Merge branch 'pyenv_kernel_tutorial' into 'master'

Pyenv kernel tutorial See merge request guimaraes1/j4j_notebooks!1

Merge branch 'pyenv_kernel_tutorial' into 'master'
e88c853e · Filipe Guimaraes · bcd08ced · 24dbe2ea · e88c853e
Commit e88c853e authored 3 years ago by Filipe Guimaraes
--- a/001-Jupyter/Create_JupyterKernel_pyenv.ipynb
+++ b/001-Jupyter/Create_JupyterKernel_pyenv.ipynb
+{
+ "cells": [
+  {
+   "attachments": {
+    "500ad0ee-8923-43bb-9336-e838a26dc2f1.jpg": {
+     "image/jpeg": 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"
+    }
+   },
+   "cell_type": "markdown",
+   "metadata": {
+    "toc-hr-collapsed": false
+   },
+   "source": [
+    "![jsc-logo.jpg](attachment:500ad0ee-8923-43bb-9336-e838a26dc2f1.jpg) \n",
+    "Author: [Filipe Guimaraes](mailto:f.guimaraes@fz-juelich.de)\n",
+    "--------------------------------------"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Create your own Jupyter pyenv-Kernel\n",
+    "\n",
+    "Often the standard kernel do not provide all features you need for your work. This might be that certain modules are not loaded or packages are not installed.\n",
+    "With your own kernel you can overcome that problem easily and define your own environment, in which you work.\n",
+    "\n",
+    "This notebook shows you how you can build your own kernel for a **pyenv environment**.\n",
+    "\n",
+    "--------------------------------------"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Building your own Jupyter pyenv-kernel is a four-step process\n",
+    "\n",
+    "1. **[Download/Install pyenv](#install)**: To start from scratch, and run the full installation.\n",
+    "2. **[Create and setup environment](#environment)**: To create an(other) environment in an existing pyenv setup.\n",
+    "3. **[Create/Edit launch script for the Jupyter kernel](#kernel)**: To setup an environment to be run via Jupyter.\n",
+    "4. **[Create/Edit Jupyter kernel configuration](#json)**: To attach your user to an existing environment via Jupyter.  "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "If `pyenv` is already installed, start at 2.\n",
+    "If the environment already exists, start at 3.\n",
+    "If the kernel launch script was already created (e.g., by some other user in the project), start at 4."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<a id='settings'></a>\n",
+    "### Settings"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "To simplifly the process, it is convenient to define a **PYENV_ROOT** path for the central pyenv installation and put on the PATH. "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**Important**: It is recommended to use a folder inside the `$PROJECT` file system, as the `$HOME` quota is low. It is also useful to share installation for different users in a single project."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "export PYENV_ROOT=${PROJECT_<projectid>}/.pyenv\n",
+    "export PATH=\"$PYENV_ROOT/bin:$PATH\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Also the environment name can be set in an environment variable **PYENV_ENV** to simplify the process:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "export PYENV_ENV=my_env"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "These lines can be added to `~/.bash_profile` (and then `source ~/.bash_profile`) to automatically set the PATH in case of restarting the shell."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "---\n",
+    "<a id='install'></a>\n",
+    "## 1. Download/Install pyenv"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Installing and setting up pyenv from scratch is very simple. A simple command is needed to install pyenv in **$PYENV_ROOT**:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "curl https://pyenv.run | bash"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "---\n",
+    "<a id='environment'></a>\n",
+    "## 2. Create and setup pyenv environment"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The following steps describe how to create and setup a new pyenv environment to be used as a jupyter kernel. They can be repeated if multiple environments are required."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "* 2.1 - Activate pyenv and virtual envs"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Since it is necessary to activate the environment to install the required modules, the following commands should be added to `~/.bash_profile` to activate pyenv and the virtual environments:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "eval \"$(pyenv init --path)\"\n",
