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Here's an example:
import markdown
example_content = """# Test
>>> print('hi')
hi
The above is valid MarkDown."""
output = markdown.markdown(example_content, extensions=['markdown.extensions.codehilite'])
print(output)
As you can see, my example file includes a Markdown example with > characters. Unfortunately, with Codehilite enabled, it produces doubly-escaped content. Here's the output of that script:
<h1>Test</h1>
<div class="codehilite"><pre><span></span>&gt;&gt;&gt; print('hi')
hi
</pre></div>
<p>The above is valid MarkDown.</p>
See those &> parts? That means your HTML output includes the > characters escaped twice. It should be just >>>, not &gt;&gt;&gt;.
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