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I've run into some issues with markdown.py, some of which looked like fixing might be quite difficult. My initial attempts to email the maintainer ended up bouncing. At that point I started looking into a re-write. I later noticed that markdown.py is hosted on GitHub. (TODO: create issues there and link to them here.)
TODO: mention the safe_mode thing and recent HTML sanitization discussions
For fun. Who doesn't like writing parsing code. :)