ENH: add wkt / wkb ufuncs by jorisvandenbossche · Pull Request #45 · pygeos/pygeos

jorisvandenbossche · 2019-09-27T13:41:37Z

Start for adding from_wkt / to_wkt / from_wkb / to_wkt ufuncs.

They are right now already defined on the Geometry object, but those are useful as ufuncs as well.
We can probably remove the implementation in pygeom.c to avoid duplication. But the question is whether we want to keep those as methods in the public API?

I should maybe also move this into a separate .c file, as the ufuncs.c is starting to become quite long? (although it are ufuncs)

Still need to make the nice Python functions, only the barebone ufuncs for now for the readers.
Also still need to do proper error handling (ensure that I destroy the reader when there is an error)

jorisvandenbossche · 2019-09-27T13:45:04Z

Some other questions:

Do we want to keep the hex / non-hex in a single ufunc? I suppose checking for each element individually which of the two it is will give some overhead. Also, you will typically either have all bytes or all hex, not a mixture?
The hex input is also bytes, while you might typically have this as a string? (not sure myself) For example the shapely.wkb.dumps( hex=True) gives a string.

caspervdw · 2019-09-27T18:21:24Z

src/ufuncs.c

+    GEOSWKTWriter_setRoundingPrecision_r(context_handle, writer, precision);
+    GEOSWKTWriter_setTrim_r(context_handle, writer, trim);
+    GEOSWKTWriter_setOutputDimension_r(context_handle, writer, dimension);
+    GEOSWKTWriter_setOld3D_r(context_handle, writer, use_old_3d);


I think these should be available as arguments to the functions. The only way I know to do that, is to actually add them to the ufunc inputs. So you'll get 5 input arguments.

I do think they should e scalars, we don't want to call these 4 methods in the inner loop. I encountered the same problem in the buffer function, which I solved by asserting that it is a scalar.

That means that you can't give them default values? (on the ufunc level, can still do that in the python wrapper)

caspervdw · 2019-09-27T18:23:49Z

src/ufuncs.c

+        } else {
+            wkt = GEOSWKTWriter_write_r(context_handle, writer, in1);
+            Py_XDECREF(*out);
+            *out = PyUnicode_FromFormat(format, wkt);


In this case PyUnicode_FromString is better I think

caspervdw · 2019-09-27T18:24:32Z

src/ufuncs.c

+        in1 = *(PyObject **)ip1;
+
+        /* Cast the PyObject (only bytes) to char* */
+        if (!PyBytes_Check(in1)) {


I guess we also need to accept Py_None

caspervdw · 2019-09-27T18:25:43Z

src/ufuncs.c

+            is_hex = ((wkb[0] == 48) | (wkb[0] == 49));
+        } else {
+            is_hex = 0;
+        }


I think the performance hit here is negligible, so keep it imho

caspervdw · 2019-09-27T18:26:26Z

src/ufuncs.c

+        else if (PyUnicode_Check(in1)) {
+            wkt = PyUnicode_AsUTF8(in1);
+            if (wkt == NULL) { return; }
+        } else {


Same comment as above, we should also accept None

caspervdw · 2019-09-27T18:27:22Z

src/ufuncs.c

+    unsigned char *wkb;
+    size_t size;
+
+    int dimension = 3;


See comment in the to_wkt function, I think these should be arguments

caspervdw · 2019-09-27T18:28:22Z

pygeos/test/test_readers_writers.py

+)
+
+
+def test_from_wkt():


There is some of overlap with the wkb/wkt tests in test_geometry, ideally these should be merged

caspervdw · 2019-09-27T18:31:01Z

Thanks for this addition! I think the wkt/wkb functions on the Geometry object should either be dropped, or should make use of the ufuncs. I don't like the duplicate code.