+    "eval \"$(pyenv init -)\"\n",
+    "eval \"$(pyenv virtualenv-init -)\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "And activate the lines"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "source ~/.bash_profile"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "* 2.2 - Install a python version (e.g. `3.10.1`)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pyenv install 3.10.1"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Note: This step may take a few minutes to complete the installation."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "* 2.3 - Create a new environment **$PYENV_ENV**"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The environment is created using the python version installed above"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pyenv virtualenv 3.10.1 $PYENV_ENV"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "* 2.4 - Activate and setup the environment"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Jupyter requires the `ipykernel` module and its dependencies. To install them, first activate the environment:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pyenv activate $PYENV_ENV"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "When the environment is successfully activated, the name of the environment is shown between parenthesis in the command line, e.g. `(my_env)`. (To deactivate the environment, use `pyenv deactivate $PYENV_ENV`.)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The python version can be checked using"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "(my_env)$ python --version\n",
+    "Python 3.10.1"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The list of python modules is still empty"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "(my_env)$ pip list\n",
+    "Package    Version\n",
+    "---------- -------\n",
+    "pip        21.2.4\n",
+    "setuptools 58.1.0"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "To create a Jupyter kernel, the `ipykernel` and its dependencies are required. `pip` can be used to install it:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pip install ipykernel"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Many modules are installed:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "(my_env)$ pip list\n",
+    "Package           Version\n",
+    "----------------- -------\n",
+    "backcall          0.2.0\n",
+    "debugpy           1.5.1\n",
+    "decorator         5.1.1\n",
+    "entrypoints       0.3\n",
+    "ipykernel         6.6.1\n",
+    "ipython           7.31.0\n",
+    "jedi              0.18.1\n",
+    "jupyter-client    7.1.0\n",
+    "jupyter-core      4.9.1\n",
+    "matplotlib-inline 0.1.3\n",
+    "nest-asyncio      1.5.4\n",
+    "parso             0.8.3\n",
+    "pexpect           4.8.0\n",
+    "pickleshare       0.7.5\n",
+    "pip               21.1.1\n",
+    "prompt-toolkit    3.0.24\n",
+    "ptyprocess        0.7.0\n",
+    "Pygments          2.11.2\n",
+    "python-dateutil   2.8.2\n",
+    "pyzmq             22.3.0\n",
+    "setuptools        56.0.0\n",
+    "six               1.16.0\n",
+    "tornado           6.1\n",
+    "traitlets         5.1.1\n",
+    "wcwidth           0.2.5"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "---\n",
+    "<a id='kernel'></a>\n",
+    "## 3. Create/Edit launch script for the Jupyter kernel"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The following steps describe how to create and configure the launch script of a new Jupyter kernel using a pyenv environment. If the environment was created in the $PROJECT folder, many users of the project can follow these steps to create the kernel. The steps assume the variables described in the **[Settings section](#settings)** are set up. Here, they don't need to be set in `~/.bash_profile` or `~/.bashrc`."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<a id='launch'></a>\n",
+    "* 3.1 - Create kernel script to allow access to the pyenv environment"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "echo '#!/bin/bash\n",
+    "\n",
+    "module purge\n",
+    "\n",
+    "export PYENV_ROOT='\"$PYENV_ROOT\"'\n",
+    "export PATH='\"$PYENV_ROOT\"'/bin:'\"$PATH\"'\n",
+    "eval \"$(pyenv init --path)\"\n",
+    "eval \"$(pyenv init -)\"\n",
+    "eval \"$(pyenv virtualenv-init -)\"\n",
+    "\n",
+    "# Activate your Python virtual environment\n",
+    "pyenv activate '\"${PYENV_ENV}\"'\n",
+    "\n",
