comments removal

Author: mohdsaid497566

.github/workflows/pmd.yml

@@ -29,7 +29,50 @@ jobs:
           - name: Running PMD
             run: |
               alias pmd="$HOME/pmd/bin/pmd"
-              pmd cpd -l fortran pr/src/*  > ../pmd-fort.txt
+
+              SOURCE_DIR="${1:-pr/src}"
+              total_files=$(find "$SOURCE_DIR" -type f \( -name "*.f" -o -name "*.f90" -o -name "*.for" -o -name "*.fpp" -o -name "*.F" -o -name "*.F90" \) | wc -l)
+              processed=0
+
+              find "$SOURCE_DIR" -type f \( -name "*.f" -o -name "*.f90" -o -name "*.for" -o -name "*.fpp" -o -name "*.F" -o -name "*.F90" \) -print0 | 
+              while IFS= read -r -d $'\0' file; do
+                  processed=$((processed + 1))
+                  echo -e "[$processed/$total_files] Processing ${file}..."
+                  
+                  # Create a temporary file with same permissions as original
+                  TMP_FILE=$(mktemp)
+                  if [ $? -ne 0 ]; then
+                      echo -e "Failed to create temporary file for $file, skipping"
+                      continue
+                  fi
+                  
+                  # Copy permissions from original file
+                  chmod --reference="$file" "$TMP_FILE"
+                  
+                  # More comprehensive sed command to handle different Fortran comment styles:
+                  # 1. Replace lines that are entirely comments with an empty line:
+                  #    - Lines starting with '!' (free form comments)
+                  #    - Lines starting with 'c', 'C', '*', 'd', 'D' in column 1 (fixed form comments)
+                  # 2. Remove end-of-line comments (anything after '!' that isn't in a string)
+                  # 3. Preserve strings containing '!' characters
+                  sed -E \
+                      -e '/^\s*!/s/.*//' \
+                      -e '/^[cC*dD]/s/.*//' \
+                      -e '/^[ \t]*[cC*dD]/s/.*//' \
+                      -e 's/([^"'\'']*("[^"]*"[^"'\'']*|'\''[^'\'']*'\''[^"'\'']*)*[^"'\'']*)[!].*$/\1/' \
+                      "$file" > "$TMP_FILE"
+                  
+                  # Check if file was actually modified before replacing
+                  if cmp -s "$file" "$TMP_FILE"; then
+                      echo -e "No changes needed for $file"
+                      rm "$TMP_FILE"
+                  else
+                      # Overwrite the original file with the processed content
+                      mv "$TMP_FILE" "$file"
+                      echo -e "Successfully processed $file"
+                  fi
+              done
+              pmd cpd -l fortran /*  > ../pmd-fort.txt
               pmd cpd -l python pr/toolchain/*  > ../pmd-py.txt
 
           - name: Display PMD Reports