[Done] Adapt set_precision API and fix remaining GEOS 3.10 tests#410
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jorisvandenbossche merged 28 commits intopygeos:masterfrom Oct 26, 2021
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[Done] Adapt set_precision API and fix remaining GEOS 3.10 tests#410jorisvandenbossche merged 28 commits intopygeos:masterfrom
jorisvandenbossche merged 28 commits intopygeos:masterfrom
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Only 4 failing tests remaining: I guess they just have to be made a bit more robust because of float imprecisions: Edit: I fixed them too, they were indeed all at the edge of a float imprecision. There are probably others that are not robust too, but the aim here was to get tests working with GEOS 3.10 working. |
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Thanks for this!
Looks good, added a few comments (I think there is a mistake with the mapping of old to new keyword, but I am not writing this with a high degree of certainty :))
I guess they just have to be made a bit more robust because of float imprecisions:
Yes, that was my conclusion as well
CHANGELOG.rst
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| **API Changes** | ||
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| * The default behaviour of ``pygeos.set_precision`` is now to always return valid geometries. | ||
| Before, pygeos did the opposite: it preserved topology. This behaviour can be modified |
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Not sure this is very important (since the GEOS devs indicated that the behaviour of the flag was not very clear), but this might be a bit confusing as currently preserve_topology=False was the default (so not preserving topology, according to that flag)
pygeos/geometry.py
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| .. deprecated:: 0.11 | ||
| Use ``mode`` instead. | ||
| mode : {'make_valid', 'pointwise', 'keep_collapsed'}, default 'make_valid' | ||
| This parameter determines how to handle invalid geometries. There are |
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Maybe clarify this is about geometries that became invalid during the simplification process, not invalid geometries in the input.
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| SetPrecisionMode.pointwise | ||
| if preserve_topology | ||
| else SetPrecisionMode.make_valid |
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I found this very confusing and always mixing them up when exploring this in #233, so I might be doing that here again :). But shouldn't this be the other way around?
The current default of preserve_topology=False matched with setting GEOS_PREC_NO_TOPO, which is what is called "pointwise" here? So if the user passed preserve_topology=True before, they got what is now "make_valid", I think (the new default).
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I had it the other way around at some point but I think it is correct like this. “Preserve_topology” is the opposite of “make_valid”. When you make a geometry valid, you may not preserve the topology (e.g. a polygon becomes a multi polygon, or a line becomes empty).
The confusion might arise from the “no_topo” mode. According to the clarification in #233 this means that every coordinate is snapped to the grid, without checking the validity of the outcome. The name “no_topo” is confusing, but I think it means “no topological change”. Even then I think “topology” is not the right word, it is just the geometry type and amount of coordinates that is preserved. As recommended in #233 I named it “pointwise” to sidestep the confusion.
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“Preserve_topology” is the opposite of “make_valid”. When you make a geometry valid, you may not preserve the topology (e.g. a polygon becomes a multi polygon, or a line becomes empty).
This sounds logical, but AFAIK that's not what the code did (that's also the reason I think that Paul said the "preserve topology" is confusing / ambiguous and shouldn't be used).
On master, the default is preserve_topology=False. We translated this in the C code to set the GEOS_PREC_NO_TOPO flag, i.e. flag=1 (which made sense bases on our limited understanding). And also on master, setting preserve_topology=True did us set flag=0. Is this correct up to now?
The new default "make_valid" in this PR also translates to flag=0.
So effectively that makes that the old preserve_topology=True is the new mode="make_valid" (even if that doesn't make much sense in wording (but that's because our unfortunate choice of terminology before), that's how I understand what the code is doing)
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Ah I see! So that should be swapped. Very confusing indeed.
It is a good thing that the default behaviour doesn’t need to change then :) edit: ….. the default behaviour does change
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It is a good thing that the default behaviour doesn’t need to change then :)
It actually does! (although we previously called preserve_topology, that that's the whole confusing thing :)) We want flag=0 as the default, and so that's a change. Now, since previously the preserve_topology=False actually did result in collapsed empty geometries (and no longer in GEOS 3.10, which is the change that triggered us to look into it), there might be less changes in practice ..
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Because of all the confusion it might be best to remove the mapping and just emit a warning that the “preserve_topology” is being ignored. I don’t think implementing it wrong now is good, even from the perspective of backwards compatibility. One could argue we are fixing a bug here.