+    "exec python -m ipykernel $@' > ${PYENV_ROOT}/versions/${PYENV_ENV}/kernel.sh"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Note: the `export` and `eval` lines are repeated here as they are not required to be in `~/.bash_profile` on these steps."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Add executable permission to the script:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "chmod +x ${PYENV_ROOT}/versions/${PYENV_ENV}/kernel.sh"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "---\n",
+    "## 4. Create/Edit Jupyter kernel configuration"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "These steps describe how to create a Jupyter kernel configuration file, to be able to access the environment via a Jupyter notebook. To access an existing pyenv environment located in **$PROJECT**, only these steps are necessary. The steps assume the variables described in the **[Settings section](#settings)** are set up."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "* 4.1 - Create a folder for the kernel"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mkdir -p $HOME/.local/share/jupyter/kernels/pyenv_${PYENV_ENV}"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "* 4.2 - Create and adjust the kernel.json file"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "echo '{\n",
+    " \"argv\": [\n",
+    "  \"'\"${PYENV_ROOT}\"'/versions/'\"${PYENV_ENV}\"'/kernel.sh\",\n",
+    "  \"-f\",\n",
+    "  \"{connection_file}\"\n",
+    " ],\n",
+    " \"display_name\": \"pyenv_'\"${PYENV_ENV}\"'\",\n",
+    " \"language\": \"python\"\n",
+    "}' > $HOME/.local/share/jupyter/kernels/pyenv_${PYENV_ENV}/kernel.json"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Restart of JupyterLab might be necessary to see the kernel in the kernel selection overview."
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Bash",
+   "language": "bash",
+   "name": "bash"
+  },
+  "language_info": {
+   "codemirror_mode": "shell",
+   "file_extension": ".sh",
+   "mimetype": "text/x-sh",
+   "name": "bash"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
+%% Cell type:markdown id: tags:
+
+![jsc-logo.jpg](attachment:500ad0ee-8923-43bb-9336-e838a26dc2f1.jpg)
+Author: [Filipe Guimaraes](mailto:f.guimaraes@fz-juelich.de)
+--------------------------------------
+
+%% Cell type:markdown id: tags:
+
+# Create your own Jupyter pyenv-Kernel
+
+Often the standard kernel do not provide all features you need for your work. This might be that certain modules are not loaded or packages are not installed.
+With your own kernel you can overcome that problem easily and define your own environment, in which you work.
+
+This notebook shows you how you can build your own kernel for a **pyenv environment**.
+
+--------------------------------------
+
+%% Cell type:markdown id: tags:
+
+## Building your own Jupyter pyenv-kernel is a four-step process
+
+1. **[Download/Install pyenv](#install)**: To start from scratch, and run the full installation.
+2. **[Create and setup environment](#environment)**: To create an(other) environment in an existing pyenv setup.
+3. **[Create/Edit launch script for the Jupyter kernel](#kernel)**: To setup an environment to be run via Jupyter.
+4. **[Create/Edit Jupyter kernel configuration](#json)**: To attach your user to an existing environment via Jupyter.
+
+%% Cell type:markdown id: tags:
+
+If `pyenv` is already installed, start at 2.
+If the environment already exists, start at 3.
+If the kernel launch script was already created (e.g., by some other user in the project), start at 4.
+
+%% Cell type:markdown id: tags:
+
+<a id='settings'></a>
+### Settings
+
+%% Cell type:markdown id: tags:
+
+To simplifly the process, it is convenient to define a **PYENV_ROOT** path for the central pyenv installation and put on the PATH.
+
+%% Cell type:markdown id: tags:
+
+**Important**: It is recommended to use a folder inside the `$PROJECT` file system, as the `$HOME` quota is low. It is also useful to share installation for different users in a single project.
+
+%% Cell type:code id: tags:
+
+``` bash
+export PYENV_ROOT=${PROJECT_<projectid>}/.pyenv
+export PATH="$PYENV_ROOT/bin:$PATH"
+```
+
+%% Cell type:markdown id: tags:
+
+Also the environment name can be set in an environment variable **PYENV_ENV** to simplify the process:
+
+%% Cell type:code id: tags:
+
+``` bash
+export PYENV_ENV=my_env
+```
+
+%% Cell type:markdown id: tags:
+
+These lines can be added to `~/.bash_profile` (and then `source ~/.bash_profile`) to automatically set the PATH in case of restarting the shell.
