Fibertree Notebooks

This repository contains various Jupyter notebooks that illustrate the implemention of various sparse (and dense) computations using the fibertree abstraction.

Run in Google Colab

The notebooks in this repo can be run in Google Colab and will bootstrap an environment using fibertree-bootstrap.

To run them, go to the notebooks directory in the fibertree notebooks repo and pick a notebook to open in Colab, which is very convenient using the "Open in Colab" Chrome extension.

Some notebooks that you can run in Colab directly are:

• startup page - a directory of notebooks
• fibertree demo - an initial tutorial notebook

Run in a Docker container

The fibertree-docker repository provides a Docker container with a preinstalled copy of the fibertree package and where one can run the fibertree notebooks without additional local installation.

Manual local installation

See the fibertree repository for instructions on installing the fibertree Python package.

Then clone this repository and run the Jupyter notebooks:

cd fibertree-notebooks/notebooks
jupyter lab .

Browse in the various subdirectories and invoke a notebook. A good place to start is basic/01-01.overview.ipynb

See FAQ below for addressing some problems.

Python virtual environment installation

Create virtual environment and install required packages

python -m venv <directory-for-venv>
source <directory-for-venv>/bin/activate

python3 -m pip install --upgrade pip
python3 -m pip install git+https://github.com/Fibertree-Project/fibertree

Get the fibertree notebooks

git clone https://github.com/Fibertree-Project/fibertree-notebooks

cd fibertree-notebooks/notebooks
jupyter lab .

When done, deactivate the virtual environment

deactivate

Development

To clear out the outputs from modified notebooks, from the root of repository run the following:

for i in `git diff --name-only`; do jupyter nbconvert --clear-output --inplace $i; done

FAQ

Q: How do I fix font-related errors when displaying graphics?

A: On Ubuntu/Debian systems you can try installing fonts-freefon-ttf with:

sudo apt install fonts-freefont-ttf

If you know where the fonts are on your system then you can set the environment variable FIBERTREE_FONT in Python code you can do this with something like:

   import os

   os.environ['FIBERTREE_FONT'] = 'Pillow/Tests/fonts/FreeMono.ttf'

Q: How can I get the Jupyter widgets to work?

A1: For classic Jupyter notebooks, try the following command:

jupyter nbextension enable --py widgetsnbextension

A2: To get widgets to work in Jupyter lab, try the following:

curl -o- https://raw.githubusercontent.com/creationix/nvm/v0.33.6/install.sh | bash
# restart bash
nvm install node
jupyter labextension install @jupyter-widgets/jupyterlab-manager