Merge pull request #2390 from farid-zare/CI

Ci

Author: farid-zare

.github/workflows/codecov.yml

@@ -1,37 +1,50 @@
-name: Code Coverage
+name: MATLAB Tests and Code Coverage
+
 on:
-  push:
-    branches: [develop]
   pull_request:
-    branches: [develop]
+    branches:
+      - '**'
+
 jobs:
-  test:
-    runs-on: ubuntu-latest
+  build:
+    runs-on: self-hosted
     steps:
-      - uses: actions/checkout@v3
-      
-      - name: Set up MATLAB
-        uses: matlab-actions/setup-matlab@v1
-        with:
-          release: R2022a
-      
-      - name: Install MOcov
+
+      - name: Checkout PR Code
+        uses: actions/checkout@v4
+
+      - name: Merge PR with Develop
+        run: |
+          git fetch origin develop
+          git checkout -b test-branch
+          git merge origin/develop --no-edit
+
+      - name: Clone COBRA Toolbox
         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
+          git clone https://github.com/opencobra/cobratoolbox.git cobratoolbox
+
+      - name: Run MATLAB Tests
         run: |
-          matlab -batch "addpath(genpath(pwd)); run_coverage_tests"
-      
-      - name: Upload coverage to Codecov
+          matlab -batch "run('cobratoolbox/initCobraToolbox.m'); diary('test_results.txt'); run('cobratoolbox/testAll.m'); diary off;"
+
+      - name: Upload Test Report
+        uses: actions/upload-artifact@v4
+        with:
+          name: test-report
+          path: test_results.txt
+
+      - name: Upload Coverage to Codecov
+        if: always()  # Ensure it runs even if tests fail
         uses: codecov/codecov-action@v3
         with:
-          files: ./coverage.xml
-          flags: matlab
+          files: CodeCovTestResults.xml
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true
+          flags: matlab
           comment: true
+
+      - name: Upload Test Results to Codecov
+        if: always()
+        uses: codecov/test-results-action@v1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/testall.yml

@@ -1,4 +1,5 @@
 name: MATLAB Tests
+
 on:
   pull_request:
     branches:
@@ -8,13 +9,21 @@ jobs:
   build:
     runs-on: self-hosted
     steps:
-    - uses: actions/checkout@v2
+    
+    - name: Checkout PR Code
+      uses: actions/checkout@v4
+
+    - name: Merge PR with Develop
+      run: |
+        git fetch origin develop
+        git checkout -b test-branch
+        git merge origin/develop --no-edit
 
     - name: Clone COBRA Toolbox
       run: |
         git clone https://github.com/opencobra/cobratoolbox.git cobratoolbox
 
-    - name: Run MATLAB tests
+    - name: Run MATLAB Tests
       run: |
         matlab -batch "run('cobratoolbox/initCobraToolbox.m'); diary('test_results.txt'); run('cobratoolbox/runTestsAndGenerateReport.m'); diary off;"
 

test/testAll.m

@@ -15,7 +15,7 @@
 
 % request explicitly from the user to launch test suite locally
 % if contains(getenv('HOME'), 'vmhadmin') || contains(getenv('HOME'), 'jenkins')
-if contains(getenv('HOME'), 'cobratoolbox')
+if contains(getenv('HOME'), 'saleh')
     % Running in CI environment
 %    fprintf('Running test in Jenkins/CI environment\n');
      fprintf('Running test in cobratoolbox/CI environment\n');
@@ -182,6 +182,55 @@
         sumFailed = sum(resultTable.Failed);
 
         fprintf(['\n > ', num2str(sumFailed), ' tests failed. ', num2str(sumSkipped), ' tests were skipped due to missing requirements.\n\n']);
+        %% NEW: Generate JUnit XML report for Codecov
+        xmlFileName = 'CodeCovTestResults.xml';
+        fid = fopen(xmlFileName, 'w');
+        if fid == -1
+            error('Could not open file for writing: %s', xmlFileName);
+        end
+
+        fprintf(fid, '<?xml version="1.0" encoding="UTF-8"?>\n');
+        
+        numTests = height(resultTable);
+        numFailures = sum(resultTable.Failed);
+        numSkipped = sum(resultTable.Skipped);
+        totalTime = 0;
+        for i = 1:numTests
+            if isnan(resultTable.Time(i))
+                tVal = 0;
+            else
+                tVal = resultTable.Time(i);
+            end
+            totalTime = totalTime + tVal;
+        end
+
+        fprintf(fid, '<testsuite name="COBRA Toolbox Test Suite" tests="%d" failures="%d" skipped="%d" time="%.3f">\n', ...
+            numTests, numFailures, numSkipped, totalTime);
+
+        for i = 1:numTests
+            testName = resultTable.TestName{i};
+            if isnan(resultTable.Time(i))
+                tVal = 0;
+            else
+                tVal = resultTable.Time(i);
+            end
+            fprintf(fid, '  <testcase classname="COBRA Toolbox" name="%s" time="%.3f"', testName, tVal);
+            if resultTable.Passed(i)
+                fprintf(fid, '/>\n');
+            else
+                fprintf(fid, '>\n');
+                if resultTable.Skipped(i)
+                    fprintf(fid, '    <skipped message="%s"/>\n', escapeXML(resultTable.Details{i}));
+                else
+                    fprintf(fid, '    <failure message="%s"/>\n', escapeXML(resultTable.Details{i}));
+                end
+                fprintf(fid, '  </testcase>\n');
+            end
+        end
+
+        fprintf(fid, '</testsuite>\n');
+        fclose(fid);
+        %% End of XML generation
 
         % count the number of covered lines of code
         if COVERAGE
@@ -291,3 +340,16 @@
     % explicit 'exit' required for R2018b in non-interactive mode to avoid SEGV near end of test
     exit
 end
+
+%% Local helper function to escape XML special characters.
+function out = escapeXML(in)
+    if isempty(in)
+        out = '';
+        return;
+    end
+    out = strrep(in, '&', '&amp;');
+    out = strrep(out, '<', '&lt;');
+    out = strrep(out, '>', '&gt;');
+    out = strrep(out, '"', '&quot;');
+    out = strrep(out, '''', '&apos;');
+ens