+
+%% Cell type:markdown id: tags:
+
+---
+<a id='install'></a>
+## 1. Download/Install pyenv
+
+%% Cell type:markdown id: tags:
+
+Installing and setting up pyenv from scratch is very simple. A simple command is needed to install pyenv in **$PYENV_ROOT**:
+
+%% Cell type:code id: tags:
+
+``` bash
+curl https://pyenv.run | bash
+```
+
+%% Cell type:markdown id: tags:
+
+---
+<a id='environment'></a>
+## 2. Create and setup pyenv environment
+
+%% Cell type:markdown id: tags:
+
+The following steps describe how to create and setup a new pyenv environment to be used as a jupyter kernel. They can be repeated if multiple environments are required.
+
+%% Cell type:markdown id: tags:
+
+* 2.1 - Activate pyenv and virtual envs
+
+%% Cell type:markdown id: tags:
+
+Since it is necessary to activate the environment to install the required modules, the following commands should be added to `~/.bash_profile` to activate pyenv and the virtual environments:
+
+%% Cell type:code id: tags:
+
+``` bash
+eval "$(pyenv init --path)"
+eval "$(pyenv init -)"
+eval "$(pyenv virtualenv-init -)"
+```
+
+%% Cell type:markdown id: tags:
+
+And activate the lines
+
+%% Cell type:code id: tags:
+
+``` bash
+source ~/.bash_profile
+```
+
+%% Cell type:markdown id: tags:
+
+* 2.2 - Install a python version (e.g. `3.10.1`)
+
+%% Cell type:code id: tags:
+
+``` bash
+pyenv install 3.10.1
+```
+
+%% Cell type:markdown id: tags:
+
+Note: This step may take a few minutes to complete the installation.
+
+%% Cell type:markdown id: tags:
+
+* 2.3 - Create a new environment **$PYENV_ENV**
+
+%% Cell type:markdown id: tags:
+
+The environment is created using the python version installed above
+
+%% Cell type:code id: tags:
+
+``` bash
+pyenv virtualenv 3.10.1 $PYENV_ENV
+```
+
+%% Cell type:markdown id: tags:
+
+* 2.4 - Activate and setup the environment
+
+%% Cell type:markdown id: tags:
+
+Jupyter requires the `ipykernel` module and its dependencies. To install them, first activate the environment:
+
+%% Cell type:code id: tags:
+
+``` bash
+pyenv activate $PYENV_ENV
+```
+
+%% Cell type:markdown id: tags:
+
+When the environment is successfully activated, the name of the environment is shown between parenthesis in the command line, e.g. `(my_env)`. (To deactivate the environment, use `pyenv deactivate $PYENV_ENV`.)
