Mark slow tests, update __eq__ methods, pin reqs

.github/workflows/test.yml

@@ -25,7 +25,7 @@ jobs:
     timeout-minutes: 40
     defaults:
       run:
-        shell: bash -l {0} 
+        shell: bash -l {0}
     env:
       PYTHON_VERSION: ${{ matrix.python-version }}
       CHANS_DEV: "-c pyviz/label/dev"
@@ -64,7 +64,7 @@ jobs:
           conda activate test-environment
           conda list
           doit develop_install ${{ env.CHANS_DEV }} -o tests
-          pip install hilbertcurve 
+          pip install hilbertcurve
       - name: doit env_capture
         run: |
           eval "$(conda shell.bash hook)"

.gitignore

@@ -106,3 +106,9 @@ venv.bak/
 *.parq
 .idea/
 spatialpandas/.version
+
+.vscode/
+
+monkeytype.sqlite3
+
+.doit.db

.isort.cfg

@@ -0,0 +1,7 @@
+[settings]
+multi_line_output=3
+include_trailing_comma=True
+force_grid_wrap=0
+use_parentheses=True
+known_local_folder=spatialpandas
+known_first_party=spatialpandas

CHANGELOG.md

@@ -1,3 +1,25 @@
+Version 0.4.0
+=============
+
+### Added
+ - Add HoloViz build infrastructure. ([#50](https://github.com/holoviz/spatialpandas/pull/50))
+ - Add `--skip-slow` and `--run-slow` options, slow tests are still run by default. ([#60](https://github.com/holoviz/spatialpandas/pull/60))
+ - Add some type hints to parquet functions. ([#60](https://github.com/holoviz/spatialpandas/pull/60))
+
+### Fixed
+ - Fix compatibility with latest pandas. ([#55](https://github.com/holoviz/spatialpandas/pull/55))
+ - Fix certain tests fail due to hypothesis health check. ([#60](https://github.com/holoviz/spatialpandas/pull/60))
+ - Pin numpy and dask on MacOS to pass tests. ([#60](https://github.com/holoviz/spatialpandas/pull/60))
+
+
+### Updated
+ - Allow using cx indexer without spatial index. ([#54](https://github.com/holoviz/spatialpandas/pull/54))
+ - Switch to GitHub Actions. ([#55](https://github.com/holoviz/spatialpandas/pull/55))
+ - Updated Geometry class __eq__ method so that if other object is a container, the equality method on the container is called, so now performing an equality check between a geometry object and a geometry array should return correct results, which should be a bool array, whereas previously it would simply return False because the objects were not the same immediate type. ([#60](https://github.com/holoviz/spatialpandas/pull/60))
+ - Update GeometryArray class __eq__ method to allow comparison of an individual element to all objects in the array, returning an array of bool. ([#60](https://github.com/holoviz/spatialpandas/pull/60))
+ - Add NotImplementedError for __contains__ method. ([#60](https://github.com/holoviz/spatialpandas/pull/60))
+
+
 Version 0.3.6
 =============
 

conftest.py

@@ -0,0 +1,33 @@
+"""Configuration for pytest."""
+import pytest
+
+
+_DEFAULT_SKIPSLOW = False
+
+
+def pytest_addoption(parser):
+    """Add command-line flags for pytest."""
+    parser.addoption(
+        "--skip-slow",
+        action="store_true",
+        help="skips slow tests",
+        default=_DEFAULT_SKIPSLOW,
+    )
+    parser.addoption(
+        "--run-slow",
+        action="store_true",
+        default=False,  # Only used for cli override
+        help="run slow tests",
+    )
+
+
+def pytest_configure(config):
+    config.addinivalue_line("markers", "slow: mark test as slow to run")
+
+
+def pytest_collection_modifyitems(config, items):
+    if not config.getoption("--run-slow") and config.getoption("--skip-slow"):
+        skip_slow = pytest.mark.skip(reason="Skipping slow tests")
+        for item in items:
+            if "slow" in item.keywords:
+                item.add_marker(skip_slow)

setup.py

@@ -1,41 +1,58 @@
-from setuptools import setup, find_packages
+import sys
+
 import param
+from setuptools import find_packages, setup
 
 extras_require = {
     'tests': [
-        'pytest',
         'codecov',
-        'pytest-cov',
         'flake8',
+        'geopandas',
         'hypothesis',
+        'pytest-cov',
+        'pytest',
         'scipy',
         'shapely',
-        'geopandas',
     ],
     'examples': [
-        'geopandas',
-        'matplotlib',
-        'descartes',
         'datashader',
+        'descartes',
+        'geopandas',
         'holoviews',
+        'matplotlib',
     ]
 }
 
 install_requires = [
-    'pandas>=0.25',
-    'dask[complete] >=2.0',
+    'fsspec',
     'numba',
-    'numpy',
-    'pyarrow>=0.15',
+    'pandas>=0.25',
     'param',
-    'fsspec',
+    'pyarrow>=0.15',
     'retrying',
+    'snappy',
 ]
 
