Maintenance for R2024b

1) Update GitHub workflow with reports published as Pages
2) Update .gitignore to support new workflow
3) Add CollectData to Function Library rather than as local function to
   aid in testing
4) Remove hard-coded colors in cnPDE and explicitPDE
5) Include solutions in InstructorResources
6) Update testing structures in SoftwareTests
7) Minor updates to scripts
8) Reorganize the project to start/stop the ProjectStartupApp

Author: eszmw

.github/workflows/ci.yml

@@ -8,16 +8,22 @@ on:
     branches: [ release ]
   workflow_dispatch:
 
+# Add permission to write GitHub pages
+permissions:
+  contents: write
+  pages: write
+  id-token: write
+
 jobs:
   test:
     strategy: 
       fail-fast: false
       matrix:
-        MATLABVersion: [R2021a,R2021b,R2022a,R2022b,R2023a,R2023b,R2024a]
+        MATLABVersion: [R2024a,R2024b]
     runs-on: ubuntu-latest
     steps:
       # Checks-out your repository
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       # Sets up a display server
       - name: Start display server
@@ -32,14 +38,14 @@ jobs:
         uses: matlab-actions/setup-matlab@v2
         with:
           release: ${{ matrix.MATLABVersion }}
-          products: 
+          products: >
             Symbolic_Math_Toolbox
             Image_Processing_Toolbox
-            Computer_Vision_Toolbox 
-            Statistics_and_Machine_Learning_Toolbox 
-            Curve_Fitting_Toolbox 
+            Statistics_and_Machine_Learning_Toolbox
+            Curve_Fitting_Toolbox
             Automated_Driving_Toolbox
 
+
       # Run all the tests
       - name: Run SmokeTests
         uses: matlab-actions/run-command@v2
@@ -48,10 +54,12 @@ jobs:
 
       # Upload the test results as artifact
       - name: Upload TestResults
-        uses: actions/[email protected]
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v4
         with:
-          name: TestResults
-          path: ./SoftwareTests/TestResults_${{ matrix.MATLABVersion }}.txt
+          name: TestResults_${{ matrix.MATLABVersion }}
+          path: ./public/*
+          overwrite: true
 
   badge:
     if: ${{ always() }}
@@ -62,26 +70,38 @@ jobs:
     steps: 
 
       # Checks-out your repository
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       # Sets up R2023b
       - name: Setup MATLAB
-        uses: matlab-actions/setup-matlab@v1
+        uses: matlab-actions/setup-matlab@v2
         with:
-          release: R2023b
+          release: R2024b
 
       # Download the test results from artifact
-      - name: Download TestResults
-        uses: actions/download-artifact@v2.1.1
+      - name: Download All TestResults
+        uses: actions/download-artifact@v4
         with:
-          name: TestResults
-          path: ./SoftwareTests/
-
+          path: public
+          pattern: TestResults_*
+          merge-multiple: true
+          
       # Create the test results badge
-      - name: Run CreateBadge
-        uses: matlab-actions/run-command@v1
+      - name: Run PostSmokeTest
+        uses: matlab-actions/run-command@v2
+        with:
+          command: openProject(pwd); PostSmokeTest;
+      
+      # Deploy reports to GitHub pages
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
+      - name: Upload pages artifact
+        uses: actions/upload-pages-artifact@v3
         with:
-          command: openProject(pwd); CreateBadge;
+          path: public
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
 
       # Commit the JSON for the MATLAB releases badge 
       - name: Commit changed files

.gitignore

@@ -52,8 +52,5 @@ Data/allStorms.csv
 Scripts/myLakeData.mat
 myLakeData.mat
 
-# Test results
-SoftwareTests/TestResults_*
-
 # GitLab page folder
 public/

.gitlab-ci.yml

@@ -24,42 +24,30 @@ smoke-test:
     # Make sure that the runner you plan to use matches the tags
       - matlab
     stage: test
+    parallel:
+      matrix:
+        - VERSION: [R2024a,R2024b]
     script: 
-      - matlab -batch "openProject(pwd);RunAllTests(true)"
+      - Set-Alias -Name matlab -Value "C:\Program Files\MATLAB\$VERSION\bin\matlab.exe"
+      - matlab -batch "openProject(pwd);RunAllTests"
     when: always
     allow_failure: true
     artifacts:
+      name: "$VERSION"
       paths:
         - public/*
-      expire_in: 1 years
+      when:  always
+
 
 pages:
     tags:
       - matlab
     stage: deploy
     script:
-      - echo 'Deploying pages'
+      - matlab -batch "openProject(pwd);PostSmokeTest;"
     artifacts:
         paths:
             - public
-
-smoke-test-solution:
-    tags:
-      - matlab
-    stage: release
-    script: 
-      - matlab -batch "proj = openProject(pwd); 
-        addpath(genpath(proj.RootFolder));
-        results = runtests(fullfile('InternalFiles','Tests','CI','SolnSmokeTests.m'));
-        disp(table(results)); assertSuccess(results);"
-    rules:
-# This test should always run when merging to main
-# And be available for manual running on any push
-      - if: $CI_MERGE_REQUEST_TARGET_BRANCH_NAME == $CI_DEFAULT_BRANCH
-        when: always
-      - if: $CI_MERGE_REQUEST_TARGET_BRANCH_NAME != $CI_DEFAULT_BRANCH
-        when: manual
-    allow_failure: true
 
 file-test:   
     tags:
@@ -87,6 +75,7 @@ release-testing:
       - matlab -batch "proj = openProject(pwd); 
         cd ..;
         addpath(genpath(fullfile('utilities','TestingResources')));
+        addpath(genpath(fullfile('utilities','Tools')));
         runCMTests"
     rules:
 # This test should always run when merging to main

