docker-stacks/docs/using/recipes.md

# Contributed Recipes

Users sometimes share interesting ways of using the Jupyter Docker Stacks.
We encourage users to [contribute these recipes](../contributing/recipes.md) to the documentation in case they prove helpful to other community members by submitting a pull request to `docs/using/recipes.md`.
The sections below capture this knowledge.

## Using `sudo` within a container

Password authentication is disabled for the `NB_USER` (e.g., `jovyan`).
We made this choice to avoid distributing images with a weak default password that users ~might~ will forget to change before running a container on a publicly accessible host.

You can grant the within-container `NB_USER` passwordless `sudo` access by adding `--user root` and `-e GRANT_SUDO=yes` to your Docker command line or appropriate container orchestrator config.

For example:

```bash
docker run -it --rm \
    --user root \
    -e GRANT_SUDO=yes \
    jupyter/minimal-notebook
```

**You should only enable `sudo` if you trust the user and/or if the container is running on an isolated host.**
See [Docker security documentation](https://docs.docker.com/engine/security/userns-remap/) for more information about running containers as `root`.

## Using `mamba install` or `pip install` in a Child Docker image

Create a new Dockerfile like the one shown below.

```dockerfile
# Start from a core stack version
FROM jupyter/datascience-notebook:2023-02-28
# Install in the default python3 environment
RUN pip install --no-cache-dir 'flake8==3.9.2' && \
    fix-permissions "${CONDA_DIR}" && \
    fix-permissions "/home/${NB_USER}"
```

Then build a new image.

```bash
docker build --rm -t jupyter/my-datascience-notebook .
```

To use a requirements.txt file, first, create your `requirements.txt` file with the listing of
packages desired.
Next, create a new Dockerfile like the one shown below.

```dockerfile
# Start from a core stack version
FROM jupyter/datascience-notebook:2023-02-28
# Install from the requirements.txt file
COPY --chown=${NB_UID}:${NB_GID} requirements.txt /tmp/
RUN pip install --no-cache-dir --requirement /tmp/requirements.txt && \
    fix-permissions "${CONDA_DIR}" && \
    fix-permissions "/home/${NB_USER}"
```

For conda, the Dockerfile is similar:

```dockerfile
# Start from a core stack version
FROM jupyter/datascience-notebook:2023-02-28
# Install from the requirements.txt file
COPY --chown=${NB_UID}:${NB_GID} requirements.txt /tmp/
RUN mamba install --yes --file /tmp/requirements.txt && \
    mamba clean --all -f -y && \
    fix-permissions "${CONDA_DIR}" && \
    fix-permissions "/home/${NB_USER}"
```

Ref: [docker-stacks/commit/79169618d571506304934a7b29039085e77db78c](https://github.com/jupyter/docker-stacks/commit/79169618d571506304934a7b29039085e77db78c#r15960081)

## Add a custom conda environment and Jupyter kernel

The default version of Python that ships with the image may not be the version you want.
The instructions below permit adding a conda environment with a different Python version and making it accessible to Jupyter.

```dockerfile
# Choose your desired base image
FROM jupyter/minimal-notebook:latest

# name your environment and choose the python version
ARG conda_env=python37
ARG py_ver=3.7

# you can add additional libraries you want mamba to install by listing them below the first line and ending with "&& \"
RUN mamba create --yes -p "${CONDA_DIR}/envs/${conda_env}" python=${py_ver} ipython ipykernel && \
    mamba clean --all -f -y

# alternatively, you can comment out the lines above and uncomment those below
# if you'd prefer to use a YAML file present in the docker build context

# COPY --chown=${NB_UID}:${NB_GID} environment.yml "/home/${NB_USER}/tmp/"
# RUN cd "/home/${NB_USER}/tmp/" && \
#     mamba env create -p "${CONDA_DIR}/envs/${conda_env}" -f environment.yml && \
#     mamba clean --all -f -y

# create Python kernel and link it to jupyter
RUN "${CONDA_DIR}/envs/${conda_env}/bin/python" -m ipykernel install --user --name="${conda_env}" && \
    fix-permissions "${CONDA_DIR}" && \
    fix-permissions "/home/${NB_USER}"

# any additional pip installs can be added by uncommenting the following line
# RUN "${CONDA_DIR}/envs/${conda_env}/bin/pip" install --no-cache-dir

# if you want this environment to be the default one, uncomment the following line:
# RUN echo "conda activate ${conda_env}" >> "${HOME}/.bashrc"
```

