ENH: include predicates in STRtree.query() by brendan-ward · Pull Request #87 · pygeos/pygeos

brendan-ward · 2020-01-13T04:32:31Z

This PR adds support for several geometric predicates into the STRtree query() function. In addition to querying geometries from the tree that have envelopes that intersect the envelope of the input geometry, this now allows you to test the predicate relationships between the input geometry and the returned geometries from the tree:

intersects
within
contains
overlaps
crosses
touches

This intentionally does not include other binary predicates, since they don't seem useful in this context (e.g., disjoint).

This should make it easier to implement spatial joins on top of pygeos.

This could be further improved by using prepared geometries and vectorizing the query function, but those should be handled in a separate PR.

Most of the code here is in tests, to verify that the predicates are being evaluated correctly. These could be improved further by adding more combinations of geometry types.

In order to preserve the existing behavior where querying the tree with a geometry of None returns an empty array, I specifically handle that in the wrapper function since there is no need to step into C code for that.

jorisvandenbossche · 2020-01-13T09:41:35Z

@brendan-ward thanks a lot for looking at this!

First gut reaction: is there a performance difference compared to doing this filtering in python using pygeos?

geoms = ...
geometry = ...
tree = pygeos.STRtree(geoms)
indices = tree.query(geometry)
subset = pygeos.intersects(geoms[indices], geometry)

This PR avoids creating the full indices array (before further filtering) and the subsetting of the geoms numpy array in python. But I am wondering if this is significant performance wise to do it in C (as it adds complexity)

brendan-ward · 2020-01-13T19:41:46Z

@jorisvandenbossche

Right now, the performance (based on a few contrived tests) between either approach is nearly equivalent. I was a little surprised, I was expecting a bit better performance by doing more of this in C. There might be something I'm doing in C that is slowing it down.

I think the bigger benefits may be building off this to use prepared geometries after querying the tree and before testing the predicate functions. I think it would be possible to first query the tree, then for any geometry that had > N (arbitrary threshold) of results from the tree, to create a prepared geometry and then use that for the predicate function. My hope there was that the use of prepared geometries in that case was handled automatically (from the user's perspective), rather than something they needed to do before using the ufunc predicates.

But until I can get a working version of prepared geometries (needs more digging) as a ufunc, it's hard to compare the two approaches.

I was also hoping this would make it easier to implement #52, though the bigger issue here is how to effectively vectorize querying the tree and testing the predicate.

brendan-ward · 2020-01-14T04:41:42Z

Using prepared geometries in the query with predicates is ~ 550x faster than without prepared geometries, for my contrived test case (polygon against 280,000 line segments, ~1,500 of which overlap the envelope of the polygon and ~500 intersect the polygon).

Comparison to ufunc predicate using prepared geometries depends on more work in #84.

Adding prepared geometries to this PR proved to be pretty easy.

caspervdw · 2020-01-14T09:16:45Z

This is great, I really like your tests also @brendan-ward thanks for being so thorough.

I am 👍 on merging and leaving the prepared geometry stuff for a later PR

brendan-ward · 2020-01-14T21:09:39Z

Thanks @caspervdw

Don't merge yet - I've got prepared geometries in place and now just trying to cleanup a few compiler warnings about pointer types...

It might be good to hold off on merging this until after I can get a first pass of #84 working so we can compare. I fully take @jorisvandenbossche 's point about added complexity vs performance tradeoffs. (it's easy to add complexity, it's harder to take it away later... though you aren't yet up against API compatibility promises)

Resolved compiler warnings where possible

brendan-ward · 2020-01-31T22:24:35Z

@jorisvandenbossche thanks to your POC for prepared geometries, I was able to do a little testing between predicate + prepared geometries within query() in this PR vs query() as it exists currently followed by intersects_prepared. For the latter, I prepared the geometries before creating the tree.

I might have been doing something wrong, but for a crude spatial join that produces ~149k intersections with the target geometries, I was seeing:

this PR: 2.2 - 2.37s
regular query() followed by intersects_prepared: 2.5 - 3s

It seems like the bit of extra complexity in C is reasonable given the performance (in this limited test) suggests it is a little better. And using the prepared geometries here gives us a huge performance win.

jorisvandenbossche · 2020-02-07T15:09:29Z

pygeos/strtree.py

+            querying the tree.
+        predicate : str, optional (default: None)
+            The predicate to use for testing geometries from the tree
+            that are within the input geometry's envelope.


