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Pass mode to all h5py.File calls

Duncan Macleod requested to merge github/fork/duncanmmacleod/h5py-file-mode into master

This PR adds explicit mode=<> keyword arguments to all h5py.File calls. The default mode is changing in h5py-3.0.0 from 'a' to 'r', so we need this to make sure nothing breaks - this should be backwards-compatible.

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