What do you think?
And about the warnings -I vaguely remember not using DeprecationWarnings because they tend to not end up at the user. Does (geo)pandas have any policies on that?
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In practice, if people used this keyword, it would probably be for setting preserve_topology=True. Since this behaviour is now the default, "mapping" it to the new one or ignoring results in the same result, so in practice it probably doesn't matter too much. So no strong opinion here, I am fine with ignoring it (with a warning) as well.
And about the warnings -I vaguely remember not using DeprecationWarnings because they tend to not end up at the user. Does (geo)pandas have any policies on that?
Yes, for that reason we tend to use FutureWarning instead of DeprecationWarning if it's something the end user needs to see.
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Thanks Casper! |
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…o version 2.0.0
0phoff (1):
to_shapely and from_shapely updates (pygeos/pygeos#312)
Adam J. Stewart (1):
Add Python 3.10 wheels for additional platforms (#1373)
Alan D. Snow (2):
REF: Use pkg_resources instead of distutils (pygeos/pygeos#393)
CI: Use pushd/popd when installing GEOS (pygeos/pygeos#405)
Ariel Kadouri (4):
Update segmentize tolerance parameter to max segment length (#1506)
Alias geometry.base buffer styles to geometry.constructive enums (#1508)
ENH: Remove Repeated Points (#1546)
ENH: Add directed parameter to line merge (#1592)
Bas Couwenberg (1):
Fix versioneer configuration (#1654)
Ben Beasley (1):
MAINT: Remove descartes from requirements-dev.txt (#1591)
Brendan Ward (42):
ENH: include predicates in STRtree.query() (pygeos/pygeos#87)
ENH: Added total_bounds() (pygeos/pygeos#107)
ENH: query tree with multiple input geometries (pygeos/pygeos#108)
Remove compiler warnings (pygeos/pygeos#115)
ENH: only add non-empty geometries to STRtree (pygeos/pygeos#147)
Add shapely-rfc link for latest proposal on integration (pygeos/pygeos#170)
ENH: Add more predicates to STRtree query (pygeos/pygeos#157)
Drop Python 3.5 from Travis-CI matrix (pygeos/pygeos#211)
ENH: set up Cython support + get parts of multipart geometries (pygeos/pygeos#197)
TST: Add Github Action for CI testing using conda (pygeos/pygeos#222)
API change: return 0 for None values in geometry counting functions (pygeos/pygeos#220)
Integrate previously prepared geometries into tree query
ENH: Reduce compiler warnings from Cython extensions (pygeos/pygeos#228)
Update changelog
CLN: remove Cythonized and compiled extension files on python setup.py clean (pygeos/pygeos#239)
CNL: Remove unnecessary filtering of counts from get_num_geometries (pygeos/pygeos#248)
ENH: Adds reverse function for GEOS >= 3.7 (pygeos/pygeos#254)
CLN: Migrate resizeable vector types and functions to dedicated files (pygeos/pygeos#247)
ENH: Add STRtree benchmarks (pygeos/pygeos#270)
ENH: STRtree: use addresses of tree geometries to calculate their index (pygeos/pygeos#265)
ENH: Add get / set precision ufuncs (pygeos/pygeos#257)
ENH: Add fixed precision set operations for GEOS >= 3.9 (pygeos/pygeos#276)
Fix signed char portability issue (pygeos/pygeos#293)
TST: Handle GEOS version strings with dev / beta qualifiers in the tests (pygeos/pygeos#301)
ENH: Add densify ufunc (pygeos/pygeos#299)
ENH: add STRtree nearest neighbor(s) function (pygeos/pygeos#272)
DOC: clarify overlaps versus crosses predicates (pygeos/pygeos#288)
ENH: Consolidate validation of enum values and raise ValueError on invalid values (pygeos/pygeos#263)
Add box ufunc based on create_box C function (pygeos/pygeos#308)
