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Clear signs after autopep8
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autoload/pymode/lint.vim

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@@ -11,6 +11,7 @@ fun! pymode#lint#auto() "{{{
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PymodePython from pymode import auto
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PymodePython auto()
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cclose
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call g:PymodeSigns.clear()
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edit
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call pymode#wide_message("AutoPep8 done.")
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endfunction "}}}

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