PERF: Use GEOSCoordSeq_copyFromBuffer for creating simple geometries by jorisvandenbossche · Pull Request #436 · pygeos/pygeos

jorisvandenbossche · 2021-11-18T11:30:38Z

Experiment in using the new GEOSCoordSeq_copyFromBuffer for creating CoordinateSequences instead of setting each ordinate individually.

This requires GEOS 3.10, so will require #255 to use this in cython.

I was benchmarking it with the US census polygons (tl_2019_us_zcta510.zip, 33144 (multi)polygons, with on average ~1200 coordinates per ring).

Focusing on LinearRing creation (the actual creation of (Multi)Polygons from those rings will of course see less of a difference):

I saved the coordinates and offsets in a numpy file, to load them again to benchmark (see https://nbviewer.org/gist/jorisvandenbossche/4fab9c94525dcb5ddda8a89b4a5ad9f3 for the full notebook):

import numpy as np
import pygeos

with np.load("pygeos-benchmark-linearrings.npz") as data:
    offsets = data["offsets"]
    coords = data["coords"]

ring_lengths = np.diff((offsets / 2).astype(int))
ring_indices = np.repeat(np.arange(len(ring_lengths)), ring_lengths)
rings = pygeos.linearrings(coords, indices=ring_indices)

and this gives:

In [2]: %timeit pygeos.linearrings(coords, indices=ring_indices)
1.13 s ± 6.86 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)   # <-- master
558 ms ± 2.35 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)  # <-- PR

I had maybe hoped on a bit more :), but it's certainly a nice speed-up.

…instead of setting each ordinate individually

jorisvandenbossche · 2021-11-18T11:34:11Z

pygeos/_geometry.pyx

        raise ValueError("The indices must be sorted.")  

-    cdef double[:, :] coord_view = coordinates
+    cdef double[:] coord_view = coordinates.ravel()


We would need to ensure the correct layout here (row major (XYXY), i.e. C contiguous). I suppose this is simply .ravel(order="C"), although that might actually already be the default.

jorisvandenbossche · 2021-11-18T11:38:53Z

pygeos/_geometry.pyx

+                # if ring_closure == 1:
+                #     if _set_xyz(geos_handle, seq, geom_size, dims, coord_view, idx - geom_size) == 0:
+                #         GEOSCoordSeq_destroy_r(geos_handle, seq)
+                #         return  # GEOSException is raised by get_geos_handle


When using the GEOSCoordSeq_copyFromBuffer_r, I am note sure we should automatically add a coordinate for ring closure.

(although I suppose it is still possible; we can first copy in one extra element (the first of the next geometry?) and then overwrite that later?)

Personally I think that when you already are providing indices, it should also be a rare use case (eg if you got those indices from one of our functions that returns indices, this will never be a problem).
We could of course still check for it (now I also commented out that code).

This could maybe also be an option of the function?

jorisvandenbossche · 2021-11-18T11:46:50Z

Doing a profile of the above benchmark with py-spy gives the following (not interactive here on github unfortunately):

So this confirms that inside pygeos.linearrings now most time is spent in GEOSCoordSeq_copyFromBuffer (66%). Another 25% is from np.bincount, and another 8% is from the comparison indices[1:] < indices[:indices.shape[0] - 1](validating the indices are sorted)

brendan-ward · 2021-11-18T14:44:58Z

Thanks for working on this! The results are promising (though a bummer that we spend so much time just validating inputs).

I wonder if it would be easier to introduce this first in the ufuncs (e.g., lib.linestrings) where we can use the C macros to guard the GEOS version? That would unblock the dependency on adding GEOS version control mechanisms to Cython in order to first start using GEOSCoordSeq_copyFromBuffer in pygeos? That said, we'll certainly want this in Cython too, just was trying to think through smaller steps to bringing this in.

jorisvandenbossche · 2021-11-18T14:49:26Z

I wonder if it would be easier to introduce this first in the ufuncs (e.g., lib.linestrings) where we can use the C macros to guard the GEOS version?

