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Fix build break
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@joseph-hellerstein
joseph-hellerstein committed May 30, 2024
1 parent a255da1 commit ea66a8f
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Showing 2 changed files with 58 additions and 5 deletions.
50 changes: 50 additions & 0 deletions examples/Controlling-Glucose-Metabolis-in-Yeast.ipynb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1903,6 +1903,56 @@
"design_result = ctlsb.plotGridDesign(grid, setpoint=SETPOINT, num_restart=5)"
]
},
{
"cell_type": "code",
"execution_count": 38,
"id": "d4b7e00f-be81-4086-8530-ba4013f0a04f",
"metadata": {},
"outputs": [
{
"ename": "AttributeError",
"evalue": "'DataFrame' object has no attribute 'dataframe'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m/var/folders/02/lb248q1j50dch2pthzkvxmpr0000gn/T/ipykernel_18984/2487768355.py\u001b[0m in \u001b[0;36m?\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mctlsb\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplotAllDesignResults\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdf\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m~/home/Technical/repos/controlSBML/src/controlSBML/control_sbml.py\u001b[0m in \u001b[0;36m?\u001b[0;34m(self, design_result, title, figsize, columns, round_digit, is_plot)\u001b[0m\n\u001b[1;32m 753\u001b[0m \u001b[0mPersists\u001b[0m \u001b[0mthe\u001b[0m \u001b[0mclosed\u001b[0m \u001b[0mloop\u001b[0m \u001b[0mdesign\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mkP\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkI\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkD\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkF\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0ma\u001b[0m \u001b[0mdesign\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0mfound\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 754\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 755\u001b[0m \u001b[0mArgs\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 756\u001b[0m \u001b[0mgrid\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mGrid\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mgrid\u001b[0m \u001b[0mof\u001b[0m \u001b[0mvalues\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mthe\u001b[0m \u001b[0mcontrol\u001b[0m \u001b[0mparameters\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 757\u001b[0;31m \u001b[0msetpoint\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mfloat\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mregulation\u001b[0m \u001b[0mpoint\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 758\u001b[0m \u001b[0msign\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mfloat\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mdirection\u001b[0m \u001b[0mof\u001b[0m \u001b[0mfeedback\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 759\u001b[0m \u001b[0mtimes\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mnumpy\u001b[0m \u001b[0marray\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mtimes\u001b[0m \u001b[0mof\u001b[0m \u001b[0msimulation\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 760\u001b[0m \u001b[0mnum_process\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mint\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mnumber\u001b[0m \u001b[0mof\u001b[0m \u001b[0mprocesses\u001b[0m \u001b[0mto\u001b[0m \u001b[0muse\u001b[0m\u001b[0;34m;\u001b[0m \u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m \u001b[0mmeans\u001b[0m \u001b[0muse\u001b[0m \u001b[0mall\u001b[0m \u001b[0mavailable\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/home/Technical/repos/controlSBML/ctl/lib/python3.9/site-packages/pandas/core/generic.py\u001b[0m in \u001b[0;36m?\u001b[0;34m(self, name)\u001b[0m\n\u001b[1;32m 6200\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mname\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_accessors\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 6201\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_info_axis\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_can_hold_identifiers_and_holds_name\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 6202\u001b[0m ):\n\u001b[1;32m 6203\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 6204\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mobject\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__getattribute__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;31mAttributeError\u001b[0m: 'DataFrame' object has no attribute 'dataframe'"
]
}
],
"source": [
"ctlsb.plotAllDesignResults(df)"
]
},
{
"cell_type": "code",
"execution_count": 33,
"id": "29eec4da-b7b0-447d-a1e6-bbf9f8fc30d6",
"metadata": {},
"outputs": [
{
"ename": "AttributeError",