## Dask JupyterLab Extension

[Dask JupyterLab Extension](https://github.com/dask/dask-labextension) provides a JupyterLab extension to manage Dask clusters, as well as embed Dask's dashboard plots directly into JupyterLab panes.
Create the Dockerfile as:

```dockerfile
# Start from a core stack version
FROM jupyter/scipy-notebook:latest

# Install the Dask dashboard
RUN pip install --no-cache-dir dask-labextension && \
    fix-permissions "${CONDA_DIR}" && \
    fix-permissions "/home/${NB_USER}"

# Dask Scheduler & Bokeh ports
EXPOSE 8787
EXPOSE 8786

ENTRYPOINT ["jupyter", "lab", "--ip=0.0.0.0", "--allow-root"]
```

And build the image as:

```bash
docker build -t jupyter/scipy-dasklabextension:latest .
```

Once built, run using the command:

```bash
docker run -it --rm \
    -p 8888:8888 \
    -p 8787:8787 jupyter/scipy-dasklabextension:latest
```

Ref: <https://github.com/jupyter/docker-stacks/issues/999>

## Let's Encrypt a Notebook server

See the README for a basic automation here
<https://github.com/jupyter/docker-stacks/tree/main/examples/make-deploy>
which includes steps for requesting and renewing a Let's Encrypt certificate.

Ref: <https://github.com/jupyter/docker-stacks/issues/78>

## Slideshows with Jupyter and RISE

[RISE](https://github.com/damianavila/RISE) allows via an extension to create live slideshows of your
notebooks, with no conversion, adding javascript Reveal.js:

```bash
# Add Live slideshows with RISE
RUN mamba install --yes -c damianavila82 rise && \
    mamba clean --all -f -y && \
    fix-permissions "${CONDA_DIR}" && \
    fix-permissions "/home/${NB_USER}"
```

Credit: [Paolo D.](https://github.com/pdonorio) based on
[docker-stacks/issues/43](https://github.com/jupyter/docker-stacks/issues/43)

## xgboost

You need to install conda-forge's gcc for Python xgboost to work correctly.
Otherwise, you'll get an exception about libgomp.so.1 missing GOMP_4.0.

```bash
mamba install --yes gcc && \
    mamba clean --all -f -y && \
    fix-permissions "${CONDA_DIR}" && \
    fix-permissions "/home/${NB_USER}"

pip install --no-cache-dir xgboost && \
    fix-permissions "${CONDA_DIR}" && \
    fix-permissions "/home/${NB_USER}"

# run "import xgboost" in python
```

## Running behind an nginx proxy

Sometimes it is helpful to run the Jupyter instance behind an nginx proxy, for example:

- you would prefer to access the notebook at a server URL with a path
  (`https://example.com/jupyter`) rather than a port (`https://example.com:8888`)
- you may have many services in addition to Jupyter running on the same server
  and want nginx to help improve server performance in managing the connections

Here is a [quick example of NGINX configuration](https://gist.github.com/cboettig/8643341bd3c93b62b5c2) to get started.
You'll need a server, a `.crt` and `.key` file for your server, and `docker` & `docker-compose` installed.
Then download the files at that gist and run `docker-compose up -d` to test it out.
Customize the `nginx.conf` file to set the desired paths and add other services.

## Host volume mounts and notebook errors

If you are mounting a host directory as `/home/jovyan/work` in your container,
and you receive permission errors or connection errors when you create a notebook,
be sure that the `jovyan` user (`UID=1000` by default) has read/write access to the directory on the host.
Alternatively, specify the UID of the `jovyan` user on container startup using the `-e NB_UID` option
described in the [Common Features, Docker Options section](common.md#docker-options)