That would indeed certainly be easier, but in practice those ufuncs are not super useful for general IO (except for points), since you almost never have all polygons of the same size (eg I couldn't have done my benchmark with real world data as I did above). So that's the reason I wanted to start looking at the non-ufunc versions.
(but we certainly want to add it to the ufuncs as well)

jorisvandenbossche · 2021-11-18T14:53:33Z

though a bummer that we spend so much time just validating inputs

It's not actually only validation, but also the calculation of the size of each CoordSeq that takes quite a bit of time. That's a consequence of how we expect the indices to be laid out (as [0, 0, 0, 0, 1, 1, 2, 2, 2] instead of [0, 4, 6, 9]).
Long term, I think it would be nice to also have a routine that takes that kind of offsets (since this is what Arrow will natively store).

The validation indeed also takes some time. We could maybe add a keyword to disable this, if you already know for sure that this is the case (but with a default to always validate).

brendan-ward · 2021-11-18T14:59:53Z

Likely crazy idea, not yet thought through: what if we exposed a function from pygeos C API that we consume in Cython so that it takes the same inputs as are now being passed into GEOSCoordSeq_copyFromBuffer. Then, instead of using this function direction from GEOS, we call back into pygeos C API, which then uses C Macros to version-guard the underlying GEOS functions used. I'm thinking that what we add would be lightweight wrappers around some of these important low-level GEOS functions where they are only available in certain recent versions of GEOS.

I.e., instead of adding shims to Cython build system to conditionally make certain GEOS functions available to Cython, we provide Cython C function shims that are implemented back in C on our end.

I don't know yet how the complexity of that would differ vs just making the Cython build system GEOS version aware.

jorisvandenbossche · 2021-11-18T15:07:00Z

That's not so crazy I think :)

We could indeed have a C function that either is a simple call of GEOSCoordSeq_copyFromBuffer or either creates a CoordSeq manually and fills this in iteratively, depending on the GEOS version (which is easy to do in C). And then we can call that in the cython code. This is basically the _set_xyz + the loop in which it is called that we now do custom in cython.

That might indeed end up simpler.

caspervdw · 2021-11-19T16:02:13Z

Thanks for investigating this and doing the benchmarks! Interesting results. For sure the new GEOS function gives significant improvements. And we have some handles to optimize even further.

We could indeed make an optional “offsets” keyword argument that is preferred above the “indices”. It depends on your use case which representation is fastest, apparently here “offsets” is a better match. This is material for another issue I guess.

For the coordinates -> coordseq conversion I think the proposed solution of @brendan-ward is not crazy at all. I think that is the way to go.

jorisvandenbossche · 2021-11-21T11:17:01Z

I did a first attempt to write a generic "create and fill in coord seq" function that can be used in in the ufuncs (and then later in the cython code as well). Some complications: the ufuncs can also handle differently strided arrays (so I have to check if the steps are correct to use the copyFromBuffer), and needed some casts back and forth between *double and *char (the steps are expressed in bytes, not for * double). This can probably be cleaned up a bit more.

jorisvandenbossche · 2021-11-21T13:12:51Z

Quick performance check for the ufunc as well (not compared with master, but comparing with itself but triggering the copyFromBuffer path by providing unclosed vs closed ring coordinates):

In [15]: coords1 = np.random.randn(10000, 100, 2)

In [16]: %timeit pygeos.linearrings(coords1)
17.2 ms ± 603 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)

In [17]: coords1[:, [99], :] = coords1[: , [0], :]

In [18]: %timeit pygeos.linearrings(coords1)   # <-- closed rings, uses the copyFromBuffer fast path
8.93 ms ± 598 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)

and with fewer but larger rings:

In [19]: coords1 = np.random.randn(100, 10000, 2)

In [20]: %timeit pygeos.linearrings(coords1)
10.8 ms ± 111 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)