"evalue": "'DataFrame' object has no attribute 'dataframe'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m/var/folders/02/lb248q1j50dch2pthzkvxmpr0000gn/T/ipykernel_18984/3759151062.py\u001b[0m in \u001b[0;36m?\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mdf\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mdesign_result\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdesigns\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdataframe\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloc\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mrange\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m100\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 4\u001b[0m \u001b[0;32mdel\u001b[0m \u001b[0mdf\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"reason\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0mctlsb\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplotAllDesignResults\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdf\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/home/Technical/repos/controlSBML/src/controlSBML/control_sbml.py\u001b[0m in \u001b[0;36m?\u001b[0;34m(self, design_result, title, figsize, columns, round_digit, is_plot)\u001b[0m\n\u001b[1;32m 753\u001b[0m \u001b[0mPersists\u001b[0m \u001b[0mthe\u001b[0m \u001b[0mclosed\u001b[0m \u001b[0mloop\u001b[0m \u001b[0mdesign\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mkP\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkI\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkD\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkF\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0ma\u001b[0m \u001b[0mdesign\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0mfound\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 754\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 755\u001b[0m \u001b[0mArgs\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 756\u001b[0m \u001b[0mgrid\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mGrid\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mgrid\u001b[0m \u001b[0mof\u001b[0m \u001b[0mvalues\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mthe\u001b[0m \u001b[0mcontrol\u001b[0m \u001b[0mparameters\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 757\u001b[0;31m \u001b[0msetpoint\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mfloat\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mregulation\u001b[0m \u001b[0mpoint\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 758\u001b[0m \u001b[0msign\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mfloat\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mdirection\u001b[0m \u001b[0mof\u001b[0m \u001b[0mfeedback\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 759\u001b[0m \u001b[0mtimes\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mnumpy\u001b[0m \u001b[0marray\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mtimes\u001b[0m \u001b[0mof\u001b[0m \u001b[0msimulation\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 760\u001b[0m \u001b[0mnum_process\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mint\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mnumber\u001b[0m \u001b[0mof\u001b[0m \u001b[0mprocesses\u001b[0m \u001b[0mto\u001b[0m \u001b[0muse\u001b[0m\u001b[0;34m;\u001b[0m \u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m \u001b[0mmeans\u001b[0m \u001b[0muse\u001b[0m \u001b[0mall\u001b[0m \u001b[0mavailable\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/home/Technical/repos/controlSBML/ctl/lib/python3.9/site-packages/pandas/core/generic.py\u001b[0m in \u001b[0;36m?\u001b[0;34m(self, name)\u001b[0m\n\u001b[1;32m 6200\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mname\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_accessors\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 6201\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_info_axis\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_can_hold_identifiers_and_holds_name\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 6202\u001b[0m ):\n\u001b[1;32m 6203\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 6204\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mobject\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__getattribute__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;31mAttributeError\u001b[0m: 'DataFrame' object has no attribute 'dataframe'"
]
}
],
"source": [
"df = design_result.designs.dataframe.loc[range(100), :]\n",
"del df[\"reason\"]\n",
"ctlsb.plotAllDesignResults(df)"
]
},
{
"cell_type": "code",
"execution_count": 4,
Expand Down
13 changes: 8 additions & 5 deletions tests/test_sbml_system.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -217,11 +217,14 @@ def testPlotSISOClosedLoop(self):
"noise_S1_S3_ot",
"disturbance_S1_S3_ot"
]
ts, _ = system.simulateSISOClosedLoop(input_name="S1", output_name="S3", kP=2, kI=0.8, kF=0.5,
selections=selections,
setpoint=setpoint, end_time=100, num_point=1000)
self.system.plotSISOClosedLoop(ts, setpoint, figsize=(5,5), markers=["+", "o"], selections=selections,
title="Closed Loop", is_plot=IS_PLOT, legend=selections)
for _ in range(5):
ts, _ = system.simulateSISOClosedLoop(input_name="S1", output_name="S3", kP=2, kI=0.8, kF=0.5,
selections=selections,
setpoint=setpoint, end_time=100, num_point=1000)
if ts is not None:
self.system.plotSISOClosedLoop(ts, setpoint, figsize=(5,5), markers=["+", "o"], selections=selections,
title="Closed Loop", is_plot=IS_PLOT, legend=selections)
break

def testGetValidSymbolsInput(self):
if IGNORE_TEST:
Expand Down

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