From 0a01bde091838c6610e09b3cbc05c2b526f5ede3 Mon Sep 17 00:00:00 2001
From: "Frank T. Bergmann" <fbergman@caltech.edu>
Date: Tue, 5 Apr 2022 14:27:21 +0200
Subject: [PATCH] #18 : add support for global variables in custom output on
 time courses

---
 basico/task_timecourse.py         |  2 +-
 tests/tellurium_sim.sbml          | 47 +++++++++++++++++++++++++++++++
 tests/test_parameterestimation.py |  2 +-
 tests/test_timecourse.py          | 19 +++++++++++++
 4 files changed, 68 insertions(+), 2 deletions(-)
 create mode 100644 tests/tellurium_sim.sbml
 create mode 100644 tests/test_timecourse.py

diff --git a/basico/task_timecourse.py b/basico/task_timecourse.py
index 476b1ee..955464a 100644
--- a/basico/task_timecourse.py
+++ b/basico/task_timecourse.py
@@ -223,7 +223,7 @@ def create_data_handler(output_selection, during=None, after=None, before=None,
                 logging.warning('no object for name {0}'.format(name))
                 continue
 
-            if isinstance(obj, COPASI.CModel):
+            if obj.getObjectType() != 'Reference':
                 obj = obj.getValueReference()
 
             cn = obj.getCN().getString()
diff --git a/tests/tellurium_sim.sbml b/tests/tellurium_sim.sbml
new file mode 100644
index 0000000..2a31db1
--- /dev/null
+++ b/tests/tellurium_sim.sbml
@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+  <model metaid="__main" id="__main">
+    <listOfCompartments>
+      <compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="S1" compartment="default_compartment" initialAmount="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="S2" compartment="default_compartment" initialAmount="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="k1" value="0" constant="false"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction id="_J0" reversible="true" fast="false">
+        <listOfProducts>
+          <speciesReference species="S2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <ci> k1 </ci>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+    <listOfEvents>
+      <event id="_E0" useValuesFromTriggerTime="true">
+        <trigger initialValue="false" persistent="true">
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <gt/>
+              <ci> S1 </ci>
+              <cn type="integer"> 1 </cn>
+            </apply>
+          </math>
+        </trigger>
+        <listOfEventAssignments>
+          <eventAssignment variable="k1">
+            <math xmlns="http://www.w3.org/1998/Math/MathML">
+              <cn type="integer"> 1 </cn>
+            </math>
+          </eventAssignment>
+        </listOfEventAssignments>
+      </event>
+    </listOfEvents>
+  </model>
+</sbml>
diff --git a/tests/test_parameterestimation.py b/tests/test_parameterestimation.py
index 3a8a0d4..ae92b17 100644
--- a/tests/test_parameterestimation.py
+++ b/tests/test_parameterestimation.py
@@ -62,7 +62,7 @@ def test_get_data(self):
     @unittest.skipIf(sys.version_info < (3, 6, 0), 'This test requires assertLogs which is not available before')
     def test_change_bounds(self):
         basico.set_fit_parameters([{'name': '(R1).k2', 'lower': 1, 'upper': 0.01}])
-        with self.assertLogs(level='ERROR') as cm:
+        with self.assertLogs(level='ERROR') as _:
             sol = basico.as_dict(basico.run_parameter_estimation())
         self.assertTrue(np.isnan(sol['sol']))
 
diff --git a/tests/test_timecourse.py b/tests/test_timecourse.py
new file mode 100644
index 0000000..a5e6089
--- /dev/null
+++ b/tests/test_timecourse.py
@@ -0,0 +1,19 @@
+import unittest
+import basico
+import os
+
+THIS_DIR = os.path.dirname(__file__)
+
+
+class TestTimeCourse(unittest.TestCase):
+    def setUp(self):
+        basico.load_model(os.path.join(THIS_DIR, 'tellurium_sim.sbml'))
+
+    def test_custom_output(self):
+        tc = basico.run_time_course_with_output(['Time', '[S1]', '[S2]', 'Values[k1]'], 0, 5, 5)
+        self.assertIsNotNone(tc)
+        self.assertListEqual(tc.columns.to_list(), ['Time', '[S1]', '[S2]', 'Values[k1]'])
+
+
+if __name__ == '__main__':
+    unittest.main()