The Phillies in-house Twitter account, as well as several of the beat writers, reported Thompson on Wednesday evening that Thompson had been optioned. I wouldn't put much stock in the fact that mlb.com's transactions page and roster haven't been updated - that is (unfortunately) fairly normal for mlb.com.
Assuming the option is real, it would have been effective on July 5th (it was announced after the game on the 4th). Thompson would be ineligible to be recalled for 10 days (July 5 through 14). He could be recalled for games beginning July 15th.
There are exceptions - he could be recalled earlier, with the approval of the Commissioner's office, to replace a player added to the DL (note: a player added to the DL after July 4th!); he could also be recalled earlier if he's being traded.