bump pytables to 3.5.1 pandas-dev#24839

Author: fangchenli

doc/source/getting_started/install.rst

@@ -280,7 +280,7 @@ psycopg2                  2.7                PostgreSQL engine for sqlalchemy
 pyarrow                   0.15.0             Parquet, ORC, and feather reading / writing
 pymysql                   0.7.11             MySQL engine for sqlalchemy
 pyreadstat                                   SPSS files (.sav) reading
-pytables                  3.4.4              HDF5 reading / writing
+pytables                  3.5.1              HDF5 reading / writing
 pyxlsb                    1.0.6              Reading for xlsb files
 qtpy                                         Clipboard I/O
 s3fs                      0.4.0              Amazon S3 access

doc/source/whatsnew/v1.2.0.rst

@@ -181,7 +181,7 @@ Optional libraries below the lowest tested version may still work, but are not c
 +-----------------+-----------------+---------+
 | pymysql         | 0.7.11          |    X    |
 +-----------------+-----------------+---------+
-| pytables        | 3.4.4           |    X    |
+| pytables        | 3.5.1           |    X    |
 +-----------------+-----------------+---------+
 | s3fs            | 0.4.0           |         |
 +-----------------+-----------------+---------+

pandas/tests/io/pytables/test_complex.py

@@ -3,17 +3,13 @@
 import numpy as np
 import pytest
 
-import pandas.util._test_decorators as td
-
 import pandas as pd
 from pandas import DataFrame, Series
 import pandas._testing as tm
 from pandas.tests.io.pytables.common import ensure_clean_path, ensure_clean_store
 
 from pandas.io.pytables import read_hdf
 
-# GH10447
-
 
 def test_complex_fixed(setup_path):
     df = DataFrame(
@@ -62,7 +58,6 @@ def test_complex_table(setup_path):
         tm.assert_frame_equal(df, reread)
 
 
-@td.xfail_non_writeable
 def test_complex_mixed_fixed(setup_path):
     complex64 = np.array(
         [1.0 + 1.0j, 1.0 + 1.0j, 1.0 + 1.0j, 1.0 + 1.0j], dtype=np.complex64

pandas/tests/io/pytables/test_store.py

@@ -909,7 +909,6 @@ def test_put_integer(self, setup_path):
         df = DataFrame(np.random.randn(50, 100))
         self._check_roundtrip(df, tm.assert_frame_equal, setup_path)
 
-    @td.xfail_non_writeable
     def test_put_mixed_type(self, setup_path):
         df = tm.makeTimeDataFrame()
         df["obj1"] = "foo"
@@ -1518,9 +1517,7 @@ def test_to_hdf_with_min_itemsize(self, setup_path):
                 pd.read_hdf(path, "ss4"), pd.concat([df["B"], df2["B"]])
             )
 
-    @pytest.mark.parametrize(
-        "format", [pytest.param("fixed", marks=td.xfail_non_writeable), "table"]
-    )
+    @pytest.mark.parametrize("format", ["fixed", "table"])
     def test_to_hdf_errors(self, format, setup_path):
 
         data = ["\ud800foo"]
@@ -1956,7 +1953,6 @@ def test_pass_spec_to_storer(self, setup_path):
             with pytest.raises(TypeError):
                 store.select("df", where=[("columns=A")])
 
-    @td.xfail_non_writeable
     def test_append_misc(self, setup_path):
 
         with ensure_clean_store(setup_path) as store:
@@ -2164,7 +2160,6 @@ def test_unimplemented_dtypes_table_columns(self, setup_path):
             with pytest.raises(TypeError):
                 store.append("df_unimplemented", df)
 
-    @td.xfail_non_writeable
     @pytest.mark.skipif(
         LooseVersion(np.__version__) == LooseVersion("1.15.0"),
         reason=(
@@ -2399,7 +2394,6 @@ def test_float_index(self, setup_path):
         s = Series(np.random.randn(10), index=index)
         self._check_roundtrip(s, tm.assert_series_equal, path=setup_path)
 
-    @td.xfail_non_writeable
     def test_tuple_index(self, setup_path):
 
         # GH #492
@@ -2412,7 +2406,6 @@ def test_tuple_index(self, setup_path):
             simplefilter("ignore", pd.errors.PerformanceWarning)
             self._check_roundtrip(DF, tm.assert_frame_equal, path=setup_path)
 
-    @td.xfail_non_writeable
     @pytest.mark.filterwarnings("ignore::pandas.errors.PerformanceWarning")
     def test_index_types(self, setup_path):
 
@@ -2474,7 +2467,6 @@ def test_timeseries_preepoch(self, setup_path):
         except OverflowError:
             pytest.skip("known failer on some windows platforms")
 
-    @td.xfail_non_writeable
     @pytest.mark.parametrize(
         "compression", [False, pytest.param(True, marks=td.skip_if_windows_python_3)]
     )
@@ -2508,7 +2500,6 @@ def test_frame(self, compression, setup_path):
         # empty
         self._check_roundtrip(df[:0], tm.assert_frame_equal, path=setup_path)
 
-    @td.xfail_non_writeable
     def test_empty_series_frame(self, setup_path):
         s0 = Series(dtype=object)
         s1 = Series(name="myseries", dtype=object)
@@ -2522,7 +2513,6 @@ def test_empty_series_frame(self, setup_path):
         self._check_roundtrip(df1, tm.assert_frame_equal, path=setup_path)
         self._check_roundtrip(df2, tm.assert_frame_equal, path=setup_path)
 
-    @td.xfail_non_writeable
     @pytest.mark.parametrize(
         "dtype", [np.int64, np.float64, object, "m8[ns]", "M8[ns]"]
     )
@@ -2608,7 +2598,6 @@ def test_store_series_name(self, setup_path):
             recons = store["series"]
             tm.assert_series_equal(recons, series)
 
-    @td.xfail_non_writeable
     @pytest.mark.parametrize(
         "compression", [False, pytest.param(True, marks=td.skip_if_windows_python_3)]
     )
@@ -4176,7 +4165,6 @@ def test_pytables_native2_read(self, datapath, setup_path):
             d1 = store["detector"]
             assert isinstance(d1, DataFrame)
 
-    @td.xfail_non_writeable
     def test_legacy_table_fixed_format_read_py2(self, datapath, setup_path):
         # GH 24510
         # legacy table with fixed format written in Python 2
@@ -4350,7 +4338,6 @@ def test_unicode_longer_encoded(self, setup_path):
             result = store.get("df")
             tm.assert_frame_equal(result, df)
 
-    @td.xfail_non_writeable
     def test_store_datetime_mixed(self, setup_path):
 
         df = DataFrame({"a": [1, 2, 3], "b": [1.0, 2.0, 3.0], "c": ["a", "b", "c"]})

pandas/util/_test_decorators.py

@@ -75,21 +75,6 @@ def safe_import(mod_name: str, min_version: Optional[str] = None):
     return False
 
 
-# TODO:
-# remove when gh-24839 is fixed.
-# this affects numpy 1.16 and pytables 3.4.4
-tables = safe_import("tables")
-xfail_non_writeable = pytest.mark.xfail(
-    tables
-    and LooseVersion(np.__version__) >= LooseVersion("1.16")
-    and LooseVersion(tables.__version__) < LooseVersion("3.5.1"),
-    reason=(
-        "gh-25511, gh-24839. pytables needs a "
-        "release beyond 3.4.4 to support numpy 1.16.x"
-    ),
-)
-
-
 def _skip_if_no_mpl():
     mod = safe_import("matplotlib")
     if mod: