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I'm using the excellent Elpy. I have with a Python project with a .flake8 config file at the top of the project source tree. I have this content in the .flake8 file:

[flake8] ignore = E251, E501, E303, E271, E221, E226 per-file-ignores = admin/export-data:E241,E304

(export-data is a Python script in the subdirectory admin/ of the project.) Elpy running Flymake clearly reads the configuration file and correctly reads the globally-ignored error codes: I can see the effect of adding or removing error code values in the ignore line. However, the per-file settings for the file admin/export-data are not being recognized. At first, I thought the problem was the file path, so I tried variations such as just export-data, using the absolute path to export-data, and so on, and nothing seems to change the behavior: the per-file-ignores setting is itself ignored. Yet it works if I run flake8 in a terminal, outside of Emacs.

Is there a trick to getting the flake8/Elpy/Flymake combination to recognize the per-file-ignores setting?

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flymake doesn't call flake8 directly. Instead it builds a python3 command-line and (if I remember correctly) feeds it the buffer contents via stdin. Naturally there's no filename in this case, but flymake handles this by using flake8's --stdin-display-name= option. According to this issue at the flymake repo, this works in the case of simple filenames, but there is apparently a flake8 bug in recognizing relative paths.

tl;dr: It sorta works, but in your case it's not working because of an outstanding flake8 bug.

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