Allow s390x to fail; not yet handled in GEOS (pygeos/pygeos#316)
raise error on nonscalar inputs to STRtree::nearest_all (pygeos/pygeos#313)
TST: Really allow s390x to fail on Travis CI (pygeos/pygeos#319)
Raise warning and return None on invalid WKB/WKT instead of raising exception (pygeos/pygeos#321)
ENH: add dwithin to STRtree (pygeos/pygeos#425)
BUG: Fix STRtree memory leaks (pygeos/pygeos#434)
TST: Update benchmarks for pygeos=>shapely (#1424)
ENH: Update STRtree API (merge query / query-bulk, return only indices) (#1422)
ENH: Remove "shapely" name and duplicate WKT type from __repr__ (#1412)
ENH: Update STRtree nearest neighbor API (#1428)
ENH: Remove Geometry() constructor usage and use concrete geometry type constructors or from_wkt (#1414)
Fix: update geometry repr used in docstrings to pass doctests (#1451)
DOC: Improve STRtree docstrings (#1626)
Casper van der Wel (256):
First commit to pygeos
Fix indentation in README
Add Gd_G functions (e.g. simplify)
Redo the list of functions
WIP on uint32 functions
Implement integer fucntions
Clean
Changes for distribution
Changes for distribution
WIP
Add extension type
Working contains2
New Geometry constructor
Working intersection2
Working YY_b and YY_Y funcs
Refactor
Add Y_b functions
Some tests
Add Y_Y functions
Y_d functions
Add Y_l functions
Y_B functions
Distance functions
Add Yd_Y functions
Add Yl_Y
More strict int types
Project functions
Add special functions
Add normalize
Clean and readme
Bump to 0.2
Fix readme and geometry construction
Add point construction ufunc
Minor fixes
Rename Point to points
Point from tuples
Make use of generalized ufunc
Added test for dimensionality
Implement points, linearrings, linestrings and improve exception handling
Finish linearring
Polygons
Polygeons and collections
Readme
Package static files
NaN / None handling
Deal with nan for predicates
Version to dev
Skip NaN in collection creation
Optimization
WKT and WKB writers
Finish WKB/WKT IO
Typo
Tests and safety for GEOSGeometry
Readme and bump
Setup travis and code formatting
Version to dev
Add numpy include
Add pygeos.ufuncs as package
Add build_ext
Setup Travis and attempt to set up Appveyor (pygeos/pygeos#13)
Rewrite setup.py enabling compilation on windows
Readme
Repair build, remove construction from ptr
Also deallocate arrays
Fix warnings
Use master badge
Attempt fix for win
Simplify appveyor
Fix RAISE_NO_MALLOC
Haussdorf distance
Buffer with style
Refactor
Refactor + buffer
Docstrings
Fix readme
Refactor functions into separate modules
Refactor into submodules
Add voronoi and delaunay functions
Free WKT and WKB buffers; tested with valgrind
Appveyor fix attempt
Add documentation for Y_b functions
Add documentation to unary predicates
Finish unary predicates
Fix doctests
PyPI badge
Skip doctest on Py3.5
WIP
Docs for predicates
Update README.rst (pygeos/pygeos#20)
RTD docs build
Install . on RTD
Fix indentation
Only install GEOS using conda
Try with setup.py install
Typos and fixes in docs
Document the boundary function
Document buffer
Document centroid and remove clone
Document convex_hull
Add constructive to API docs
Add envelope docs
Simplify and snap
Finish constructive docs
Pin numpydoc to 0.7.0 on RTD
Rewrite constructive tests + fixes
Fix travis
Syntax fix for Py3.5
Docs WIP
Finish setop docs
Fix tests
Simplify
Fix
Tests for set operations
Integrate get element functions
Finish element counters and getters
Also fix get_exterior_ring
Move has_z, remove normalize, finish get_x and get_y
Docs
Unittests
Document and test measurement funcs
Tests for pygeos.length
Fix doctest rounding
WIP On separating Missing and Empty
Fix and finish
Fix readme
Some docs
PR Changes after review
