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The tests should run in both python version. They do not have to pass in both versions, though.
Note that, because of how the DCD reader was imported, the tests probably do run on python 3 now. Indeed, the library tries to import the DCD reader, succeed, and therefore do not skip the tests.
However, skipping the tests should not be an option. In practice, it means removing the try/except in mda.coordinates.__init__, and removing all the skips that are there because of DCD.
All the skips are identical, so it should even be doable automatically. It may be better for you to do it progressively in your other PRs, though. To avoid having to deal with conflicts.
Now that #1372 is merged, there is no reason not to load DCD on python 3. Currently, python 3 tries to load the DCD and LAMMPS reader and let it go if it fails. See https://github.com/MDAnalysis/mdanalysis/blob/develop/package/MDAnalysis/coordinates/__init__.py. The DCD and LAMMPS reader should be loaded as the others, now.
With the two modules loaded normally, there is no reason to skip the tests involving DCD. The skips should be phased out.
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