In [21]: coords1[:, [9999], :] = coords1[: , [0], :]

In [22]: %timeit pygeos.linearrings(coords1)
3.54 ms ± 44.6 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)

caspervdw · 2021-11-27T18:46:29Z

src/geos.c

+    int hasZ = dims == 3;
+    coord_seq = GEOSCoordSeq_copyFromBuffer_r(ctx, buf, size, hasZ, 0);
+    return coord_seq;
+  }


I think we could use GEOSCoordSeq_copyFromArrays here if (cs1 == 8) && (cs2 == size * 8)

in that case x = buf, y = buf + cs2, z = (dims == 3) ? buf + 2 * cs2 : NULL

This could come in handy for fortran-ordered arrays

Looking into this, I am not sure it would actually work. At least not for "standard" fortran ordered arrays, because the strides are not exactly how we would need it:

>>> coords = np.asarray(np.random.randn(10, 4, 2), order="F") >>> coords.shape (10, 4, 2) >>> coords.strides (8, 80, 320)

So the cs1 and cs2 is actually total_size * 8 and total_size * size * 8 here, with total_size being 10 in this case (the total number of geometries that are going to be created), and that's something you don't know in the ufunc inner function + then it won't have the contiguous layout for CopyFromArrays anyway

So I could easily add the check you suggested, but I am not sure how useful it would be in practice. I need to do quite some axis wrangling in numpy to get an array with the correct strides to make use of this:

>>> coords = np.asarray(np.random.randn(4, 2, 10), order="F") >>> coords = np.swapaxes(np.swapaxes(coords, 0, 2), 1, 2) >>> coords.shape (10, 4, 2) >>> coords.strides (64, 8, 32)

I see. I guess it would 'work' for two-dimensional input arrays (scalar outputs), but in those cases you probably can't tell which GEOS function was used as the Python interpreter overhead would take up most of the time

That's actually a good point. When creating a relatively large LineString or LinearRing (tested 1000 vertices), the difference is actually notable also in Python. So added that, and a test case using a scalar.

caspervdw · 2021-11-29T19:45:52Z

Looks good to merge! Can you add a line to the changelog?

…ygeos/pygeos#436)

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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)

PERF: Use GEOSCoordSeq_copyFromBuffer for creating simple geometries …

03ba32d

…instead of setting each ordinate individually

jorisvandenbossche commented Nov 18, 2021

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caspervdw mentioned this pull request Nov 21, 2021

Add “offsets” as an alternative to “indices” #438

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try using GEOSCoordSeq_copyFromBuffer_r in ufuncs if possible

5af5b46

jorisvandenbossche added 2 commits November 21, 2021 13:37

expose helper in C api in use in cython simple_geometries_1d

29fbd94

clean-up

5f1827b

jorisvandenbossche marked this pull request as ready for review November 21, 2021 12:58

caspervdw reviewed Nov 27, 2021

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caspervdw approved these changes Nov 29, 2021

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jorisvandenbossche added 3 commits November 29, 2021 21:25

add GEOSCoordSeq_copyFromArrays_r as well

c9f41cf

Merge remote-tracking branch 'upstream/master' into frombuffer

9dcbc34

add changelog entry

2b9e288

caspervdw merged commit 6833e5e into pygeos:master Nov 30, 2021

jorisvandenbossche deleted the frombuffer branch November 30, 2021 08:18

jorisvandenbossche added a commit to shapely/shapely that referenced this pull request Dec 1, 2021

PERF: Use GEOSCoordSeq_copyFromBuffer for creating simple geometries (p…

b541ffd

…ygeos/pygeos#436)

jorisvandenbossche mentioned this pull request Dec 17, 2021

BUG: creating LineString from array with invalid dimensions uses wrong coordinates shapely/shapely#1267

Closed

jorisvandenbossche mentioned this pull request Aug 28, 2022

PERF: use GEOSCoordSeq_copyToBuffer for get_coordinates (GEOS >= 3.10) shapely/shapely#1511

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