Ref: <https://github.com/jupyter/docker-stacks/issues/199>

## Manpage installation

Most containers, including our Ubuntu base image, ship without manpages installed to save space.
You can use the following Dockerfile to inherit from one of our images to enable manpages:

```dockerfile
# Choose your desired base image
ARG BASE_CONTAINER=jupyter/datascience-notebook:latest
FROM $BASE_CONTAINER

USER root

# `/etc/dpkg/dpkg.cfg.d/excludes` contains several `path-exclude`s, including man pages
# Remove it, then install man, install docs
RUN rm /etc/dpkg/dpkg.cfg.d/excludes && \
    apt-get update --yes && \
    dpkg -l | grep ^ii | cut -d' ' -f3 | xargs apt-get install --yes --no-install-recommends --reinstall man && \
    apt-get clean && rm -rf /var/lib/apt/lists/*

USER ${NB_UID}
```

Adding the documentation on top of the existing single-user image wastes a lot of space
and requires reinstalling every system package,
which can take additional time and bandwidth.
The `datascience-notebook` image has been shown to grow by almost 3GB when adding manpages in this way.
Enabling manpages in the base Ubuntu layer prevents this container bloat.
To achieve this, use the previous `Dockerfile`'s commands with the original `ubuntu` image as your base container:

```dockerfile
ARG BASE_CONTAINER=ubuntu:22.04
```

For Ubuntu 18.04 (bionic) and earlier, you may also require to a workaround for a mandb bug, which was fixed in mandb >= 2.8.6.1:

```dockerfile
# https://git.savannah.gnu.org/cgit/man-db.git/commit/?id=8197d7824f814c5d4b992b4c8730b5b0f7ec589a
# https://launchpadlibrarian.net/435841763/man-db_2.8.5-2_2.8.6-1.diff.gz

RUN echo "MANPATH_MAP ${CONDA_DIR}/bin ${CONDA_DIR}/man" >> /etc/manpath.config && \
    echo "MANPATH_MAP ${CONDA_DIR}/bin ${CONDA_DIR}/share/man" >> /etc/manpath.config && \
    mandb
```

Be sure to check the current base image in `base-notebook` before building.

## JupyterHub

We also have contributed recipes for using JupyterHub.

### Use JupyterHub's dockerspawner

In most cases for use with DockerSpawner, given an image that already has a notebook stack set up,
you would only need to add:

1. install the jupyterhub-singleuser script (for the correct Python version)
2. change the command to launch the single-user server

Swapping out the `FROM` line in the `jupyterhub/singleuser` Dockerfile should be enough for most
cases.

Credit: [Justin Tyberg](https://github.com/jtyberg), [quanghoc](https://github.com/quanghoc), and
[Min RK](https://github.com/minrk) based on
[docker-stacks/issues/124](https://github.com/jupyter/docker-stacks/issues/124) and
[docker-stacks/pull/185](https://github.com/jupyter/docker-stacks/pull/185)

### Containers with a specific version of JupyterHub

To use a specific version of JupyterHub, the version of `jupyterhub` in your image should match the
version in the Hub itself.

```dockerfile
FROM jupyter/base-notebook:2023-02-28
RUN pip install --no-cache-dir jupyterhub==1.4.1 && \
    fix-permissions "${CONDA_DIR}" && \
    fix-permissions "/home/${NB_USER}"
```

Credit: [MinRK](https://github.com/jupyter/docker-stacks/issues/423#issuecomment-322767742)

Ref: <https://github.com/jupyter/docker-stacks/issues/177>

## Spark

A few suggestions have been made regarding using Docker Stacks with spark.

### Using PySpark with AWS S3

Using Spark session for Hadoop 2.7.3

```python
import os

# !ls /usr/local/spark/jars/hadoop* # to figure out what version of Hadoop
os.environ[
    "PYSPARK_SUBMIT_ARGS"
] = '--packages "org.apache.hadoop:hadoop-aws:2.7.3" pyspark-shell'

import pyspark

myAccessKey = input()
mySecretKey = input()

spark = (
    pyspark.sql.SparkSession.builder.master("local[*]")
    .config("spark.hadoop.fs.s3a.access.key", myAccessKey)
    .config("spark.hadoop.fs.s3a.secret.key", mySecretKey)
    .getOrCreate()
)

df = spark.read.parquet("s3://myBucket/myKey")
```

