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Merged
ChezJe merged 2 commits into from
Feb 3, 2026
Merged

Dev je #39

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1d1b9a7
added deploy.yml
Feb 3, 2026
f0c481a
updated repo
Feb 3, 2026
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52 changes: 6 additions & 46 deletions .github/workflows/ci.yml
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@@ -1,19 +1,17 @@
# This is a basic workflow to help you get started with MATLAB Actions
name: MATLAB Build
name: CI

# Controls when the action will run.
on:
# Triggers the workflow on push or pull request events, but only for the main branch
push:
branches: [ main ]
# Triggers the workflow on pull request events, but only for the main branch
pull_request:
branches: [ main ]

# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:

env:
PRODUCT_LIST: MATLAB MATLAB_Test
PRODUCT_LIST: MATLAB MATLAB_Test SimBiology Statistics_and_Machine_Learning_Toolbox

# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
permissions:
Expand All @@ -24,20 +22,15 @@ permissions:
# Only allow one build of this type to run at a time
# Ensure results publishing completes without being interrupted/overwritten
concurrency:
group: "test and publish results"
group: "test"
cancel-in-progress: false

jobs:
# This workflow contains a single job called "build"
build:

# Set up URLs for GitHub Pages report
environment:
name: github-pages
url: ${{ steps.deployment.outputs.page_url }}
test:

# The type of runner that the job will run on
runs-on: ubuntu-latest
runs-on: windows-latest

# Steps represent a sequence of tasks that will be executed as part of the job
steps:
Expand All @@ -57,36 +50,3 @@ jobs:
uses: matlab-actions/run-build@v2
with:
tasks: test

# Configure GitHub Pages to accept your artifact uploads
- name: Setup Pages
uses: actions/configure-pages@v5

# Upload testing and code coverage reports to your repository
- name: Upload pages
uses: actions/upload-pages-artifact@v4
with:
path: results # Upload results

# Publish reports to GitHub Pages so they can be viewed in a browser
- name: Deploy to GitHub Pages
id: deployment
uses: actions/deploy-pages@v4



# ==================================== #
# Alternate ways to run commands in CI #
# ==================================== #

## Runs your tests using `runtests` command
#- name: Run all tests
# uses: matlab-actions/run-tests@v2
# with:
# source-folder: code

## Executes custom MATLAB scripts, functions, or statements
#- name: Run custom testing procedure
# uses: matlab-actions/run-command@v2
# with:
# command: disp('Running my custom testing procedure!'); addpath('code'); results = runtests('IncludeSubfolders', true); assertSuccess(results);
99 changes: 99 additions & 0 deletions .github/workflows/deploy.yml
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@@ -0,0 +1,99 @@
# This is a basic workflow to help you get started with MATLAB Actions
name: MATLAB Build

# Controls when the action will run.
on:
# Triggers the workflow on push events, but only for the main branch
push:
branches: [ main ]

# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:

env:
PRODUCT_LIST: MATLAB MATLAB_Test SimBiology Statistics_and_Machine_Learning_Toolbox

# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
permissions:
contents: read
pages: write
id-token: write

# Only allow one build of this type to run at a time
# Ensure results publishing completes without being interrupted/overwritten
concurrency:
group: "test and publish results"
cancel-in-progress: false

jobs:

build:

# Set up URLs for GitHub Pages report
environment:
name: github-pages
url: ${{ steps.deployment.outputs.page_url }}

# The type of runner that the job will run on
runs-on: windows-latest

# Steps represent a sequence of tasks that will be executed as part of the job
steps:

# Check out your repository
- uses: actions/checkout@v5

# Set up MATLAB on a GitHub-hosted runner
- name: Setup MATLAB
uses: matlab-actions/setup-matlab@v2
with:
products: ${{ env.PRODUCT_LIST }}
cache: true

# Run the MATLAB build tool to build and test your code
- name: Run buildtool
uses: matlab-actions/run-build@v2
with:
tasks: test

# Configure GitHub Pages to accept your artifact uploads
- name: Setup Pages
if: always()
uses: actions/configure-pages@v5

