Description: HDF5 and Stata I/O are broken on some architectures Fix some issues, warn on use and xfail tests for the remainder armhf TestHDF5Store::test*encoding only sometimes crashes (1.1.3+dfsg-1 passed on build but failed autopkgtest) HDF5 and Stata are known to fail on big-endian architectures Stata also fails on qemu-ppc64el, but not real ppc64el Author: Andreas Tille , Graham Inggs , Yaroslav Halchenko , Rebecca N. Palmer Bug-Debian: https://bugs.debian.org/877419 Forwarded: no --- a/pandas/io/pytables.py +++ b/pandas/io/pytables.py @@ -9,6 +9,10 @@ import os import re from typing import TYPE_CHECKING, Any, Dict, List, Optional, Tuple, Type, Union import warnings +import platform +import re +from pandas.compat import is_platform_little_endian +warn_hdf_platform = "Non-x86 system detected, HDF(5) format I/O may give wrong results (particularly on files created with older versions) or crash - https://bugs.debian.org/877419" if not bool(re.match('i.?86|x86',platform.uname()[4])) else False import numpy as np @@ -527,6 +531,8 @@ class HDFStore: fletcher32: bool = False, **kwargs, ): + if warn_hdf_platform: + warnings.warn(warn_hdf_platform) if "format" in kwargs: raise ValueError("format is not a defined argument for HDFStore") @@ -766,7 +772,10 @@ class HDFStore: self._handle.flush() if fsync: try: - os.fsync(self._handle.fileno()) + if is_platform_little_endian(): + os.fsync(self._handle.fileno()) + else: + os.sync() # due to a pytables bad-cast bug, fileno is invalid on 64-bit big-endian except OSError: pass --- a/pandas/io/stata.py +++ b/pandas/io/stata.py @@ -29,6 +29,9 @@ from typing import ( Union, ) import warnings +import platform +import re +warn_stata_platform = "Non-x86 system detected, Stata format I/O may give wrong results (particularly on strings) - https://bugs.debian.org/877419" if not bool(re.match('i.?86|x86',platform.uname()[4])) else False from dateutil.relativedelta import relativedelta import numpy as np @@ -875,6 +878,8 @@ class StataParser: # NOTE: the byte type seems to be reserved for categorical variables # with a label, but the underlying variable is -127 to 100 # we're going to drop the label and cast to int + if warn_stata_platform: + warnings.warn(warn_stata_platform) self.DTYPE_MAP = dict( list(zip(range(1, 245), [np.dtype("a" + str(i)) for i in range(1, 245)])) + [ --- a/pandas/tests/io/pytables/test_store.py +++ b/pandas/tests/io/pytables/test_store.py @@ -54,6 +54,10 @@ from pandas.io.pytables import ( from pandas.io import pytables as pytables # noqa: E402 isort:skip from pandas.io.pytables import TableIterator # noqa: E402 isort:skip +import platform +import re +import sys +is_crashing_arch=bool((platform.uname()[4].startswith('arm') or platform.uname()[4].startswith('aarch')) and sys.maxsize<2**33) # meant for armhf, though this form will also skip on armel - uname = kernel arch _default_compressor = "blosc" @@ -1088,6 +1092,7 @@ class TestHDFStore: check("table", index) check("fixed", index) + @pytest.mark.xfail(condition=is_crashing_arch,reason="https://bugs.debian.org/790925",strict=False,run=False) @pytest.mark.skipif( not is_platform_little_endian(), reason="reason platform is not little endian" ) @@ -1120,6 +1125,7 @@ class TestHDFStore: ], ) @pytest.mark.parametrize("dtype", ["category", object]) + @pytest.mark.xfail(condition=is_crashing_arch,reason="https://bugs.debian.org/790925",strict=False,run=False) def test_latin_encoding(self, setup_path, dtype, val): enc = "latin-1" nan_rep = "" @@ -1305,6 +1311,7 @@ class TestHDFStore: # still read from it. pd.read_hdf(store, "k1") + @pytest.mark.xfail(condition=is_crashing_arch,reason="https://bugs.debian.org/790925",strict=False,run=False) def test_append_frame_column_oriented(self, setup_path): with ensure_clean_store(setup_path) as store: @@ -3921,6 +3928,7 @@ class TestHDFStore: df.iloc[3:5, 1:3] = np.nan df.iloc[8:10, -2] = np.nan + @pytest.mark.xfail(condition=is_crashing_arch,reason="https://bugs.debian.org/790925",strict=False,run=False) def test_select_filter_corner(self, setup_path): df = DataFrame(np.random.randn(50, 100)) @@ -4177,6 +4185,7 @@ class TestHDFStore: assert isinstance(d1, DataFrame) @td.xfail_non_writeable + @pytest.mark.xfail(condition=not is_platform_little_endian(),reason="known failure of hdf on non-little endian",strict=False,raises=AttributeError) def test_legacy_table_fixed_format_read_py2(self, datapath, setup_path): # GH 24510 # legacy table with fixed format written in Python 2 @@ -4191,6 +4200,7 @@ class TestHDFStore: ) tm.assert_frame_equal(expected, result) + @pytest.mark.xfail(condition=not is_platform_little_endian(),reason="known failure