Improve PMD use (#889)

Co-authored-by: mohdsaid497566 <mohdsaid497566@gmail.com>

Author: Malmahrouqi3

.github/workflows/pmd.yml

@@ -30,7 +30,105 @@ jobs:
               unzip -q pmd.zip
               PMD_HOME="pmd-bin-${PMD_VERSION}"
           
+              SOURCE_DIR="${1:-src}"
+              total_files=$(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" "$TMP_FILE"
+                  
+                  # More comprehensive sed command to handle different Fortran comment styles:
+                  # 1. Replace lines that are entirely comments with an empty line:
+                  #    - Lines starting with '!' (free form comments)
+                  #    - Lines starting with 'c', 'C', '*', 'd', 'D' in column 1 (fixed form comments)
+                  # 2. Remove end-of-line comments (anything after '!' that isn't in a string)
+                  # 3. Preserve strings containing '!' characters                  
+                  sed -E '
+                    # First handle & continuation style (modern Fortran)
+                    :ampersand_loop
+                    /&[[:space:]]*$/ {
+                      N
+                      s/&[[:space:]]*\n[[:space:]]*(&)?/ /g
+                      tampersand_loop
+                    }
+                    
+                    # Handle fixed-form continuation (column 6 indicator)
+                    :fixed_form_loop
+                    /^[[:space:]]{0,5}[^[:space:]!&]/ {
+                      N
+                      s/\n[[:space:]]{5}[^[:space:]]/ /g
+                      tfixed_form_loop
+                    }
+                    
+                    # Remove any remaining continuation markers
+                    s/&//g
+                    
+                    # Normalize spacing - replace multiple spaces with single space
+                    s/[[:space:]]{2,}/ /g
+                    
+                    # Remove spaces around mathematical operators
+                    s/[[:space:]]*\*[[:space:]]*/*/g
+                    s/[[:space:]]*\+[[:space:]]*/+/g
+                    s/[[:space:]]*-[[:space:]]*/-/g
+                    s/[[:space:]]*\/[[:space:]]*/\//g
+                    s/[[:space:]]*\*\*[[:space:]]*/\*\*/g
+                    
+                    # Remove spaces in common Fortran constructs (array indexing, function calls)
+                    s/\([[:space:]]*([^,)[:space:]]+)[[:space:]]*,/(\1,/g      # First argument
+                    s/,[[:space:]]*([^,)[:space:]]+)[[:space:]]*,/,\1,/g       # Middle arguments
+                    s/,[[:space:]]*([^,)[:space:]]+)[[:space:]]*\)/,\1)/g      # Last argument
+                    s/\([[:space:]]*([^,)[:space:]]+)[[:space:]]*\)/(\1)/g     # Single argument
+                    
+                    # Remove spaces around brackets and parentheses
+                    s/\[[[:space:]]*/</g
+                    s/\[[[:space:]]*/>/g
+                    s/\[[[:space:]]*/</g
+                    s/[[:space:]]*\]/]/g
+                    s/\([[:space:]]*/(/g
+                    s/[[:space:]]*\)/)/g
+
+                    # Remove spaces around comparison operators
+                    s/[[:space:]]*<=[[:space:]]*/</g
+                    s/[[:space:]]*>=[[:space:]]*/>/g
+                    s/[[:space:]]*<[[:space:]]*/</g
+                    s/[[:space:]]*>[[:space:]]*/>/g
+                    s/[[:space:]]*==[[:space:]]*/==/g
+
+                    # Remove full-line comments
+                    /^\s*!/d
+                    /^[cC*dD]/d
+                    /^[ \t]*[cC*dD]/d
+                    /^[[:space:]]*$/d
+
+                    # Remove end-of-line comments, preserving quoted strings
+                    s/([^"'\''\\]*("[^"]*")?('\''[^'\'']*'\''?)?[^"'\''\\]*)[!].*$/\1/
+                  ' "$file" > "$TMP_FILE"
+                
+                  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_HOME}/bin/pmd" cpd \
                 --dir src \
                 --language fortran \
-                --minimum-tokens=40
+                --minimum-tokens=20 \
+                --no-fail-on-violation \
+                --no-fail-on-error