FunctionLibrary/.gitkeep

@@ -12,4 +12,4 @@
 roi = drawpolygon(ax);
 x = roi.Position(:,1);
 y = roi.Position(:,2);
-end
+end

FunctionLibrary/CollectData.m

@@ -69,11 +69,7 @@
     % To visualize the outputs
     hold on
     delete(ax.Children(1:end-1));
-    try
-        plot(xVals,[alpha(j*dt);u;beta(j*dt)],LineWidth=1,SeriesIndex="none")
-    catch % If using R2023a or earlier
-        plot(xVals,[alpha(j*dt);u;beta(j*dt)],"k",LineWidth=1)
-    end
+    plot(xVals,[alpha(j*dt);u;beta(j*dt)],LineWidth=1,SeriesIndex="none")
     subtitle("$t = $"+dt*j)
     drawnow
     pause(0.1)     

FunctionLibrary/cnPDE.m

@@ -66,11 +66,7 @@
     % To visualize the outputs
     hold on
     delete(ax.Children(1:end-1));
-    try
-        plot(xVals,[alpha((j+1)*dt);u;beta((j+1)*dt)],LineWidth=4,SeriesIndex="none")
-    catch % If using R2023a or earlier
-        plot(xVals,[alpha((j+1)*dt);u;beta((j+1)*dt)],"k",LineWidth=4)
-    end
+    plot(xVals,[alpha((j+1)*dt);u;beta((j+1)*dt)],"LineWidth",4,SeriesIndex="none")
     subtitle("$t = $"+dt*(j+1))
     drawnow
     pause(0.1)     

FunctionLibrary/explicitPDE.m

@@ -0,0 +1,80 @@
+function u = cnPDESoln(f,alpha,beta,tEnd,dx,gamma,L)
+% Solve the 1D heat equation u_t = gamma*u_{xx} on a rod of length L
+%   using the Crank-Nicolson method
+%   u(t,0) = alpha(t)
+%   u(t,L) = beta(t)
+%   u(0,x) = f(x)
+%   The desired spatial resolution is dx
+%   Output is u = u(tEnd,x_m), a vector of values on the mesh points
+
+% Define dt with reference to both error and stability concerns
+% Optimal dt for stability
+dtOpt = dx;
+% Forcing an integer numbers of dt steps that terminate at tEnd
+dt = tEnd/ceil(tEnd/dtOpt);
+
+% % testing %%%%%%%%%%
+% dt = 0.005;
+ 
+% Set up the helper values for defining the required matrices
+numRows = L/dx-1;
+mu = gamma*dt/(dx^2);
+baseDiag = ones(1,numRows);
+
+% Define modA for the explicit updating rule 
+% modA-I = (A-I)/2, where I is the identity matrix
+modA = gallery('tridiag',0.5*mu*baseDiag(1:end-1),(1-mu)*baseDiag,0.5*mu*baseDiag(1:end-1));
+
+% Define modB for the implicit updating rule 
+% modB-I = (B-I)/2, where I is the identity matrix
+modB = gallery('tridiag',-0.5*mu*baseDiag(1:end-1),(1+mu)*baseDiag,-0.5*mu*baseDiag(1:end-1));
+
+% Initialize bAvg = b^(j)+b^(j+1) as a vector of zeros
+bAvg = zeros(numRows,1);
+
+% Define a spatial mesh vector
+xVals = linspace(0,L,round(L/dx)+1);
+
+% Set up a column vector u0 of the initial values of u when t=0
+u0 = f(xVals)';
+
+% Initialize the output to the interior points of u0 
+u = u0(2:end-1);
+
+% To visualize the outputs
+p = plot(xVals,u0,"LineWidth",2,"SeriesIndex",1);
+ax = p.Parent;
+
+% Set the y limits to reasonable fixed values
+minAlpha = min(alpha(0:dt:tEnd));
+maxAlpha = max(alpha(0:dt:tEnd));
+minBeta = min(beta(0:dt:tEnd));
+maxBeta = max(beta(0:dt:tEnd));
+yLower = min([ax.YLim(1),minAlpha,minBeta]);
+yUpper = max([ax.YLim(2),maxAlpha,maxBeta]);
+scale = (yUpper-yLower)*0.05;
+ax.YLim = [yLower-scale yUpper+scale];
+
+title("Solving $\frac{\partial u}{\partial t} = \gamma \frac{\partial^2 u}{\partial x^2}$ with Crank-Nicolson","Interpreter","latex")
+subtitle("$t=0$","Interpreter","latex")
+xlabel("$x$","Interpreter","latex")
+ylabel("$u$","Interpreter","latex")
+
+% Compute new values for halfB*u^(j+1)-b^(j+1) = halfA*u^(j)+b^(j)
+% Loop over timesteps to reach tEnd
+for j = 1:(tEnd/dt)
+    bAvg(1) = mu*(alpha((j-1)*dt)+alpha(j*dt))/2;
+    bAvg(end) = mu*(beta((j-1)*dt)+beta(j*dt))/2;
+    u = modB\(modA*u+bAvg);   
+    % To visualize the outputs
+    hold on
+    delete(ax.Children(1:end-1));
+    plot(xVals,[alpha(j*dt);u;beta(j*dt)],"LineWidth",2,"SeriesIndex",2)
+    subtitle("$t = $"+dt*j)
+    drawnow
+    pause(0.1)     
+    hold off
+    % End visualization code
+end
+legend(["u(0,x)","u(t,x)"],"Location","north")
+end

