source/SOView/Installation.ipynb

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   "source": [
    "# Installation"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This tutorial demonstrates how to install Pysodb on SOVIew (a spatial omics visualization tool).\n",
    "\n",
    "Reference tutorials can be found at https://soview-doc.readthedocs.io/en/latest/index.html \n",
    "and https://github.com/TencentAILabHealthcare/pysodb."
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Installing softwares and tools"
   ]
  },
  {
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   "cell_type": "markdown",
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   "source": [
    "### 1. The first step is to install Visual Studio Code, Conda and Jupyter notebook in advance."
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Reference tutorials presents how to install Visual Studio Code, Conda and Jupyter notebook,respectively. And they can be found at https://code.visualstudio.com/Docs/setup/setup-overview, https://code.visualstudio.com/docs/python/environments#_activating-an-environment-in-the-terminal and https://code.visualstudio.com/docs/datascience/data-science-tutorial."
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 2. Launch Visual Studio Code and open a terminal window. "
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Henceforth, various packages or modules will be installed via the command line"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Installation SOVIew"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 3. Select the installation path and open it"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "cd <path>"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 4. Create a conda environment"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "conda create -n <environment_name> python=3.8"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 5. Activate a conda environment"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Run the following command on the terminal to activate the conda environment:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "conda activate <environment_name>"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 6. Clone SOView code"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "git clone https://github.com/yuanzhiyuan/SOView"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "If cloning the code fails through git, please download it at https://github.com/yuanzhiyuan/SOView, upload it to the folder created above, and extract it."
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 7. Open the SOView directory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "cd SOView"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 8. Install SOView package from source code"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "pip install ."
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Installation Pysodb"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Keep the conda environment active"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 9. Clone Pysodb code"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "git clone https://github.com/TencentAILabHealthcare/pysodb.git"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "If cloning the code fails through git, please download it at https://github.com/TencentAILabHealthcare/pysodb, upload it to the folder created above, and extract it."
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 10. Open the Pysodb directory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "cd pysodb"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 11. Install a Pysodb package from source code"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "python setup.py install"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "If \"error: urllib3 2.0.0a3 is installed but urllib3<1.27,>=1.21.1 is required by {'requests'}\" appears, users can execute the following commands,respectively."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "pip install 'urllib3>=1.21.1,<1.27'\n",
    "python setup.py install"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "finish！\n"
     ]
    }
   ],
   "source": [
    "print('finish！')"
   ]
  }
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