Return NaN for distance to EMPTY
Added is_valid_input
Docstrings
Setup versioneer
Add geos_version
Add LICENSE to MANIFEST
RLS: 0.4
ENH: Get and set coordinates as a array of floats (pygeos/pygeos#44)
Finish API docs (pygeos/pygeos#53)
Moved to pygeos org (pygeos/pygeos#56)
Rewrite Travis CI script (pygeos/pygeos#59)
Add extern in header files (pygeos/pygeos#79)
ENH: Add STRtree (pygeos/pygeos#58)
[ENH] Add bounds function (pygeos/pygeos#69)
ENH: Implement from_shapely (pygeos/pygeos#61)
Textual changes + test
Fix strtree header file (pygeos/pygeos#91)
CI: Test on python 3.8 (pygeos/pygeos#101)
Gitignore
ENH: Add any pygeos/*.dll files for Windows binary .whl files (pygeos/pygeos#103)
Benchmarking suite (asv) (pygeos/pygeos#96)
BUG: Check types in create_collections (pygeos/pygeos#86)
Fix segfault in strtree test_flush_geometries (pygeos/pygeos#100)
ENH: Implement hash, eq, neq (pygeos/pygeos#102)
Include GEOS license info (pygeos/pygeos#118)
RLS: 0.7.1
Version conditional: make_valid (pygeos/pygeos#120)
Eliminate global GEOS context and release GIL (pygeos/pygeos#113)
Add release notes (pygeos/pygeos#158)
Fix memleak in strtree creation (introduced in pygeos/pygeos#144) (pygeos/pygeos#162)
Fix memory leak in from_shapely (introduced in pygeos/pygeos#144) (pygeos/pygeos#163)
Release the GIL for geometry-creating operations (pygeos/pygeos#156)
Memory leak testing using valgrind (pygeos/pygeos#159)
DOC: Update docs, add multithreading section (pygeos/pygeos#169)
FIX: Accept linearrings in pygeos.multilinestrings (pygeos/pygeos#168)
Raise ValueError on to_wkt of multipoint with empty point (pygeos/pygeos#171)
[DONE] Fix POINT EMPTY to_wkb (pygeos/pygeos#179)
Fix segfault on linestring/linearring/polygon creation (pygeos/pygeos#187)
Accept multi geometries in boundary() (pygeos/pygeos#188)
Update classifiers in setup.py
RLS: 0.8
Fix release date in changelog
Add Zenodo badge
Limit WKT length in repr (pygeos/pygeos#189)
Support pickling (pygeos/pygeos#190)
Fix bug when setting coordinates on an empty point (pygeos/pygeos#199)
Implement is_ccw for GEOS >= 3.7.0 (pygeos/pygeos#201)
Minor doc changes (pygeos/pygeos#202)
Re-add GeometryType -1 (but name it MISSING) (pygeos/pygeos#204)
Format C code using clang-format with Google style (pygeos/pygeos#203)
Release GIL for is_geometry, is_missing and is_valid_input (pygeos/pygeos#207)
Fix line_interpolate_point for multilinestrings (pygeos/pygeos#208)
Add Cython to RTD build (pygeos/pygeos#236)
CI: Cull windows tests and shorten name (pygeos/pygeos#237)
FIX: Consistent behaviour for all reduction set_operations (pygeos/pygeos#249)
ENH: Add is_prepared (pygeos/pygeos#252)
[API] Set None as default axis for reduction operations (pygeos/pygeos#266)
Update changes (pygeos/pygeos#282)
Fix mistake in changes
RLS: 0.9
Prepare 0.10
Add travis for different CPU archs (pygeos/pygeos#296)
NaN equality tests for GEOS 3.10 (pygeos/pygeos#304)
Pin endianness in to_wkb tests (pygeos/pygeos#305)
Also clean build/lib.*/pygeos in setup.py clean (pygeos/pygeos#307)
Fix badges
Fix creation error handling and release GIL (pygeos/pygeos#310)
Accept indices in collection constructors (pygeos/pygeos#290)
Enable "return_index" in get_coordinates (pygeos/pygeos#318)
Create simple geometries from coordinates and indices (pygeos/pygeos#322)
Fix the badges
Only run doctests on conda-forge, latest Py38 (pygeos/pygeos#325)
Add flake8 linter and format repo (pygeos/pygeos#328)
DOC: Add kwargs where necessary and document it (pygeos/pygeos#327)
Release the GIL in shared_paths (missing decorator) (pygeos/pygeos#331)
Create polygons from indices (pygeos/pygeos#326)
Show docstrings for functions decorated with requires_geos (pygeos/pygeos#341)
