Update requirements

ModelEngineering · Feb 2, 2025 · 7ceb979 · 7ceb979
1 parent 69e2b38
commit 7ceb979
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Showing 3 changed files with 8 additions and 3 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -9,6 +9,7 @@ requires-python = ">=3.6"
 
 dependencies = [
     "coverage",
+    "colour",
     "control",
     "docstring-expander",
     "jupyterlab",

diff --git a/requirements.txt b/requirements.txt
@@ -18,6 +18,7 @@ scikit-learn
 seaborn
 statsmodels
 sympy
+symmathSBML
 tabulate
 tellurium
 toml

diff --git a/src/controlSBML/control_sbml.py b/src/controlSBML/control_sbml.py
@@ -138,7 +138,8 @@
 DesignResult = namedtuple("DesignResult", ["timeseries", "antimony_builder", "design_df"])
 ModelResult = namedtuple("ModelResult", ["timeseries"])
 StaircaseResponseResult = namedtuple("StaircaseResponseResult", ["timeseries", "antimony_builder"])
-TransferFunctionFitResult = namedtuple("TransferFunctionFitResult", ["timeseries", "antimony_builder"]) 
+TransferFunctionFitResult = namedtuple("TransferFunctionFitResult",
+                                       ["timeseries", "antimony_builder", "transfer_function"]) 
 
 
 class ControlSBML(object):
@@ -154,7 +155,7 @@ def __init__(self, model_reference:str,
                  fitter_method:Optional[str]=OPTION_DCT[cn.O_FITTER_METHOD],
                  setpoint:Optional[float]=OPTION_DCT[cn.O_SETPOINT],
                  sign:Optional[int]=OPTION_DCT[cn.O_SIGN],
-                 times:Optional[np.ndarray[float]]=None,
+                 times:Optional[np.ndarray]=None,
                  **kwargs):
         """
         model_reference: str
@@ -460,7 +461,7 @@ def _initializeStaircaseOptions(self, initial_value=None, final_value=None, num_
 
     ############ PLOTTERS ##############
     def plotModel(self, 
-                  times:Optional[np.ndarray[float]]=None,
+                  times:Optional[np.ndarray]=None,
                   selections:Optional[List[str]]=OPTION_DCT[cn.O_SELECTIONS],
                   **kwargs)->ModelResult:
         """
@@ -562,6 +563,7 @@ def plotTransferFunctionFit(self,
             TransferFunctionFitResult
                 timeseries: Timeseries (predicted, staircase input, simulated output)
                 antimony_builder: AntimonyBuilder
+                transfer_function: control.TransferFunction
         """
         # Check the options
         self._checkKwargs(valids=PLOT_KEYS, **kwargs)
@@ -602,6 +604,7 @@ def plotTransferFunctionFit(self,
         return TransferFunctionFitResult(
                 timeseries=self._fitter_result.time_series, 
                 antimony_builder=self._fitter_result.antimony_builder,
+                transfer_function=self._fitter_result.transfer_function,
         )
 
     def _plotClosedLoop(self,