Minimal Trap Spaces computation using Maximal Siphons
Project description
Trappist is a tool for computing minimal trap spaces of a Boolean model.
Install
You can install trappist with pip
directly from the Package Index:
$ python3 -m pip install trappist
or grab the very latest version from the source:
$ python3 -m pip install -e git+https://github.com/soli/trap-spaces-as-siphons.git
You will also need the clingo
ASP solver in your PATH for the asp
method of computing the trap spaces (default). Instructions are provided directly on the Potassco pages.
Note that Trappist does install the PySAT module so that the sat
method is always available even if you do not have clingo
.
Run trappist in a Binder image
Latest version, with 2022-12-01 colomoto-docker image:
Read about trappist
The first article describing trappist is here
Run trappist from the command line
After installing trappist
(and maybe clingo
), just run
$ trappist -h
usage: trappist [-h] [-d] [-v] [-m MAX] [-p PARALLEL] [-t TIME] [-s {asp,cp,ilp,sat,naive}] [infile]
Compute minimal trap-spaces of a Petri-net encoded Boolean model. Copyright (C) 2022 Sylvain.Soliman@inria.fr and
giang.trinh91@gmail.com GPLv3
positional arguments:
infile Boolnet (.bnet) file of the model or Petri-net (PNML) file of its Petri net encoding.
options:
-h, --help show this help message and exit
-d, --debug Print debugging information.
-v, --version show program's version number and exit
-m MAX, --max MAX Maximum number of solutions (0 for all).
-p PARALLEL, --parallel PARALLEL
Maximum number of cores to use [only for naive method] (0 for no-limit).
-t TIME, --time TIME Maximum number of seconds for search (0 for no-limit).
-s {asp,cp,ilp,sat,naive}, --solver {asp,cp,ilp,sat,naive}
Solver to compute the Maximal conflict-free siphons. 'asp' requires clingo, 'cp' requires minizinc.
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