# Upload testing and code coverage reports to your repository
- name: Upload pages
if: always()
uses: actions/upload-pages-artifact@v4
with:
path: results # Upload results

# # Upload compiled CTF file to deploy Web App
# - name: Upload CTF file
# uses: actions/upload-pages-artifact@v4
# with:
# name: WebApp_CTF
# path: WebAppArchive/*.ctf

# Publish reports to GitHub Pages so they can be viewed in a browser
- name: Deploy to GitHub Pages
id: deployment
if: always()
uses: actions/deploy-pages@v4


# ==================================== #
# Alternate ways to run commands in CI #
# ==================================== #

## Runs your tests using `runtests` command
#- name: Run all tests
# uses: matlab-actions/run-tests@v2
# with:
# source-folder: code

## Executes custom MATLAB scripts, functions, or statements
#- name: Run custom testing procedure
# uses: matlab-actions/run-command@v2
# with:
# command: disp('Running my custom testing procedure!'); addpath('code'); results = runtests('IncludeSubfolders', true); assertSuccess(results);
7 changes: 3 additions & 4 deletions buildfile.m
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Expand Up @@ -7,7 +7,6 @@
% CodeIssues task
plan("check") = CodeIssuesTask(Results=["results/codeissues.sarif"; ...
"results/codeissues.mat"]);

% Test task
tTask = TestTask("tests", ...
SourceFiles = "code", ...
Expand All @@ -34,7 +33,7 @@
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").Inputs = fullfile(proj.RootFolder,"code",["*.mat","*.mlapp","*.m"]);
plan("compile").Outputs = fullfile(proj.RootFolder,"WebAppArchive");

% Set default task
Expand Down Expand Up @@ -62,9 +61,9 @@ function compileTask(~)

MATfilename = dir(fullfile(rootFolder,"code","*.mat"));
MATfilename = fullfile(rootFolder,"code",MATfilename.name);
load(MATfilename,"dependenciesSimFun");
s = load(MATfilename,"dependenciesSimFun");

appDependencies = [MATfilename; dependenciesSimFun; ...
appDependencies = [MATfilename; s.dependenciesSimFun; ...
codeFiles; imgFiles];
appfilename = fullfile(rootFolder,"code","TMDDApp.mlapp");

Expand Down
20 changes: 13 additions & 7 deletions code/ConcTimecourseView.m
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Expand Up @@ -2,15 +2,18 @@

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} )
properties ( Hidden )
% Leave these properties Hidden but public to enable access for any test generated
% with Copilot during workshop
Axes

% line handles
lhDrug
lhReceptor
Expand All @@ -35,13 +38,16 @@
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,:));
obj.lhDrug = plot(ax, NaN, NaN, '-','Linewidth',2,'Color',obj.ConcColors(1,:),'DisplayName','Drug');
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,:));
obj.lhReceptor = plot(ax, NaN, NaN, '-','Linewidth',2,'Color',obj.ConcColors(2,:),'DisplayName','Receptor');
obj.lhComplex= plot(ax, NaN, NaN, '-','Linewidth',2,'Color',obj.ConcColors(3,:),'DisplayName','Complex');
hold(ax,'off');
lh = legend(ax,{'Drug','Receptor','Complex'},'FontName',obj.FontName);
lh.Box = 'off';
lgd = legend(ax,'show','FontName',obj.FontName,'Color','none');
lgd.Box = "off";

ax.XLimitMethod = "padded";
ax.YLimitMethod = "padded";

% instantiate listener
dataListener = event.listener( model, 'DataChanged', ...
Expand Down
4 changes: 3 additions & 1 deletion code/LampView.m
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Expand Up @@ -9,7 +9,9 @@
LampColorFailure = [0.85, 0.33, 0.10] % color of lamp if RO not between thresholds after day 1
end

properties ( SetAccess=private, GetAccess={?tTMDDApp} )
properties ( Hidden )
% Leave these properties Hidden but public to enable access for any test generated
% with Copilot during workshop
LampObj
end

