Update codecov.yml

.github/workflows/codecov.yml

@@ -10,59 +10,55 @@ jobs:
     runs-on: self-hosted
     steps:
       - name: Checkout PR Code
-        uses: actions/checkout@v4  # Fetches the PR branch
+        uses: actions/checkout@v4
 
-      - name: Rebase PR Branch on Top of Develop
+      - name: Connect to King Server & Setup Rebase
         run: |
-          git fetch origin develop  # Fetch latest develop
-          if [[ "${{ github.event.pull_request.head.repo.full_name }}" == "${{ github.repository }}" ]]; then
-            # PR is from the same repo
-            git fetch origin ${{ github.event.pull_request.head.ref }}
-            git checkout ${{ github.event.pull_request.head.ref }}
-          else
-            # PR is from a forked repo
-            git remote add pr_repo ${{ github.event.pull_request.head.repo.clone_url }}
-            git fetch pr_repo ${{ github.event.pull_request.head.ref }}
-            git checkout -b test-rebase FETCH_HEAD
+          ssh saleh@king << 'EOF'
+          # Navigate to home directory
+          cd ~
+
+          # Clone or update COBRA Toolbox
+          if [ ! -d "cobratoolbox" ]; then
+            git clone https://github.com/opencobra/cobratoolbox.git
           fi
-          git rebase origin/develop
-          git push origin +HEAD:test-rebase --force  # Push rebased branch
+          cd cobratoolbox
 
-      - name: Clone Rebased Branch on King Server
-        run: |
-          ssh saleh@king "rm -rf cobratoolbox && git clone -b test-rebase https://github.com/opencobra/cobratoolbox.git cobratoolbox"
+          # Ensure develop is up-to-date
+          git fetch origin develop
+          git checkout develop
+          git reset --hard origin/develop  
 
-      - name: Run MATLAB Tests on King Server
-        run: |
-          ssh saleh@king "matlab -batch \"run('cobratoolbox/initCobraToolbox.m'); diary('test_results.txt'); run('cobratoolbox/test/testAll.m'); diary off;\""
+          # Fetch and rebase the PR branch
+          git fetch origin ${{ github.event.pull_request.head.ref }}
+          git checkout -b pr-rebase FETCH_HEAD
+          git rebase develop
 
-      - name: Retrieve Test Results from Server
-        run: |
-          scp saleh@king:cobratoolbox/test_results.txt .
+          # If rebase fails, abort and exit
+          if [ $? -ne 0 ]; then
+            git rebase --abort
+            exit 1
+          fi
+
+          # Run MATLAB tests
+          matlab -batch "run('cobratoolbox/initCobraToolbox.m'); diary('test_results.txt'); run('cobratoolbox/test/testAll.m'); diary off;"
+
+          # Exit SSH session
+          exit
+          EOF
 
       - name: Upload Test Report
         uses: actions/upload-artifact@v4
         with:
           name: test-report
-          path: test_results.txt
+          path: ~/cobratoolbox/test_results.txt
 
       - name: Upload Coverage to Codecov
         if: always()
         uses: codecov/codecov-action@v3
         with:
-          files: ${{ github.workspace }}/CodeCovTestResults.xml
+          files: ~/cobratoolbox/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 }}
-
-      - name: Cleanup Temporary Rebased Branch
-        if: always()
-        run: |
-          git push origin --delete test-rebase || true  # Delete the test-rebase branch after tests