I think we should clarify here in which order the predicate is evaluated (predicate(passed_geometry, tree_geometry) vs predicate(tree_geometry, passed_geometry))

(it's not directly self-evident which of the two it would be I think)

I tried to clarify this, and also added an example to the docstring.

jorisvandenbossche · 2020-02-07T15:10:21Z

pygeos/strtree.py

-        return self._tree.query(envelope)
+
+        if geometry is None:
+            return np.array([], dtype="int")


This is no longer handled on the C level?

And if done here, you can use dtype=np.intp for consistency in the dtype

I had assumed (but not sure I tested) that passing None would be problematic for parsing the function arguments via PyArg_ParseTuple(args, "O!i", &GeometryType, &geometry, &predicate)

According to the docs for O!, a TypeError would be raised if we pass in something of NoneType instead of GeometryType, and failing out here returns NULL instead of an empty array.

I'm not that familiar with PyArg_ParseTuple, so if there is a better way we can handle None we could deal with at the C level.

Can certainly change the dtype though.

Confirmed, passing None to the C function as it is now raises
TypeError: argument 1 must be pygeos.lib.GEOSGeometry, not None

jorisvandenbossche · 2020-02-07T15:11:27Z

pygeos/strtree.py

 __all__ = ["STRtree"]


+class UnaryPredicate(IntEnum):


BinaryPredicate instead of UnaryPredicate?

jorisvandenbossche · 2020-02-07T15:23:41Z

src/strtree.c

+    // iterate from last value to first to get back original order
+    for (i = size - 1; i >= 0; i--) {
+        ptr = PyArray_GETPTR1(result, i);
+        *ptr = (npy_intp)kv_a(npy_intp, *arr, i);


Is there a reason you use kv_a here instead of kv_pop? (I assume the use of kv_pop was also the reason to iterate backwards; I don't know if there was a performance reason to use kv_pop over kv_a)

I did not test the performance of either variant. I had assumed there might be allocations involved in kv_pop as you remove items from the vector, but looking more closely at the implementation I don't believe that happens. I just wanted to access an element, not remove it from the vector.

I use kv_A below instead of kv_a, so I wasn't very consistent either.

Looping backwards was probably a holdover from using kv_pop.

I'll standardize to kv_pop - the implementation is much simpler so it theoretically should be marginally faster.

Changed my mind, went with kv_A in both cases. It's function signature looks low complexity, so it should be as fast as kv_pop, and allows us to iterate forward in arrays.

jorisvandenbossche · 2020-02-07T15:37:28Z

@brendan-ward thanks for the timings! And after thinking more about this, apart from a small speed-up, I think this also gives a nice usability improvement, of not needing to do the actual predicate check manually in a follow-up step. So certainly +1 on this PR.

I added some minor comments / questions.

In principle, this doesn't need to be blocked by the prepared geoms PR #92 I think? Once that lands, we can update this to reuse cached prepared geometries if they exist.
But thinking on that topic, what would you ideally need from #92? Something like a get_geom_prepared that gets the cached prepared pointer or if that doesn't exist yet prepares the geometry, caches it, and returns that?
In psuedo code, I mean (+handling of None):

char get_geom_prepared(GeometryObject *obj, GEOSPreparedGeometry **out) {
    if obj->prepared_ptr != NULL:
        *out = obj->prepared_ptr
    else:
        obj->prepared_ptr = GEOSPrepare(handle, obj->ptr)
        *out = obj->prepared_ptr
}

and with that you don't need to prepare geometries and destroy the prepared geometries inside the STRtree query ?

brendan-ward · 2020-02-08T02:36:57Z

@jorisvandenbossche thanks for the review!

I think I have addressed everything from your comments. I updated the documentation settings for STRtree so that it outputs what we want.

It looks like there is potentially a difference in behavior for MultiPoint intersections between GEOS 3.5 and 3.6+, since that is what is failing on Travis-CI.

brendan-ward · 2020-02-08T03:02:53Z

If I follow this issue, this was an issue with prepared MultiPoints resolved in GEOS 3.6.

Not isolated to this PR, it got detected here only because we're using prepared geometries.

