Merge branch 'develop' of github.com:stochss/stochss into develop

Dockerfile

@@ -29,10 +29,10 @@ COPY --chown=jovyan:users jupyter_notebook_config.py $JUPYTER_CONFIG_DIR/jupyter
 
 USER root
 
-RUN wget -q https://julialang-s3.julialang.org/bin/linux/x64/1.4/julia-1.4.2-linux-x86_64.tar.gz \
-    && tar -xvzf julia-1.4.2-linux-x86_64.tar.gz \
-    && mv julia-1.4.2 /usr/local/ \
-    && chown -R jovyan:users /usr/local/julia-1.4.2/
+RUN wget -q https://julialang-s3.julialang.org/bin/linux/x64/1.4/julia-1.4.2-linux-x86_64.tar.gz
+RUN tar -xvzf julia-1.4.2-linux-x86_64.tar.gz
+RUN mv julia-1.4.2 /usr/local/
+RUN chown -R jovyan:users /usr/local/julia-1.4.2/
 
 USER jovyan
 

client/templates/includes/editInitialCondition.pug

@@ -8,13 +8,13 @@ tr
 
   td
 
-    if this.model.icType === "Place"
+    div(data-hook="place-details")
       span <b>Location:</b>
       div
         div.inline(data-hook="x-container")
         div.inline(data-hook="y-container")
         div.inline(data-hook="z-container")
-    else
+    div(data-hook="scatter-details")
       span <b>Active in Types:</b>
       div(data-hook="initial-condition-types")
 

client/templates/includes/spatialSpeciesEditor.pug

@@ -20,6 +20,26 @@ div#species-editor.card.card-body
 
       tbody(data-hook="specie-list")
 
+    table.table
+      thead
+        tr
+          th(scope="col", colspan="3") 
+
+            div
+
+              div.inline Model Mode
+
+              div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.spatialSpeciesMode) <sup><svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="info" class="svg-inline--fa fa-info fa-w-6" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 192 512"><path fill="currentColor" d="M20 424.229h20V279.771H20c-11.046 0-20-8.954-20-20V212c0-11.046 8.954-20 20-20h112c11.046 0 20 8.954 20 20v212.229h20c11.046 0 20 8.954 20 20V492c0 11.046-8.954 20-20 20H20c-11.046 0-20-8.954-20-20v-47.771c0-11.046 8.954-20 20-20zM96 0C56.235 0 24 32.235 24 72s32.235 72 72 72 72-32.235 72-72S135.764 0 96 0z"></path></svg></sup>
+
+      tbody
+        tr
+          td
+            input(type="radio", name="species-mode", data-hook="all-continuous", data-name="continuous") 
+            |  Concentration
+          td
+            input(type="radio", name="species-mode", data-hook="all-discrete", data-name="discrete")
+            |  Population
+
     button.btn.btn-outline-primary.box-shadow(data-hook="add-species") Add Variable
 
     button.btn.btn-outline-primary.box-shadow.ml-2(data-hook="save-species") Save Variables

client/tooltips.js

@@ -29,6 +29,9 @@ module.exports = {
     speciesMode: "Concentration - Variables will only be represented using continuous (floating point) values.<br>Population - Variables will only be represented "+
         "using discrete (integer count) values.<br>Hybrid Concentration/Population - Allows a variables to be represented using continuous and/or discrete values.",
 
+    spatialSpeciesMode: "Concentration - Variables will only be represented using continuous (floating point) values.<br>Population - Variables will only be represented "+
+        "using discrete (integer count) values.",
+
     mode: "Concentration - Variables will only be represented using continuous (floating point) values.<br>Population - Variables will only be represented "+
         "using discrete (integer count) values.<br>Hybrid Concentration/Population - Allows a variables to be represented using continuous and/or discrete values.",
 

