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Demos and tutorials for Free and Practical Software for Algebraic Combinatorics 2019

This is a tentative list of software demonstrations and tutorials that will be run during the conference. For each piece of software, there typically will be a flash demo (~5 minutes) early in the week in front of the whole audience, to attract participants to tutorials and/or longer demos later in the week.

If you are interested in one of them, or in presenting or helping out for one of them, please add your name in the corresponding section. Please add new demos and tutorials that you would like to participate in or present!

Presenters: please edit your entry to recall briefly what the software is about, and add relevant material: documents the attendees will be following, links, … If it grows beyond a few lines, you can make it a separate page.

The Jupyter ecosystem

Self guided tutorial 1: getting started with Jupyter

Go to http://opendreamkit.org/try, pick your favorite system train yourself with Jupyter, and ask for help whenever needed! If in doubt start with Try Python.

Jupyter

Project Jupyter exists to develop open-source software, open standards, and services for interactive computing across dozens of programming languages.

The Jupyter Notebook is an open-source web application to create and share documents that contain live code, equations, visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning, and much more.

Jupyter is now the default user interface for SageMath, and can be used as user interface for many other mathematical systems such as GAP, Pari/GP, Singular, …

JupyterLab

JupyterLab is the next-generation web-based user interface for Project Jupyter.

JupyterLab enables you to work with documents and activities such as Jupyter notebooks, text editors, terminals, and custom components in a flexible, integrated, and extensible manner. You can arrange multiple documents and activities side by side in the work area using tabs and splitters. Documents and activities integrate with each other, enabling new workflows for interactive computing.

  • Demo: Monday morning
  • Presenter(s): Stephan Pfannerer
  • Participants: Wencin, Oliver, Balthazar, Henri, Antonio, Andrés David,
  • Documentation

CoCalc

CoCalc (Collaborative Calculation) is an online service that gives access to a wealth of computational systems, with extra goodies for teaching. It's free for basic usage.

Summary: CoCalc can do a lot more than just run Sage workbooks! It can also be a substitute for Overleaf for writing LaTeX documents, Skype for video chatting, Dropbox for file sharing, iMessage for text chatting about confusions, etc… Perhaps if you are working on a collaborative project with a substantial computational component, it is worth a look as a semi-convenient way to organize all the various components of your project!

  • Demo: Friday morning, 9:20 - 10:00 am (Room 202)
  • Presenter(s): Oliver, Can, Mee Seong
  • Participants: Jiayuan + 20 participants

Binder

Binder is a service that lets you run Jupyter notebooks online on top of an arbitrary software stack. Sessions are free, anonymous, and temporary.

Explainer video
Explainervideo

Explainer comics
Binder comics|

About this tutorial: in the version control tutorial you published a notebook. We will now guide you through the process of enabling Binder so that anyone can play with it online.

Follow-up: sharing code as packages.

  • Tutorial: Wednesday morning
  • Helper(s): Nicolas
  • Participants: Pauline, Nadia, Émile, Antonio, Wencin, Anne, Abolape
  • Material: see this blog

Repositories that were binder-enabled during the conference

Thebelab

ThebeLab is a tool for embedding live code blocks in a web page. For SageMath, there is also the analog SageCell tool.

  • Presenter(s): Nicolas?
  • Participants: Anne, Tom Roby

Planetaryum

Planetaryum is a Python package for publishing Jupyter notebook collections.

  • Presenter(s): ?
  • Participants: Anne

Math Computational Systems & Databases

Getting started with computational systems

Go to http://opendreamkit.org/try , pick your favorite system, and ask for help whenever needed!

GAP

Groups, Algorithms, Programming - a System for Computational Discrete Algebra

SageMath

SageMath is a general purpose computational mathematics system developed by a worldwide community of hundreds of researchers, teachers and engineers. It's based on the Python programming language and includes GAP, PARI/GP, Singular, and dozens of other specialized libraries.