I marked them as xfail here, but once a minimum supported version of GEOS is set, those can be removed.

jorisvandenbossche

Thanks for the updates! (and for the great PR!)

jorisvandenbossche · 2020-02-19T09:38:40Z

I only noticed now when building locally, but this introduces a build warning:

src/strtree.c: In function ‘STRtree_query’:
/home/joris/miniconda3/envs/geo-dev/lib/python3.8/site-packages/numpy/core/include/numpy/__multiarray_api.h:840:10: warning: return from incompatible pointer type [-Wincompatible-pointer-types]
         (*(PyObject * (*)(PyTypeObject *, int, npy_intp const *, int, npy_intp const *, void *, int, int, PyObject *)) \
/home/joris/miniconda3/envs/geo-dev/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:130:9: note: in expansion of macro ‘PyArray_New’
         PyArray_New(&PyArray_Type, nd, dims, typenum, NULL, NULL, 0, 0, NULL)
         ^~~~~~~~~~~
src/strtree.c:157:16: note: in expansion of macro ‘PyArray_SimpleNew’
         return PyArray_SimpleNew(1, dims, NPY_INTP);
                ^~~~~~~~~~~~~~~~~

Something to look into at some point.

brendan-ward · 2020-02-19T16:50:49Z

src/strtree.c

+    npy_intp *ptr;
+
+    npy_intp dims[1] = {size};
+    // the following raises a compiler warning based on how the macro is defined


@jorisvandenbossche I flagged the same compiler error you found. I did a bit of digging into it, and couldn't resolve; it appears to come from numpy this way.

see this and this

I believe the compiler warning was there originally?

