Merge branch 'development' into test_rerun

OpenSourceBrain · Jan 8, 2025 · 8551de6 · 8551de6
2 parents 9c3f600 + 1838933
commit 8551de6
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Showing 99 changed files with 3,162 additions and 1,081 deletions.
diff --git a/BioModels/BIOMD0000000001/BIOMD0000000001_url.sedml b/BioModels/BIOMD0000000001/BIOMD0000000001_url.sedml
@@ -4,7 +4,7 @@
     <model id="BIOMD0000000001_url" language="urn:sedml:language:sbml" source="BIOMD0000000001_url.xml"/>
   </listOfModels>
   <listOfSimulations>
-    <uniformTimeCourse id="auto_ten_seconds" initialTime="0.001" outputStartTime="0.001" outputEndTime="10000" numberOfSteps="100000">
+    <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
       <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
@@ -616,18 +616,18 @@
       <xAxis name="Time" type="linear"/>
       <yAxis name="Species" type="linear"/>
       <listOfCurves>
-        <curve id="autogen_curve_task1_BLL" name="BLL" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_BLL"/>
-        <curve id="autogen_curve_task1_IL" name="IL" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_IL"/>
-        <curve id="autogen_curve_task1_AL" name="AL" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_AL"/>
-        <curve id="autogen_curve_task1_A" name="A" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_A"/>
-        <curve id="autogen_curve_task1_BL" name="BL" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_BL"/>
-        <curve id="autogen_curve_task1_B" name="B" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_B"/>
-        <curve id="autogen_curve_task1_DLL" name="DLL" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_DLL"/>
-        <curve id="autogen_curve_task1_D" name="D" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_D"/>
-        <curve id="autogen_curve_task1_ILL" name="ILL" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_ILL"/>
-        <curve id="autogen_curve_task1_DL" name="DL" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_DL"/>
-        <curve id="autogen_curve_task1_I" name="I" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_I"/>
-        <curve id="autogen_curve_task1_ALL" name="ALL" logX="true" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_ALL"/>
+        <curve id="autogen_curve_task1_BLL" name="BLL" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_BLL"/>
+        <curve id="autogen_curve_task1_IL" name="IL" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_IL"/>
+        <curve id="autogen_curve_task1_AL" name="AL" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_AL"/>
+        <curve id="autogen_curve_task1_A" name="A" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_A"/>
+        <curve id="autogen_curve_task1_BL" name="BL" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_BL"/>
+        <curve id="autogen_curve_task1_B" name="B" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_B"/>
+        <curve id="autogen_curve_task1_DLL" name="DLL" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_DLL"/>
+        <curve id="autogen_curve_task1_D" name="D" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_D"/>
+        <curve id="autogen_curve_task1_ILL" name="ILL" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_ILL"/>
+        <curve id="autogen_curve_task1_DL" name="DL" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_DL"/>
+        <curve id="autogen_curve_task1_I" name="I" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_I"/>
+        <curve id="autogen_curve_task1_ALL" name="ALL" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_ALL"/>
       </listOfCurves>
     </plot2D>
   </listOfOutputs>

diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_local/amici_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_local/amici_autogen_plot_for_task1.pdf
diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_local/copasi_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_local/copasi_autogen_plot_for_task1.pdf
diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_local/pysces_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_local/pysces_autogen_plot_for_task1.pdf
diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_local/tellurium_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_local/tellurium_autogen_plot_for_task1.pdf
diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_local/vcell_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_local/vcell_autogen_plot_for_task1.pdf
diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_remote/amici_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_remote/amici_autogen_plot_for_task1.pdf
diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_remote/copasi_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_remote/copasi_autogen_plot_for_task1.pdf
diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_remote/masspy_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_remote/masspy_autogen_plot_for_task1.pdf
diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_remote/pysces_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_remote/pysces_autogen_plot_for_task1.pdf
diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_remote/tellurium_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_remote/tellurium_autogen_plot_for_task1.pdf
diff --git a/BioModels/BIOMD0000000001/tests/d1_plots_remote/vcell_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000001/tests/d1_plots_remote/vcell_autogen_plot_for_task1.pdf
diff --git a/BioModels/BIOMD0000000001/tests/results_compatibility_biosimulators.md b/BioModels/BIOMD0000000001/tests/results_compatibility_biosimulators.md
diff --git a/BioModels/BIOMD0000000001/tests/results_local.json b/BioModels/BIOMD0000000001/tests/results_local.json
diff --git a/BioModels/BIOMD0000000001/tests/results_remote.json b/BioModels/BIOMD0000000001/tests/results_remote.json
diff --git a/BioModels/BIOMD0000000138/BIOMD0000000138_url.sedml b/BioModels/BIOMD0000000138/BIOMD0000000138_url.sedml
@@ -4,7 +4,7 @@
     <model id="BIOMD0000000138_url" language="urn:sedml:language:sbml" source="BIOMD0000000138_url.xml"/>
   </listOfModels>
   <listOfSimulations>
-    <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="3000" numberOfSteps="100000">
+    <uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
       <algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
     </uniformTimeCourse>
   </listOfSimulations>
@@ -414,24 +414,12 @@
         <dataSet id="autogen_task1_reaction_0000004" label="reaction_0000004" dataReference="auto_dg_for_task1_reaction_0000004"/>
       </listOfDataSets>
     </report>
-    <plot2D id="autogen_plot1" name="c">
+    <plot2D id="autogen_plot_for_task1" name="Auto-generated plot for task1, including all species.">
       <xAxis name="Time" type="linear"/>
       <yAxis name="Species" type="linear"/>
       <listOfCurves>
         <curve id="autogen_curve_task1_c" name="c" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_c"/>
-          </listOfCurves>
-    </plot2D>
-    <plot2D id="autogen_plot2" name="V">
-      <xAxis name="Time" type="linear"/>
-      <yAxis name="Species" type="linear"/>
-      <listOfCurves>
-         <curve id="autogen_curve_for_task1_V" name="V" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_V"/>
       </listOfCurves>
     </plot2D>
-
-    <plot2D id="autogen_plot3" name="vk">
-      <xAxis name="Time" type="linear"/>
-      <yAxis name="Species" type="linear"/>
-    </plot2D>
   </listOfOutputs>
 </sedML>
diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_local/amici_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_local/amici_autogen_plot_for_task1.pdf
diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_local/copasi_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_local/copasi_autogen_plot_for_task1.pdf
diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_local/pysces_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_local/pysces_autogen_plot_for_task1.pdf
diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_local/tellurium_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_local/tellurium_autogen_plot_for_task1.pdf
diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_local/vcell_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_local/vcell_autogen_plot_for_task1.pdf
diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_remote/amici_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_remote/amici_autogen_plot_for_task1.pdf
diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_remote/copasi_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_remote/copasi_autogen_plot_for_task1.pdf
diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_remote/masspy_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_remote/masspy_autogen_plot_for_task1.pdf
diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_remote/pysces_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_remote/pysces_autogen_plot_for_task1.pdf
diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_remote/tellurium_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_remote/tellurium_autogen_plot_for_task1.pdf
diff --git a/BioModels/BIOMD0000000138/tests/d1_plots_remote/vcell_autogen_plot_for_task1.pdf b/BioModels/BIOMD0000000138/tests/d1_plots_remote/vcell_autogen_plot_for_task1.pdf