Wraps GEOS geometry functions in numpy ufuncs.

Last update: Dec 23, 2022

Related tags

Geolocation pygeos

Overview

PyGEOS

PyGEOS is a C/Python library with vectorized geometry functions. The geometry operations are done in the open-source geometry library GEOS. PyGEOS wraps these operations in NumPy ufuncs providing a performance improvement when operating on arrays of geometries.

Note: PyGEOS is a very young package. While the available functionality should be stable and working correctly, it's still possible that APIs change in upcoming releases. But we would love for you to try it out, give feedback or contribute!

What is a ufunc?

A universal function (or ufunc for short) is a function that operates on n-dimensional arrays in an element-by-element fashion, supporting array broadcasting. The for-loops that are involved are fully implemented in C diminishing the overhead of the Python interpreter.

Multithreading

PyGEOS functions support multithreading. More specifically, the Global Interpreter Lock (GIL) is released during function execution. Normally in Python, the GIL prevents multiple threads from computing at the same time. PyGEOS functions internally releases this constraint so that the heavy lifting done by GEOS can be done in parallel, from a single Python process.

Examples

Compare an grid of points with a polygon:

>>> geoms = points(*np.indices((4, 4)))
>>> polygon = box(0, 0, 2, 2)

>>> contains(polygon, geoms)

  array([[False, False, False, False],
         [False,  True, False, False],
         [False, False, False, False],
         [False, False, False, False]])

Compute the area of all possible intersections of two lists of polygons:

>>> from pygeos import box, area, intersection

>>> polygons_x = box(range(5), 0, range(10, 15), 10)
>>> polygons_y = box(0, range(5), 10, range(10, 15))

>>> area(intersection(polygons_x[:, np.newaxis], polygons_y[np.newaxis, :]))

array([[100.,  90.,  80.,  70.,  60.],
     [ 90.,  81.,  72.,  63.,  54.],
     [ 80.,  72.,  64.,  56.,  48.],
     [ 70.,  63.,  56.,  49.,  42.],
     [ 60.,  54.,  48.,  42.,  36.]])

See the documentation for more: https://pygeos.readthedocs.io

Relationship to Shapely

Both Shapely and PyGEOS are exposing the functionality of the GEOS C++ library to Python. While Shapely only deals with single geometries, PyGEOS provides vectorized functions to work with arrays of geometries, giving better performance and convenience for such usecases.

There is active discussion and work toward integrating PyGEOS into Shapely:

latest proposal: https://github.com/shapely/shapely-rfc/pull/1
prior discussion: https://github.com/Toblerity/Shapely/issues/782

For now PyGEOS is developed as a separate project.

References

GEOS: http://trac.osgeo.org/geos
Shapely: https://shapely.readthedocs.io/en/latest/
Numpy ufuncs: https://docs.scipy.org/doc/numpy/reference/ufuncs.html
Joris van den Bossche's blogpost: https://jorisvandenbossche.github.io/blog/2017/09/19/geopandas-cython/
Matthew Rocklin's blogpost: http://matthewrocklin.com/blog/work/2017/09/21/accelerating-geopandas-1

Copyright & License

Comments

ENH: set up Cython support + get parts of multipart geometries
Closes #127, closes #128

This is the Cython counterpart to #130.
This borrows heavily from #93 - thanks @jorisvandenbossche ! (note: there are some changes here that may be useful there)

This is about 3.5 times faster than a pure python loop implementation (100 randomly generated multipoints with 1000 points each); surprisingly, it also looks a bit faster than the original C implementation in #130 (not quite 2 times as fast).

get_parts supports returning either the parts as an array (default) or a tuple of parts and indexes in the source geometry array.

I know there was discussion around naming in #130 and #128, but it felt like a get_* function was most consistent with similar functions here. dump and explode both feel out of place.

A few points to consider / discuss specific to Cython:

I put Cython files under pygeos/ext. Unlike projects like fiona which use a naming scheme like _module.pyx in the main folder with Python sources, I wanted the Python files at the root in pygeos folder to represent the top-level API. We can use something other than ext - but for imports to work properly, I think it has to be a subfolder of pygeos rather than a sibling.

Cython functions are wrapped in top-level Python functions; this is similar to patterns in other libraries that use Cython (fiona, etc)

declarations of functions / types intended to be used across modules are stored in *.pxd files; those that were only needed within a given implementation are in the *.pyx file that uses it. These wrap functions / types from GEOS and source files here. We will likely tune how this is setup over time.

