redirect canonical

functions.php

1. // use the page url and append the CPT template file you would like to redirect canoncial URL's

add_action( 'template_redirect', 'insight_template_redirect', 1 );
function insight_template_redirect() {
    if ( is_paged() && is_single( 'yourwebsite.com/category' ) ) {
        remove_action( 'template_redirect', 'redirect_canonical' );
    }
}

2. // Declare pagination function and use paged parameter in wp_query

function pagination($prev = '«', $next = '»') {
  global $wp_query, $wp_rewrite;
  $wp_query->query_vars['paged'] >2 ? $current = $wp_query->query_vars['paged'] : $current = 1;
  $pagination = array(
      'base' => @add_query_arg('paged','%#%'),
      'format' => '',
      'total' => $wp_query->max_num_pages,
      'current' => $current,
      'prev_text' => __($prev),
      'next_text' => __($next),
      'paged' => $current,
      'type' => 'plain'
);
  if( $wp_rewrite->using_permalinks() )
      $pagination['base'] = user_trailingslashit( trailingslashit( remove_query_arg( 's', get_pagenum_link( 1 ) ) ) . 'page/%#%/', 'paged' );
      remove_filter('template_redirect', 'redirect_canonical');

  if( !empty($wp_query->query_vars['s']) )
      $pagination['add_args'] = array( 's' => get_query_var( 's' ) );

  echo paginate_links( $pagination );
};