src/base/solvers/getSetSolver/changeCobraSolver.m

.github/workflows/TestAll_and_Code_Coverage_CI.md

@@ -0,0 +1,217 @@
+
+# TestAll and Code Coverage CI - GitHub Actions Workflow
+
+This repository contains the **Code Coverage CI** GitHub Actions workflow, which automates the process of running MATLAB tests and generating code coverage reports using MOcov and Codecov. The workflow is triggered on pushes and pull requests to the `develop` branch.
+
+## Table of Contents
+
+- [Overview](#overview)
+- [Prerequisites](#prerequisites)
+- [Setup Instructions](#setup-instructions)
+- [Workflow Breakdown](#workflow-breakdown)
+  - [Trigger Configuration](#trigger-configuration)
+  - [Jobs Definition](#jobs-definition)
+  - [Steps Breakdown](#steps-breakdown)
+- [Project Structure](#project-structure)
+
+
+## Overview
+
+The **Code Coverage CI** workflow automates testing and code coverage reporting. It ensures that code changes are tested and that code coverage metrics are updated automatically using [MOcov](https://github.com/MOxUnit/MOcov) and [Codecov](https://codecov.io/).
+
+## Prerequisites
+
+- **MATLAB R2022a**: The workflow uses MATLAB R2022a. Ensure your code is compatible with this version.
+- **MOcov**: An open-source code coverage tool for MATLAB. It will be installed as part of the workflow.
+- **Codecov Account**: Sign up for a [Codecov](https://codecov.io/) account to access code coverage reports.
+- **Codecov Token**: Obtain a `CODECOV_TOKEN` from Codecov for authentication (required for private repositories).
+
+## Setup Instructions
+
+1. **Clone the Repository** (if not already):
+
+   ```bash
+   git clone https://github.com/opencobra/cobratoolbox.git
+   ```
+
+2. **Add the Workflow File**:
+
+   - Save the provided workflow YAML file as `.github/workflows/codecov.yml` in the repository.
+
+3. **Store Codecov Token**:
+
+   - In the repository, go to **Settings** > **Secrets and variables** > **Actions**.
+   - Click on **New repository secret**.
+   - Add `CODECOV_TOKEN` as the name and paste the Codecov token as the value.
+
+4. **Add MOcov to Your Project** (Optional for local testing):
+
+   - **Clone MOcov**:
+
+     ```bash
+     git clone https://github.com/MOxUnit/MOcov.git /path/to/MOcov
+     ```
+
+   - **Add MOcov to MATLAB Path**:
+
+     ```matlab
+     addpath(genpath('/path/to/MOcov'));
+     ```
+
+5. **Create `run_coverage_tests.m` Script**:
+
+   - Add the `run_coverage_tests.m` script to the root of the repository. This script runs tests and generates the coverage report using MOcov.
+
+6. **Organize Project**:
+
+   - **Source Code**: Place your MATLAB source code in the `src` directory.
+   - **Tests**: Place test files in the `test` directory. Ensure `testAll.m` or your main test script is in this directory.
+
+7. **Push Changes**:
+
+   ```bash
+   git add .
+   git commit -m "Add Code Coverage CI workflow with MOcov"
+   git push origin develop
+   ```
+
+## Workflow Breakdown
+
+### Trigger Configuration
+
+The workflow is triggered on push events and pull requests to the `develop` branch.
+
+```yaml
+on:
+  push:
+    branches: [develop]
+  pull_request:
+    branches: [develop]
+```
+
+### Jobs Definition
+
+The workflow defines a job named `test` that runs on the latest Ubuntu environment.
+
+```yaml
+jobs:
+  test:
+    runs-on: ubuntu-latest
+```
+
+### Steps Breakdown
+
+1. **Checkout Repository**
+
+   Checks out thr repository code so the workflow can access it.
+
+   ```yaml
+   - uses: actions/checkout@v3
+   ```
+
+2. **Set Up MATLAB**
+
+   Installs MATLAB R2022a on the runner to execute MATLAB scripts and functions.
+
+   ```yaml
+   - name: Set up MATLAB
+     uses: matlab-actions/setup-matlab@v1
+     with:
+       release: R2022a
+   ```
+
+3. **Install MOcov**
+
+   Clones the MOcov repository and sets the appropriate permissions.
+
+   ```yaml
+   - name: Install MOcov
+     run: |
+       git clone https://github.com/MOxUnit/MOcov.git /opt/MOcov
+       sudo chmod -R 755 /opt/MOcov
+   ```
+
+4. **Run MATLAB Tests and Generate Coverage**
+
+   Executes MATLAB tests using MOcov to generate a code coverage report in XML format.
+
+   ```yaml
+   - name: Run MATLAB tests and generate coverage
+     run: |
+       matlab -batch "addpath(genpath(pwd)); run_coverage_tests"
+   ```
+
+   **Contents of `run_coverage_tests.m`:**
+
+   ```matlab
+   function run_coverage_tests()
+       % Add MOcov to path
+       addpath(genpath('/opt/MOcov'));
+       
+       try
+           % Run tests and capture results
+           disp('Running tests with coverage...');
+           
+           % Run tests directly first to capture results
+           results = runtests('test/testAll.m');
+           passed = all([results.Passed]);
+           
+           % Now run MOcov with a simpler expression that just runs the tests
+           test_expression = 'runtests(''test/testAll.m'')';
+           
+           % Run MOcov for coverage analysis
+           mocov('-cover', '.', ...
+                 '-cover_xml_file', 'coverage.xml', ...
+                 '-expression', test_expression);
+           
+           % Check results
+           if ~passed
+               error('Some tests failed. Check the test results for details.');
+           end
+           
+           disp('All tests passed successfully!');
+           disp(['Number of passed tests: ' num2str(sum([results.Passed]))]);
+           
+           exit(0);
+       catch e
+           disp('Error running tests:');
+           disp(getReport(e));
+           exit(1);
+       end
+   end
+   ```
+
+5. **Upload Coverage to Codecov**
+
+   Uploads the generated coverage report to Codecov for analysis.
+
+   ```yaml
+   - name: Upload coverage to Codecov
+     uses: codecov/codecov-action@v3
+     with:
+       files: ./coverage.xml
+       flags: matlab
+       token: ${{ secrets.CODECOV_TOKEN }}
+       fail_ci_if_error: true
+       comment: true
+   ```
+
+
+
+## Project Structure
+
+Organize your project as follows:
+
+```
+your-repository/
+├── .github/
+│   └── workflows/
+│       └── codecov.yml
+├── src/
+│   └── (MATLAB source code)
+├── test/
+│   └── testAll.m
+├── run_coverage_tests.m
+└── (Other project files)
+```
+

