Dev je

README.md

@@ -1,6 +1,6 @@
-[![MATLAB](https://github.com/simkaryote/MATLAB-SimBiology-DevOps-Workflow-Example/actions/workflows/ci.yml/badge.svg)](https://github.com/simkaryote/MATLAB-SimBiology-DevOps-Workflow-Example/actions/workflows/ci.yml)
-[![Tests](https://img.shields.io/badge/Tests-Open_Test_Report-blue)](https://simkaryote.github.io/MATLAB-SimBiology-DevOps-Workflow-Example/tests/)
-[![Coverage](https://img.shields.io/badge/Coverage-Open_Code_Coverage_Report-orange)](https://simkaryote.github.io/MATLAB-SimBiology-DevOps-Workflow-Example/coverage/)
+[![MATLAB](https://github.com/ChezJe/MATLAB-SimBiology-DevOps-Workflow-Example/actions/workflows/ci.yml/badge.svg)](https://github.com/ChezJe/MATLAB-SimBiology-DevOps-Workflow-Example/actions/workflows/ci.yml)
+[![Tests](https://img.shields.io/badge/Tests-Open_Test_Report-blue)](https://ChezJe.github.io/MATLAB-SimBiology-DevOps-Workflow-Example/tests/)
+[![Coverage](https://img.shields.io/badge/Coverage-Open_Code_Coverage_Report-orange)](https://ChezJe.github.io/MATLAB-SimBiology-DevOps-Workflow-Example/coverage/)
 
 # Generating Tests for Your MATLAB<sup>&reg;</sup> Code Workshop
 

buildfile.m

@@ -1,22 +1,20 @@
 function plan = buildfile
-
 import matlab.buildtool.tasks.*
 
+% Extract tasks from local functions
 plan = buildplan(localfunctions);
 
-% Set default task
-plan.DefaultTasks = "test";
-
-
 % CodeIssues task
-plan("check") = CodeIssuesTask();
+plan("check") = CodeIssuesTask(Results=["results/codeissues.sarif"; ...
+                                        "results/codeissues.mat"]);
 
 % Test task
 tTask = TestTask("tests", ...
     SourceFiles = "code", ...
     IncludeSubfolders = true,...
-    TestResults = fullfile("results","tests","index.html"), ...
-    Dependencies = "check");
+    TestResults = fullfile("results","tests","index.html"),...
+    RunOnlyImpactedTests=true); 
+
 tTaskWithMatlabTest = tTask.addCodeCoverage( ...
     fullfile("results","coverage","index.html"), ...
     MetricLevel = "condition"); % Note: Change MetricLevel to "statement" 
@@ -26,4 +24,52 @@
 % Clean task
 plan("clean") = CleanTask();
 
+% Define dependencies
+plan("compile").Dependencies = "test";
+plan("test").Dependencies = "generateSimFun";
+plan("generateSimFun").Dependencies = "check";
+
+% Define inputs and outputs
+proj = currentProject;
+plan("generateSimFun").Inputs = fullfile(proj.RootFolder,"code","*.sbproj");
+plan("generateSimFun").Outputs = fullfile(proj.RootFolder,"code","*.mat");
+plan("test").Inputs = fullfile(proj.RootFolder,"code","*");
+plan("compile").Inputs = fullfile(proj.RootFolder,"code",["*.mat","*.mlapp","graystyle.m"]);
+plan("compile").Outputs = fullfile(proj.RootFolder,"WebAppArchive");
+
+% Set default task
+plan.DefaultTasks = "compile";
+
+
+end
+
+function generateSimFunTask(~)
+    % Generate SimFunction and associated MAT file for app to run
+    generateSimFun();
+end
+
+function compileTask(~)
+    % Compile App into Web App
+
+    proj = currentProject;
+    rootFolder = proj.RootFolder; % Get the root folder of the project
+
+    imgFiles = dir(fullfile(rootFolder,"code","images","*.*"));
+    imgFiles = string({imgFiles.name}');
+    imgFiles = fullfile(rootFolder,"code","images",imgFiles(~matches(imgFiles,[".",".."])));
+    codeFiles = dir(fullfile(rootFolder,"code","*.m"));
+    codeFiles = string({codeFiles.name}');
+    codeFiles = fullfile(rootFolder,"code",setdiff(codeFiles,"generateSimFun.m"));
+
+    MATfilename = dir(fullfile(rootFolder,"code","*.mat"));
+    MATfilename = fullfile(rootFolder,"code",MATfilename.name);
+    load(MATfilename,"dependenciesSimFun");
+
+    appDependencies = [MATfilename; dependenciesSimFun; ...
+        codeFiles; imgFiles];
+    appfilename = fullfile(rootFolder,"code","TMDDApp.mlapp");
+
+    compiler.build.webAppArchive(appfilename,...
+        AdditionalFiles=appDependencies,OutputDir="WebAppArchive");
+
 end

