Comment #4 on issue 326 by fritzoph...@gmail.com: filetype plugin not loaded when file opened from within vim rather than from command line
https://code.google.com/p/vim/issues/detail?id=326

I rescind my statement. Probably the problem is something in YOUR settings is overwriting the filetype plugin somehow. Apparently the ftplugin sets "expandtab tabstop=8 softtabstop=4 shiftwidth=4" which should be applying 4-space indent.

I couldn't tell you where in PEP8 the tabstop of 8 comes from. I don't develop the python plugin nor do I code in python more than a couple times in a month. All I know is there was a change to the runtime files somewhat recently that applied these settings in the python file. I also know filetype plugins load perfectly fine on every single python file for almost every single Vim user. So probably something is wrong with your setup. Check ":verbose set expandtab?" to see where this was apparently unset in your config.

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