Merge polygons_1d into collections_1d + finish implementation for rls 0.10 (pygeos/pygeos#346)
Remove minimum_rotated_rectangle duplicate + fix docstrings (pygeos/pygeos#350)
Exclude Cythonized .c files from distributions (pygeos/pygeos#351)
Contributors
RLS: 0.10
Back to 0.11 dev
FIX: Testing on Pypy (pygeos/pygeos#353)
FIX: Handle NULL in object-dtype arrays (pygeos/pygeos#374)
Build wheels on CI with cibuildwheel (pygeos/pygeos#365)
RLS: 0.10.2a1
RLS: 0.10.2a2
Fix requires_geos with methods (pygeos/pygeos#376)
RLS: 0.10.2
Back to 0.11dev [skip ci]
Handle linearrings in is_closed (pygeos/pygeos#379)
Handle 'out' keyword argument in constructors if indices are given (pygeos/pygeos#380)
Add pygeos.empty (pygeos/pygeos#381)
Replace appveyor with gh actions (pygeos/pygeos#382)
Fix WKB/WKT of empty (multi)points on GEOS 3.9 (pygeos/pygeos#392)
Write docs for runtime library finding + clean CI runners (pygeos/pygeos#387)
Trigger build
Disallow linearrings with 3 coordinates in GEOS 3.10 (pygeos/pygeos#378)
CI: Fix GEOS main caching (pygeos/pygeos#399)
Force 2D/3D (pygeos/pygeos#396)
Fix 3D empty WKT serialization (pygeos/pygeos#403)
Fix GEOS 3.10 tests for linearring construction (pygeos/pygeos#408)
Update docstring of STRTree
assert_geometries_equal (pygeos/pygeos#401)
Adapt set_precision API and fix remaining GEOS 3.10 tests (pygeos/pygeos#410)
Fix segfault when getting coordinates from empty points (pygeos/pygeos#415)
Revert GEOS 3.8 version in test runner
wheels: Add Python 3.10 and GEOS 3.10.0 (pygeos/pygeos#416)
RLS: 0.11
Back to 0.12 development [ci skip]
RLS: 0.11.1
GeoJSON IO for GEOS 3.10 (pygeos/pygeos#413)
Fix tests for GEOS main (pygeos/pygeos#419)
Revert Win32 CI version for faster builds (pygeos/pygeos#420)
Reinstate may_segfault for from_geojson (pygeos/pygeos#418)
dwithin for GEOS 3.10.0 (pygeos/pygeos#417)
Revert changes from pygeos/pygeos#418 (pygeos/pygeos#426)
OSX arm64 and universal2 wheels (pygeos/pygeos#427)
Fix error handling in STRtree (pygeos/pygeos#432)
Change linearring closing logic (pygeos/pygeos#431)
Documentation fixes (pygeos/pygeos#430)
Solve RuntimeWarnings in tests (pygeos/pygeos#441)
Arm64 wheel builds on Travis (pygeos/pygeos#444)
Clean the NoticeHandler (#1329)
CI: Fix the release workflows (GHA and travis CI) (#1253)
Fix segfault in reduction functions (#1517)
ENH: Check signals every 10000 ufunc iteration (#1370)
COMPAT: Add compat for unpickling shapely<2 geometries (#1657)
Ewout ter Hoeven (4):
CI: Enable Python 3.11, update used actions (#1560)
release CI: Update used actions to latest versions / Python 3.11 wheels (#1561)
Add Dependabot configuration for GitHub Actions updates (#1597)
release CI: Use release/v1 branch for PyPI publish action (#1646)
Geir Arne Hjelle (1):
ENH: Add concave_hull() function (#1518)
James Gaboardi (1):
CI: flake8 has migrated to GH – update .pre-commit (#1614)
James Myatt (1):
DOC: Fix docstring for get_coordinates (pygeos/pygeos#340)
Joris Van den Bossche (199):
Split single ufuncs.c file in multiple files
cleanup 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)
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This adapts the API of set_precision as discussed in #233 and fixes the tests.
There were too many differences in the “test_set_precision_collapse” tests between GEOS versions so I chose to skip those for pre-3.10. Also, 1 test segfaults and another gives a wrong result. These are in a trac ticket at GEOS: https://trac.osgeo.org/geos/ticket/1135
Lastly, empty geometries after collapsing became 3D! I added force_2d to the tests. GEOS ticket: https://trac.osgeo.org/geos/ticket/1137
Builds on #401Closes #233