Demos and tutorials for [Free and Practical Software for Algebraic Combinatorics 2019](https://wiki.sagemath.org/fpsac19)

--- tags: OpenDreamKit, FPSAC, Sage, GAP, workshop --- # Demos and tutorials for [Free and Practical Software for Algebraic Combinatorics 2019](https://wiki.sagemath.org/fpsac19) 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](http://jupyter.org) 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](https://jupyterlab.readthedocs.io/) 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](https://hackmd.io/NLuOxF6aRBCDzpr5ej5KRw?view) ### [CoCalc](http://cocalc.com) 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](http://mybinder.org) 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](https://opendreamkit.org/public/images/use-cases/reproducible_logbook_scenario.png =60%x)](https://drive.google.com/file/d/1AoyCP7CSfxHvLvRZjI9GjXZSxRnIAnrc/view) **Explainer comics** [![Binder comics](https://opendreamkit.org/public/images/use-cases-binder-logbook-solution.png =60%x)](https://opendreamkit.org/public/images/use-cases-binder-logbook-solution.png)| About this tutorial: in the [version control tutorial](#Version-control-with-git) 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](#Sharing-code-as-packages). - Tutorial: Wednesday morning - Helper(s): Nicolas - Participants: Pauline, Nadia, Émile, Antonio, Wencin, Anne, Abolape - Material: see [this blog](https://opendreamkit.org/2018/07/23/live-online-slides-with-sagemath-jupyter-rise-binder/) #### Repositories that were binder-enabled during the conference - Lorenzo's [Cross-flips_and_balanced_library](https://github.com/LorenzoVenturello/Cross-flips_and_balanced_library/) SageMath library - Duncan Levear's [generating functions demo](https://github.com/dlevear/sagedays2019_gf_talk/) [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/dlevear/sagedays2019_gf_talk/master) - Wencin Poh's [FPSAC'19 software demonstration](https://github.com/wencin-poh/fpsac-2019-crystals-demo) - Jang Soo Kim's q-integer factorization: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jangsookim/q-integer-factorization/master?filepath=Factorization%20into%20q-integers.ipynb) - Aram's latex with sage presentation: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/thecaligarmo/SageTutorials/master?filepath=Latexifying%20(on%20steroids).ipynb) - Aram's introduction to python: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/thecaligarmo/SageTutorials/master?filepath=Introduction%20to%20Python%20with%20Sage.ipynb) #### Links: - [Reproducible Research with Interactive Jupyter Dashboards](https://annefou.github.io/jupyter_dashboards/), a [Software Carpentry Lesson](https://software-carpentry.org/). See in particular the [a binder tutorial](https://annefou.github.io/jupyter_dashboards/06-sharing-binder/index.html). - [a nice guide on building binder images](https://build-a-binder.github.io/) - [a conversation about Binder workshops](https://discourse.jupyter.org/t/binder-binderhub-workshops-help-wanted/313/19) ### [Thebelab](https://thebelab.readthedocs.io/en/latest/) ThebeLab is a tool for embedding live code blocks in a web page. For SageMath, there is also the analog [SageCell](http://cell.sagemath.org/) tool. - Presenter(s): Nicolas? - Participants: Anne, Tom Roby ### [Planetaryum](https://github.com/OpenDreamKit/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](http://www.gap-system.org/) Groups, Algorithms, Programming - a System for Computational Discrete Algebra - Presenter(s): - Participants: Tomer, Balthazar, Andrés David, - **Demo**: - **Getting started tutorial** - [GAP homepage](https://www.gap-system.org) - [GAP source code](https://github.com/gap-system/gap) - [GAP.app](https://cocoagap.sourceforge.io/) an alternative version of GAP for MAC users - tutorial links - [Software carpentry lesson: Programming with GAP](http://alex-konovalov.github.io/gap-lesson/) -- intro to the GAP language, good place to start - [Official GAP tutorial](https://www.gap-system.org/Manuals/doc/tut/chap0.html) - [Using GAP](https://www.math.colostate.edu/~hulpke/paper/gap4tut.pdf) -- Older tutorial from 2000; quick spotlight on many GAP features and concepts - [Using GAP Effectively: Some Tips and Pitfalls](https://github.com/alex-konovalov/gap-teaching/blob/master/notebooks/TipsAndPitfalls.ipynb) - [More learning material](https://www.gap-system.org/Doc/Learning/learning.html) - **Some advanced tutorial?** -- please let us know if you are interested in tutorials on any specific topics - **[Francy](https://github.com/gap-packages/francy): Visual tools for Jupyter**: Sebastian [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/gap-packages/francy/master) ### [SageMath](http://sagemath.org) 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. - **[Getting started tutorial](https://more-sagemath-tutorials.readthedocs.io/en/latest/tutorial-start-here.html#tutorial-start-here)** Try it online: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/sagemath/more-sagemath-tutorials/master?filepath=tutorial-start-here.ipynb) [Download as notebook](https://more-sagemath-tutorials.readthedocs.io/en/latest/tutorial-start-here.ipynb) - **[Exploring further](https://more-sagemath-tutorials.readthedocs.io/en/latest/tutorial-start-here.html#exploring-further)** At the end of the above tutorial, you can find links to many more tutorials, books, online references, ... - **[SageManifolds](https://nbviewer.jupyter.org/github/egourgoulhon/SageMathTour/blob/master/Notebooks/demo_manifolds.ipynb)** [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/egourgoulhon/SageMathTour/master?filepath=Notebooks%2Fdemo_manifolds.ipynb) - **[Elementary