Use profiles for different environments (dev, prod)
7. Enable hooks selectively: Start with after_shell for logging
8. Review approval policy: Balance security and automation
9. Use memories sparingly: Enable only for long-running projects
10. Document workflows: Create .md files showing Agent → Skill patterns

Resources

• Official Docs: https://developers.openai.com/codex/overview
• This Repo: https://github.com/shanraisshan/codex-cli-best-practice
• MCP Spec: https://modelcontextprotocol.io
• Community Skills: https://github.com/topics/codex-cli-skills
• Plugin Marketplace: Built into Codex CLI (/plugins)