Build fixes

ModelEngineering · Mar 31, 2024 · 72317f7 · 72317f7
1 parent 09762a3
commit 72317f7
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Showing 3 changed files with 312 additions and 172 deletions.
diff --git a/examples/Regulating-Cell-Cycle-Xenpus-Laevis.ipynb b/examples/Regulating-Cell-Cycle-Xenpus-Laevis.ipynb
diff --git a/src/controlSBML/siso_transfer_function_fitter.py b/src/controlSBML/siso_transfer_function_fitter.py
@@ -147,7 +147,8 @@ def simulateTransferFunction(self,
         out_arr = self.out_arr - out_mean
         # Specify initial state for the transfer function, just the initial output
         X0 = np.zeros(len(transfer_function.den[0][0])-1)  # type: ignore
-        X0[-1] = out_arr[0]  # state position for undifferentiated output
+        if len(X0) > 0:
+            X0[-1] = out_arr[0]  # state position for undifferentiated output
         # Do the simulation
         warnings.filterwarnings("ignore")
         result_input = control.forced_response(transfer_function, T=self.times, U=in_arr, X0=X0)

diff --git a/tests/test_gpz_fitter.py b/tests/test_gpz_fitter.py
@@ -138,7 +138,8 @@ def testFitDCGain(self):
     def testFitPoles(self):
         if IGNORE_TEST:
             return
-        ts, _ = BUILDER.makeStaircaseResponse(staircase=STAIRCASE, times=np.linspace(0, 5, 50))
+        builder = BUILDER.copy()
+        ts, _ = builder.makeStaircaseResponse(staircase=STAIRCASE, times=np.linspace(0, 5, 50))
         fitter = GPZFitter(ts, num_zero=0, num_pole=2)
         fitter._fitDCGain()
         fitter._fitPoles()
@@ -184,8 +185,8 @@ def plot(self, in_fitter=None, title=""):
         plt.show()
 
     def testFitTransferFunctionBug(self):
-        #if IGNORE_TEST:
-        #    return
+        if IGNORE_TEST:
+            return
         URL = "https://www.ebi.ac.uk/biomodels/services/download/get-files/MODEL1304160000/2/BIOMD0000000449_url.xml"
         ctlsb = ControlSBML(URL,
               input_name="IR", output_name="GLUT4", is_fixed_input_species=True, is_plot=False)