code/ConcTimecourseView.m

@@ -0,0 +1,75 @@
+classdef ConcTimecourseView < handle
+
+    properties ( Access = private ) 
+        Model
+        Axes
+
+        ConcColors = [0.30,0.75,0.93;...
+                      0.86,0.55,0.41;...
+                      0.91,0.73,0.42]; % colors to plot concentrations
+        FontName = "Helvetica";
+    end
+
+    properties ( SetAccess=private, GetAccess={?tTMDDApp} )
+        % line handles
+        lhDrug
+        lhReceptor
+        lhComplex
+
+    end
+
+    properties( Access = private )
+        DataListener % listener
+    end
+
+    methods
+        function obj = ConcTimecourseView(parent, model)
+
+            arguments
+                parent 
+                model (1,1) SimulationModel
+            end
+
+            ax = uiaxes(parent);
+            graystyle(ax);
+            xlabel(ax, "Time (hours)", 'FontName',obj.FontName);
+            ylabel(ax, "Concentrations (nanomole/liter)",'FontName',obj.FontName);
+
+            obj.lhDrug = plot(ax, NaN, NaN, '-','Linewidth',2,'Color',obj.ConcColors(1,:));
+            hold(ax,'on');
+            obj.lhReceptor = plot(ax, NaN, NaN, '-','Linewidth',2,'Color',obj.ConcColors(2,:));
+            obj.lhComplex= plot(ax, NaN, NaN, '-','Linewidth',2,'Color',obj.ConcColors(3,:));
+            hold(ax,'off');
+            lh = legend(ax,{'Drug','Receptor','Complex'},'FontName',obj.FontName);
+            lh.Box = 'off';
+
+            % instantiate listener
+            dataListener = event.listener( model, 'DataChanged', ...
+                @obj.update );
+
+            % store listeners
+            obj.DataListener = dataListener;
+
+            % save objects
+            obj.Model = model;
+            obj.Axes = ax;
+
+        end % constructor
+
+
+    end % public methods
+
+    methods ( Access = private )
+
+        function update(obj,~,~)
+            t = obj.Model.SimDataTable;
+
+            set(obj.lhDrug,'XData',t.Time, 'YData',t.Drug);
+            set(obj.lhReceptor,'XData',t.Time, 'YData',t.Receptor);
+            set(obj.lhComplex,'XData',t.Time, 'YData',t.Complex);
+
+        end % update
+
+    end % private method
+end % class
+