Using Spark context for Hadoop 2.6.0

```python
import os

os.environ[
    "PYSPARK_SUBMIT_ARGS"
] = "--packages com.amazonaws:aws-java-sdk:1.10.34,org.apache.hadoop:hadoop-aws:2.6.0 pyspark-shell"

import pyspark

sc = pyspark.SparkContext("local[*]")

from pyspark.sql import SQLContext

sqlContext = SQLContext(sc)

hadoopConf = sc._jsc.hadoopConfiguration()
myAccessKey = input()
mySecretKey = input()
hadoopConf.set("fs.s3.impl", "org.apache.hadoop.fs.s3native.NativeS3FileSystem")
hadoopConf.set("fs.s3.awsAccessKeyId", myAccessKey)
hadoopConf.set("fs.s3.awsSecretAccessKey", mySecretKey)

df = sqlContext.read.parquet("s3://myBucket/myKey")
```

Ref: <https://github.com/jupyter/docker-stacks/issues/127>

### Using Local Spark JARs

```python
import os

os.environ[
    "PYSPARK_SUBMIT_ARGS"
] = "--jars /home/jovyan/spark-streaming-kafka-assembly_2.10-1.6.1.jar pyspark-shell"
import pyspark
from pyspark.streaming.kafka import KafkaUtils
from pyspark.streaming import StreamingContext

sc = pyspark.SparkContext()
ssc = StreamingContext(sc, 1)
broker = "<my_broker_ip>"
directKafkaStream = KafkaUtils.createDirectStream(
    ssc, ["test1"], {"metadata.broker.list": broker}
)
directKafkaStream.pprint()
ssc.start()
```

Ref: <https://github.com/jupyter/docker-stacks/issues/154>

### Using spark-packages.org

If you'd like to use packages from [spark-packages.org](https://spark-packages.org/), see
[https://gist.github.com/parente/c95fdaba5a9a066efaab](https://gist.github.com/parente/c95fdaba5a9a066efaab)
for an example of how to specify the package identifier in the environment before creating a
SparkContext.

Ref: <https://github.com/jupyter/docker-stacks/issues/43>

### Use jupyter/all-spark-notebooks with an existing Spark/YARN cluster

```dockerfile
FROM jupyter/all-spark-notebook

# Set env vars for pydoop
ENV HADOOP_HOME /usr/local/hadoop-2.7.3
ENV JAVA_HOME /usr/lib/jvm/java-8-openjdk-amd64
ENV HADOOP_CONF_HOME /usr/local/hadoop-2.7.3/etc/hadoop
ENV HADOOP_CONF_DIR  /usr/local/hadoop-2.7.3/etc/hadoop

USER root
# Add proper open-jdk-8 not the jre only, needed for pydoop
RUN echo 'deb https://cdn-fastly.deb.debian.org/debian jessie-backports main' > /etc/apt/sources.list.d/jessie-backports.list && \
    apt-get update --yes && \
    apt-get install --yes --no-install-recommends -t jessie-backports openjdk-8-jdk && \
    rm /etc/apt/sources.list.d/jessie-backports.list && \
    apt-get clean && rm -rf /var/lib/apt/lists/* && \
# Add Hadoop binaries
    wget https://mirrors.ukfast.co.uk/sites/ftp.apache.org/hadoop/common/hadoop-2.7.3/hadoop-2.7.3.tar.gz && \
    tar -xvf hadoop-2.7.3.tar.gz -C /usr/local && \
    chown -R "${NB_USER}:users" /usr/local/hadoop-2.7.3 && \
    rm -f hadoop-2.7.3.tar.gz && \
# Install os dependencies required for pydoop, pyhive
    apt-get update --yes && \
    apt-get install --yes --no-install-recommends build-essential python-dev libsasl2-dev && \
    apt-get clean && rm -rf /var/lib/apt/lists/* && \
# Remove the example hadoop configs and replace
# with those for our cluster.
# Alternatively, this could be mounted as a volume
    rm -f /usr/local/hadoop-2.7.3/etc/hadoop/*

# Download this from ambari/cloudera manager and copy it here
COPY example-hadoop-conf/ /usr/local/hadoop-2.7.3/etc/hadoop/

# Spark-Submit doesn't work unless I set the following
RUN echo "spark.driver.extraJavaOptions -Dhdp.version=2.5.3.0-37" >> /usr/local/spark/conf/spark-defaults.conf  && \
    echo "spark.yarn.am.extraJavaOptions -Dhdp.version=2.5.3.0-37" >> /usr/local/spark/conf/spark-defaults.conf && \
    echo "spark.master=yarn" >>  /usr/local/spark/conf/spark-defaults.conf && \
    echo "spark.hadoop.yarn.timeline-service.enabled=false" >> /usr/local/spark/conf/spark-defaults.conf && \
    chown -R "${NB_USER}:users" /usr/local/spark/conf/spark-defaults.conf && \
    # Create an alternative HADOOP_CONF_HOME so we can mount as a volume and repoint
    # using ENV var if needed
    mkdir -p /etc/hadoop/conf/ && \
    chown "${NB_USER}":users /etc/hadoop/conf/

USER ${NB_UID}

# Install useful jupyter extensions and python libraries like :
# - Dashboards
# - PyDoop
# - PyHive
RUN pip install --no-cache-dir jupyter_dashboards faker && \
    jupyter dashboards quick-setup --sys-prefix && \
    pip2 install --no-cache-dir pyhive pydoop thrift sasl thrift_sasl faker && \
    fix-permissions "${CONDA_DIR}" && \
    fix-permissions "/home/${NB_USER}"

USER root
# Ensure we overwrite the kernel config so that toree connects to cluster
RUN jupyter toree install --sys-prefix --spark_opts="\
    --master yarn \
    --deploy-mode client \
    --driver-memory 512m \
    --executor-memory 512m \
    --executor-cores 1 \
    --driver-java-options \
    -Dhdp.version=2.5.3.0-37 \
    --conf spark.hadoop.yarn.timeline-service.enabled=false \
"
USER ${NB_UID}
```

