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add_filter( 'the_content', 'remove_empty_p', 20, 1 );
function remove_empty_p( $content ){
	// clean up p tags around block elements
	$content = preg_replace( array(
		'#<p>\s*<(div|aside|section|article|header|footer)#',
		'#</(div|aside|section|article|header|footer)>\s*</p>#',
		'#</(div|aside|section|article|header|footer)>\s*<br ?/?>#',
		'#<(div|aside|section|article|header|footer)(.*?)>\s*</p>#',
		'#<p>\s*</(div|aside|section|article|header|footer)#',
	), array(
		'<$1',
		'</$1>',
		'</$1>',
		'<$1$2>',
		'</$1',
	), $content );

	return preg_replace('#<p>(\s|&nbsp;)*+(<br\s*/*>)?(\s|&nbsp;)*</p>#i', '', $content);
}

function shortcode_empty_paragraph_fix( $content ) {

    // define your shortcodes to filter, '' filters all shortcodes
    $shortcodes = array( 'your_shortcode_1', 'your_shortcode_2' );

    foreach ( $shortcodes as $shortcode ) {

        $array = array (
            '<p>[' . $shortcode => '[' .$shortcode,
            '<p>[/' . $shortcode => '[/' .$shortcode,
            $shortcode . ']</p>' => $shortcode . ']',
            $shortcode . ']<br />' => $shortcode . ']'
        );

        $content = strtr( $content, $array );
    }

    return $content;
}

add_filter( 'the_content', 'shortcode_empty_paragraph_fix' );