BUG: Fix HDFStore empty keys on native HDF5 file by adding keyword include

doc/source/whatsnew/v1.1.0.rst

@@ -962,6 +962,7 @@ I/O
 - Bug in :meth:`~DataFrame.to_excel` could not handle the column name `render` and was raising an ``KeyError`` (:issue:`34331`)
 - Bug in :meth:`~SQLDatabase.execute` was raising a ``ProgrammingError`` for some DB-API drivers when the SQL statement contained the `%` character and no parameters were present (:issue:`34211`)
 - Bug in :meth:`~pandas.io.stata.StataReader` which resulted in categorical variables with difference dtypes when reading data using an iterator. (:issue:`31544`)
+- :meth:`HDFStore.keys` has now an optional `include` parameter that allows the retrieval of all native HDF5 table names (:issue:`29916`)
 
 Plotting
 ^^^^^^^^

pandas/io/pytables.py

@@ -580,16 +580,39 @@ def __enter__(self):
     def __exit__(self, exc_type, exc_value, traceback):
         self.close()
 
-    def keys(self) -> List[str]:
+    def keys(self, include: str = "pandas") -> List[str]:
         """
         Return a list of keys corresponding to objects stored in HDFStore.
 
+        Parameters
+        ----------
+
+        include : str, default 'pandas'
+                When kind equals 'pandas' return pandas objects
+                When kind equals 'native' return native HDF5 Table objects
+
+                .. versionadded:: 1.1.0
+
         Returns
         -------
         list
             List of ABSOLUTE path-names (e.g. have the leading '/').
+
+        Raises
+        ------
+        raises ValueError if kind has an illegal value
         """
-        return [n._v_pathname for n in self.groups()]
+        if include == "pandas":
+            return [n._v_pathname for n in self.groups()]
+
+        elif include == "native":
+            assert self._handle is not None  # mypy
+            return [
+                n._v_pathname for n in self._handle.walk_nodes("/", classname="Table")
+            ]
+        raise ValueError(
+            f"`include` should be either 'pandas' or 'native' but is '{include}'"
+        )
 
     def __iter__(self):
         return iter(self.keys())

pandas/tests/io/pytables/test_store.py

@@ -341,6 +341,40 @@ def create_h5_and_return_checksum(track_times):
         # checksums are NOT same if track_time = True
         assert checksum_0_tt_true != checksum_1_tt_true
 
+    def test_non_pandas_keys(self, setup_path):
+        class Table1(tables.IsDescription):
+            value1 = tables.Float32Col()
+
+        class Table2(tables.IsDescription):
+            value2 = tables.Float32Col()
+
+        class Table3(tables.IsDescription):
+            value3 = tables.Float32Col()
+
+        with ensure_clean_path(setup_path) as path:
+            with tables.open_file(path, mode="w") as h5file:
+                group = h5file.create_group("/", "group")
+                h5file.create_table(group, "table1", Table1, "Table 1")
+                h5file.create_table(group, "table2", Table2, "Table 2")
+                h5file.create_table(group, "table3", Table3, "Table 3")
+            with HDFStore(path) as store:
+                assert len(store.keys(include="native")) == 3
+                expected = {"/group/table1", "/group/table2", "/group/table3"}
+                assert set(store.keys(include="native")) == expected
+                assert set(store.keys(include="pandas")) == set()
+                for name in expected:
+                    df = store.get(name)
+                    assert len(df.columns) == 1
+
+    def test_keys_illegal_include_keyword_value(self, setup_path):
+        with ensure_clean_store(setup_path) as store:
+            with pytest.raises(
+                ValueError,
+                match="`include` should be either 'pandas' or 'native' "
+                "but is 'illegal'",
+            ):
+                store.keys(include="illegal")
+
     def test_keys_ignore_hdf_softlink(self, setup_path):
 
         # GH 20523