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holoviz / spatialpandas

Pandas extension arrays for spatial/geometric operations
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Tests failing with `ValueError: Cannot mask with a boolean indexer containing NA values` #41

Closed brl0 closed 4 years ago

brl0 commented 4 years ago

The following tests fail with this error: ValueError: Cannot mask with a boolean indexer containing NA values

TestGeometryGetitem.test_getitem_boolean_na_treated_as_false ``` self = data = [ Point([0.0, 1.0]), Point([1.0, 2.0]), Point([3.0, 4.0]), None, Point([-1.0, -2.0])... Point([1.0, 2.0]), Point([3.0, 4.0]), None, Point([-1.0, -2.0])] Length: 100, dtype: point[float64] def test_getitem_boolean_na_treated_as_false(self, data): # https://github.com/pandas-dev/pandas/issues/31503 mask = pd.array(np.zeros(data.shape, dtype="bool"), dtype="boolean") mask[:2] = pd.NA mask[2:4] = True > result = data[mask] ../../miniconda3/envs/default/lib/python3.7/site-packages/pandas/tests/extension/base/getitem.py:167: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = [ Point([0.0, 1.0]), Point([1.0, 2.0]), Point([3.0, 4.0]), None, Point([-1.0, -2.0])... Point([1.0, 2.0]), Point([3.0, 4.0]), None, Point([-1.0, -2.0])] Length: 100, dtype: point[float64] item = [ , , True, True, False, False, False, False, False, False, False, False, False, False, Fal...alse, False, False, False, False, False, False, False, False, False, False, False, False] Length: 100, dtype: boolean def __getitem__(self, item): err_msg = ("Only integers, slices and integer or boolean" "arrays are valid indices.") if isinstance(item, Integral): item = int(item) if item < -len(self) or item >= len(self): raise IndexError("{item} is out of bounds".format(item=item)) else: # Convert negative item index if item < 0: item += len(self) value = self.data[item].as_py() if value is not None: return self._element_type(value, self.numpy_dtype) else: return None elif isinstance(item, slice): if item.step is None or item.step == 1: # pyarrow only supports slice with step of 1 return self.__class__(self.data[item], dtype=self.dtype) else: selected_indices = np.arange(len(self))[item] return self.take(selected_indices, allow_fill=False) elif isinstance(item, Iterable): if isinstance(item, (np.ndarray, ExtensionArray)): # Leave numpy and pandas arrays alone kind = item.dtype.kind else: item = pd.array(item) kind = item.dtype.kind if len(item) == 0: return self.take([], allow_fill=False) elif kind == 'b': # Check mask length is compatible if len(item) != len(self): raise IndexError( "boolean mask length ({}) doesn't match array length ({})" .format(len(item), len(self)) ) # check for NA values if any(pd.isna(item)): raise ValueError( > "Cannot mask with a boolean indexer containing NA values" ) E ValueError: Cannot mask with a boolean indexer containing NA values spatialpandas/geometry/base.py:385: ValueError ```