I guess the hex input might also be a string indeed. Maybe best to try to parse both bytes and strings in the ufunc.

src/ufuncs.c

jorisvandenbossche · 2019-09-29T12:20:28Z

Thanks for the comments!
I already addressed them partly. For to_wkt, I already added the parameters. But, that brings up a new question: what should be the defaults?
For now, I used the defaults as they are in GEOS. But, those are not necessarily the most user friendly defaults (shapely also uses trim=True and output_dimension=3 as default, which deviates from GEOS).

caspervdw · 2019-09-30T06:33:00Z

I agree that it is better here to deviate from the GEOS defaults. In the ToWKB I wrote earlier I used:

char trim = 1;
int precision = 6;
int dimension = 3;
int use_old_3d = 0;

caspervdw · 2019-09-30T06:39:38Z

The ToWKT part is good to go. I like the docstring!

jorisvandenbossche · 2019-09-30T06:43:46Z

So I will:

remove the methods on the Geometry object (and see how to use the to_wkt ufunc in the repr of that object, this might be a hard one)
convert the existing tests for those to use the ufuncs / consolidate it with my tests
also add python wrappers for the from_wkt/from_wkb/to_wkb functions

That sounds good?

jorisvandenbossche · 2019-09-30T06:51:21Z

For the hex/bytes question, I will add accepting hex-strings instead of only bytes. However, for the actual bytes representation, I would personally only accept bytes, and not strings to be interpreted as bytes (that feels cleaner).

I think the performance hit here is negligible, so keep it imho

Yes, it's indeed only a minor overhead (2-3% when I checked, but that is also in the uncertainty range).
A reason to still have it as a keyword instead of automatic detection, is that I would find it very strange to have a mixture of bytes / hex in a single array. I am not sure we should support that.

BTW, I did some performance timings in general, and this PR gives exactly the same performance (as expected) as the cython version I wrote before, and it gives around a 20x speed-up for from_wkb/to_wkb and a 10x speed-up for from_wkt/to_wkt (for an array of Points, so which is the "easiest" (where the looping is relatively more overhead compared to the actual GEOS call), with bigger geoms the speed-up will be a bit less).

caspervdw · 2019-10-07T15:10:47Z

However, for the actual bytes representation, I would personally only accept bytes, and not strings to be interpreted as bytes (that feels cleaner).

I agree, WKB should always be bytes and never string. WKT could be both.

Yes, it's indeed only a minor overhead (2-3% when I checked, but that is also in the uncertainty range). I would find it very strange to have a mixture of bytes / hex in a single array. I am not sure we should support that.

The mixture of both would be odd indeed, but that's no reason to not implement it in this way, right? Maybe adding it as a keyword argument (hex=True/False) like in the ToWKB is the way to go then. I would be happy with both options.

jorisvandenbossche · 2019-10-08T12:18:37Z

OK, made a bunch of updates:

added python wrappers for the other methods as well
added parameters to to_wkb
consolidated the tests (and added a str(Geometry) functionality to the GeometryObject to return default WKT)
return hex as string in to_wkb, and accept strings in from_wkb

I already updated the tests to no longer use the Geometry.to/from_wkb/wkt methods, but did no yet finally remove the methods, because I am running in to the following issue where Geometry.from_wkb works, but the ufunc version pygeos.from_wkb does not (so the tests that I converted to use the ufuncs are failing):

In [1]: import pygeos

In [2]: p = pygeos.points(1, 1)

In [3]: p.to_wkb() == pygeos.to_wkb(p) 
Out[3]: True

In [4]: p.to_wkb(byte_order=0) == pygeos.to_wkb(p, byte_order=0)
Out[4]: True

In [5]: wkb = pygeos.to_wkb(p, byte_order=0)

In [6]: pygeos.Geometry.from_wkb(wkb) 
Out[6]: <pygeos.Geometry POINT (1 1)>

In [7]: pygeos.from_wkb(wkb) 
---------------------------------------------------------------------------
GEOSException                             Traceback (most recent call last)
<ipython-input-7-7d2b49c9458f> in <module>
----> 1 pygeos.from_wkb(wkb)

~/scipy/repos/pygeos/pygeos/io.py in from_wkb(geometry, **kwargs)
    172 
    173     """
--> 174     return lib.from_wkb(geometry, **kwargs)

