{
 "cells": [
  {
   "cell_type": "markdown",
   "source": [
    "# Anaconda"
   ],
   "metadata": {
    "collapsed": false
   },
   "id": "dcc77f4c10a8ea56"
  },
  {
   "cell_type": "markdown",
   "source": [
    "\n",
    "IMPORTANT: In order to have conda environments persisting between sessions, you need to create them under your home folder ( `/home/maia-user/` ).\n",
    "\n",
    "To create a new conda environment, you can use the following command:"
   ],
   "metadata": {
    "collapsed": false
   },
   "id": "28d56401ca1796d6"
  },
  {
   "cell_type": "code",
   "source": [
    "%%bash\n",
    "\n",
    "/opt/conda/bin/conda create --prefix ~/.conda/envs/<ENV_NAME> -y"
   ],
   "metadata": {
    "collapsed": false,
    "is_executing": true
   },
   "id": "44167bd15429ee0c",
   "outputs": [],
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "To create a conda environment from a specific `environment.yml` file, you can first upload the file to the JupyterLab environment and then run the following command:"
   ],
   "metadata": {
    "collapsed": false
   },
   "id": "4feb6ae09ffa872e"
  },
  {
   "cell_type": "code",
   "source": [
    "%%bash\n",
    "\n",
    "/opt/conda/bin/conda env create --prefix ~/.conda/envs/<ENV_NAME> --file <ENV_YML_FILE> -y"
   ],
   "metadata": {
    "collapsed": false
   },
   "id": "ca7a9678660225fd",
   "outputs": [],
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "In order to be able to use the conda environment on a Jupyter notebook, you will need to create a corresponding Jupyter Kernel. To create a Jupyter kernel from a conda environment, you can use the following command:"
   ],
   "metadata": {
    "collapsed": false
   },
   "id": "3c8aa931767a549a"
  },
  {
   "cell_type": "code",
   "source": [
    "%%bash\n",
    "/opt/conda/bin/conda install --prefix ~/.conda/envs/<ENV_NAME> -c anaconda ipykernel -y\n",
    "\n",
    "~/.conda/envs/<ENV_NAME>/bin/python -m ipykernel install --user --name=<ENV_NAME>"
   ],
   "metadata": {
    "collapsed": false,
    "is_executing": true
   },
   "id": "bbce5ea14a2a1a2a",
   "outputs": [],
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "To install a pip package in the conda environment, you can use the following command:\n"
   ],
   "metadata": {
    "collapsed": false
   },
   "id": "146f993892196b67"
  },
  {
   "cell_type": "code",
   "source": [
    "import sys\n",
    "!{sys.executable} -m pip install <PACKAGE>"
   ],
   "metadata": {
    "collapsed": false
   },
   "id": "e4046a60ff426e9c",
   "outputs": [],
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "## Mamba\n",
    "\n",
    "If you prefer to use `mamba` instead of `conda`, you can install it by running the following command:"
   ],
   "metadata": {
    "collapsed": false
   },
   "id": "6ec39f423cceaf0a"
  },
  {
   "cell_type": "code",
   "source": [
    "%%bash\n",
    "\n",
    "/opt/conda/bin/conda install -c conda-forge mamba -y"
   ],
   "metadata": {
    "collapsed": false,
    "is_executing": true
   },
   "id": "adf9f056f71f6745",
   "outputs": [],
   "execution_count": null
  },
  {
   "cell_type": "markdown",
   "source": [
    "## Anaconda Navigator\n",
    "\n",
    "To install Anaconda Navigator, you can run the following command:"
   ],
   "metadata": {
    "collapsed": false
   },
   "id": "2edcdc2f4267370f"
  },
  {
   "cell_type": "code",
   "source": [
    "%%bash\n",
    "\n",
    "/opt/conda/bin/conda install anaconda-navigator -y"
   ],
   "metadata": {
    "collapsed": false
   },
   "id": "987defd8f6c697d4",
   "outputs": [],
   "execution_count": null
  }
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