I made research but I couldn't find any way to get most popular rune for specific champion. There are many rune websites that do this but I don't know whether they use their own rune pages or they use api. So I need a way to get most popular rune for specific champion in League of Legends. Is it possible to do this via riot api or another python package?
No, it's not possible to filter by runes in the API itself. You CAN fetch as many matches as you can and analyze them for the specific champion and his runes. Then you have a small amount of data to work with and read out popular / good runes. This is how the rune websites work too.
To answer your question: I don't think there is a library for this, you can easily program a match fetcher by yourself and save the queries in a databse.