# Sébastien Labbé’s Research Code¶

## README¶

This is an optional package for SageMath containing code I wrote for research. It contains modules on the following topics.

**Discrete dynamical systems**- diophantine approximation, Markov transformations, Wang tilings, Lyapunov exponents, matrix cocycles, multidimensional continued fraction algorithms, polyhedron exchange transformations,
**Combinatorics**- 2d substitutions, bispecial factors, bond percolation, Dyck word in 3D, words, Joyal bijection, languages, Oldenburger sequence, ostrowski numeration, partial injections,
**Digital geometry**- Christoffel graph, discrete subset, discrete plane, double square tiles, polyhedron partitions,
**Vizualization**- tikzpicture
**Miscellaneous**- analyze Sage build time, fruit Python classes example, ranking scale

Links:

- documentation: http://www.slabbe.org/docs/
- PyPI: http://pypi.python.org/pypi/slabbe
- github: http://github.com/seblabbe/slabbe
- www: http://www.slabbe.org/Sage/

### Prerequisites¶

Installing slabbe requires a working SageMath installation (with Cython and gcc). Depending on the usage, it might be necessary to install the optional packages dot2tex, glucose, cryptominisat and latte_int:

```
sage -i dot2tex glucose cryptominisat latte_int
```

as well as the external packages ImageMagick, Graphviz and Gurobi. See this thematic tutorial to use Gurobi in SageMath.

On Debian or Ubuntu, one may do:

```
sudo apt install graphviz imagemagick
```

On OSX, one may do after installing Homebrew:

```
sudo brew install graphviz imagemagick
```

Note that graphviz must be installed *before* dot2tex.

### Installation¶

The module is distributed on PyPI and is easily installed through the Python package manager pip:

```
sage -pip install slabbe
```

To install the module in your user space (which does not require administrator rights):

```
sage -pip install slabbe --user
```

To install the most recent development version:

```
sage -pip install --upgrade git+https://github.com/seblabbe/slabbe
```

Usage:

```
sage: from slabbe import *
```

### It builds on SageMath¶

It depends heavily on the SageMath library as it uses the following modules: combinat, functions, geometry, graphs, matrix, misc, modules, numerical, parallel, plot, probability, rings, sat, sets, structure, symbolic.

SageMath is free open source math software that supports research and teaching in algebra, geometry, number theory, cryptography, and related areas.

### Follows the Best practices for scientific computing¶

It follows as much as possible the SageMath general conventions and the
Best Practices for Scientific Computing. Each module is fully documented
and doctested. Before each new release, we make sure that all examples are
working. As the ReScience Journal says: “*Reproducible science is good.
Replicated Science is better*”.

### Future inclusion into Sage¶

Some modules may have a wider interest to the SageMath community
(`tikz_picture.py`

for example) and could be included in SageMath at some
point. Please contact the author if you want to act as a reviewer for some
module(s) and I will create a ticket on trac for its inclusion into SageMath.

### Release history¶

*Version 0.6 (November 22, 2019)*- Make the package work with Python 3. Most of the tests pass with Python 3 now.
*Version 0.5.1 (May 30, 2019)*- Few fixes for the publication of “Induction of \(Z^2\)-actions on partitions of the 2-torus”. Improved html documentation.
*Version 0.5 (April 10, 2019)*- Few fixes for the version 2 of “Substitutive structure of Jeandel-Rao aperiodic tilings”. New additions includes solving Wang tilings problem using SAT solvers and a class for Polyhedron exchange transformations.
*Version 0.4.4 (September 28, 2018)*- Make
`import slabbe`

work in Sage with Python 3. *Version 0.4.3 (August 22, 2018)*- Few fixes for the publication of “Substitutive structure of Jeandel-Rao aperiodic tilings”.
*Version 0.4.2 (July 20, 2018)*- Few fixes for the version 2 of “A self-similar aperiodic set of 19 Wang tiles”.
*Version 0.4.1 (February 9, 2018)*- Few fixes for the publication of “A self-similar aperiodic set of 19 Wang tiles”. New module to solve the Magic hexagon problem.
*Version 0.4 (January 20, 2018)*- Version
`0.4`

includes new modules for Wang tilings, 2d substitutions, polyhedron partitions, partial injections, ostrowski numeration and many improvements to other modules. *Version 0.3b2 (December 11, 2016)*- Version
`0.3b2`

includes a new module for diophantine approximations, random point generation inside polytopes, analyzing sage building time, and many improvements to previous modules. *Version 0.3b1 (June 12, 2016)*- Version
`0.3b1`

is now a Python package available in the Python Package Index (PyPI). It was migrated from the previous sage optional spkg old-style format. It also adds code to deal with bispecial factors, some new methods of graphs, substitutions and matrices. *Version 0.2 (November 25, 2015)*- slabbe-0.2.spkg (documentation) provides modules on multidimensional continued fraction algorithms, matrix cocycles, languages and tikzpictures.

*Version 0.1.1 (June 3, 2015)*- slabbe-0.1.1.spkg fixes a bug with
`gcd`

import error.

*Version 0.1 (August 27, 2014)*- slabbe-0.1.spkg (documentation) contains modules on digital geometry, combinatorics on words and more.

## Module documentation¶

This reference manual contains many examples that illustrate the usage of the slabbe package. The examples are all tested at each release and should produce exactly the same output as in this manual.

This work is licensed under a Creative Commons Attribution-Share Alike 3.0 License.