There seems to be a problem with using certain Python packages and the application resume feature of recent macOS versions. Specifically, whenever I "import matplotlib.plyplot" or run the magic command "%matplotlib" in IPython, I get the following warning message:

2018-02-22 10:35:38.287 Python[4145:281298] ApplePersistenceIgnoreState: Existing state will not be touched. New state will be written to (null)

There's an issue in the matplotlib repo (https://github.com/matplotlib/matplotlib/issues/6242), but I don't think this problem can be fixed by matplotlib. Instead, according to this SO post (https://stackoverflow.com/a/21567601/1112283), the following command fixes the behavior:

defaults write org.python.python ApplePersistenceIgnoreState NO

Since this problem also comes up with Homebrew, I created an issue (https://github.com/Homebrew/homebrew-core/issues/24424), but the maintainers indicated that (1) this might be a Python issue and should be addressed upstream, and (2) the solution above is not a real fix and the correct behavior should be implemented programmatically by Python itself.