Credit: [britishbadger](https://github.com/britishbadger) from [docker-stacks/issues/369](https://github.com/jupyter/docker-stacks/issues/369)

## Run Jupyter Notebook/Lab inside an already secured environment (i.e., with no token)

(Adapted from [issue 728](https://github.com/jupyter/docker-stacks/issues/728))

The default security is very good.
There are use cases, encouraged by containers, where the jupyter container and the system it runs within lie inside the security boundary.
It is convenient to launch the server without a password or token in these use cases.
In this case, you should use the `start.sh` script to launch the server with no token:

For JupyterLab:

```bash
docker run -it --rm \
    jupyter/base-notebook:2023-02-28 \
    start.sh jupyter lab --LabApp.token=''
```

For jupyter classic:

```bash
docker run -it --rm \
    jupyter/base-notebook:2023-02-28 \
    start.sh jupyter notebook --NotebookApp.token=''
```

## Enable nbextension spellchecker for markdown (or any other nbextension)

NB: this works for classic notebooks only

```dockerfile
# Update with your base image of choice
FROM jupyter/minimal-notebook:latest

USER ${NB_UID}

RUN pip install --no-cache-dir jupyter_contrib_nbextensions && \
    jupyter contrib nbextension install --user && \
    # can modify or enable additional extensions here
    jupyter nbextension enable spellchecker/main --user && \
    fix-permissions "${CONDA_DIR}" && \
    fix-permissions "/home/${NB_USER}"
```

Ref: <https://github.com/jupyter/docker-stacks/issues/675>

## Enable Delta Lake in Spark notebooks

Please note that the [Delta Lake](https://delta.io/) packages are only available for Spark version > `3.0`.
By adding the properties to `spark-defaults.conf`, the user no longer needs to enable Delta support in each notebook.

```dockerfile
FROM jupyter/pyspark-notebook:latest

ARG DELTA_CORE_VERSION="1.2.1"
RUN pip install --no-cache-dir delta-spark==${DELTA_CORE_VERSION} && \
     fix-permissions "${HOME}" && \
     fix-permissions "${CONDA_DIR}"

USER root

RUN echo 'spark.sql.extensions io.delta.sql.DeltaSparkSessionExtension' >> "${SPARK_HOME}/conf/spark-defaults.conf" && \
    echo 'spark.sql.catalog.spark_catalog org.apache.spark.sql.delta.catalog.DeltaCatalog' >> "${SPARK_HOME}/conf/spark-defaults.conf"

USER ${NB_UID}

# Trigger download of delta lake files
RUN echo "from pyspark.sql import SparkSession" > /tmp/init-delta.py && \
    echo "from delta import *" >> /tmp/init-delta.py && \
    echo "spark = configure_spark_with_delta_pip(SparkSession.builder).getOrCreate()" >> /tmp/init-delta.py && \
    python /tmp/init-delta.py && \
    rm /tmp/init-delta.py
```