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init_geom_type signature + remove unreachable code in GeometryObject_new Add LICENSE BLD: use angle bracket include for numpy Update README to include conda-forge installation instructions Refactor ufuncs module into lib module (pygeos/pygeos#48) ENH: add wkt / wkb ufuncs (pygeos/pygeos#45) ENH: add equals_exact predicate (pygeos/pygeos#57) Ensure to only use GEOS reentrant API (pygeos/pygeos#63) RLS: 0.5 Small updates to the README (pygeos/pygeos#68) RLS: 0.6 RLS: 0.7 ENH: add normalize (pygeos/pygeos#123) Fix spacing in README (pygeos/pygeos#173) Rename get_coordinate_dimension (dimensions -> dimension) (pygeos/pygeos#176) ENH: ability to get z-coordinates in get_coordinates (pygeos/pygeos#178) Release the GIL for STRtree bulk_query (pygeos/pygeos#174) ENH: Add get_z ufunc (pygeos/pygeos#175) ENH: Add subclass registry (enable subclassing pygeos.Geometry) (pygeos/pygeos#182) ENH: add relate() function (pygeos/pygeos#186) Delay shapely import (pygeos/pygeos#193) BLD: allow GEOS_CONFIG env variable to override PATH (pygeos/pygeos#200) BUG: Fix error handling for line_locate_point (GEOSProject(Normalized)) (pygeos/pygeos#216) ENH: add minimum_clearance (pygeos/pygeos#223) TST: Fix make_valid tests for OverlayNG (normalize result/expected) (pygeos/pygeos#232) ENH: offset_curve (pygeos/pygeos#229) ENH: support z-coordinates in apply (coordinate transformation) (pygeos/pygeos#221) CI: move Travis linux builds to Github Actions (pygeos/pygeos#240) ENH: prepared geometry as additional (cached) attribute on GeometryObject (pygeos/pygeos#92) CLN: deduplicate some code with macros in geometry-creating ufuncs (pygeos/pygeos#230) ENH: relate_pattern (pygeos/pygeos#245) ENH: clip_by_rect (pygeos/pygeos#273) Update for compatibility with numpy 1.20 (builtin type aliases, array coercion) (pygeos/pygeos#269) TST: fix from_shapely test for numpy 1.20 (pygeos/pygeos#278) CI: add GEOS 3.9.0 build to linux CI (pygeos/pygeos#279) DOC: fix style issue with numpydoc parameter names and sphinx_rtd_theme (pygeos/pygeos#283) Update ASV configuration (pygeos/pygeos#285) ENH: add contains_properly predicate function (pygeos/pygeos#267) Change default STRtree leaf size (node capacity) to 10 (pygeos/pygeos#286) Update pin for numpy version for Python 3.9 in pyproject.toml (pygeos/pygeos#295) ENH: add polygonize ufunc (pygeos/pygeos#275) Add back pygeos.strtree.VALID_PREDICATES for now (pygeos/pygeos#309) ENH: add polygonize_full (pygeos/pygeos#298) Add pre-commit configuration (pygeos/pygeos#330) DOC: clarify that set_coordinates modifies array of geometries in place (pygeos/pygeos#335) Explode polygons into rings: get_rings (pygeos/pygeos#342) Fix use of C logical operator (pygeos/pygeos#348) ENH: Add shortest_line (nearest_points) ufunc (pygeos/pygeos#334) Fix multi-threaded STRtree query by ensuring it is built on creation (pygeos/pygeos#362) BUG: fix no inplace output check for box and set_precision (pygeos/pygeos#367) RLS: update changelog for bug-fix release (pygeos/pygeos#369) Release workflow: automate sdist creation / GitHub release (pygeos/pygeos#370) Fix tag selector for release workflow RLS: 0.10.1 CI: Fix failing Windows github actions (pygeos/pygeos#406) [2.0] Remove mutability of geometries (#960) [2.0] Remove deprecated asShape / adapter classes (#961) [2.0] Remove public ctypes and array interface (#977) [2.0] Remove iteration / getitem from multi-part geometries (#982) Refactor Geometry classes to subclass the C extension type (#983) Refactor affine_transform: use general function apply on coordinates (#1019) Clean-up use of impl/lgeos/delegated/exceptNull in shapely/geometry/ (#1020) Remove cython code: remove the speedups module + refactor the vectorized module (#1036) Refactor shapely.prepared to use prepared base geometries (#1039) Clean-up impl: remove impl.py + all helper classes (#1052) Remove usage of lgeos in shapely.validation (#1067) [2.0] Remove len() (__len__) for multi-part geometries (#1114) Refactor shapely.ops to not use lgeos (#1065) Refactor pickling of LinearRing to not use lgeos (#1162) [2.0] Disallow setting custom attributes on geometry objects (#1181) Refactor strtree to not use lgeos / ctypes (#1161) [2.0] Remove shapely.geos.lgeos ctypes interface to GEOS (#1163) TST: fix tests on Windows for python >= 3.8 (#1213) Update GEOS url (pygeos/pygeos#435) Clean-up old/unused files and scripts (#1219) PERF: Use GEOSCoordSeq_copyFromBuffer for creating simple geometries (pygeos/pygeos#436) Migration to Shapely: rename conflicting files Move pygeos/* files into shapely/ python package Rename pygeos -> shapely in the python package Minimal changes (setup.py, rename geometry.py(x)) for working package Remove PyGEOS/Shapely conversion layer (from/to_shapely functions) (#1238) Minimal pygeos->shapely renaming in C code to get cython API working (#1240) TST: fix search/replace mistake in test_empty (#1244) BUG: fixup the hashability of geometries (#1239) Remove now unused shapely._buildcfg module (#1222) CI: consolidate the build scripts and github actions tests workflow (#1241) Replace Toblerity/Shapely -> shapely/shapely (#1255) Linting: blacken shapely code (#1242) TST: Move + clean-up tests for the scalar geometry subclasses (#1257) Update .gitignore for Shapely->shapely repo rename Linting: update pre-commit and setup.cfg configuration + pass black / flake8 / isort (#1265) CLN: remove deprecation