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I have set up Emacs (on Mac Catalina) with Elpy to handle Python. I also managed to get Jupyter notebooks (.ipynb files) working with Elpy via Ein. Both .py and .ipynb compile and use Flycheck correctly.

I have problems with .ipynb notebooks:

I find that Flycheck does not work properly because of the In [ ]:

I found flake8_nb (and not 'flake8`) works fine with them from the command line:

flake8_nb name.ipynb

My question now is: How can I set up Emacs/elpy to use flake8 with py files and flake8_nb with .ipynb?

From what I have understood, Elpy calls flake8 through python-flake8 but I cannot find an option to make it use flake8_nb with .ipynb files.

Can you please help me?

This is my .emacs Python part:

    (use-package elpy
      :ensure t
      :init
      (elpy-enable))

    (when(require 'ein)
    (setq ein:use-auto-complete-superpack t))

    (when (require 'flycheck nil t)
      (setq elpy-modules (delq 'elpy-module-flymake elpy-modules))
      (add-hook 'elpy-mode-hook 'flycheck-mode))

    (add-hook 'after-init-hook #'global-flycheck-mode)

    (require 'py-autopep8)
    (add-hook 'elpy-mode-hook 'py-autopep8-enable-on-save)

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