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I looked into this a while back after seeing a similar issue. Internally, pip-autoremove can't see when something is installed with extras (in this case woff is the extra), it can only see that the base package was installed. This appears to be a limitation of pkg_resources.get_distribution which is what is used to build up the dependency graph.
Not remove all unused dependencies:
Using pip-autoremove:
These 2 libs (brotli and zopfli) deps from fonttools not auto uninstalled:
Versão:
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