TestGeometryGetitem.test_getitem_boolean_na_treated_as_false ``` self = data = [ Line([0.0, 1.0]), Line([1.0, 2.0, 3.0, 4.0]), None, Line([-1.0, ... None, Line([-1.0, -2.0]), Line([])] Length: 100, dtype: line[float64] def test_getitem_boolean_na_treated_as_false(self, data): # https://github.com/pandas-dev/pandas/issues/31503 mask = pd.array(np.zeros(data.shape, dtype="bool"), dtype="boolean") mask[:2] = pd.NA mask[2:4] = True > result = data[mask] ../../miniconda3/envs/default/lib/python3.7/site-packages/pandas/tests/extension/base/getitem.py:167: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = [ Line([0.0, 1.0]), Line([1.0, 2.0, 3.0, 4.0]), None, Line([-1.0, ... None, Line([-1.0, -2.0]), Line([])] Length: 100, dtype: line[float64] item = [ , , True, True, False, False, False, False, False, False, False, False, False, False, Fal...alse, False, False, False, False, False, False, False, False, False, False, False, False] Length: 100, dtype: boolean def __getitem__(self, item): err_msg = ("Only integers, slices and integer or boolean" "arrays are valid indices.") if isinstance(item, Integral): item = int(item) if item < -len(self) or item >= len(self): raise IndexError("{item} is out of bounds".format(item=item)) else: # Convert negative item index if item < 0: item += len(self) value = self.data[item].as_py() if value is not None: return self._element_type(value, self.numpy_dtype) else: return None elif isinstance(item, slice): if item.step is None or item.step == 1: # pyarrow only supports slice with step of 1 return self.__class__(self.data[item], dtype=self.dtype) else: selected_indices = np.arange(len(self))[item] return self.take(selected_indices, allow_fill=False) elif isinstance(item, Iterable): if isinstance(item, (np.ndarray, ExtensionArray)): # Leave numpy and pandas arrays alone kind = item.dtype.kind else: item = pd.array(item) kind = item.dtype.kind if len(item) == 0: return self.take([], allow_fill=False) elif kind == 'b': # Check mask length is compatible if len(item) != len(self): raise IndexError( "boolean mask length ({}) doesn't match array length ({})" .format(len(item), len(self)) ) # check for NA values if any(pd.isna(item)): raise ValueError( > "Cannot mask with a boolean indexer containing NA values" ) E ValueError: Cannot mask with a boolean indexer containing NA values spatialpandas/geometry/base.py:385: ValueError ```
Installed packages ``` # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_llvm conda-forge abseil-cpp 20200225.2 he1b5a44_0 conda-forge adal 1.2.4 pyh9f0ad1d_0 conda-forge aiohttp 3.6.2 py37h516909a_0 conda-forge alabaster 0.7.12 py_0 conda-forge alembic 1.4.2 pyh9f0ad1d_0 conda-forge appdirs 1.4.3 py_1 conda-forge arrow-cpp 0.17.1 py37h1234567_10_cpu conda-forge asn1crypto 1.3.0 py37hc8dfbb8_1 conda-forge astroid 2.3.3 pypi_0 pypi async-timeout 3.0.1 py_1000 conda-forge async_generator 1.10 py_0 conda-forge attrs 19.3.0 py_0 conda-forge aws-logging-handlers 2.0.3 pypi_0 pypi aws-sdk-cpp 1.7.164 hc831370_1 conda-forge awscli 1.18.94 py37hc8dfbb8_0 conda-forge babel 2.8.0 py_0 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge bandit 1.6.2 py37_0 conda-forge beautifulsoup4 4.9.1 py37hc8dfbb8_0 conda-forge black 19.10b0 py37_0 conda-forge bleach 3.1.5 pyh9f0ad1d_0 conda-forge blessed 1.17.5 pypi_0 pypi blinker 1.4 py_1 conda-forge blosc 1.19.0 he1b5a44_0 conda-forge bokeh 1.4.0 py_0 bokeh boost-cpp 1.72.0 h8e57a91_0 conda-forge boto 2.49.0 py_0 conda-forge boto3 1.14.17 pyh9f0ad1d_0 conda-forge botocore 1.17.17 pyh9f0ad1d_0 conda-forge bottleneck 1.3.2 py37h03ebfcd_1 conda-forge brotli 1.0.7 he1b5a44_1002 conda-forge brotlipy 0.7.0 py37h8f50634_1000 conda-forge bzip2 1.0.8 h516909a_2 conda-forge c-ares 1.15.0 h516909a_1001 conda-forge ca-certificates 2020.6.20 hecda079_0 conda-forge cachetools 4.1.1 py_0 conda-forge cairo 1.16.0 hcf35c78_1003 conda-forge cartopy 0.17.0 py37hd759880_1006 