Biobalm

Latest version: v0.4.2

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0.4.2

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).

0.4.1

None

0.4.0

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**: https://github.com/jcrozum/biobalm/compare/v0.3.1...v0.4.0

0.3.1

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**: https://github.com/jcrozum/biobalm/compare/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".


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