## Add Custom Fonts in Scipy notebook

The example below is a Dockerfile to load Source Han Sans with normal weight, usually used for the web.

```dockerfile
FROM jupyter/scipy-notebook:latest

RUN PYV=$(ls "${CONDA_DIR}/lib" | grep ^python) && \
    MPL_DATA="${CONDA_DIR}/lib/${PYV}/site-packages/matplotlib/mpl-data" && \
    wget --quiet -P "${MPL_DATA}/fonts/ttf/" https://mirrors.cloud.tencent.com/adobe-fonts/source-han-sans/SubsetOTF/CN/SourceHanSansCN-Normal.otf && \
    sed -i 's/#font.family/font.family/g' "${MPL_DATA}/matplotlibrc" && \
    sed -i 's/#font.sans-serif:/font.sans-serif: Source Han Sans CN,/g' "${MPL_DATA}/matplotlibrc" && \
    sed -i 's/#axes.unicode_minus: True/axes.unicode_minus: False/g' "${MPL_DATA}/matplotlibrc" && \
    rm -rf "/home/${NB_USER}/.cache/matplotlib" && \
    python -c 'import matplotlib.font_manager;print("font loaded: ",("Source Han Sans CN" in [f.name for f in matplotlib.font_manager.fontManager.ttflist]))'
```

## Enable clipboard in pandas on Linux systems

```{admonition} Additional notes
    This solution works on Linux host systems.
    It is not required on Windows and won't work on macOS.
```

To enable the `pandas.read_clipboard()` functionality, you need to have `xclip` installed
(installed in `minimal-notebook` and all the inherited images)
and add these options when running `docker`: `-e DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix`, i.e.:

```bash
docker run -it --rm \
    -e DISPLAY \
    -v /tmp/.X11-unix:/tmp/.X11-unix \
    jupyter/minimal-notebook
```

## Add ijavascript kernel to container

The example below is a Dockerfile to install the [ijavascript kernel](https://github.com/n-riesco/ijavascript).

```dockerfile
# use one of the Jupyter Docker Stacks images
FROM jupyter/scipy-notebook:2023-02-28

# install ijavascript
RUN npm install -g ijavascript
RUN ijsinstall
```

## Add Microsoft SQL Server ODBC driver

The following recipe demonstrates how to add functionality to read from and write to an instance of Microsoft SQL server in your notebook.

```dockerfile
ARG BASE_IMAGE=jupyter/tensorflow-notebook

FROM $BASE_IMAGE

USER root

ENV MSSQL_DRIVER "ODBC Driver 18 for SQL Server"
ENV PATH="/opt/mssql-tools18/bin:${PATH}"

RUN apt-get update --yes && \
    apt-get install --yes --no-install-recommends gnupg2 && \
    wget -qO- https://packages.microsoft.com/keys/microsoft.asc | gpg --dearmor > /usr/share/keyrings/microsoft.gpg && \
    apt-get purge --yes gnupg2 && \
    echo "deb [arch=amd64,armhf,arm64 signed-by=/usr/share/keyrings/microsoft.gpg] https://packages.microsoft.com/ubuntu/22.04/prod jammy main" > /etc/apt/sources.list.d/microsoft.list && \
    apt-get update --yes && \
    ACCEPT_EULA=Y apt-get install --yes --no-install-recommends msodbcsql18 && \
    apt-get clean && rm -rf /var/lib/apt/lists/*

# Switch back to jovyan to avoid accidental container runs as root
USER ${NB_UID}

RUN pip install --no-cache-dir pyodbc
```

You can now use `pyodbc` and `sqlalchemy` to interact with the database.

Pre-built images are hosted in the [realiserad/jupyter-docker-mssql](https://github.com/Realiserad/jupyter-docker-mssql) repository.