A few things to note:

there is some unrelated formatting in setup.py via black

this does not yet attempt to handle multithreading; guidance there welcome (have not yet figured out how to adapt recent work at the C level to Cython)

I have not yet checked to verify there are no memory leaks and there are not yet sufficient tests to prove that we won't get segfaults in some cases. Tests TBD.

using Cython introduces a bunch of compiler warnings; have not yet investigated these yet (some are from numpy by way of Cython and not our fault here)

TODO:

[x] Tests

[x] Reduce compiler warnings

[x] GeometryCollection support

[x] CI setup

[ ] Packaging (may need some help with this)
opened by brendan-ward 48

Failures with GEOS master / 3.10

I was testing with GEOS master (in light of the new OverlayNG), and next to 2 failures related to the new overlay implementation (which I am fixing in https://github.com/pygeos/pygeos/pull/232), there are also 2 other failures:

_______________________________________ test_points_invalid_ndim ________________________________________

    def test_points_invalid_ndim():
        with pytest.raises(pygeos.GEOSException):
>           pygeos.points([0, 1, 2, 3])
E           Failed: DID NOT RAISE <class 'pygeos.GEOSException'>

pygeos/test/test_creation.py:41: Failed
_______________________________________ test_from_wkb_empty[POLYGON EMPTY] _____________________________

wkt = 'POLYGON EMPTY'

    @pytest.mark.parametrize(
        "wkt", ("POINT EMPTY", "LINESTRING EMPTY", "POLYGON EMPTY", "GEOMETRYCOLLECTION EMPTY")
    )
    def test_from_wkb_empty(wkt):
        wkb = pygeos.to_wkb(pygeos.Geometry(wkt))
        geom = pygeos.from_wkb(wkb)
        assert pygeos.is_geometry(geom).all()
        assert pygeos.is_empty(geom).all()
>       assert pygeos.to_wkb(geom) == wkb
E       AssertionError: assert b'\x01\x03\x0...0\x00\x00\x00' == b'\x01\x03\x0...0\x00\x00\x00'
E         At index 4 diff: b'\x80' != b'\x00'
E         Use -v to get the full diff

pygeos/test/test_io.py:121: AssertionError

The first case now seems to ignore the 4th dimension, and create a POINT Z:

(Pdb) pygeos.points([0, 1, 2, 3])
<pygeos.Geometry POINT Z (0 1 2)>

In the second case, the WKB of an empty polygon differs depending on whether the empty polygon was created from WKT or WKB:

(Pdb) geom1 = pygeos.Geometry("POLYGON EMPTY")
(Pdb) geom1
<pygeos.Geometry POLYGON EMPTY>
(Pdb) pygeos.to_wkb(geom1)
b'\x01\x03\x00\x00\x00\x00\x00\x00\x00'
(Pdb) geom2 = pygeos.from_wkb(pygeos.to_wkb(geom1))
(Pdb) geom2
<pygeos.Geometry POLYGON EMPTY>
(Pdb) pygeos.to_wkb(geom2)
b'\x01\x03\x00\x00\x80\x00\x00\x00\x00'

opened by jorisvandenbossche 35

ENH: prepared geometry as additional (cached) attribute on GeometryObject
@brendan-ward @caspervdw I experimented today with a possible alternative approach on supporting prepared geometries, compared with https://github.com/pygeos/pygeos/pull/84

I added a second static attribute to the GeometryObject struct, which can optionally (for a prepared geom) be populated.

For me, the main reason I wanted to test this approach is that this keeps the geometry and its prepared version together. This means that the user doesn't need to keep track of a separate array with the prepared versions of their data (which could then get out of sync, etc): you just have your single array of geometries, that also can be prepared.

The ufuncs that I added here are just a quick hack to get something working. But from a quick test, it seems to be working:

import geopandas import pygeos df = geopandas.read_file(geopandas.datasets.get_path("naturalearth_lowres")) countries = pygeos.from_shapely(np.array(df.geometry)) df2 = geopandas.read_file(geopandas.datasets.get_path("naturalearth_cities")) cities = pygeos.from_shapely(np.array(df2.geometry))

# the current intersects result In [10]: pygeos.lib.intersects(countries, cities[:, None]) Out[10]: array([[False, False, False, ..., False, False, False], [False, False, False, ..., False, False, False], [False, False, False, ..., False, False, False], ..., [False, False, False, ..., False, False, False], [False, False, False, ..., False, False, False], [False, False, False, ..., False, False, False]]) # timing the existing function In [14]: %timeit pygeos.lib.intersects(countries, cities[:, None]) 18.8 ms ± 91.4 µs per loop (mean ± std. dev. of 7 runs, 100 loops each) # timing the prepared version (but without prepared geoms -> just an extra if check) In [16]: %timeit pygeos.lib.intersects_prepared(countries, cities[:, None]) 18.9 ms ± 62 µs per loop (mean ± std. dev. of 7 runs, 100 loops each) # preparing the geometries In [18]: temp = pygeos.lib.prepare(countries) # calling the prepared version again, but now with prepared geoms In [19]: %timeit pygeos.lib.intersects_prepared(countries, cities[:, None]) 1.27 ms ± 3.16 µs per loop (mean ± std. dev. of 7 runs, 1000 loops each)

So that shows a POC of having the prepared geometries in the same array, and also shows the nice speed-up that you can get from that!

Some additional thoughts on this:

It gives some additional memory usage, also when not using prepared geometries (the extra static attribute). If your geometries have a certain size (eg for polygons), this will probably not be very significant, but for points it might be more substantial.

