[backport 2.3.x] ENH: Enable pytables to round-trip with StringDtype (#60663) (#60771)

ENH: Enable pytables to round-trip with StringDtype (#60663)

Co-authored-by: William Ayd <[email protected]>
(cherry picked from commit 60325b8)

Co-authored-by: Richard Shadrach <[email protected]>

Author: jorisvandenbossche

doc/source/whatsnew/v2.3.0.rst

@@ -35,6 +35,7 @@ Other enhancements
 - The semantics for the ``copy`` keyword in ``__array__`` methods (i.e. called
   when using ``np.array()`` or ``np.asarray()`` on pandas objects) has been
   updated to raise FutureWarning with NumPy >= 2 (:issue:`60340`)
+- :meth:`~Series.to_hdf` and :meth:`~DataFrame.to_hdf` now round-trip with ``StringDtype``  (:issue:`60663`)
 - The :meth:`~Series.cumsum`, :meth:`~Series.cummin`, and :meth:`~Series.cummax` reductions are now implemented for ``StringDtype`` columns when backed by PyArrow (:issue:`60633`)
 - The :meth:`~Series.sum` reduction is now implemented for ``StringDtype`` columns (:issue:`59853`)
 

pandas/io/pytables.py

@@ -86,12 +86,16 @@
     DatetimeArray,
     PeriodArray,
 )
+from pandas.core.arrays.string_ import BaseStringArray
 import pandas.core.common as com
 from pandas.core.computation.pytables import (
     PyTablesExpr,
     maybe_expression,
 )
-from pandas.core.construction import extract_array
+from pandas.core.construction import (
+    array as pd_array,
+    extract_array,
+)
 from pandas.core.indexes.api import ensure_index
 from pandas.core.internals import (
     ArrayManager,
@@ -2955,6 +2959,9 @@ def read_array(self, key: str, start: int | None = None, stop: int | None = None
 
         if isinstance(node, tables.VLArray):
             ret = node[0][start:stop]
+            dtype = getattr(attrs, "value_type", None)
+            if dtype is not None:
+                ret = pd_array(ret, dtype=dtype)
         else:
             dtype = _ensure_decoded(getattr(attrs, "value_type", None))
             shape = getattr(attrs, "shape", None)
@@ -3193,6 +3200,11 @@ def write_array(
         elif lib.is_np_dtype(value.dtype, "m"):
             self._handle.create_array(self.group, key, value.view("i8"))
             getattr(self.group, key)._v_attrs.value_type = "timedelta64"
+        elif isinstance(value, BaseStringArray):
+            vlarr = self._handle.create_vlarray(self.group, key, _tables().ObjectAtom())
+            vlarr.append(value.to_numpy())
+            node = getattr(self.group, key)
+            node._v_attrs.value_type = str(value.dtype)
         elif empty_array:
             self.write_array_empty(key, value)
         else:
@@ -3225,7 +3237,11 @@ def read(
         index = self.read_index("index", start=start, stop=stop)
         values = self.read_array("values", start=start, stop=stop)
         result = Series(values, index=index, name=self.name, copy=False)
-        if using_string_dtype() and is_string_array(values, skipna=True):
+        if (
+            using_string_dtype()
+            and isinstance(values, np.ndarray)
+            and is_string_array(values, skipna=True)
+        ):
             result = result.astype(StringDtype(na_value=np.nan))
         return result
 
@@ -3294,7 +3310,11 @@ def read(
 
             columns = items[items.get_indexer(blk_items)]
             df = DataFrame(values.T, columns=columns, index=axes[1], copy=False)
-            if using_string_dtype() and is_string_array(values, skipna=True):
+            if (
+                using_string_dtype()
+                and isinstance(values, np.ndarray)
+                and is_string_array(values, skipna=True)
+            ):
                 df = df.astype(StringDtype(na_value=np.nan))
             dfs.append(df)
 
@@ -4682,9 +4702,13 @@ def read(
                 df = DataFrame._from_arrays([values], columns=cols_, index=index_)
             if not (using_string_dtype() and values.dtype.kind == "O"):
                 assert (df.dtypes == values.dtype).all(), (df.dtypes, values.dtype)
-            if using_string_dtype() and is_string_array(
-                values,  # type: ignore[arg-type]
-                skipna=True,
+            if (
+                using_string_dtype()
+                and isinstance(values, np.ndarray)
+                and is_string_array(
+                    values,
+                    skipna=True,
+                )
             ):
                 df = df.astype(StringDtype(na_value=np.nan))
             frames.append(df)

pandas/tests/io/pytables/test_put.py

@@ -3,8 +3,6 @@
 import numpy as np
 import pytest
 
-from pandas._config import using_string_dtype
-
 from pandas._libs.tslibs import Timestamp
 
 import pandas as pd
@@ -26,7 +24,6 @@
 
 pytestmark = [
     pytest.mark.single_cpu,
-    pytest.mark.xfail(using_string_dtype(), reason="TODO(infer_string)", strict=False),
 ]
 
