fix: fixed recording time courses with initial time != 0

biosimulators · Aug 10, 2021 · 41303d9 · 41303d9
1 parent 7838c6e
commit 41303d9
Show file tree

Hide file tree

Showing 4 changed files with 8 additions and 6 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -14,7 +14,7 @@
 # Base OS
 FROM python:3.9-slim-buster
 
-ARG VERSION="0.1.27"
+ARG VERSION="0.1.28"
 ARG SIMULATOR_VERSION=4.33.246
 
 # metadata

diff --git a/biosimulators_copasi/_version.py b/biosimulators_copasi/_version.py
@@ -1 +1 @@
-__version__ = '0.1.27'
+__version__ = '0.1.28'
diff --git a/biosimulators_copasi/core.py b/biosimulators_copasi/core.py
@@ -214,7 +214,8 @@ def exec_sed_task(task, variables, log=None):
 
     copasi_problem = copasi_task.getProblem()
     copasi_model.setInitialTime(sim.initial_time)
-    copasi_problem.setOutputStartTime(sim.output_start_time - sim.initial_time)
+    copasi_model.forceCompile()
+    copasi_problem.setOutputStartTime(sim.output_start_time)
     copasi_problem.setDuration(sim.output_end_time - sim.initial_time)
     if sim.output_end_time == sim.output_start_time:
         if sim.output_start_time == sim.initial_time:
@@ -263,9 +264,6 @@ def exec_sed_task(task, variables, log=None):
     for i_step in range(number_of_recorded_points):
         step_values = copasi_data_handler.getNthRow(i_step)
         for variable, value in zip(variables, step_values):
-            if variable.symbol == Symbol.time.value:
-                value += sim.initial_time
-
             variable_results[variable.id][i_step] = value
 
     if sim.output_end_time == sim.output_start_time and sim.output_start_time == sim.initial_time:

diff --git a/tests/test_core_main.py b/tests/test_core_main.py
@@ -207,6 +207,7 @@ def test_exec_sed_task_correct_time_course_attrs(self):
                 task=task),
         ]
 
+        # initial time == 0, output start time == initial time
         task.simulation.initial_time = 0.
         task.simulation.output_start_time = 0.
         task.simulation.output_end_time = 20.
@@ -217,6 +218,7 @@ def test_exec_sed_task_correct_time_course_attrs(self):
             numpy.linspace(task.simulation.output_start_time, task.simulation.output_end_time, task.simulation.number_of_points + 1),
             rtol=1e-4)
 
+        # initial time == 0, output start time != initial time
         task.simulation.initial_time = 0.
         task.simulation.output_start_time = 10.
         task.simulation.output_end_time = 20.
@@ -228,6 +230,7 @@ def test_exec_sed_task_correct_time_course_attrs(self):
             rtol=1e-4)
         numpy.testing.assert_allclose(second_half_variable_results['A'], full_variable_results['A'][10:], rtol=1e-4)
 
+        # initial time != 0, output start time == initial time
         task.simulation.initial_time = 5.
         task.simulation.output_start_time = 5.
         task.simulation.output_end_time = 25.
@@ -239,6 +242,7 @@ def test_exec_sed_task_correct_time_course_attrs(self):
             rtol=1e-4)
         numpy.testing.assert_allclose(offset_full_variable_results['A'], full_variable_results['A'], rtol=1e-4)
 
+        # initial time != 0, output start time != initial time
         task.simulation.initial_time = 5.
         task.simulation.output_start_time = 15.
         task.simulation.output_end_time = 25.