InstructorResources/Solutions/FunctionLibrarySolutions/cnPDESoln.m

@@ -0,0 +1,77 @@
+function u = cnPDE(u0,alpha,beta,tEnd,dx,gamma,L,t0)
+% Solve the 1D heat equation u_t = gamma*u_{xx} on a rod of length L
+%   using the Crank-Nicolson method
+%   u(t,0) = alpha(t)
+%   u(t,L) = beta(t)
+%   u(t0,x) = u0
+%   The desired spatial resolution is dx
+%   Output is u = u(tEnd,x_m), a vector of values on the mesh points
+
+% Define dt with reference to both error and stability concerns
+% Optimal dt for stability
+dtOpt = dx;
+% Forcing an integer numbers of dt steps that terminate at tEnd
+dt = tEnd/ceil((tEnd-t0)/dtOpt);
+
+% % testing %%%%%%%%%%
+% dt = 0.005;
+ 
+% Set up the helper values for defining the required matrices
+numRows = L/dx-1;
+mu = gamma*dt/(dx^2);
+baseDiag = ones(1,numRows);
+
+% Define modA for the explicit updating rule 
+% modA-I = (A-I)/2, where I is the identity matrix
+modA = gallery('tridiag',0.5*mu*baseDiag(1:end-1),(1-mu)*baseDiag,0.5*mu*baseDiag(1:end-1));
+
+% Define modB for the implicit updating rule 
+% modB-I = (B-I)/2, where I is the identity matrix
+modB = gallery('tridiag',-0.5*mu*baseDiag(1:end-1),(1+mu)*baseDiag,-0.5*mu*baseDiag(1:end-1));
+
+% Initialize bAvg = b^(j)+b^(j+1) as a vector of zeros
+bAvg = zeros(numRows,1);
+
+% Define a spatial mesh vector
+xVals = linspace(0,L,round(L/dx)+1);
+
+% Initialize the output to the interior points of u0 
+u = u0(2:end-1);
+
+% To visualize the outputs
+p = plot(xVals,u0,"LineWidth",4);
+ax = p.Parent;
+
+% Set the y limits to reasonable fixed values
+minAlpha = min(alpha(0:dt:tEnd));
+maxAlpha = max(alpha(0:dt:tEnd));
+minBeta = min(beta(0:dt:tEnd));
+maxBeta = max(beta(0:dt:tEnd));
+yLower = min([ax.YLim(1),minAlpha,minBeta]);
+yUpper = max([ax.YLim(2),maxAlpha,maxBeta]);
+scale = (yUpper-yLower)*0.05;
+ax.YLim = [yLower-scale yUpper+scale];
+
+title("Solving $\frac{\partial u}{\partial t} = \gamma \frac{\partial^2 u}{\partial x^2}$","Interpreter","latex")
+subtitle("$t=0$","Interpreter","latex")
+xlabel("$x$","Interpreter","latex")
+ylabel("$u$","Interpreter","latex")
+
+% Compute new values for halfB*u^(j+1)-b^(j+1) = halfA*u^(j)+b^(j)
+% Loop over timesteps to reach tEnd
+for j = 0:(tEnd/dt - 1)
+    bAvg(1) = mu*(alpha(j*dt)+alpha((j+1)*dt))/2;
+    bAvg(end) = mu*(beta(j*dt)+beta((j+1)*dt))/2;
+    u = modB\(modA*u+bAvg);   
+    % To visualize the outputs
+    hold on
+    delete(ax.Children(1:end-1));
+    plot(xVals,[alpha((j+1)*dt);u;beta((j+1)*dt)],"LineWidth",4,SeriesIndex="none")
+    subtitle("$t = $"+dt*(j+1))
+    drawnow
+    pause(0.1)     
+    hold off
+    % End visualization code
+end
+
+end