Algebraic Combinatorics in SageMath

Lie superalgebras

  • Presenter(s):
  • Participants: Mee Seong

Kac-Moody algebras

  • Presenter(s):
  • Participants: Oliver

reflection group, Coxeter groups, Hecke algebras

  • Presenter(s): Robin (This will be an elementary talk, perhaps most interesting for beginners)
  • Participants: Kyle, Jiayuan, João, Sun-mi, Justine

generating function and solving system of equation (used sage to find the coefficients of a generating function, in one or two variables; this is helpful for doing combinatorics since we sometimes need to look at the first few coefficients of a power series)

  • Time: Tuesday 15:30 Slides/Notebook: Binder
  • Presenter(s): Duncan
  • Participants: Émile, Nadia, Hugo + 50 participants

Graph algorithm (both combinatorial and spectral)

  • Presenter(s):
  • Participants: Reza, Abolape

Graph algorithm (resolvable graph decomposition, domination and metric dimension of graphs)

  • Presenter(s):
  • Participants: Abolape, Reza

Tableaux and their generalization

  • Presenter(s):
  • Participants: Se-jin, Reza

DiscreteZOO - accessing precomputed graphs (and eventually other objects) from Sage

  • Presenter: Janoš
  • Participants: Abolape

Finding triangulations of combinatorial manifolds

Problem: Find triangulations of combinatorial manifolds (2- and 3-dimensional) on few vertices which are balanced, i.e., their 1-skeleton can be colored with dimension plus one colors.

Solution: A computer program, implemented in Sage; apply local operations to a balanced triangulation which preserve the homeomorphism type and the coloring, and reduce the number of vertices.

  • Time: Tuesday July 9, 9:00 am
  • Presenter: Alexander Wang
  • Participants: Lorenzo, …

Visualisation and interactive computing

Jupyter Widgets

Widget basics demo

  • Presenter(s):
  • Participants:

Sage-Combinat widgets

A set of interactive, configurable widgets for visualizing combinatorial objects.

  • Demo: Monday afternoon

  • Presenter(s): Odile Bénassy

  • Participants: Émile, Nadia, Henri, Harrison

  • Tutorial/coding sprint: Tuesday from 10:30 + from 15:30, room 202

  • Demo: Wednesday 13:30 room 202

    • Parallelogram Polyominos Binder

Installation:

​​​​sage -pip install sage_combinat_widgets

Francy

Graph vizualization in GAP, Python, and SageMath

  • Demo: Monday afternoon
  • Presenter(s): Odile
  • Participants:

Creating LaTeX view of an object using TikZ

We will cover various ways to output objects in Sage. The content of the talk can be found here on binder: Binder and the notebook is here.

  • Presenter(s): Aram Dermenjian
  • Participants: EG (my hope is to do this for frieze patterns, perfect matchings of graphs, and planar triangulations), Robin, Oliver, Sun-mi, Justine, Odile, Inês, Can Ozan

Basic skills

Using the shell

  • Tutorial: Tuesday 13:30, room 203
  • Presenter(s): Émile
  • Participants: Balthazar, Justine, Reza, Inês, Andrés David

We will cover basic directory structure of Unix systems and the command to navigate inside it, edit file and make basic research

Ressources for the tutorial

Version control with git

If you are not familiar with the shell, we recommand that you attend the shell presentation before starting learning about Git.

Smart text editors (vim|emacs)

  • Presenter(s): Duncan, Odile
  • Participants: Wencin, Tomer, Balthazar, Émile

Some best practices for computer exploration

Slides

  • Wednesday morning
  • Presenter(s): Nicolas, …
  • Participants: Émile, Antonio, Nadia, Balthazar, Reza, Andrés David + ~20

Programming, development

Introduction to Python using Sage

An introduction to programming with python. Goes over the very basics of programming and shows how to use various variable types, how to use loops, how to make functions, etc.