warning for setattr (which now raises) (#1266) BUG: Polygon constructor with multiple variable-sized holes (#1229) Fix doctests to be more robust with different versions of GEOS (#1228) TST: test that Geometry subclasses properly return NotImplemented in comparison with non-geometry (#1282) BUG: fix Polygon() constructor from a LineString (#1277) BUG: fix linestring/linearring creation (copyFromBuffer usage) to check for dimension (#1274) TST: Move + clean-up more geometry-class specific tests (#1275) TST: remove filterwarnings for numpy 1.21 (#1304) Pickling: fix SRID handling + update linearring test (#1245) PERF: speed-up bounds function with GEOSGeom_getXMin et al (GEOS >= 3.7.0) (#1299) CLN: remove no longer used custom error classes (#1306) REF: Move ShapelyError base class to C, GEOSException becomes subclass (#1314) Consolidate error class for unsupported GEOS version functionality (#1305) Remove logging related tests (#1308) Expose the geometry subclasses in the top-level namespace (#1339) Deprecate calling the BaseGeometry constructor + EmptyGeometry class (#1303) CI: update black to fix click compat issue (#1355) TST: update tests to pass with numpy 1.22 and pytest 8 (#1356) Remove deprecation warning from GeometryTypeError (#1358) API: update STRtree interface (merge shapely/pygeos features) (#1251) TST: fix tests for GEOS main (#1357) Update repr for the Geometry classes (#1302) CI: only build Travis on the main branch (not PRs) (#1382) CI: fix Travis tests (#1384) DOC: Move pygeos doc pages into shapely docs (#1377) DEPR: deprecate the GeometryType attribute (#1375) CI: fix tests with latest setuptools (#1388) CLN: remove unused vendored packaging, consolidate gitignore, remove old pygeos pyproject.toml (#1389) DOC: replace pygeos -> shapely in the reference docs (#1394) DOC: update class (init/new) docstrings of Geometry subclasses (#1395) DOC: fix / consolidate the readthedocs configuration (#1397) Update LICENSE file and copyright holder (#1403) Add aliases for project/interpolate/representative_point methods (#1340) Change simplify() preserve_topology default to True (match the Geometry method) (#1392) API: change the bounds of an empty geometry from empty tuple to tuple of NaNs (#1416) API: all-empty GeometryCollection .geoms to return empty subgeoms (#1420) API: remove __geom__, keep _geom read-only access to GEOS pointer (#1417) Consolidate setup.py metadata, remove old setup.py files (#1376) DOC: restructure the combined docs + new theme (#1402) DOC: update the installation documentation (#1396) Rename shapely.apply to shapely.transform (#1393) CLN: removed unused shape_factory + HeterogeneousGeometrySequence (#1421) CLN: remove unused _geos.pxi GEOS cython declarations (#1419) Consolidate README files (#1378) DOC: update examples in manual.rst (#1391) DOC: fix repr in example (#1452) RLS: 2.0a1 ENH: expose fixed precision overlay (grid_size keyword) in the Geometry methods as well (#1468) CLN: actually remove the base class Geometry() constructor (#1476) DOC: add changelog for Shapely 2.0 (#1442) PERF: use GEOSCoordSeq_copyToBuffer for get_coordinates (GEOS >= 3.10) (#1511) DOC/CLN: clean-up conf.py and unused docs files (#1519) ENH: expose dwithin on the Geometry subclasses (#1496) DOC/RLS: update CHANGES.txt with last releases, move old releases to docs (#1520) PERF: use GEOSGeom_getExtent for GEOS>=3.11 in bounds ufunc (#1477) API: use quad_segs for buffer keyword instead of resolution (#1512) RLS/CI: update GEOS to 3.11.0 for wheels (#1527) COMPAT: keep old exception sublcasses as (deprecated) ShapelyError aliases (#1538) COMPAT: keep (deprecated) geom_factory for downstream packages (cartopy) (#1534) Add unary_union alias for top-level union_all (#1536) CLN: remove custom minimum_rotated_rectangle implementation + add oriented_envelope alias (#1532) DOC: update offset_curve (parallel_offset) documentation regarding direction of the resulting line (#1537) DOC: autogenerate separate reference pages per function with autosummary (#1529) ENH: shapely.plotting module with basic matplotlib-based functionality (+ updated docs to use this) (#1497) DOC/CI: fix doc build for latex + re-enable epub and htmlzip (#1549) PERF: improve performance of Point(x, y) constructor (#1547) Make Geometry objects weakref-able (#1535) CI: add PyPI token for travis wheel uploads (splitted secret) (#1554) API: restore unary_union behaviour on empty list to return empty GeometryCollection (#1553) DOC: various small fixes to sphinx building (#1558) PERF: reintroduce global context and use in GeometryObject dealloc (#1530) DOC: add migration guide for PyGEOS users (#1557) Refactor reducing set operations as gufuncs + return emtpy collection for empty/all-None input (#1562) CI: update cibuildwheel version in travis as well (#1574) RLS: 2.0b1 BUG: move weakref-able implementation to base C extension type (fix PyPy) (#1577) CI: fix Travis deploy step for non-wheel jobs + try avoid building sdist (#1576) API: rename 'radius' -> 'distance' keyword in shapely.buffer() for consistency (#1589) Allow passing len-1 array for x and y coordinates in Point(..) (compat with 1.8) (#1590) RLS: 2.0b2 DOC: automatically fill in correct version (#1595) CI: ensure doctests are running (#1596) Document Point(..) constructor change no longer allowing coordinate sequence of len > 1 (#1600) ENH: allow Geometry methods to return arrays if passed array as argument (#1599) ENH: Add node