v1.1.0

Introduces a new phenotype classification method: Now, you can pick between classify_phenotypes and classify_attractor_phenotypes, where the second option actually classifies each attractor in isolation, so you get a better idea of the actual possible behaviors (the first option only detects if a phenotype is possible at all).

v1.0.1

Compared to 1.0.0, updates the lib-bdd dependency to version 0.5.21. This does not add any new significant functionality, but it fixes a performance problem in the implementation of mk_dnf/mk_cnf. It also uses a new, improved to_dnf algorithm. Finally, to_dnf now has a size_limit argument which interrupts the method if the DNF becomes too large.

What's Changed

• Update lib-bdd to 0.5.21 by @daemontus in #24

Full Changelog: v1.0.0...v1.0.1

v1.0.0

This is essentially a complete rewrite of the Python wrappers. Much has been added. Please consult the API documentation regarding the new interface: https://biodivine.fi.muni.cz/docs/aeon-py/latest/biodivine_aeon.html

0.0.9-alpha2

0.0.9a2

v0.4.0a5

0.4.0-alphaa5

0.4.0a5

v0.4.0a4

0.4.0-alpha4

0.4.0a4

Phenotype control alpha release 3

0.4.0-alpha3

versions

0.3.0

This release adds some new functionality and incorporates a lot of the latest changes in biodivine libraries. As opposed to the transition from 0.1.0 to 0.2.0, transition to 0.3.0 should not have any breaking changes.

Complete list of changes:

• Added bindings for HCTL and attractor property classification:
  • run_hctl_classification, run_attractor_classification: compute HCTL or attractor classification map.
  • save_class_archive, load_class_archive: load/store classification results for later use or GUI analysis.
  • get_model_assertions, get_model_properties: read HCTL assertions/properties from an annotated .aeon model.
• Added bindings for HCTL model checking:
  • A HctlTreeNode class is used to manipulate and represent HCTL formulas at runtime.
  • get_extended_stg: extends a SymbolicAsyncGraph with a collection of symbolic variables necessary for model checking.
  • model_check, model_check_multiple: Basic model checking.
  • model_check_extended, model_check_extended_multiple: Model checking, but with "extended" propositions that can map to arbitrary subsets of states.
  • mc_analysis, mc_analysis_multiple: Run model checking with progress printing, sanitization, etc.
• Fixed #13, so BddValuation and BddPartialValuation are now actually iterable objects.
• Added BddVariableSet::transfer_from, SymbolicContext::transfer_from, and SymbolicAsyncGraph::transfer_from/SymbolicAsyncGraph::transfer_colors_from/SymbolicAsyncGraph::transfer_vertices_from. These methods are used to translate a Bdd or a symbolic set between two symbolic domains.
• Added BooleanNetwork::inline_variable and FnUpdate::substitute_variable, which can be used to implement network reduction.
• Added three new example workflow notebooks:
  • classification.ipynb: Classification of network instantiations based on HCTL and attractor properties.
  • file-formats.ipynb: A quick overview of supported file formats and their properties/limitations.
  • model-checking.ipynb: Model checking of HCTL properties on (partially specified) Boolean networks.
  • Examples for the network reduction process will be added later once we resolve a few remaining issues in the Rust backend.

Phenotype control alpha release 2

0.4.0-alpha2

Improved interface for control

Phenotype control alpha release

0.4.0-alphaa1

Bump lib version