This is more or less the final content and format of the Shapely 1.0 manual. I struggled a bit with the choice of format and writer to use. If it had any math I'd probably have reverted to LaTeX, but I'm dodging the math with links to the Java Topology Suite docs and evasive statements like "just go ask Martin Dr J(ts) Davis". OOWriter's HTML export didn't cut it and there was little support for Python code syntax highlighting. Proprietary software or formats were out of the question. Finally I settled on docutils, restructured text, Pygments, and the Pygments code-blocking version of rst2html in the docutils sandbox (also included in the current Trac). The restructured text source is at manual.txt. It works well and looks sharp thanks to a stylesheet from Dave Kuhlman's odtwriter page.
If you're using Shapely, I'd appreciate your feedback on the manual. It's the last ticket on the Shapely 1.0 milestone.