Expand Down
4 changes: 3 additions & 1 deletion code/NCAView.m
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Expand Up @@ -7,7 +7,9 @@

end

properties ( SetAccess=private, GetAccess={?tTMDDApp} )
properties ( Hidden )
% Leave these properties Hidden but public to enable access for any test generated
% with Copilot during workshop
NCAtable
end

Expand Down
11 changes: 7 additions & 4 deletions code/ROTimecourseView.m
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Expand Up @@ -8,7 +8,10 @@
'FontWeight','bold','LabelVerticalAlignment','middle'}; % style for threshold lines
end

properties ( GetAccess = {?tTMDDApp} )
properties ( Hidden, SetAccess=private)
% Leave these properties Hidden but public to enable access for any test generated
% with Copilot during workshop

% line handles
lhRO
end
Expand Down Expand Up @@ -39,12 +42,12 @@
ylabel(ax, "RO (%)",'FontName',obj.FontName);

obj.lhRO = plot(ax, NaN, NaN, 'Color', obj.ROColors,'Linewidth',2);
yline(ax,model.ThresholdValues(1), '--','efficacy','FontName',obj.FontName,obj.ThresholdStyle{:});
yline(ax,model.ThresholdValues(2), '--','safety','FontName',obj.FontName,obj.ThresholdStyle{:});
% yline(ax,model.ThresholdValues(1), '--','efficacy','FontName',obj.FontName,obj.ThresholdStyle{:});
% yline(ax,model.ThresholdValues(2), '--','safety','FontName',obj.FontName,obj.ThresholdStyle{:});


% set limits
xlim(ax,'auto');
ax.XLimitMethod = "padded";
ylim(ax,[-5, 105]);

% instantiate listener
Expand Down
42 changes: 26 additions & 16 deletions code/SimulationModel.m
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@@ -1,17 +1,6 @@
classdef SimulationModel < handle
% Class to simulate the TMDD model

properties ( SetAccess = private )
DoseTable % daily dose to apply to simulate
SimFun % exported SimFunction

SimData
SimDataTable

ThresholdValues = [20, 80] % threshold values

end

properties
% original values for resetting
Amount0 (1,1) double
Expand All @@ -20,10 +9,28 @@
Kel0 (1,1) double
Kdeg0 (1,1) double
Interval0 (1,1) double
end

properties ( Dependent )
ROIsBetweenThresholds (1,1) logical
end

events ( NotifyAccess = private )
properties ( Hidden )
% Leave these properties Hidden but public to enable access for any test generated
% with Copilot during workshop

DoseTable % daily dose to apply to simulate
SimFun % exported SimFunction

SimDataTable
SimData

ThresholdValues = [20, 80] % threshold values
end

events ( NotifyAccess = public )
% Leave this notification public to enable access for any test generated
% with Copilot during workshop
DataChanged
end

Expand Down Expand Up @@ -73,10 +80,6 @@ function simulate(obj, parameters)
idxNotIncreasing = diff(t.Time)<=0; % remove duplicates
t(idxNotIncreasing,:) = [];

% logical value to check whether or not RO remains between thresholds after day 1
aboveThreshold1 = all(t.RO(t.Time >= 24) >= obj.ThresholdValues(1)/100);
belowThreshold2 = all(t.RO(t.Time >= 24) <= obj.ThresholdValues(2)/100);
obj.ROIsBetweenThresholds = aboveThreshold1 && belowThreshold2;

obj.SimData = sd;
obj.SimDataTable = t;
Expand All @@ -85,6 +88,13 @@ function simulate(obj, parameters)

end % simulate

function value = get.ROIsBetweenThresholds(obj)
% logical value to check whether or not RO remains between thresholds after day 1
timeAfter24h = obj.SimDataTable.Time >= 24;
ROAfter24h = obj.SimDataTable.RO(timeAfter24h);
value = all(ROAfter24h >= obj.ThresholdValues(1)/100) && ...
all(ROAfter24h <= obj.ThresholdValues(2)/100);
end % get.ROIsBetweenThresholds()

end % public methods

Expand Down
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