+# Checking for platform explicitly because
+# pyctdev does not handle dependency conditions
+# such as 'numpy<1.20;platform_system=="Darwin"'
+if sys.platform == 'darwin':
+    install_requires.extend([
+        'dask[complete]>=2.0,<2020.12',
+        'numpy<1.20',
+    ])
+else:
+    install_requires.extend([
+        'dask[complete]>=2.0',
+        'numpy',
+    ])
+
 setup_args = dict(
     name='spatialpandas',
     version=param.version.get_setup_version(
-        __file__, "spatialpandas", archive_commit="$Format:%h$"
+        __file__,
+        "spatialpandas",
+        archive_commit="$Format:%h$",
     ),
     description='Pandas extension arrays for spatial/geometric operations',
     long_description=open("README.md").read(),
@@ -49,9 +66,8 @@
     tests_require=extras_require['tests'],
     license='BSD-2-Clause',
     packages=find_packages(exclude=('tests', 'tests.*')),
-    include_package_data=True
+    include_package_data=True,
 )
 
 if __name__ == '__main__':
     setup(**setup_args)
-

spatialpandas/__init__.py

@@ -1,17 +1,21 @@
-from . import geometry, spatialindex, tools # noqa
-from .geoseries import GeoSeries # noqa
-from .geodataframe import GeoDataFrame # noqa
-from .tools.sjoin import sjoin # noqa
 import param as _param
 
+from . import geometry, spatialindex, tools  # noqa
+from .geodataframe import GeoDataFrame  # noqa
+from .geoseries import GeoSeries  # noqa
+from .tools.sjoin import sjoin  # noqa
+
 try:
-    import dask.dataframe # noqa
+    import dask.dataframe  # noqa
     # Import to trigger registration of types with Dask
-    import spatialpandas.dask # noqa
+    import spatialpandas.dask  # noqa
 except ImportError:
     # Dask dataframe not available
     pass
 
-__version__ = str(_param.version.Version(
-    fpath=__file__, archive_commit="$Format:%h$", reponame="spatialpandas")
-)
+__version__ = str(
+    _param.version.Version(
+        fpath=__file__,
+        archive_commit="$Format:%h$",
+        reponame="spatialpandas",
+    ))

spatialpandas/dask.py

@@ -1,24 +1,26 @@
+import copy
+import json
+import os
+import uuid
+from inspect import signature
+
+import numpy as np
+import pandas as pd
+import pyarrow as pa
+import pyarrow.parquet as pq
+from retrying import retry
+
+import dask
 import dask.dataframe as dd
 from dask import delayed
+from dask.dataframe.core import get_parallel_type
 from dask.dataframe.partitionquantiles import partition_quantiles
+from dask.dataframe.utils import make_array_nonempty, make_meta, meta_nonempty
 
-from spatialpandas.geometry.base import _BaseCoordinateIndexer, GeometryDtype
-from spatialpandas.spatialindex import HilbertRtree
-from .geoseries import GeoSeries
 from .geodataframe import GeoDataFrame
-import dask
-from dask.dataframe.core import get_parallel_type
-from dask.dataframe.utils import make_meta, meta_nonempty, make_array_nonempty
-import pandas as pd
-import numpy as np
-import pyarrow.parquet as pq
-import pyarrow as pa
-import os
-import uuid
-import json
-import copy
-from inspect import signature
-from retrying import retry
+from .geometry.base import GeometryDtype, _BaseCoordinateIndexer
+from .geoseries import GeoSeries
+from .spatialindex import HilbertRtree
 
 
 class DaskGeoSeries(dd.Series):

spatialpandas/geodataframe.py

@@ -1,7 +1,8 @@
 import pandas as pd
+
+from ._optional_imports import gp
 from .geometry import GeometryDtype
 from .geoseries import GeoSeries, _MaybeGeoSeries
-from ._optional_imports import gp
 
 
 class _MaybeGeoDataFrame(pd.DataFrame):