of hdf on non-little endian",strict=False,raises=AttributeError) def test_legacy_table_fixed_format_read_datetime_py2(self, datapath, setup_path): # GH 31750 # legacy table with fixed format and datetime64 column written in Python 2 @@ -4870,6 +4880,7 @@ class TestHDFStore: with pd.HDFStore(path) as store: assert os.fspath(store) == str(path) + @pytest.mark.xfail(condition=not is_platform_little_endian(),reason="known failure of hdf on non-little endian",strict=False,raises=AttributeError) def test_read_py2_hdf_file_in_py3(self, datapath): # GH 16781 --- a/pandas/tests/io/test_stata.py +++ b/pandas/tests/io/test_stata.py @@ -29,6 +29,8 @@ from pandas.io.stata import ( read_stata, ) +from pandas.compat import is_platform_little_endian +pytestmark = pytest.mark.xfail(condition=not is_platform_little_endian(),reason="known failure of test_stata on non-little endian",strict=False) @pytest.fixture() def mixed_frame(): @@ -203,7 +205,7 @@ class TestStata: # parsed_113 = self.read_dta(self.dta2_113) # Remove resource warnings - w = [x for x in w if x.category is UserWarning] + w = [x for x in w if x.category is UserWarning and not "Non-x86 system detected" in str(x.message)] # should get warning for each call to read_dta assert len(w) == 3 @@ -465,7 +467,7 @@ class TestStata: warnings.simplefilter("always", InvalidColumnName) original.to_stata(path, None, version=version) # should get a warning for that format. - assert len(w) == 1 + assert len([x for x in w if not "Non-x86 system detected" in str(x.message)]) == 1 written_and_read_again = self.read_dta(path) tm.assert_frame_equal(written_and_read_again.set_index("index"), formatted) @@ -1788,8 +1790,9 @@ has been incorrectly encoded by Stata or the string values returned are correct.""" with tm.assert_produces_warning(UnicodeWarning) as w: encoded = read_stata(self.dta_encoding_118) - assert len(w) == 151 - assert w[0].message.args[0] == msg + w2 = [x for x in w if not "Non-x86 system detected" in str(x.message)] + assert len(w2) == 151 + assert w2[0].message.args[0] == msg expected = pd.DataFrame([["Düsseldorf"]] * 151, columns=["kreis1849"]) tm.assert_frame_equal(encoded, expected) --- a/pandas/_testing.py +++ b/pandas/_testing.py @@ -6,6 +6,8 @@ from functools import wraps import gzip import operator import os +import platform +import re from shutil import rmtree import string import tempfile @@ -2612,6 +2614,8 @@ def assert_produces_warning( ) assert actual_warning.filename == caller.filename, msg else: + if actual_warning.category==UserWarning and "Non-x86 system detected" in str(actual_warning.message) and not bool(re.match('i.?86|x86',platform.uname()[4])): + continue extra_warnings.append( ( actual_warning.category.__name__, --- a/pandas/tests/io/pytables/test_timezones.py +++ b/pandas/tests/io/pytables/test_timezones.py @@ -4,6 +4,7 @@ import numpy as np import pytest import pandas.util._test_decorators as td +from pandas.compat import is_platform_little_endian import pandas as pd from pandas import DataFrame, DatetimeIndex, Series, Timestamp, date_range @@ -311,6 +312,7 @@ def test_store_timezone(setup_path): tm.assert_frame_equal(result, df) +@pytest.mark.xfail(condition=not is_platform_little_endian(),reason="known failure of hdf on non-little endian",strict=False,raises=AttributeError) def test_legacy_datetimetz_object(datapath, setup_path): # legacy from < 0.17.0 # 8260 @@ -362,6 +364,7 @@ def test_read_with_where_tz_aware_index( tm.assert_frame_equal(result, expected) +@pytest.mark.xfail(condition=not is_platform_little_endian(),reason="known failure of hdf on non-little endian",strict=False,raises=AttributeError) def test_py2_created_with_datetimez(datapath, setup_path): # The test HDF5 file was created in Python 2, but could not be read in # Python 3. --- a/pandas/tests/io/test_common.py +++ b/pandas/tests/io/test_common.py @@ -8,7 +8,7 @@ from pathlib import Path import pytest -from pandas.compat import is_platform_windows +from pandas.compat import is_platform_windows, is_platform_little_endian import pandas.util._test_decorators as td import pandas as pd @@ -230,11 +230,11 @@ bar2,12,13,14,15 "pyarrow", ("io", "data", "feather", "feather-0_3_1.feather"), ), - ( + pytest.param( pd.read_hdf, "tables", ("io", "data", "legacy_hdf", "datetimetz_object.h5"), - ), + marks=pytest.mark.xfail(condition=not is_platform_little_endian(),reason="known failure of hdf on non-little endian",strict=False,raises=AttributeError)), (pd.read_stata, "os", ("io", "data", "stata", "stata10_115.dta")), (pd.read_sas, "os", ("io", "sas", "data", "test1.sas7bdat")), (pd.read_json, "os", ("io", "json", "data", "tsframe_v012.json")),