vector calculus with SageMath](https://sagemanifolds.obspm.fr/vector_calculus.html)** ### 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](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/dlevear/sagedays2019_gf_talk/master) - 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](https://github.com/DiscreteZOO/DiscreteZOO-sage) - 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](https://jupyter.org/widgets) [Widget basics demo](https://mybinder.org/v2/gh/jdemeyer/widget_basics/master?filepath=index.ipynb) - Presenter(s): - Participants: #### [Sage-Combinat widgets](https://github.com/sagemath/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](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/git/https%3A%2F%2Fgit.died.re%2Fsagenb/03ab38365ed1f494fc8cc692095fec441fd20c6a?filepath=widgets%2FPolyomino.ipynb) Installation: sage -pip install sage_combinat_widgets #### **[Francy](https://github.com/mcmartins/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](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/thecaligarmo/SageTutorials/master?filepath=Latexifying%20(on%20steroids).ipynb) and the notebook is [here](https://github.com/thecaligarmo/SageTutorials/blob/master/Latexifying%20(on%20steroids).ipynb). - 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 - [The slides](https://github.com/enadeau/shell_sagedays_fpsac2019/raw/master/slides.pdf) - [Directory for exercises](https://github.com/enadeau/shell_sagedays_fpsac2019/raw/master/exercises_files.zip) - [Command Line Cheat Sheet](https://www.git-tower.com/blog/command-line-cheat-sheet/) - [Software Carpentry tutorial about shell](http://swcarpentry.github.io/shell-novice/) - [Game Shell](http://lama.univ-savoie.fr/~hyvernat/Enseignement/1617/info202/tp2.html) (French only) ### 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. - Tutorial: Tuesday 13:50, room 203 - Presenter(s): Pauline, Nadia - Participants: Antonio, Duncan, Wencin, Oliver, Balthazar, Andrés David, Stephan, - Slides: https://github.com/phubert/git_sagedays2019/blob/master/git-tutorial.pdf - Git repository: https://github.com/phubert/git_sagedays2019 ### Smart text editors (vim|emacs) - Presenter(s): Duncan, Odile - Participants: Wencin, Tomer, Balthazar, Émile ## [Some best practices for computer exploration](/DUiM8pdxQu2N0Zw9Wh4Stg) [Slides](https://hackmd.io/@nthiery/some-best-practices-for-computer-exploration) - 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](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/thecaligarmo/SageTutorials/master?filepath=Introduction%20to%20Python%20with%20Sage.ipynb) - 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. - Tuesday morning (1030 to 1100-ish) at 204 - Presenter(s): Wencin - Participants: Sun-mi, Reza, Andrés David, + 20 people - Binder link: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/wencin-poh/fpsac2019-sage-oop/master?filepath=Object%20Oriented%20Programming%20tutorial.ipynb) - [GitHub repo (with demo during tutorial)](https://github.com/wencin-poh/fpsac2019-sage-oop) Going further: - [Sage's thematic tutorials on programming](https://doc.sagemath.org/html/en/thematic_tutorials/index.html#introduction-to-python) ### 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](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/hchapman/sagedays-cython-tutorial/master?urlpath=lab/tree/Cython%20demo.ipynb) - 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](#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](https://github.com/sagemath/sage_sample). - 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: - [SageMath packages](https://wiki.sagemath.org/SageMathExternalPackages) wiki page. - Some thoughts on [code sharing workflows](https://wiki.sagemath.org/CodeSharingWorkflow) ### 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: - [Contributing to SageMath (by Franco Saliola)](https://saliola.github.io/contributing-to-sage/) - [The Sage Trac server](https://trac.sagemath.org/), where all the development is achieved - [Sage coding convention](http://doc.sagemath.org/html/en/developer/coding_basics.html#sage-documentation-style) - [Sage git trac tutorial](https://doc.sagemath.org/html/en/developer/git_trac.html) - [Git trac repository on github](https://github.com/sagemath/git-trac-command) - [The tutorial we are editing](http://doc.sagemath.org/html/en/thematic_tutorials/tutorial-comprehensions.html) ## 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](https://github.com/sagemath/sagetex) Mixing Sage Code and LaTeX - Presenter(s): Pauline - Participants: Julian, Duncan, Antonio, Tomer (project: add built-in support to [LyX](https://www.lyx.org/)), Odile, Justine, Andrés David, Josh, Inês - Slides : https://phubert.github.io/sagetex-tutorial.pdf ### [nbgrader](https://nbgrader.readthedocs.io/) [Jessica Hammrick's talk](https://youtu.be/5WUm0QuJdFw) (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](https://github.com/nbgallery/ordo) Visual feedback for exercises in Jupyter notebooks - Presenter(s): Nicolas - Participants: Odile ## Hosted class management in CoCalc - Presenter(s): - Participants: ## Other tools ### [pypersist](https://github.com/mtorpey/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](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/mtorpey/pypersist/master?filepath=binder/demo.ipynb)

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