This is a demonstration of a post that does not render properly (the lack of hyperlink):
code code code
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[logging module] (http://docs.python.org/library/logging.html)
You'll want to drop that
 and go with this:
To get this:
This looks like markdown doesn't want to parse links in a block immediately preceding a section surrounded by <pre> tags. Your [foo]1 label with footnote looks fine, and inserting one with the hyperlink WYSIWYG tool generates the same format (which also doesn't work).
I noticed you used <code> and <pre> tags -- it's generally easier to just indent your text by four spaces (which the binary button at the top of the editing window will do for you).
text using code and pre tags
Here is a link that does not work... through experimentation, it would seem that it is the <pre> tag following that screws things up.
...stuff inside a pre tag
text using four spaces of indentation
Here is a link that does work.
From what I see of your raw post text, you have not used valid Markdown.
Please refer to the editing help, which is linked: