Module: Jupyter

Launch Jupyter notebook server with Pigsty, a web-based interactive scientific notebook.
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Run jupyter notebook with docker, you have to:

    1. change the default password in .env: JUPYTER_TOKEN
    1. create data dir with proper permission: make dir, owned by 1000:100
    1. make up to pull up jupyter with docker compose
cd ~/pigsty/app/jupyter ; make dir up

Visit http://lab.pigsty or http://10.10.10.10:8888, the default password is pigsty

Prepare

Create a data directory /data/jupyter, with the default uid & gid 1000:100:

make dir   # mkdir -p /data/jupyter; chown -R 1000:100 /data/jupyter

Connect to Postgres

Use the jupyter terminal to install psycopg2-binary & psycopg2 package.

pip install psycopg2-binary psycopg2

# install with a mirror
pip install -i https://pypi.tuna.tsinghua.edu.cn/simple psycopg2-binary psycopg2

pip install --upgrade pip
pip config set global.index-url https://pypi.tuna.tsinghua.edu.cn/simple

Or installation with conda:

conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/

then use the driver in your notebook

import psycopg2

conn = psycopg2.connect('postgres://dbuser_dba:[email protected]:5432/meta')
cursor = conn.cursor()
cursor.execute('SELECT * FROM pg_stat_activity')
for i in cursor.fetchall():
    print(i)

Alias

make up         # pull up jupyter with docker compose
make dir        # create required /data/jupyter and set owner
make run        # launch jupyter with docker
make view       # print jupyter access point
make log        # tail -f jupyter logs
make info       # introspect jupyter with jq
make stop       # stop jupyter container
make clean      # remove jupyter container
make pull       # pull latest jupyter image
make rmi        # remove jupyter image
make save       # save jupyter image to /tmp/docker/jupyter.tgz
make load       # load jupyter image from /tmp/docker/jupyter.tgz

Last modified 2024-09-02: update extension list (8681a8ce)