.github/workflows/codecov.yml

@@ -0,0 +1,37 @@
+name: Code Coverage
+on:
+  push:
+    branches: [develop]
+  pull_request:
+    branches: [develop]
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up MATLAB
+        uses: matlab-actions/setup-matlab@v1
+        with:
+          release: R2022a
+
+      - name: Install MOcov
+        run: |
+          git clone https://github.com/MOxUnit/MOcov.git /opt/MOcov
+          sudo chmod -R 755 /opt/MOcov
+      
+      - name: Verify MATLAB installation
+        run: matlab -batch "version"
+
+      - name: Run MATLAB tests
+        run: |
+          matlab -batch "addpath(genpath(pwd)); run_coverage_tests"
+      
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          files: ./coverage.xml
+          flags: matlab
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true
+          comment: true

codecov.yml

@@ -1,6 +1,20 @@
+# codecov.yml
+
+# Comment settings
+comment:
+  layout: "reach, diff, flags, files"
+  behavior: default  # Shows the comment only on the first push of a pull request
+  require_changes: true  # Only comment if there are coverage changes
+
+# Coverage status checks
 coverage:
   status:
     project:
       default:
-        threshold: 15
-    patch: off
+        target: auto  # Automatically adjust coverage goal
+        threshold: 1%  # Fail PRs that reduce coverage by more than 1%
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+

runTestsAndGenerateReport.m

@@ -1,6 +1,6 @@
 % Run your tests
-testResults = runtests('./test/testAll_ghActions.m');
-
+% testResults = runtests('./test/testAll_ghActions.m');
+testResults = runtests('./test/testAll.m');
 % Open a file for writing
 fid = fopen('test_results.txt', 'w');
 

run_coverage_tests.m

@@ -0,0 +1,35 @@
+function run_coverage_tests()
+    % Add MOcov to path
+    addpath(genpath('/opt/MOcov'));
+
+    try
+        % Run tests and capture results
+        disp('Running tests with coverage...');
+
+        % Run tests directly first to capture results
+        results = runtests('test/test_myfunction.m');
+        passed = all([results.Passed]);
+
+        % Now run MOcov with a simpler expression that just runs the tests
+        test_expression = 'runtests(''test/test_myfunction.m'')';
+
+        % Run MOcov for coverage analysis
+        mocov('-cover', '.', ...
+              '-cover_xml_file', 'coverage.xml', ...
+              '-expression', test_expression);
+
+        % Check results
+        if ~passed
+            error('Some tests failed. Check the test results for details.');
+        end
+
+        disp('All tests passed successfully!');
+        disp(['Number of passed tests: ' num2str(sum([results.Passed]))]);
+
+        exit(0);
+    catch e
+        disp('Error running tests:');
+        disp(getReport(e));
+        exit(1);
+    end
+end

src/analysis/exploration/findRxnsFromSubSystem.m

@@ -15,18 +15,29 @@
 %    rxnPos:                A double array of positions of the reactions in
 %                           reactionNames in the model (same order).
 %
-% USAGE:
-%    %Obtain all reactions with Glycolysis in their respective subSystems
-%     field.
+% EXAMPLE:
+%
+%    Obtain all reactions with Glycolysis in their respective subSystems
+%    field.
 %    [reactionNames,rxnPos]  = findRxnsFromSubSystem(model,'Glycolysis')
 %
-% .. Author: - Thomas Pfau Nov 2017, Ronan MT. Fleming, 2022
+% .. Author: - Thomas Pfau Nov 2017, 
+%            - Ronan MT. Fleming, 2022
+%            - Farid Zare, 2024/08/14     updated the code to support rxn2subSystem field
+%
 
-charBool = cellfun(@(x) ischar(x), model.subSystems);
-if all(charBool)
-    present = strcmp(model.subSystems,subSystem);
-else
-    present = cellfun(@(x) any(ismember(x,subSystem)),model.subSystems);
+% Check to see if model already has these fields
+if ~isfield(model, 'rxn2subSystem')
+    warning('The "rxn2subSystem" field has been generated because it was not in the model.')
+    model = buildRxn2subSystem(model);
 end
-reactionNames = model.rxns(present);
-rxnPos = find(present);
+
+% Get subSystem ids
+subSystemID = ismember(model.subSystemNames, subSystem);
+
+% Get corresponding reactions
+rxn2subSystemMat = model.rxn2subSystem(:, subSystemID);
+rxnID = logical(sum(rxn2subSystemMat, 2));
+
+reactionNames = model.rxns(rxnID);
+rxnPos = find(rxnID);