JupyterLab + SoS Suite setup
Install miniconda3 the Python development environment
We recommend using miniconda
over anaconda
and customize your installation as needed after install this minimal version of conda
.
To install please follow instructions on this page. Please go for miniconda3
.
After you successfully installed the latest version of miniconda3
, please follow prompts below to setup
a JupyterLab + SoS Suite environment for daily computing.
Jupyter Notebook kernels
Bash kernel
pip install bash_kernel --no-cache-dir
python -m bash_kernel.install
Markdown kernel
pip install markdown-kernel --no-cache-dir
python -m markdown_kernel.install
R kernel
R --slave -e "install.packages('IRkernel'); IRkernel::installspec()"
A ipynb to docx converter
This will allow you to save ipynb
file to a docx
file for various purposes
pip install jupyter-docx-bundler --no-cache-dir
jupyter bundlerextension enable --py jupyter_docx_bundler --sys-prefix
nbdime to work with git
This will override the default git diff
and display better the changes to IPython notebooks
pip install nbdime
nbdime config-git --enable --global
SoS Suite
pip install docker markdown wand graphviz imageio pillow nbformat jupyterlab feather-format --no-cache-dir
pip install sos sos-notebook sos-r sos-python sos-bash -U --no-cache-dir
python -m sos_notebook.install
jupyter labextension install transient-display-data
jupyter labextension install jupyterlab-sos
If the last command fails and complains about missing nodejs
you can use conda
to install it,
conda install -c conda-forge nodejs
Install Docker
We use Docker a lot running various software that are hard to install. SoS also provides an interface to run Docker images.
To install Docker (tested on Linux but might work on Mac too – can someone confirm and fix?),
- Run commands below:
curl -fsSL get.docker.com -o get-docker.sh
sudo sh get-docker.sh
sudo usermod -aG docker $USER
- Log out and log back in (no need to reboot computer)