function (#1431) PERF: restore speed of LineString(..) from numpy array of coordinates (#1602) ENH: expose contains_properly on the Geometry subclasses (#1605) ENH: faster contains_xy/intersects_xy predicates special casing for point coordinates (#1548) CLN: clean c code - remove unused variables / functions (#1619) CI/TST: fix tests for voronoi_diagram for latest GEOS (#1625) CI/TST: fix tests for changed numpy error from creating ragged array (#1627) ENH: convert to / construct from ragged array (flat coordinates and offset arrays) (#1559) ENH: expose flavor keyword in to_wkb (#1628) CI/RLS: set up CircleCI to build Linux aarch64 wheels (instead of Travis CI) (#1624) RLS: 2.0rc1 CI/RLS: ensure to run CircleCI on tags (#1634) TST: fix test_to_wkb_flavor to use fixed byte_order to pass on big endian machine (#1635) CI: fix circle config syntax CLN: remove shapely/examples submodule (#1645) TST: fix tests for GEOS changes in M handling (#1647) RLS: 2.0rc2 DEV: update valgrind Dockerfile (#1649) DOC: add note about prepare + touches to contains_xy/intersects_xy docstrings (#1631) RLS: 2.0rc3 TST: skip intermittent remove_repeated_points failure for GEOS 3.11 (#1656) DOC/RLS: update release notes for final 2.0.0 (#1659) RLS: 2.0.0 Keith Jenkins (1): fix typo (#1465) Kian Meng Ang (1): Fix typos (#1212) Krishna Chaitanya (5): Implement constructive.build_area (GEOS 3.8.0+) (pygeos/pygeos#141) Implement wrappers for Fréchet distance under measurement module (3.7.0+) (pygeos/pygeos#144) Fix typo in haussdorf -> hausdorff (pygeos/pygeos#151) Refactor GEOS_SINCE_3X0 to GEOS_SINCE_3_X_0 (pygeos/pygeos#152) Implement GEOSCoverageUnion_r under set_operations (GEOS 3.8.0+) (pygeos/pygeos#142) Kyle Barron (1): DOC: Fix typo in `from_ragged_array` docstring (#1658) Martin Fleischmann (3): DOC: add missing modules (pygeos/pygeos#136) ENH: add minimum_bounding_circle and minimum_bounding_radius (pygeos/pygeos#315) ENH: add oriented_envelope (minimum rotated rectangle) (pygeos/pygeos#314) Martin Lackner (1): Fix typos in docstring of pygeos.creation.box (pygeos/pygeos#191) Mike Taves (38): MAINT,DOC: change RTD channel to just 'defaults', pin versions (pygeos/pygeos#106) Rename normalize -> normalized in linear referencing functions (pygeos/pygeos#209) TST: Use native CI build tools to allow flexible GEOS versions (pygeos/pygeos#219) FIX: handle non-integer GEOS_VERSION_PATCH like 0beta1 as 0 (pygeos/pygeos#262) CI: bump versions to latest GEOS-3.9.1 (pygeos/pygeos#300) TST: ubuntu-16.04 about to reach EOL; upgrade to ubuntu-latest (pygeos/pygeos#347) TST: rename head branch for GEOS from 'master' to 'main' (pygeos/pygeos#360) Increment testing for geos, python and numpy versions for 2021 (pygeos/pygeos#409) Update README for 'main' branch (#1209) CI: upgrade GEOS versions, fix "Run doctests" (pygeos/pygeos#422) DOC: Update URLs for GEOS, PostGIS and use HTTPS for Code of Conduct TST: linearring closing logic was changed with pygeos (#1232) BUG/TST: fix hashing for Polygon + update tests (#1250) Update MANIFEST.in to enable 'python -m build` to work (#1249) Fix GitHub Actions badge svg, remove appveyor placeholder (#1273) CI: upgrade GEOS patch versions for tests and release (#1408) CI: add testing for 2022, including GEOS-3.11 (#1437) PERF: use numpy matmul for affine transformation (#1418) Require Python 3.7+, NumPy 1.14+ (#1453) CI: macOS-10.15 is deprecated, upgrade to macOS-11 (#1458) Move static metadata from setup.py to pyproject.toml, add sdist check (#1426) MAINT: remove workarounds when numpy was optional (#1461) MAINT: use modern Python coding styles (from pyupgrade) (#1462) CLN: Rename `__p__`→`_parent`, clean-up `gtag`, `_factory` and `__rings__` (#1467) DEPR: deprecate the type attribute (#1492) DOC: update migration guide to use 'packaging' instead of 'distutils' (#1502) TST: change WKT tests with inconsistent dimensionality for GEOS 3.12 (#1542) Add CITATION.cff, remove CITATION.txt (#1455) TST: clean-up test_doctests (with binascii_hex), refactor test_hash (#1586) Raise ValueError for non-finite distance to buffer/offset_curve (#1522) ENH: add `__format__` specification for geometry types (#1556) MAINT: Add Python 3.11 classifier and upgrade to GEOS 3.11.1; other CI upgrades (#1607) MAINT: remove requirements-dev.txt; expand optional dependencies in pyproject.toml (#1606) DOC: clean-up docstrings and Sphinx markup for deprecated functions (#1611) DEP: remove 'preserve_topology' from 'set_precision()' (#1612) DEP: change `almost_equals()` to be removed from version 2.0 to 2.1 (#1604) CLN/DOC: credits, miscellaneous clean-up, file modes, doc touchup (#1629) BLD: pin to Cython~=0.29, ignore .c and .pyx files in wheels (#1632) Phil Chiu (1): PERF: vectorized implementation for signed area (#1323) Tom Clancy (1): Add additional benchmarks (pygeos/pygeos#145) dependabot[bot] (4): Bump actions/setup-python from 2 to 4 (#1640) Bump actions/checkout from 2 to 3 (#1644) Bump pre-commit/action from 2.0.0 to 3.0.0 (#1642) Bump pypa/cibuildwheel from 2.10.2 to 2.11.2 (#1643) enrico ferreguti (3): TST: rewrite tests using pytest assert (#1505) Make parallel_offset an alias for offset_curve (#1510) TST: assert rewriting in tests (#1514) gpapadok (2): ENH: Add segmentize method to BaseGeometry (#1434) ENH: Add reverse method to BaseGeometry (#1457) mattijn (1): Reintroduce shared_paths (pygeos/pygeos#77) odidev (1): Add linux aarch64 wheel build support (pygeos/pygeos#386)