conda-forge certifi 2020.6.20 py37hc8dfbb8_0 conda-forge certipy 0.1.3 py_0 conda-forge cffi 1.14.0 py37hd463f26_0 conda-forge cfgv 3.1.0 py_0 conda-forge cfitsio 3.470 hb60a0a2_2 conda-forge cftime 1.2.0 py37h03ebfcd_1 conda-forge chardet 3.0.4 py37hc8dfbb8_1006 conda-forge click 7.1.2 pyh9f0ad1d_0 conda-forge click-plugins 1.1.1 py_0 conda-forge cligj 0.5.0 py_0 conda-forge cloudpickle 1.4.1 py_0 conda-forge colorama 0.4.3 py_0 conda-forge colorcet 2.0.2 py_0 pyviz/label/dev conda-lock 0.2.2 pypi_0 pypi configurable-http-proxy 4.2.1 node13_he01fd0c_0 conda-forge coverage 5.2 py37h8f50634_0 conda-forge croniter 0.3.30 py_0 conda-forge cryptography 2.9.2 py37hb09aad4_0 conda-forge cssselect 1.1.0 py_0 conda-forge curl 7.68.0 hf8cf82a_0 conda-forge cycler 0.10.0 py_2 conda-forge cython 0.29.20 py37h3340039_0 conda-forge cytoolz 0.10.1 py37h516909a_0 conda-forge dask 2.20.0 py_0 conda-forge dask-core 2.20.0 py_0 conda-forge dask-glm 0.2.0 py_1 conda-forge dask-kubernetes 0.10.1 py_0 conda-forge dask-labextension 2.0.1 pypi_0 pypi dask-ml 1.5.0 py_0 conda-forge datashader 0.11.0 py_0 pyviz/label/dev datashape 0.5.4 py_1 conda-forge dbus 1.13.6 he372182_0 conda-forge decorator 4.4.2 py_0 conda-forge defusedxml 0.6.0 py_0 conda-forge descartes 1.1.0 py_4 conda-forge dill 0.3.2 pyh9f0ad1d_0 conda-forge distlib 0.3.1 pyh9f0ad1d_0 conda-forge distributed 2.20.0 py37hc8dfbb8_0 conda-forge docker-py 4.2.2 py37hc8dfbb8_0 conda-forge 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hb6868eb_1001 conda-forge geoviews 1.7.0 py_0 pyviz/label/dev geoviews-core 1.7.0 py_0 pyviz/label/dev gettext 0.19.8.1 hc5be6a0_1002 conda-forge gflags 2.2.2 he1b5a44_1002 conda-forge giflib 5.1.7 h516909a_1 conda-forge gitdb 4.0.5 py_0 conda-forge gitpython 3.1.3 py_0 conda-forge glib 2.65.0 h6f030ca_0 conda-forge glog 0.4.0 h49b9bf7_3 conda-forge google-auth 1.17.2 py_0 conda-forge googlemaps 2.5.1 py_0 conda-forge graphite2 1.3.13 he1b5a44_1001 conda-forge graphviz 2.42.3 h0511662_0 conda-forge grpc-cpp 1.30.0 h9ea6770_0 conda-forge gst-plugins-base 1.14.5 h0935bb2_2 conda-forge gstreamer 1.14.5 h36ae1b5_2 conda-forge h5py 2.10.0 nompi_py37h513d04c_102 conda-forge harfbuzz 2.4.0 h9f30f68_3 conda-forge haversine 2.2.0 py_0 conda-forge hdf4 4.2.13 hf30be14_1003 conda-forge hdf5 1.10.5 nompi_h3c11f04_1104 conda-forge heapdict 1.0.1 py_0 conda-forge holoviews 1.13.3 py_0 pyviz/label/dev html5lib 1.1 pyh9f0ad1d_0 conda-forge hvplot 0.6.0 py_0 pyviz/label/dev hypothesis 5.19.0 py_0 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xorg-libsm 1.2.3 h84519dc_1000 conda-forge xorg-libx11 1.6.9 h516909a_0 conda-forge xorg-libxau 1.0.9 h14c3975_0 conda-forge xorg-libxdmcp 1.1.3 h516909a_0 conda-forge xorg-libxext 1.3.4 h516909a_0 conda-forge xorg-libxpm 3.5.13 h516909a_0 conda-forge xorg-libxrender 0.9.10 h516909a_1002 conda-forge xorg-libxt 1.1.5 h516909a_1003 conda-forge xorg-renderproto 0.11.1 h14c3975_1002 conda-forge xorg-xextproto 7.3.0 h14c3975_1002 conda-forge xorg-xproto 7.0.31 h14c3975_1007 conda-forge xz 5.2.5 h516909a_0 conda-forge yaml 0.1.7 h14c3975_1001 conda-forge yapf 0.29.0 py_0 conda-forge yarl 1.3.0 py37h516909a_1000 conda-forge zeromq 4.3.2 he1b5a44_2 conda-forge zict 2.0.0 py_0 conda-forge zipp 3.1.0 py_0 conda-forge zlib 1.2.11 h516909a_1006 conda-forge zstandard 0.14.0 py37h3340039_0 conda-forge zstd 1.4.4 h6597ccf_3 conda-forge ```
brl0 commented 4 years ago

Fixed in #37.