updated yml to run all analysis

.github/workflows/gtf_tests.yml

@@ -27,14 +27,37 @@ jobs:
         python -m pip install --upgrade pip
         pip install pandas
 
-    - name: Create output directory
-      run: mkdir -p test_output
+    - name: Create directories
+      run: |
+        mkdir -p test_data
+        mkdir -p test_output
+        mkdir -p test_output/comparison_files
+        mkdir -p test_data/reference_outputs
+
+    - name: Create test data
+      run: python create_test_gtfs.py
+
+    # First run: Create reference GTF if it doesn't exist
+    - name: Create reference GTF
+      if: ${{ !hashFiles('test_data/reference_outputs/reference_modified.gtf') }}
+      env:
+        PYTHONPATH: ${{ github.workspace }}/3rd-party-tools/build-indices
+      run: |
+        python modify_gtf.py \
+          -i test_data/test1.gtf \
+          -o test_data/reference_outputs/reference_modified.gtf \
+          -b Biotypes.tsv
 
-    - name: Verify required files exist
+    # Run unit tests
+    - name: Run unit tests
+      id: unit_tests
+      env:
+        PYTHONPATH: ${{ github.workspace }}/3rd-party-tools/build-indices
       run: |
-        ls test_data/test1.gtf
-        ls Biotypes.tsv
+        python -m unittest test_gtf_comparison.py -v
+      continue-on-error: true
 
+    # Run modify_gtf and comparison
     - name: Run modify_gtf script
       env:
         PYTHONPATH: ${{ github.workspace }}/3rd-party-tools/build-indices
@@ -44,21 +67,78 @@ jobs:
           -o test_output/modified_test1.gtf \
           -b Biotypes.tsv
 
-    - name: Run comparison tests
+    - name: Run comparison
+      id: comparison
       env:
         PYTHONPATH: ${{ github.workspace }}/3rd-party-tools/build-indices
       run: |
         python compare_gtfs.py \
           test_data/test1.gtf \
           test_output/modified_test1.gtf \
-          --output-prefix test_output/comparison
+          --output-prefix test_output/comparison_files/comparison
+      continue-on-error: true
 
-    - name: Upload test results
+    - name: Create comparison summary
+      run: |
+        echo "GTF Comparison Summary" > test_output/comparison_files/summary.txt
+        echo "Generated on: $(date)" >> test_output/comparison_files/summary.txt
+        echo "\nInput GTF: test_data/test1.gtf" >> test_output/comparison_files/summary.txt
+        echo "Modified GTF: test_output/modified_test1.gtf\n" >> test_output/comparison_files/summary.txt
+        
+        echo "=== Structural Differences ===" >> test_output/comparison_files/summary.txt
+        cat test_output/comparison_files/comparison_structural_diff.txt >> test_output/comparison_files/summary.txt
+        
+        echo "\n=== Gene Differences ===" >> test_output/comparison_files/summary.txt
+        cat test_output/comparison_files/comparison_gene_diff.txt >> test_output/comparison_files/summary.txt
+        
+        echo "\n=== Attribute Differences ===" >> test_output/comparison_files/summary.txt
+        cat test_output/comparison_files/comparison_attribute_diff.txt >> test_output/comparison_files/summary.txt
+
+    - name: Zip comparison results
+      run: |
+        cd test_output
+        zip -r comparison_results.zip comparison_files/
+        cd ..
+
+    - name: Upload test artifacts
       uses: actions/upload-artifact@v4
       if: always()
       with:
         name: gtf-test-results
         path: |
-          3rd-party-tools/build-indices/test_output/
+          3rd-party-tools/build-indices/test_output/comparison_results.zip
+          3rd-party-tools/build-indices/test_output/modified_test1.gtf
           3rd-party-tools/build-indices/test_data/test1.gtf
-          3rd-party-tools/build-indices/Biotypes.tsv
+          3rd-party-tools/build-indices/Biotypes.tsv
+          3rd-party-tools/build-indices/test_data/reference_outputs/reference_modified.gtf
+        compression-level: 9
+
+    - name: Check test results
+      if: always()
+      run: |
+        # Print test summary
+        echo "=== Test Results Summary ==="
+        
+        # Check unit tests result
+        if [ "${{ steps.unit_tests.outcome }}" == "success" ]; then
+          echo "✅ Unit tests passed"
+        else
+          echo "❌ Unit tests failed"
+          TESTS_FAILED=true
+        fi
+        
+        # Check comparison results
+        if [ -f test_output/comparison_files/comparison_structural_diff.txt ]; then
+          if grep -q "differs in" test_output/comparison_files/comparison_structural_diff.txt; then
+            echo "❌ GTF comparison found differences"
+            cat test_output/comparison_files/summary.txt
+            TESTS_FAILED=true
+          else
+            echo "✅ GTF comparison passed"
+          fi
+        fi
+        
+        # Fail if any tests failed
+        if [ "$TESTS_FAILED" = true ]; then
+          exit 1
+        fi