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    "## Setup\n",
    "\n",
    "\n",
    "### System structures\n",
    "\n",
    "To run PyJEM, you need Python and several supporting libraries (dependencies).\n",
    "Managing these can be complicated:\n",
    "\n",
    "**Problem without proper setup:**\n",
    "- Different Python projects need different versions of libraries\n",
    "- If library A needs version 1.0 and project B needs version 2.0 of the same library, they conflict\n",
    "- Installing libraries globally can break other projects\n",
    "\n",
    "**Solution: Use Miniconda + virtual environment (vjem)**\n",
    "\n",
    "```\n",
    "Your PC\n",
    "├── System Python (do NOT use for PyJEM)\n",
    "├── Miniconda (Python distribution with conda package manager)\n",
    "│   ├── vjem (isolated virtual environment)\n",
    "│   │   ├── Python 3.x\n",
    "│   │   ├── PyJEM\n",
    "│   │   ├── opencv-python\n",
    "│   │   ├── numpy\n",
    "│   │   └── ... (other dependencies)\n",
    "│   └── ... (other virtual environments)\n",
    "```\n",
    "\n",
    "**Benefits of this structure:**\n",
    "1. **Isolation**: PyJEM and its dependencies are contained in vjem. Other projects on your PC are unaffected.\n",
    "2. **Package management**: The `conda` package manager (in Miniconda) handles dependency conflicts automatically.\n",
    "3. **Reproducibility**: You can recreate the exact same environment on another PC.\n",
    "\n",
    "### Installation order\n",
    "The installation must follow this order because each step depends on the previous one:\n",
    "\n",
    "#### [Step 1: Install Miniconda](Miniconda.ipynb)\n",
    "- Miniconda provides the `conda` command, which you need to create virtual environments.\n",
    "- Without Miniconda, you cannot create the vjem environment.\n",
    "\n",
    "```\n",
    "PC → Miniconda (installed)\n",
    "```\n",
    "\n",
    "#### [Step 2: Install vjem(virtual environment)](vjem.ipynb)\n",
    "- Create a separate environment named “vjem” within the Miniconda environment you created in Step 1.\n",
    "- vjem is organized by Python version and includes its own Python interpreter and package space.\n",
    "- Without vjem, PyJEM would be installed globally and could conflict with other projects.\n",
    "\n",
    "```\n",
    "Miniconda → conda command → vjem (created)\n",
    "```\n",
    "\n",
    "#### [Step 3: Install PyJEM on vjem](PyJEM.ipynb)\n",
    "- You activate the vjem environment to use its isolated Python.\n",
    "- PyJEM will be installed within vjem. In some cases, dependency libraries may also be installed.\n",
    "- PyJEM can only be installed after vjem exists.\n",
    "\n",
    "```\n",
    "vjem (activated) → pip/conda install PyJEM → PyJEM ready to use\n",
    "```\n",
    "\n",
    "```{toctree}\n",
    ":maxdepth: 2\n",
    ":glob:\n",
    "\n",
    "Miniconda\n",
    "vjem\n",
    "PyJEM\n",
    "Appendix/index\n",
    "```"
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