GEOSException: ParseException: Unexpected EOF parsing WKB

This example is with a different byte order, but it also occurs with the default byte order for a different geometry type, eg:

In [8]: p = pygeos.Geometry("POLYGON ((0 0, 2 0, 2 2, 0 2, 0 0))") 

In [9]: p.to_wkb() == pygeos.to_wkb(p) 
Out[9]: True

In [10]: wkb = pygeos.to_wkb(p)

In [11]: pygeos.Geometry.from_wkb(wkb) 
Out[11]: <pygeos.Geometry POLYGON ((0 0, 2 0, 2 2, 0 2, 0 0))>

In [12]: pygeos.from_wkb(wkb) 
---------------------------------------------------------------------------
GEOSException                             Traceback (most recent call last)
<ipython-input-12-7d2b49c9458f> in <module>
----> 1 pygeos.from_wkb(wkb)

~/scipy/repos/pygeos/pygeos/io.py in from_wkb(geometry, **kwargs)
    172 
    173     """
--> 174     return lib.from_wkb(geometry, **kwargs)

GEOSException: ParseException: Unexpected EOF parsing WKB

but for other geometries this is working fine. And I don't directly see the difference between the code of the ufunc or the object's method ..

jorisvandenbossche · 2019-10-08T19:42:01Z

One additional question regarding naming: currently I am using the to_wkt / from_wkt pattern. But, it could also be as_wkt / from_wkt (more similar as the postgis terminology) or read_wkt / write_wkt (more close to GEOS terminology of WKTReader/Writer)

jorisvandenbossche · 2019-10-09T10:01:33Z

OK, looked into the failure I described above (difference between ufuncs::from_wkb and Geometry.from_wkb), by printing the wkb chars passed to the GEOS function in c:

In [1]: import pygeos 
   ...: p = pygeos.Geometry("POLYGON ((0 0, 2 0, 2 2, 0 2, 0 0))")  
   ...: wkb = pygeos.to_wkb(p)

In [2]: pygeos.from_wkb(wkb) 
Size: 77
01 03 00 00 00 01 00 00 00 05 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
00 00 00 00 00 40 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 40 00 00 00 00 00 00 00 40 00 
00 00 00 00 00 00 00 00 00 00 00 00 00 00 40 
---------------------------------------------------------------------------
GEOSException                             Traceback (most recent call last)
...
GEOSException: ParseException: Unexpected EOF parsing WKB

In [3]: pygeos.Geometry.from_wkb(wkb)
Size: 93
01 03 00 00 00 01 00 00 00 05 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
00 00 00 00 00 40 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 40 00 00 00 00 00 00 00 40 00 
00 00 00 00 00 00 00 00 00 00 00 00 00 00 40 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Out[3]: <pygeos.Geometry POLYGON ((0 0, 2 0, 2 2, 0 2, 0 0))>

So you can see that although the same python object is passed, in the working case there are additional null bytes, while those have been removed in the failing ufunc case.
And the original python object has indeed those null bytes:

In [7]: wkb
Out[7]: b'\x01\x03\x00\x00\x00\x01\x00\x00\x00\x05\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00@\x00\x00\x00\x00\x00\x00\x00
\x00\x00\x00\x00\x00\x00\x00\x00@\x00\x00\x00\x00\x00\x00\x00@\x00\x00\x00\x00\x00\x00\x00
\x00\x00\x00\x00\x00\x00\x00\x00@\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00
\x00\x00'

In [8]: len(wkb)
Out[8]: 93

And what is more, this only happens for the ufunc if you pass a scalar, not if you actually pass an array:

In [6]: pygeos.from_wkb(np.array([wkb], dtype=object))
Size: 93
01 03 00 00 00 01 00 00 00 05 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
00 00 00 00 00 40 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 40 00 00 00 00 00 00 00 40 00 
00 00 00 00 00 00 00 00 00 00 00 00 00 00 40 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Out[6]: 
array([<pygeos.Geometry POLYGON ((0 0, 2 0, 2 2, 0 2, 0 0))>],
      dtype=object)

So there seems to be going something wrong how numpy treats a non-numpy array as input to the ufunc in this case. I don't know if it is something that I am doing wrong, or if it is a bug in numpy.
But at least it provides a way to workaround it in this case.

jorisvandenbossche · 2019-10-09T10:14:27Z

I don't know if it is something that I am doing wrong, or if it is a bug in numpy.
But at least it provides a way to workaround it in this case.

