setup_environment

This script helps users set up: 1. Conda environment with required dependencies 2. API keys for LLM providers 3. Data lake directory configuration 4. MCP server setup (optional)

Skills
Scientific
0

What it does and how to use it

A skill that teaches Claude Code to do scientific tasks well. It is packaged knowledge the model uses whenever it is relevant.

Install the skill (command above).
In Claude Code, describe what you need - the skill turns on by itself when the context fits.
No commands to memorize: you talk in plain language and the skill does the rest.

Install (Claude Code)

mkdir -p .claude/skills/setup-environment-2 && curl -fsSL https://doutorai.pt/data/lib/skills__setup-environment-2.md -o .claude/skills/setup-environment-2/SKILL.md

Paste this command into the terminal, in your project folder, and the component installs automatically.

Content

#!/usr/bin/env python3
"""
Interactive setup script for biomni environment configuration.

This script helps users set up:
1. Conda environment with required dependencies
2. API keys for LLM providers
3. Data lake directory configuration
4. MCP server setup (optional)

Usage:
    python setup_environment.py
"""

import os
import sys
import subprocess
from pathlib import Path
from typing import Dict, Optional


def check_conda_installed() -> bool:
    """Check if conda is available in the system."""
    try:
        subprocess.run(
            ['conda', '--version'],
            capture_output=

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