Sébastien Labbé’s Research Code¶
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, GIFS.
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,
analyze Sage build time, fruit Python classes example, ranking scale
Prerequisites - System packages (easy to install)¶
Some functionalities of
slabbe package depend on the installation of
packages on the system such as pdflatex, lualatex (lualatex compiles large
tikzpicture exceeding the memory limits of pdflatex), pdf2svg as well as
softwares including ImageMagick (to convert pdf to png so that tikzpicture
appear directly in the Jupyter notebook), Graphviz (to draw graphs).
On Debian or Ubuntu, one may do:
sudo apt update sudo apt install texlive texlive-latex-extra texlive-luatex -qy sudo apt install graphviz imagemagick pdf2svg -y
The installation of imagemagick done above provides the command
it does not allow to convert pdf to png unless you edit the Imagemagick’s
policy.xml file which can be done as follows (thanks to Naveed’s comment
sudo sed -i '/PDF/s/none/read|write/' /etc/ImageMagick-6/policy.xml
On OSX, one should first install Homebrew. Then one can install the
above packages similarly as above using
brew instead of
sudo brew install graphviz imagemagick pdf2svg
Prerequisites - SageMath optional packages¶
Installing slabbe requires a working SageMath installation (with Cython and gcc). Depending on the usage, it might be necessary to install the optional sagemath packages dot2tex (translate dot file to tikz to draw nice graphs), glucose (SAT solver) and latte_int:
sage -i dot2tex glucose latte_int
Note that graphviz must be installed before dot2tex.
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://gitlab.com/seblabbe/slabbe
sage: from slabbe import *
Other System packages you may want to install¶
Some functionalities of
slabbe package depend on the installation of a
linear program solver such as Gurobi. See the thematic tutorial to setup the
installation of Gurobi in SageMath`.
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.
- Version 0.6.2 (December 15, 2020)
New module on Graph-directed iterated function systems (GIFS). Fixed \(TransitiveIdeal\) import error. Now using gitlab continuous integration automatic tests: installation +
import slabbetested to work on versions 8.7, 8.8, 9.0, 9.1, 9.2 of SageMath. All tests passed on versions 9.0, 9.1, 9.2 of SageMath.
- Version 0.6.1 (May 8, 2020)
New modules to deal with the coding of \(Z^d\)-action by PETs, \(d\)-dimensional sturmian configurations. Improved the computation of induced polyhedron partition and induced polyhedron exchange transformation. New modules containing the code for the articles arxiv:1903.06137 and arXiv:1906.01104
- 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)
import slabbework 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)
0.4includes 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)
0.3b2includes 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)
0.3b1is 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
- Version 0.1 (August 27, 2014)
slabbe-0.1.spkg (documentation) contains modules on digital geometry, combinatorics on words and more.
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.
- Matrix Cocycles
- Multidimensional Continued Fraction Algorithms
- Diophantine Approximation
- Lyapunov exponents (comparison)
- Markov transformations
- Polyhedron exchange transformations (PETs) and induced transformations
- 2d Substitutions
- Coding of Polyhedron exchange transformations (PETs)
- Graph-directed iterated function system (GIFS)