Ah, this is because of the default dtype inference of numpy. If you pass a bytes like object to an array (without specifying a dtype), you get a S dtyped array, and accessing a single element of that removes trailing null bytes:

In [24]: np.array(wkb) 
Out[24]: 
array(b'\x01\x03\x00\x00\x00\x01\x00\x00\x00\x05\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00
\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00@\x00\x00\x00\x00\x00\x00\x00
\x00\x00\x00\x00\x00\x00\x00\x00@\x00\x00\x00\x00\x00\x00\x00@\x00\x00\x00\x00\x00\x00\x00
\x00\x00\x00\x00\x00\x00\x00\x00@',
      dtype='|S93')

In [25]: np.array(wkb).item() 
Out[25]: b'\x01\x03\x00\x00\x00\x01\x00\x00\x00\x05\x00\x00\x00\x00\x00\x00\x00\x00\x00
\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00@\x00\x00\x00\x00\x00
\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00@\x00\x00\x00\x00\x00\x00\x00@\x00\x00\x00\x00\x00
\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00@'

In [26]: wkb 
Out[26]: b'\x01\x03\x00\x00\x00\x01\x00\x00\x00\x05\x00\x00\x00\x00\x00\x00\x00\x00\x00
\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00@\x00\x00\x00\x00\x00
\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00@\x00\x00\x00\x00\x00\x00\x00@\x00\x00\x00\x00\x00
\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00@\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'

So a roundtrip to numpy S93 and back to object removes the trailing null bytes.
Some explanation in https://stackoverflow.com/questions/37435309/numpy-trimming-trailing-zeros-in-byte-strings and numpy/numpy#3878. The reason they do that because the trailing null bytes as end-of-string is the only way to have shorter strings in a fixed-length string dtype, but for our use case this is of course totally unacceptable. So we probably should disallow those string dtypes as input.

jorisvandenbossche · 2019-10-09T13:16:24Z

@caspervdw the ufuncs are now fully working, but a remaining item: can we deduplicate the code between ufuncs.c and pygeom.c ? Because pygeom.c does still need to have basic read/write functionality for the repr and the constructor (but without options).
But I don't directly see an easy way to reuse the function we defined for the ufunc. You would need to define the arguments in the way the the ufunc function expects them, I don't directly succeed in that.

caspervdw

I left some minor comments. As a general remark I prefer the "one assert per unittest" (a unittest should fail for one reason), so whenever you can split the tests please do.

Concerning the deduplication of the WKB/WKT code, I think we should investigate the overhead if we define part of the Geometry object in pure python. Maybe create the base class in C (with the static _ptr attribute), and subclass it in Python adding extra features such as the to_wkb.

Something for a later time.

pygeos/io.py

pygeos/test/test_io.py

jorisvandenbossche · 2019-10-13T12:04:13Z

I think we should investigate the overhead if we define part of the Geometry object in pure python. Maybe create the base class in C (with the static _ptr attribute), and subclass it in Python adding extra features such as the to_wkb.

But the ufuncs would still return the base extension type. So do you mean that in the python functions, we would (for those methods that return geometries) loop through it and wrap each element in the python class?

caspervdw · 2019-10-14T20:31:30Z

Maybe we could make a kind of accessor like:

Geometry.obj

That creates a Python object with all the bells and whistles

jorisvandenbossche · 2019-10-14T20:35:23Z

Will update for your comments when having some time this week.

