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What is Zoose?

Jupyter is to Jupiter as Zoose is to Zeus.

Zoose is a Docker container image for Jupyter notebooks pre-loaded with common Python packages as well as a Neo4j web server for graph analytics with Cypher. Containerized notebooks with a standard set of packages make sharing and reproducing notebooks easier: no need for virtual environments and brittle configurations that break on Python upgrades.

Flavours

Zoose comes in a few flavours: base, neo4j, pytorch, quantum, and geo. What is included in base is always included in the rest, too.

You can run these flavours directly in VSCode from your browser with GitHub Codespaces. Only two clicks to spin up an IDE or notebook with all packages installed and ready!

Special flavours

There are also several special flavours suitable for use with Gitpod, an alternative to GitHub Codespaces.

  • base-gitpod
  • pytorch-gitpod
  • quantum-gitpod
  • geo-gitpod

To get started with these special flavours for Gitpod, please use the template to create a repository that you use to spin up a workspace from that repo.

In Gitpod, you have two options for Zoose notebooks:

  1. A VSCode experience
  2. JupyterLab, which you can start from the Gitpod workspace terminal with /jupyter.sh.

Zoose Base

  • Python 3.12
  • JupyterLab 4.3 with extensions

Python packages:

  • Beautiful Soup 4.12
  • Gower 0.1
  • Keras 3.5
  • LIME 0.2
  • Matplotlib 3.9
  • NLTK 3.9
  • Numpy 1.26
  • Pandas 2.2
  • Prince 0.13
  • Requests 2.32
  • scikit-learn 1.5
  • SciPy 1.14
  • Scrapy 2.11
  • Seaborn 0.13
  • SHAP 0.46
  • spaCy 3.7
  • StatsModels 0.14
  • thefuzz 0.22

Zoose Neo4j

Zoose Neo4j includes everything from Zoose Base as well as:

  • Neo4j Community Edition 4.4
  • neomodel 5.3.2

Zoose PyTorch

Zoose PyTorch includes everything from Zoose Base as well as:

  • Captum 0.7
  • PyTorch 2.4
  • PyTorch Audio 2.4 (CPU)
  • PyTorch Text 0.18 (CPU)
  • PyTorch Vision 0.19 (CPU)
  • Transformers 4.44

Zoose Quantum

Zoose Quantum includes everything from Zoose Base as well as:

  • Amazon Braket SDK 1.57
  • Cirq 1.4
  • OpenFermion 1.6
  • PennyLane 0.38 with plugins for Cirq, Stawberry Fields, Qiskit
  • pytket 1.32
  • Qiskit 1.2
  • QuTiP 5.0
  • Strawberry Fields 0.23

Zoose Geo

Zoose Geo includes everything from Zoose Base as well as:

  • Geopandas 1.0
  • Geoplot 0.5
  • h3 3.7
  • h5py 3.11
  • netCDF4 1.7
  • shapely 2.0
  • xarray 2024.9
  • zarr 2.18

How to use?

Execute ./zoose.sh, which launches a Jupyter notebooks session. By default it launches Zoose Base. If you want Neo4j, Geo, or Quantum, just use ./zoose.sh neo4j, ./zoose.sh geo, or ./zoose.sh quantum instead.

Please use the link from the command line to access it, as it requires a token.

If you do not want to git clone the repo, you can use the public Docker image:

docker run --rm -it \
  -v $(pwd):$(pwd) -w $(pwd) \
  -p 8888:8888 \ 
  "databaseline/zoose-base"

Please ensure that the Docker container has sufficient resources. Go to Docker Desktop > Preferences > Resources and set the number of CPUs to at least half of the total number available. Assign at least 4 GB of RAM to the container. Note that the Jupyter kernel may crash when loading large data sets (into memory). These settings apply to all local containers.

BigQuery credentials

BigQuery support has been dropped from the base image in 3.1. You can install pandas_gbq and google.auth easily from within a notebook with pip: ! pip install pandas_gbq.

If you use Zoose with BigQuery often, you may want to preserve credentials. You can do so by adding -v $(pwd)/.config:/root/.config/pandas_gbq/ to the command above.

Just make sure you ignore .config and do not share your personal credentials in a git repository!

IBMQ credentials

If you use Zoose Quantum with Qiskit often, you may want to preserve IBMQ credentials. You can do so by adding -v $(pwd)/.qiskit:/root/.qiskit to the command above. You need to execute IBMQ.save_account(...) from Zoose Quantum once to save the credentials. Afterwards, you can execute IBMQ.load_account(), provided you have mounted the .qiskit volume prior to launching Zoose Quantum.

Just make sure you ignore .qiskit and do not share your API token in a git repository!

Neo4j

Zoose also kicks off a Neo4j web server. The UI is available at localhost:7474. Please check out this value stream example to learn more about Neo4j and Cypher.

If you use Neo4j, please ensure that your Docker container has at least 6 GB of RAM allocated. This can be configured in the Docker client under 'Resources'.