spatialpandas/geometry/__init__.py

@@ -1,4 +1,4 @@
-from .polygon import Polygon, PolygonArray, PolygonDtype  # noqa 
+from .polygon import Polygon, PolygonArray, PolygonDtype  # noqa
 from .multipolygon import ( # noqa
     MultiPolygon, MultiPolygonArray, MultiPolygonDtype
 )

spatialpandas/geometry/_algorithms/bounds.py

@@ -1,6 +1,6 @@
 import numpy as np
 
-from spatialpandas.utils import ngjit
+from ...utils import ngjit
 
 
 @ngjit

spatialpandas/geometry/_algorithms/intersection.py

@@ -1,10 +1,10 @@
 import numpy as np
-
-from spatialpandas.geometry._algorithms.bounds import total_bounds_interleaved
-from spatialpandas.geometry._algorithms.orientation import triangle_orientation
-from spatialpandas.utils import ngjit, ngpjit
 from numba import prange
 
+from ...geometry._algorithms.bounds import total_bounds_interleaved
+from ...geometry._algorithms.orientation import triangle_orientation
+from ...utils import ngjit, ngpjit
+
 
 @ngjit
 def segment_intersects_point(ax0, ay0, ax1, ay1, bx, by):

spatialpandas/geometry/_algorithms/measures.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 
-from spatialpandas.utils import ngjit
+from ...utils import ngjit
 
 
 @ngjit

spatialpandas/geometry/_algorithms/orientation.py

@@ -1,7 +1,8 @@
-from spatialpandas.geometry._algorithms.measures import compute_area
-from spatialpandas.utils import ngjit
 import numpy as np
 
+from ...geometry._algorithms.measures import compute_area
+from ...utils import ngjit
+
 
 @ngjit
 def triangle_orientation(ax, ay, bx, by, cx, cy):

spatialpandas/geometry/base.py

@@ -1,18 +1,17 @@
+import re
+from collections.abc import Container, Iterable
 from numbers import Integral
-from collections.abc import Iterable
 
 import numpy as np
 import pandas as pd
 import pyarrow as pa
 from pandas.api.extensions import ExtensionArray, ExtensionDtype
 from pandas.api.types import is_array_like
 
-from spatialpandas.spatialindex import HilbertRtree
-from spatialpandas.spatialindex.rtree import _distances_from_bounds
-import re
-
-from spatialpandas.utils import ngjit
-from .._optional_imports import sg, gp
+from .._optional_imports import gp, sg
+from ..spatialindex import HilbertRtree
+from ..spatialindex.rtree import _distances_from_bounds
+from ..utils import ngjit
 
 
 def _unwrap_geometry(a, element_dtype):
@@ -144,6 +143,8 @@ def __hash__(self):
         return hash((self.__class__, np.array(self.data.as_py()).tobytes()))
 
     def __eq__(self, other):
+        if isinstance(other, Container):
+            return other == self
         if type(other) is not type(self):
             return False
         return self.data == other.data
@@ -336,11 +337,18 @@ def __eq__(self, other):
             for i in range(len(self)):
                 result[i] = self[i] == other[i]
             return result
-        else:
-            raise ValueError("""
+        if isinstance(other, (self.dtype.type, type(None))):
+            result = np.zeros(len(self), dtype=np.bool_)
+            for i in range(len(self)):
+                result[i] = self[i] == other
+            return result
+        raise ValueError("""
 Cannot check equality of {typ} of length {a_len} with:
     {other}""".format(typ=type(self).__name__, a_len=len(self), other=repr(other)))
 
+    def __contains__(self, item) -> bool:
+        raise NotImplementedError
+
     def __len__(self):
         return len(self.data)
 
@@ -499,8 +507,8 @@ def _concat_same_type(cls, to_concat):
 
     def fillna(self, value=None, method=None, limit=None):
         from pandas.api.types import is_array_like
-        from pandas.util._validators import validate_fillna_kwargs
         from pandas.core.missing import get_fill_func
+        from pandas.util._validators import validate_fillna_kwargs
 
         value, method = validate_fillna_kwargs(value, method)
 
@@ -766,10 +774,8 @@ def is_geometry_array(data):
 
 
 def to_geometry_array(data, dtype=None):
-    from . import (
-        PointArray, MultiPointArray,  LineArray, RingArray,
-        MultiLineArray, PolygonArray, MultiPolygonArray
-    )
+    from . import (LineArray, MultiLineArray, MultiPointArray,
+                   MultiPolygonArray, PointArray, PolygonArray, RingArray)
     if sg is not None:
         shapely_to_spatialpandas = {
             sg.Point: PointArray,