One more question about the naming: I now used to_wkt / from_wkt pattern. But, it could also be write_wkt / read_wkt (in line of GEOS's Writer/Reader classes) or as_wkt / to_wkt (more like postgis).

caspervdw · 2019-10-16T18:17:46Z

I don't like the "read" and "write" namings, as we also do not speak of "readers" and "writers" (that is a bit C-ish). We just convert representations of geometries.

I like the idea of aligning with PostGIS as_wkt / from_wkt, but Python packages often use the to_ and from_ prefixes (e.g. pandas.DataFrame.to_csv or numpy.ndarray.to_list)

So my preference is keeping it as is. Also the least amount of work.

jorisvandenbossche · 2019-10-20T13:02:56Z

One more question: are you OK with dropping WKB input in the Geometry(..) constructor?
For WKT it is convenient to be able to do Geometry("POINT (1 1)"), but for WKB I think people can just use from_wkb ? (then only the WKT io has some duplication in pygeom.c)

jorisvandenbossche · 2019-10-20T16:09:52Z

cleaned up empty lines
splitted tests (not to a single assert per test, but at least more splitted)
added test for empty geometries (empty point does not work for WKB, as expected, but does still give a wrong error (MemoryError), so that is still a TODO)
removed the methods on the Geometry object (and simplified the WKT code, since that doesn't need to handle with options any more -> that is covered by pygeos.to/from_wkt)

jorisvandenbossche · 2019-10-20T16:17:07Z

And the "POINT EMPTY" error in to_wkb is now also fixed: it still raises an error, but now the proper one with a informative error message:

In [2]: geom = pygeos.Geometry("POINT EMPTY") 

In [3]: pygeos.to_wkb(geom)
---------------------------------------------------------------------------
GEOSException                             Traceback (most recent call last)
<ipython-input-3-2272ebf49184> in <module>
----> 1 pygeos.to_wkb(geom)

~/scipy/repos/pygeos/pygeos/io.py in to_wkb(geometry, hex, output_dimension, byte_order, include_srid, **kwargs)
    127         np.intc(byte_order),
    128         np.bool(include_srid),
--> 129         **kwargs,
    130     )
    131 

GEOSException: IllegalArgumentException: Empty Points cannot be represented in WKB

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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)

ENH: add wkt / wkb ufuncs

108321a

add to_wkt, to_wkb

9706a84

caspervdw reviewed Sep 27, 2019

View reviewed changes

jorisvandenbossche commented Sep 28, 2019

View reviewed changes

src/ufuncs.c Show resolved Hide resolved

jorisvandenbossche added 5 commits September 28, 2019 18:24

handle None input

3f82cef

add parameters to to_wkt + python wrapper

4da285b

properly destroy reader/writer on error

ab43c51

Use PyUnicode_FromString instead of FromFormat

2a912c0

fix syntax error

dc8d76c

jorisvandenbossche added 7 commits October 8, 2019 09:24

Merge remote-tracking branch 'upstream/master' into wkt-wkb-ufuncs

fbec8e1

fixup merge

a5f48fc

add python wrappers for other functions

84deeee

add parameters to to_wkb

895a5a7

change defaults of to_wkt to more user friendly ones

85f6d11

add str for Geometry, remove methods, move WKT/WKB tests

d8f2f4e

accept hex strings in from_wkb

ec3c337

fix test and docstring

3a8ded4

fix numpy string dtype removing trailing null bytes

291e59b

jorisvandenbossche mentioned this pull request Oct 12, 2019

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

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caspervdw reviewed Oct 13, 2019

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caspervdw added this to the 0.5 milestone Oct 16, 2019

jorisvandenbossche added 2 commits October 20, 2019 17:59

clean-up tests

57bc404

Remove methods on Geometry object, simplify wkt code in pygeom.c

942e237

properly handle GEOSException in to_wkb

5ec9194

clean-up

46802df

caspervdw merged commit 2ae2813 into pygeos:master Oct 21, 2019

jorisvandenbossche deleted the wkt-wkb-ufuncs branch March 29, 2020 11:55

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

ENH: add wkt / wkb ufuncs (pygeos/pygeos#45)

8dbb15e

		)


		def test_from_wkt():

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