v0.4.3

Add a new configuration flag (auto_expand_source_nodes) which allows for the exhaustive auto-expansion of source nodes in the root to be turned off.

Also fixes a minor issue in the percolation routine which occurred if the network contained un-expanded source nodes (which was not possible with previous versions).

v0.4.2

Allow to run biobalm even if pint is not installed (previously, an import statement required pint native dependency even if pint itself was ultimately unused).

v0.4.1

Update version.

v0.4.0

Includes minor performance improvements to the attractor detection methods, plus the ability to explicitly label nodes as "skipped", which influences how they are treated by attractor detection (as opposed to not expanded nodes).

Full Changelog: v0.3.1...v0.4.0

Minor workflow fixes

This release is the same as v0.3.0 except that it uses more up-to-date GitHub actions. Also, this will help to sync the PyPI release, which now properly recognizes the new repository name.

0.3.0

Summary:

• A new "source block" expansion methods which supersedes SCC expansion, especially in the context of attractor search.
• Further tuning of the simulation candidate elimination.
• Minor refinements of some of the utility methods.
• Repository cleanup (mostly removal of unused test models).

API changes:

• Added interaction_graph_utils.source_nodes.
• SuccessionDiagram.component_subdiagrams renamed to SuccessionDiagram.component_subdiagram with a more "modular" behavior. The old method is available as SuccessionDiagram.source_scc_subdiagrams.
• Added SuccessionDiagram.expand_block, which implements the new expansion method.
• Added minimum_simulation_budget to the SuccessionDiagram configuration dictionary.

Full Diff: v0.2.0...v0.3.0

0.2.0

• Optimizing attractor detection method for improved performance (some of the previously available methods are now hidden as private).
• Added a new SD configuration object to store all the "global configuration constants".

release-setup: Merge pull request #112 from jcrozum/expansion-refactor-and-docs

Organize SCC expansion module