+
+%% Cell type:markdown id: tags:
+
+The python version can be checked using
+
+%% Cell type:code id: tags:
+
+``` bash
+(my_env)$ python --version
+Python 3.10.1
+```
+
+%% Cell type:markdown id: tags:
+
+The list of python modules is still empty
+
+%% Cell type:code id: tags:
+
+``` bash
+(my_env)$ pip list
+Package    Version
+---------- -------
+pip        21.2.4
+setuptools 58.1.0
+```
+
+%% Cell type:markdown id: tags:
+
+To create a Jupyter kernel, the `ipykernel` and its dependencies are required. `pip` can be used to install it:
+
+%% Cell type:code id: tags:
+
+``` bash
+pip install ipykernel
+```
+
+%% Cell type:markdown id: tags:
+
+Many modules are installed:
+
+%% Cell type:code id: tags:
+
+``` bash
+(my_env)$ pip list
+Package           Version
+----------------- -------
+backcall          0.2.0
+debugpy           1.5.1
+decorator         5.1.1
+entrypoints       0.3
+ipykernel         6.6.1
+ipython           7.31.0
+jedi              0.18.1
+jupyter-client    7.1.0
+jupyter-core      4.9.1
+matplotlib-inline 0.1.3
+nest-asyncio      1.5.4
+parso             0.8.3
+pexpect           4.8.0
+pickleshare       0.7.5
+pip               21.1.1
+prompt-toolkit    3.0.24
+ptyprocess        0.7.0
+Pygments          2.11.2
+python-dateutil   2.8.2
+pyzmq             22.3.0
+setuptools        56.0.0
+six               1.16.0
+tornado           6.1
+traitlets         5.1.1
+wcwidth           0.2.5
+```
+
+%% Cell type:markdown id: tags:
+
+---
+<a id='kernel'></a>
+## 3. Create/Edit launch script for the Jupyter kernel
+
+%% Cell type:markdown id: tags:
+
+The following steps describe how to create and configure the launch script of a new Jupyter kernel using a pyenv environment. If the environment was created in the $PROJECT folder, many users of the project can follow these steps to create the kernel. The steps assume the variables described in the **[Settings section](#settings)** are set up. Here, they don't need to be set in `~/.bash_profile` or `~/.bashrc`.
+
+%% Cell type:markdown id: tags:
+
+<a id='launch'></a>
+* 3.1 - Create kernel script to allow access to the pyenv environment
+
+%% Cell type:code id: tags:
+
+``` bash
+echo '#!/bin/bash
+
+module purge
+
+export PYENV_ROOT='"$PYENV_ROOT"'
+export PATH='"$PYENV_ROOT"'/bin:'"$PATH"'
+eval "$(pyenv init --path)"
+eval "$(pyenv init -)"
+eval "$(pyenv virtualenv-init -)"
+
+# Activate your Python virtual environment
+pyenv activate '"${PYENV_ENV}"'
+
+exec python -m ipykernel $@' > ${PYENV_ROOT}/versions/${PYENV_ENV}/kernel.sh
+```
+
+%% Cell type:markdown id: tags:
+
+Note: the `export` and `eval` lines are repeated here as they are not required to be in `~/.bash_profile` on these steps.
+
+%% Cell type:markdown id: tags:
+
+Add executable permission to the script:
+
+%% Cell type:code id: tags:
+
+``` bash
+chmod +x ${PYENV_ROOT}/versions/${PYENV_ENV}/kernel.sh
+```
+
+%% Cell type:markdown id: tags:
+
+---
+## 4. Create/Edit Jupyter kernel configuration
+
+%% Cell type:markdown id: tags:
+
+These steps describe how to create a Jupyter kernel configuration file, to be able to access the environment via a Jupyter notebook. To access an existing pyenv environment located in **$PROJECT**, only these steps are necessary. The steps assume the variables described in the **[Settings section](#settings)** are set up.
+
+%% Cell type:markdown id: tags:
+
+* 4.1 - Create a folder for the kernel
+
+%% Cell type:code id: tags:
+
+``` bash
+mkdir -p $HOME/.local/share/jupyter/kernels/pyenv_${PYENV_ENV}
+```
+
+%% Cell type:markdown id: tags:
+
+* 4.2 - Create and adjust the kernel.json file
+
+%% Cell type:code id: tags:
+
+``` bash
+echo '{
+ "argv": [
+  "'"${PYENV_ROOT}"'/versions/'"${PYENV_ENV}"'/kernel.sh",
+  "-f",
+  "{connection_file}"
+ ],
+ "display_name": "pyenv_'"${PYENV_ENV}"'",
+ "language": "python"
+}' > $HOME/.local/share/jupyter/kernels/pyenv_${PYENV_ENV}/kernel.json
+```
+
+%% Cell type:markdown id: tags:
+
+Restart of JupyterLab might be necessary to see the kernel in the kernel selection overview.