 
@@ -54,8 +51,8 @@ def test_api_default_format(tmp_path, setup_path):
     with ensure_clean_store(setup_path) as store:
         df = DataFrame(
             1.1 * np.arange(120).reshape((30, 4)),
-            columns=Index(list("ABCD"), dtype=object),
-            index=Index([f"i-{i}" for i in range(30)], dtype=object),
+            columns=Index(list("ABCD")),
+            index=Index([f"i-{i}" for i in range(30)]),
         )
 
         with pd.option_context("io.hdf.default_format", "fixed"):
@@ -79,8 +76,8 @@ def test_api_default_format(tmp_path, setup_path):
     path = tmp_path / setup_path
     df = DataFrame(
         1.1 * np.arange(120).reshape((30, 4)),
-        columns=Index(list("ABCD"), dtype=object),
-        index=Index([f"i-{i}" for i in range(30)], dtype=object),
+        columns=Index(list("ABCD")),
+        index=Index([f"i-{i}" for i in range(30)]),
     )
 
     with pd.option_context("io.hdf.default_format", "fixed"):
@@ -106,7 +103,7 @@ def test_put(setup_path):
         )
         df = DataFrame(
             np.random.default_rng(2).standard_normal((20, 4)),
-            columns=Index(list("ABCD"), dtype=object),
+            columns=Index(list("ABCD")),
             index=date_range("2000-01-01", periods=20, freq="B"),
         )
         store["a"] = ts
@@ -166,7 +163,7 @@ def test_put_compression(setup_path):
     with ensure_clean_store(setup_path) as store:
         df = DataFrame(
             np.random.default_rng(2).standard_normal((10, 4)),
-            columns=Index(list("ABCD"), dtype=object),
+            columns=Index(list("ABCD")),
             index=date_range("2000-01-01", periods=10, freq="B"),
         )
 
@@ -183,7 +180,7 @@ def test_put_compression(setup_path):
 def test_put_compression_blosc(setup_path):
     df = DataFrame(
         np.random.default_rng(2).standard_normal((10, 4)),
-        columns=Index(list("ABCD"), dtype=object),
+        columns=Index(list("ABCD")),
         index=date_range("2000-01-01", periods=10, freq="B"),
     )
 
@@ -197,10 +194,20 @@ def test_put_compression_blosc(setup_path):
         tm.assert_frame_equal(store["c"], df)
 
 
-def test_put_mixed_type(setup_path):
+def test_put_datetime_ser(setup_path):
+    # https://github.com/pandas-dev/pandas/pull/60663
+    ser = Series(3 * [Timestamp("20010102").as_unit("ns")])
+    with ensure_clean_store(setup_path) as store:
+        store.put("ser", ser)
+        expected = ser.copy()
+        result = store.get("ser")
+        tm.assert_series_equal(result, expected)
+
+
+def test_put_mixed_type(setup_path, using_infer_string):
     df = DataFrame(
         np.random.default_rng(2).standard_normal((10, 4)),
-        columns=Index(list("ABCD"), dtype=object),
+        columns=Index(list("ABCD")),
         index=date_range("2000-01-01", periods=10, freq="B"),
     )
     df["obj1"] = "foo"
@@ -220,13 +227,42 @@ def test_put_mixed_type(setup_path):
     with ensure_clean_store(setup_path) as store:
         _maybe_remove(store, "df")
 
-        with tm.assert_produces_warning(pd.errors.PerformanceWarning):
+        warning = None if using_infer_string else pd.errors.PerformanceWarning
+        with tm.assert_produces_warning(warning):
             store.put("df", df)
 
         expected = store.get("df")
         tm.assert_frame_equal(expected, df)
 
 
+def test_put_str_frame(setup_path, string_dtype_arguments):
+    # https://github.com/pandas-dev/pandas/pull/60663
+    dtype = pd.StringDtype(*string_dtype_arguments)
+    df = DataFrame({"a": pd.array(["x", pd.NA, "y"], dtype=dtype)})
+    with ensure_clean_store(setup_path) as store:
+        _maybe_remove(store, "df")
+
+        store.put("df", df)
+        expected_dtype = "str" if dtype.na_value is np.nan else "string"
+        expected = df.astype(expected_dtype)
+        result = store.get("df")
+        tm.assert_frame_equal(result, expected)
+
+
+def test_put_str_series(setup_path, string_dtype_arguments):
+    # https://github.com/pandas-dev/pandas/pull/60663
+    dtype = pd.StringDtype(*string_dtype_arguments)
+    ser = Series(["x", pd.NA, "y"], dtype=dtype)
+    with ensure_clean_store(setup_path) as store:
+        _maybe_remove(store, "df")
+
+        store.put("ser", ser)
+        expected_dtype = "str" if dtype.na_value is np.nan else "string"
+        expected = ser.astype(expected_dtype)
+        result = store.get("ser")
+        tm.assert_series_equal(result, expected)
+
+
 @pytest.mark.parametrize("format", ["table", "fixed"])
 @pytest.mark.parametrize(
     "index",
@@ -253,7 +289,7 @@ def test_store_index_types(setup_path, format, index):
         tm.assert_frame_equal(df, store["df"])
 
 
-def test_column_multiindex(setup_path):
+def test_column_multiindex(setup_path, using_infer_string):
     # GH 4710
     # recreate multi-indexes properly
 
@@ -264,6 +300,12 @@ def test_column_multiindex(setup_path):
     expected = df.set_axis(df.index.to_numpy())
 
     with ensure_clean_store(setup_path) as store:
+        if using_infer_string:
+            # TODO(infer_string) make this work for string dtype
+            msg = "Saving a MultiIndex with an extension dtype is not supported."
+            with pytest.raises(NotImplementedError, match=msg):
+                store.put("df", df)
+            return
         store.put("df", df)
         tm.assert_frame_equal(
             store["df"], expected, check_index_type=True, check_column_type=True