client/views/edit-initial-condition.js

@@ -16,6 +16,7 @@ You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
+let $ = require('jquery');
 var tests = require('./tests');
 //views
 var View = require('ampersand-view');
@@ -74,19 +75,19 @@ module.exports = View.extend({
   },
   renderDetailsView: function () {
     if(this.model.icType === "Place") {
+      $(this.queryByHook("scatter-details")).css("display", "none")
+      $(this.queryByHook("place-details")).css("display", "block")
       this.renderLocation();
     }else {
+      $(this.queryByHook("place-details")).css("display", "none")
+      $(this.queryByHook("scatter-details")).css("display", "block")
       this.renderTypes();
     }
   },
   renderLocation: function () {
     if(this.xCoord) {
       this.xCoord.remove();
-    }
-    if(this.yCoord) {
       this.yCoord.remove();
-    }
-    if(this.zCoord) {
       this.zCoord.remove();
     }
     this.xCoord = new InputView({parent: this, required: true,

client/views/species-editor.js

@@ -136,22 +136,24 @@ module.exports = View.extend({
   },
   setAllSpeciesModes: function (defaultMode, cb) {
     this.collection.parent.defaultMode = defaultMode;
-    if(defaultMode === "continuous") {
-      $(this.parent.queryByHook("system-volume-container")).collapse("hide")
-    }else{
-      $(this.parent.queryByHook("system-volume-container")).collapse("show")
-    }
-    this.collection.map(function (specie) { 
-      specie.mode = defaultMode
-      cb(specie)
-    });
-    if(defaultMode === "dynamic"){
-      this.renderSpeciesAdvancedView()
-      $(this.queryByHook('advanced-species')).collapse('show');
-    }
-    else{
-      this.speciesAdvancedView.views[0].updateInputValidation()
-      $(this.queryByHook('advanced-species')).collapse('hide');
+    if(!this.collection.parent.is_spatial) {
+      if(defaultMode === "continuous") {
+        $(this.parent.queryByHook("system-volume-container")).collapse("hide")
+      }else{
+        $(this.parent.queryByHook("system-volume-container")).collapse("show")
+      }
+      this.collection.map(function (specie) { 
+        specie.mode = defaultMode
+        cb(specie)
+      });
+      if(defaultMode === "dynamic"){
+        this.renderSpeciesAdvancedView()
+        $(this.queryByHook('advanced-species')).collapse('show');
+      }
+      else{
+        this.speciesAdvancedView.views[0].updateInputValidation()
+        $(this.queryByHook('advanced-species')).collapse('hide');
+      }
     }
   },
   renderEditSpeciesView: function () {

jupyterhub/Dockerfile.jupyterhub

@@ -13,11 +13,13 @@ RUN apt-get update  && apt-get install -yq --no-install-recommends \
         locales \
         python3-pip \
         python3-pycurl \
-        nodejs \
-        npm \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/*
 
+RUN curl -sL https://deb.nodesource.com/setup_14.x | bash -
+
+RUN apt-get install -y nodejs
+
 ENV SHELL=/bin/bash LC_ALL=en_US.UTF-8 LANG=en_US.UTF-8 LANGUAGE=en_US.UTF-8
 
 RUN locale-gen $LC_ALL

stochss/handlers/util/scripts/run_preview.py

@@ -96,6 +96,7 @@ def run_preview(wkfl):
         model = StochSSSpatialModel(path=args.path)
         wkfl = SpatialSimulation(path="", preview=True, species=args.species)
         wkfl.s_py_model = model.convert_to_spatialpy()
+        wkfl.s_model = model.model
     else:
         log_stm = setup_logger()
         model = StochSSModel(path=args.path)

stochss/handlers/util/spatial_simulation.py

@@ -71,6 +71,8 @@ def run(self, preview=False, verbose=False):
             #     self.species = list(self.s_py_model.get_all_species().keys())[0]
             t_ndx_list = list(range(len(os.listdir(results.result_dir)) - 1))
             plot = results.plot_species(species=self.species, t_ndx_list=t_ndx_list, animated=True,
+                                        concentration=self.s_model['defaultMode'] == "continuous",
+                                        deterministic=self.s_model['defaultMode'] == "discrete",
                                         width=None, height=None, return_plotly_figure=True,
                                         f_duration=100, t_duration=100)
             plot["layout"]["autosize"] = True