BUG: Fix HDFStore empty keys on native HDF5 file by adding keyword include
- [x] closes #29916
- [x] tests added / passed
- [x] passes `black pandas`
- [x] passes `git diff upstream/master -u -- "*.py" | flake8 --diff`
- [x] whatsnew entry

Hello @roberthdevries! Thanks for updating this PR. We checked the lines you've touched for [PEP 8](https://www.python.org/dev/peps/pep-0008) issues, and found:





There are currently no PEP 8 issues detected in this Pull Request. Cheers! :beers: 

##### Comment last updated at 2020-06-14 21:02:12 UTC > looks fine. does this solve the OP? meaning folks simply want to use .keys() to get _all_ the tables, then use .get() to read them?

We could also merge the two sets of tables. I think pandas does not use native HDF5 tables to store DataFrames. In that case the two sets are disjoint and we should be fine returning the joined set. I tried the variant with returning the combination of keys of pandas tables and HDF5 native tables, and the unit test `pandas/tests/io/pytables/test_store.py::TestHDFStore::test_copy` fails. I think the solution we have now helps the `dask` developers at least to have a work-around solution, that can work on both older and newer pandas versions by checking for the pandas version. > I tried the variant with returning the combination of keys of pandas tables and HDF5 native tables, and the unit test `pandas/tests/io/pytables/test_store.py::TestHDFStore::test_copy` fails.

Hi there, this is interesting, how did this test pass before the `keys()` method changed, i.e. it used to return all the keys in pandas < 0.24?

> I think the solution we have now helps the `dask` developers at least to have a work-around solution, that can work on both older and newer pandas versions by checking for the pandas version.

Hopefully, thanks for working on it. > don't you need this _also_ in `.groups()`?

Could be added there as well, although that use case is less typical. Most users are interested in the _tables_ in the file.
However, if this question pops up, I'll be happy to create a PR for that. @jreback tests should have run fine, except that one of the tests took too long I think. So this is my ping on sort of green thanks @roberthdevries  thanks @roberthdevries and @jreback for resolving this issue for keys, it will help my project a lot.

@roberthdevries the source files coming into my system use groups (not created by pandas) so I would need the same fix applying to .groups() as well as .keys() if at all possible.