Presentation can be found here: Binder

  • Presenter: Aram Dermenjian

(If you have any questions, feel free to come ask me =D)

Object oriented programming in Python

Implementing new objects in Python with classes.

Going further:

Object oriented programming in Sage

We will review how to create new objects in Sage. Sage being based on Python, this is based on Python's object oriented programming , just with certain additional features and twists for Sage (Parents, Elements, Categories, ..).

  • Presenter: Nicolas
  • Participants: Stephan Pfannerer, Andrés David, Can Ozan, Robin

Coercions in SageMath

E.g.: coercion of elements in different polynomial rings, character rings

  • Presenter(s):
  • Participants: Antonio, Wencin

Easily using C from Python with Cython

Do you have a library in C that you must use (either it is faster, or you do not want to reimplement it…), but much prefer experimentation in Python with Jupyter and other tools?

We'll go over how to access C libraries and C code quickly from Python using friendly Python-like syntax, and we'll see how it's easy to get started using Cython from Jupyter notebooks.

Demo Binder: Binder

  • Presenter(s): Harrison
  • Participants: Jeremy, Émile

Good practices in Python and Sage development

Sharing code as packages

This is a follow up to the Binder tutorial where we published simple notebooks with artefacts, and made them excutable online.

You have a collection of functions and classes and want to make them available? In this session, we will help you write and publish your own Sage-Package. Our base example will be Sage's sample package.

  • Helper: Nicolas, Odile
  • Participants: Mee Seong, Justine, Andrés David, Reza

Steps:

  • organize the code as a (collection of) python files.

  • publish the code on a public repository.

  • add a README.rst file describing your project; see the eponym file in sage_sample.

  • make your project into a Python package: copy the setup.py and VERSION files of sage_sample, and adapt them for your project. Install the package with:

    sage -pip install -e .

  • Add a demo notebook

  • Add Binder configuration (see the Dockerfile of sage_sample) + binder link/badge from the README

  • Write a tutorial

  • Configure sphinx for the documentation

  • More tests and documentation

  • Publish on pipy

  • Setup continuous integration (see sage_sample)

  • ? Merge into SageMath

References:

Contributing to SageMath and to other software

Trac tickets, Github/Gitlab tickets, PRs ..

  • Presenter(s): Nadia, Émile
  • Helper(s): Odile
  • Participants: Mee Seong (I've seen some of the tutorial last year but it doesn't hurt to discuss the details with others as a refresher), Hugo, Balthazar, Andrés David, Stephan Pfannerer, Robin, Pauline

Refrences:

Education tools

Authoring live documents

Jupyter notebooks, ReST documents, ThebeLab, …
NB: it'll be even more interesting if you can bring some of your math examples

  • Presenter(s): Nicolas
  • Participants: Tom Roby, Antonio, Justine, Josh,…

SageTeX

Mixing Sage Code and LaTeX

nbgrader

Jessica Hammrick's talk

(semi)automatic grading of exercise sheets in Jupyter notebooks

  • Presenter(s): Nicolas?
  • Participants: Pauline, Émile, Duncan, Antonio, Nadia, Tomer, Wencin, Anne, Odile, Justine, Josh

Installation with conda:

​​​​conda create -n nbgrader
​​​​conda activate nbgrader
​​​​conda install nbgrader

Getting started:

​​​​nbgrader quickstart mycourse
​​​​cd mycourse

Edit mycourse/nbgrader_config.py:

​​​​jupyter notebook

ordo

Visual feedback for exercises in Jupyter notebooks

  • Presenter(s): Nicolas
  • Participants: Odile

Hosted class management in CoCalc

  • Presenter(s):
  • Participants:

Other tools

pypersist

Persistent memoisation framework for Python.

Or, how to permanently store the results of a long-to-compute function?

  • Presenter(s): Aram Dermenjian
  • Participants: Émile, Wencin, Tomer, Anne, Janoš

We will go through the excellent tutorial provided by Michael Torpey through binder on how to persist data.
Binder

Select a repo