brendan-ward added 4 commits January 12, 2020 15:15

First draft of STRTree.query() with predicate functions

998c45f

add more variants of tests for STRtree.query() and query with predicates

fffa905

Add STRtree tests for within and contains predicates

dff2a1a

Added STRtree.query() overlaps and touches tests

7d77036

Use prepared geometries to speed up predicate test in STRtree.query()

4405338

Resolved compiler warnings where possible

brendan-ward mentioned this pull request Jan 30, 2020

ENH: prepared geometry as additional (cached) attribute on GeometryObject #92

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jorisvandenbossche reviewed Feb 7, 2020

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brendan-ward added 3 commits February 7, 2020 17:03

PR feedback

24970f1

Merge branch 'master' into query_predicate

4add8da

Refine documentation for STRtree

e16e9a4

Mark MultiPoint intersections as xfail (GEOS 3.5 bug)

7e93a7c

brendan-ward mentioned this pull request Feb 9, 2020

ENH: (optionally) use pygeos for vectorized GeometryArray operations geopandas/geopandas#1154

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jorisvandenbossche approved these changes Feb 19, 2020

View reviewed changes

jorisvandenbossche merged commit 56ad4d0 into pygeos:master Feb 19, 2020

jorisvandenbossche mentioned this pull request Feb 19, 2020

Port the spatial join algorithm from geopandas #52

Closed

brendan-ward commented Feb 19, 2020

View reviewed changes

brendan-ward deleted the query_predicate branch February 19, 2020 16:50

jorisvandenbossche pushed a commit to jorisvandenbossche/shapely that referenced this pull request Nov 29, 2021

ENH: include predicates in STRtree.query() (pygeos/pygeos#87)

aa68dbe

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