Trappist is a tool for computing minimal trap spaces of a Boolean model.
You can install trappist with pip directly from the Package Index:
$ python3 -m pip install trappistor grab the very latest version from the source:
$ python3 -m pip install -e git+https://github.com/soli/trap-spaces-as-siphons.gitYou 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.
CMSB 2022 Submitted version:
Latest version, with 2022-12-01 colomoto-docker image:
You can find articles describing trappist here, here and here (tsconj's improvements have been backported to trappist with conj and conj-c solvers).
After installing trappist (and maybe clingo), just run
$ trappist -h
usage: trappist [-h] [-d] [-v] [-m MAX] [-p PARALLEL] [-t TIME] [-c {min,max,fix}] [-s {asp,cp,ilp,sat,naive,conj,conj-c}] [infile]
Compute minimal trap-spaces of a Petri-net encoded Boolean model. Copyright (C) [email protected] and
[email protected] GPLv3
positional arguments:
infile Boolnet (.bnet) file of the model or Petri-net (PNML) file of its Petri net encoding. 'naive' and
'conj(-c)' solvers only handle .bnet input.
optional arguments:
-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 and conj(-c) method] (0 for no-limit).
-t TIME, --time TIME Maximum number of seconds for search (0 for no-limit).
-c {min,max,fix}, --computation {min,max,fix}
Computation option.
-s {asp,cp,ilp,sat,naive,conj,conj-c}, --solver {asp,cp,ilp,sat,naive,conj,conj-c}
Solver to compute the Maximal conflict-free siphons. 'asp', 'naive' and 'conj(-c)' require `clingo`, 'cp'
requires `minizinc`.