v0.6.5

• sanitize node names when converting to mpbn
• add support for observation on the left of non-reach operator: obs / target ensures that no configuration matching with obs can reach the target on the right.
• improvement of several ASP encodings

Full Changelog: v0.6.1...v0.6.5

0.6.1

• optimization of the trap space reprogramming methods

0.6: CEGAR-based trapspace reprogramming

New features:

• bonesis.reprogramming.marker_reprogramming uses new CEGAR-based implementation (http://arxiv.org/abs/2305.02442). The other implementation is still available using the algorithm="complementary" option.
  bonesis.reprogramming.trapspace_reprogramming is an alias.
• InfluenceGraph: option exact="unsigned" allows enforcing that the Boolean networks use all the interactions of the influence graph with unsigned edges c632b3a

Bug fixes:

• non_reach constraint in mutant contexts

0.5.7: improve compatibility with mpbn

v0.5.7

improve compatibility with mpbn

0.5.6: non-monotone Boolean network support single-model domain

Non-monotone Boolean networks can now be used as (single-model) domain for performing model-checking or reprogramming.

v0.5.5

New features

Views:

• add support for "somes" as extra parameter to extract assignments of Some objects (e.g., examples/extra_somes.py)

Language:

• inequality (!=) between Some objects (e.g., examples/extra_somes.py)

User interaction

TL;DR: support timeout and CTRL+C

• honor the timeout argument when solving (i.e., correctly interrupt clingo search)
• add settings["fail_if_timeout"] to either throw a TimeoutError exception (True, default) or silently stop the solution enumeration ( False)
• workaround the "GIL" to capture CTRL+C events during clingo search. This can be disabled with settings["clingo_gil_workaround"]=0.
• add settings["soft_interrupt"] to either throw KeyboardInterrupt exception (False, default), or silently stop the solution enumeration (True) when catching interruption signal

Bug fixes

• correct action() encoding

Full Changelog: v0.5.0...v0.5.5

v0.5.0

New features

• bo.hypercube: add min_dimension and max_dimension arguments to constrain dimension
• new bo.scope_reachability context to add constraints on admissible trajectories (monotony and maximum number of changes)
• InfluenceGraph: add rules list attribute for custom rules injection

Changes

• change default optimization strategy of clingo to branch-and-bound. Can be overridden with clingo_opt_strategy setting.

Bugfixes

• trapspace constraint with inline observations
• AEON import failed with non-monotone interactions

Full Changelog: v0.4.93...v0.5.0

0.4.93

• new feature: add scope option to configurations and hypercubes views
• bugfix for trap space reprogramming with exclude option

0.4.92

• bug fixes

0.4.91

New features:

• support for AEON.py to specify input domain
• command line interface for listing attractors (minimal trap space) from Boolean networks and ensembles
• reprogramming (API and command line), see https://github.com/bnediction/reprogramming-with-bonesis