search

jcrozum / pystablemotifs

Python library for attractor identification and control in Boolean networks
MIT License
28 stars 7 forks source link

Testing and benchmarking #3

Closed jcrozum closed 3 years ago

jcrozum commented 4 years ago
  1. Test simple models that are easy to verify by hand
  2. Test curated biological models
  3. Test "tricky" models designed to fool the code
  4. Benchmark ensemble random networks against PyBoolNet's methods and the Java implementation

See the StableMotifTest1.py, StableMotifTest2.py, and StableMotifTest3.py files for examples.

jcrozum commented 4 years ago
  1. Test to make sure the partial STG building works in all cases. Tested for the 3 examples in the root directory. Need to test the case when we can't rule out a complex attractor by other means and MUST rely on the partial STG to rule out hidden complex attractors.
jgtz commented 4 years ago

There is a new branch "testing-benchmarking" where 2 new tricky test models were added. See https://github.com/jcrozum/StableMotifs/commit/d3069b7d2227de34445fd5fd85ed6b368f84efe0

deriteidavid commented 4 years ago

Guys, I added a unit-testing script to the main folder called test_StableMotifs.py. Right now it's in a primitive state but I will gradually improve it with new tests. It's a simple, single script to run before every major commit to the code. You're also welcome to add test functions to it as you write new code.