code/LampView.m

@@ -0,0 +1,70 @@
+classdef LampView < handle
+
+    properties ( Dependent )
+        IsOn (1,1) logical
+    end
+
+    properties
+        LampColorSucess  = [0.47, 0.67, 0.19]  % color of lamp if RO between thresholds after day 1
+        LampColorFailure = [0.85, 0.33, 0.10]  % color of lamp if RO not between thresholds after day 1
+    end
+
+    properties ( SetAccess=private, GetAccess={?tTMDDApp} )
+        LampObj
+    end
+
+    properties ( Access=private )
+        Model
+    end
+
+    properties( Access = private )
+        DataListener % listener
+    end
+
+    methods
+        function obj = LampView(parent,model)
+
+            lampObj = uilamp(parent);
+            lampObj.Tooltip = compose("Target occupancy does not remain\n between thresholds");
+            lampObj.Color = obj.LampColorFailure;
+
+            % instantiate listener
+            dataListener = event.listener( model, 'DataChanged', ...
+                @obj.update );
+
+            % store listeners
+            obj.DataListener = dataListener;
+
+            obj.LampObj = lampObj;
+            obj.Model = model;
+
+        end % constructor
+
+        function set.IsOn(obj, value)
+            % color lamp according to whether or not RO remains between thresholds after day 1
+            if value
+                obj.LampObj.Color = obj.LampColorSucess;
+                obj.LampObj.Tooltip = compose("Target occupancy remains\n between thresholds");
+            else
+                obj.LampObj.Color = obj.LampColorFailure;
+                obj.LampObj.Tooltip = compose("Target occupancy does not remain\n between thresholds");
+            end
+
+            obj.LampObj.UserData = value;
+
+        end % set.IsOn
+
+        function value = get.IsOn(obj)
+                value = obj.LampObj.UserData;
+        end % get.IsOn
+
+    end % public methods
+
+    methods ( Access = private )
+
+        function update(obj,~,~)
+                obj.IsOn = obj.Model.ROIsBetweenThresholds;
+        end % update
+
+    end % private method
+end

code/NCAView.m

@@ -0,0 +1,87 @@
+classdef NCAView < handle
+
+    properties ( Access = private ) 
+        Model
+        NCApanel
+        GridLayout
+
+    end
+
+    properties ( SetAccess=private, GetAccess={?tTMDDApp} )
+        NCAtable
+    end
+
+    properties ( Access = public ) 
+        FontName                (1,1) string = "Helvetica"
+        NCAoptions              % options for NCA calculations
+        ConcentrationColumnName (1,1) string = "Complex"
+    end
+
+    properties( Access = private )
+        DataListener % listener
+    end
+
+    methods
+        function obj = NCAView(parent, model)
+
+            arguments
+                parent 
+                model (1,1) SimulationModel
+            end
+
+            ncapanel = uipanel(parent);
+            ncapanel.Title = "NCA parameters for bound target ('" + ...
+                obj.ConcentrationColumnName + "')";
+            ncapanel.BackgroundColor = [1 1 1];
+            ncapanel.FontName = obj.FontName;
+            ncapanel.BorderType = 'none';
+
+            % Create GridLayout
+            gl = uigridlayout(ncapanel);
+            gl.ColumnWidth = {'1x'};
+            gl.RowHeight = {'1x'};
+            gl.Padding = [0 0 0 0];
+            gl.BackgroundColor = [1 1 1];
+
+            % Create NCAtable
+            ncat = uitable(gl);
+
+            % save NCA options 
+            opt = sbioncaoptions;
+            opt.concentrationColumnName = obj.ConcentrationColumnName;
+            opt.timeColumnName          = 'Time';
+            opt.IVDoseColumnName        = 'Dose';
+
+            % instantiate listener
+            dataListener = event.listener( model, 'DataChanged', ...
+                @obj.update );
+
+            % store listeners
+            obj.DataListener = dataListener;
+
+            % save objects
+            obj.Model = model;
+            obj.NCAoptions = opt;
+            obj.NCApanel = ncapanel;
+            obj.GridLayout = gl;
+            obj.NCAtable = ncat;
+
+        end % constructor
+
+
+    end % public methods
+
+    methods ( Access = private )
+
+        function update(obj,~,~)
+
+            % compute NCA parameters and display them in table
+            ncaParameters = sbionca(obj.Model.SimDataTable, obj.NCAoptions);
+            obj.NCAtable.ColumnName = ncaParameters.Properties.VariableNames(2:end);
+            obj.NCAtable.Data = ncaParameters(:,2:end);
+
+        end % update
+
+    end % private method
+end % class
+