Comments (1)
Fixed in above referenced commit. Added kda.find_all_unique_cycles() which uses nx.simple_cycles() to find all cycles in a given diagram, even if some of the cycles contain the same nodes. It was discovered that previous versions of similar code in KDA were unnecessarily filtering out cycles with the same nodes, so this was fixed and implemented into cycle flux calculation code.
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Related Issues (20)
- MAINT: Change plotting function `label`/`path` behavior
- MAINT: Move single cycle/diagram plotting code into new, public plotting function
- CI: Update `codecov` configuration HOT 1
- DOC: Purge "directional partial" from function docstrings
- ENH: Change graphs to store rates as edge weights instead of attributes HOT 1
- ENH: Add `KineticModel` method for calculating net cycle fluxes HOT 3
- MAINT: create `KineticDiagram` object and move relevant functions into class body HOT 2
- CI: Add Python 3.10 to CI
- DOC: Add algorithm references to function docstrings HOT 1
- TST: Add test for transition/cycle/operational flux relations HOT 3
- ENH: Improve KDA API HOT 1
- ENH: Add thermodynamic consistency checker
- make a release HOT 10
- CI, BUG: Tests Failing on Python 3.9 HOT 1
- Replace deprecated `np.product()` function calls HOT 1
- TST: Add test which verifies number of spanning trees using Kirchhoff's Matrix-Tree Theorem HOT 3
- MAINT, TST: hypothesis FailedHealthCheck error due to multiple executors
- CI: Update CI Python versions
- BUG, MAINT: Fix `arrows=True` parameter for `nx.draw_networkx_edges` in `plotting.draw_diagrams()` HOT 1
- MAINT: Pin `mpmath` to version 1.3.0 HOT 1
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