Merge pull request #1360 from StochSS/develop

Release 2.4.11
StochSS · Aug 23, 2022 · ea29cde · ea29cde
2 parents 59b3bf9 + ca7909b
commit ea29cde
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Showing 7 changed files with 27 additions and 26 deletions.
diff --git a/client/model-view/model-view.js b/client/model-view/model-view.js
@@ -79,27 +79,24 @@ module.exports = View.extend({
       this.setReadOnlyMode("model-mode");
       this.setReadOnlyMode("system-volume");
     }else {
-      if(this.model.defaultMode === "" && !this.model.is_spatial){
-        if(this.model.is_spatial) {
-          this.model.defaultMode = "discrete";
-          $(this.queryByHook("spatial-discrete")).prop('checked', true);
-        }else{
+      if(this.model.is_spatial) {
+        this.model.defaultMode = "discrete";
+        $(this.queryByHook("spatial-discrete")).prop('checked', true);
+        let dataHooks = {
+          'continuous':'spatial-continuous',
+          'discrete':'spatial-discrete',
+          'discrete-concentration':'spatial-discrete-concentration'
+        };
+        $(this.queryByHook(dataHooks[this.model.defaultMode])).prop('checked', true);
+        $(this.queryByHook("model-mode-container")).css("display", "none");
+        $(this.queryByHook("system-volume-container")).css("display", "none");
+      }else{
+        let dataHooks = {'continuous':'all-continuous', 'discrete':'all-discrete', 'dynamic':'advanced'};
+        $(this.queryByHook("spatial-model-mode-container")).css("display", "none");
+        if (this.model.defaultMode === ""){
           this.getInitialDefaultMode();
-        }
-      }else {
-        if(this.model.is_spatial) {
-          let dataHooks = {
-            'continuous':'spatial-continuous',
-            'discrete':'spatial-discrete',
-            'discrete-concentration':'spatial-discrete-concentration'
-          };
-          $(this.queryByHook(dataHooks[this.model.defaultMode])).prop('checked', true);
-          $(this.queryByHook("model-mode-container")).css("display", "none");
-          $(this.queryByHook("system-volume-container")).css("display", "none");
         }else{
-          let dataHooks = {'continuous':'all-continuous', 'discrete':'all-discrete', 'dynamic':'advanced'};
           $(this.queryByHook(dataHooks[this.model.defaultMode])).prop('checked', true);
-          $(this.queryByHook("spatial-model-mode-container")).css("display", "none");
         }
       }
       this.model.reactions.on("change", (reactions) => {

diff --git a/...Vilar-Oscillator.proj/Vilar_Oscillator.wkgp/Vilar_Oscillator_SCIOPE_Model_Inference.ipynb b/...Vilar-Oscillator.proj/Vilar_Oscillator.wkgp/Vilar_Oscillator_SCIOPE_Model_Inference.ipynb
@@ -183,7 +183,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "model = VilarOscillator1()"
+    "model = create_vilar_oscillator()"
    ]
   },
   {

diff --git a/stochss/handlers/util/ensemble_simulation.py b/stochss/handlers/util/ensemble_simulation.py
@@ -89,7 +89,7 @@ def __update_timespan(self):
                 end = self.settings['timespanSettings']['endSim']
                 step_size = self.settings['timespanSettings']['timeStep']
                 self.g_model.timespan(
-                    TimeSpan(numpy.arange(0, end + step_size, step_size))
+                    TimeSpan.arange(step_size, t=end + step_size)
                 )
 
 

diff --git a/stochss/handlers/util/parameter_sweep.py b/stochss/handlers/util/parameter_sweep.py
@@ -121,7 +121,7 @@ def configure(self):
                 end = self.settings['timespanSettings']['endSim']
                 step_size = self.settings['timespanSettings']['timeStep']
                 self.g_model.timespan(
-                    TimeSpan(numpy(0, end + step_size, step_size))
+                    TimeSpan.arange(step_size, t=end + step_size)
                 )
         kwargs = {"model":self.g_model, "settings":run_settings}
         parameters = []

diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py
@@ -139,7 +139,7 @@ def __convert_model_settings(self):
         try:
             end = self.model['modelSettings']['endSim']
             step_size = self.model['modelSettings']['timeStep']
-            return TimeSpan(numpy.arange(0, end + step_size, step_size))
+            return TimeSpan.arange(step_size, t=end + step_size)
         except KeyError as err:
             message = "Model settings are not properly formatted or "
             message += f"are referenced incorrectly: {str(err)}"

diff --git a/stochss/handlers/util/stochss_notebook.py b/stochss/handlers/util/stochss_notebook.py
@@ -121,7 +121,11 @@ def __create_configuration_cell(self):
             else:
                 commented = False
             start = f"{pad}# " if commented else pad
-            config.append(f"{start}solver = {self.settings['solver']}(model=model)")
+            if self.nb_type in (self.MODEL_EXPLORATION, self.MODEL_INFERENCE):
+                del_dir = ", delete_directory=False"
+            else:
+                del_dir = ""
+            config.append(f"{start}solver = {self.settings['solver']}(model=model{del_dir})")
         config.append(pad + "kwargs = {")
         if self.s_model['is_spatial']:
             settings = self.__get_spatialpy_run_setting()

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
@@ -29,7 +29,7 @@
 from escapism import escape
 from spatialpy import Model, Species, Parameter, Reaction, Domain, DomainError, BoundaryCondition, \
                       PlaceInitialCondition, UniformInitialCondition, ScatterInitialCondition, \
-                      Geometry, ModelError
+                      Geometry, ModelError, TimeSpan
 
 from .stochss_base import StochSSBase
 from .stochss_errors import StochSSFileNotFoundError, FileNotJSONFormatError, DomainFormatError, \
@@ -235,8 +235,8 @@ def __convert_model_settings(self, model):
             end = self.model['modelSettings']['endSim']
             output_freq = self.model['modelSettings']['timeStep']
             step_size = self.model['modelSettings']['timestepSize']
-            tspan = numpy.arange(0, end + step_size, output_freq)
-            model.timespan(tspan, timestep_size=step_size)
+            tspan = TimeSpan.arange(output_freq, t=end + step_size, timestep_size=step_size)
+            model.timespan(tspan)
         except KeyError as err:
             message = "Spatial model settings are not properly formatted or "
             message += f"are referenced incorrectly: {str(err)}"