I now made a separate intersects_prepared version, mainly to be able to compare with the existing intersects. In principle, this can be a single function that can handle both (it seems the extra check doesn't give much slowdown, at least on this test case)

I added a ufunc to prepare the geometries (based on https://github.com/pygeos/pygeos/pull/84/). We maybe also want to "unprepare" in case you want to get rid of some memory usage. But in principle, the predicates that support prepared geoms could also "prepare on the fly". That might make it even easier for the user, but gives a bit less control. Most of the time you probably just want that pygeos does it under the hood for you, but there might be cases where prepared geoms are less interesting (I am not too familiar on this, we should probably try to get some good test data of various kinds for such things).

It modifies the Geometry objects inplace in some way. It doesn't change their meaning, though (it doesn't change coordinates), so I would say this doesn't violate the principle of an immutable geometry object.
opened by jorisvandenbossche 22
ENH: add wkt / wkb ufuncs

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)

opened by jorisvandenbossche 20
Support pickling
Closes #46

After a failed approach with __getstate__ and __setstate__, I chose for the __reduce__ route. __setstate__ does not play nice with the fact that our geometry objects are immutable. Further reading: https://docs.python.org/3/library/pickle.html#pickling-class-instances

__reduce__ should return a tuple (callable, args). A convenient way for us would be the following:

(pygeos.lib.Geometry, ("<WKT>", ))

However, WKT serialization is less efficient than WKB serialization. We could opt for:

(pygeos.lib.from_wkb, (b"<WKB>", ))

When testing these approaches, a noticed that both of them have drawbacks.

WKT does not support SRID serialization and it has an issue with empty points in multipoints (#171).

WKB does not support linearrings

I am still in favour of going the WKB route. Do we accept that linearrings gets transformed into linestrings when pickled-unpickled?

>>> import pickle, pygeos >>> g = pygeos.linearrings([[(0, 0), (0, 1), (1, 1), (0, 0)]]) >>> pickle.loads(pickle.dumps(g)) array([<pygeos.Geometry LINESTRING (0 0, 0 1, 1 1, 0 0)>], dtype=object)
opened by caspervdw 18
ENH: query tree with multiple input geometries
This adds a first pass at bulk query against STRtree instance, as the core of a spatial join function for #52.

This extends the functionality of the existing STRtree::query() method to handle multiple input geometries. It returns a tuple of source (left) indexes and target (right) indexes that either overlap the windows of the sources, or also meet the predicate function provided.

Example:

tree = pygeos.STRtree(pygeos.points(np.arange(10), np.arange(10))) tree.query_bulk([pygeos.points(1, 1)]) # returns: (array([0]), array([1]))

Multiple source geometries, first and third boxes overlap windows:

tree.query_bulk([ pygeos.box(0,0, 1,1), pygeos.box(100,100,110,110), pygeos.box(2,2,4,4) ]) # returns: (array([0, 0, 2, 2, 2]), array([0, 1, 2, 3, 4]))

This preserves the original query() function as a singular operation.

/cc: @jorisvandenbossche
opened by brendan-ward 18
Added STRtree::nearest function

This is one of a few variants of nearest neighbor functionality based on the STRtree.

This version wraps the GEOS nearest neighbor functionality and returns the index of the nearest item in the tree.

Right now this is limited to a singular geometry operation. I'm considering changing that to a bulk geometry operation (given array of source geometries, return nearest neighbor index for each), which would likely be more useful.

Other variants that return multiple neighbors for each source geometry could be handled in a later PR.

opened by brendan-ward 17

RuntimeWarning: overflow encountered in distance

I am getting RuntimeWarning: overflow encountered in distance, sometimes followed by RuntimeWarning: invalid value encountered in distance when doing distance on some real-life geometries. MRE below:

>>> x, y = 1, 6
>>> g1 = pygeos.box(x, y, x+1, y+1)
>>> g2 = pygeos.box(x-1, y-1, x-1, y-1)

>>> pygeos.distance(g1, g2)

/opt/miniconda3/envs/stable/lib/python3.9/site-packages/pygeos/measurement.py:70: RuntimeWarning: overflow encountered in distance
  return lib.distance(a, b, **kwargs)
/opt/miniconda3/envs/stable/lib/python3.9/site-packages/pygeos/measurement.py:70: RuntimeWarning: invalid value encountered in distance
  return lib.distance(a, b, **kwargs)
1.4142135623730951

The result is correct but the errors are confusing and tend to spam the feed. I see the same on macOS and Ubuntu (details below).

macOS environemnt:

SYSTEM INFO
-----------
python     : 3.9.6 | packaged by conda-forge | (default, Jul 11 2021, 03:36:15)  [Clang 11.1.0 ]
executable : /opt/miniconda3/envs/stable/bin/python
machine    : macOS-11.6-x86_64-i386-64bit

GEOS, GDAL, PROJ INFO
---------------------
GEOS       : 3.9.1
GEOS lib   : /opt/miniconda3/envs/stable/lib/libgeos_c.dylib
GDAL       : 3.3.1
GDAL data dir: /opt/miniconda3/envs/stable/share/gdal
PROJ       : 8.0.1
PROJ data dir: /opt/miniconda3/envs/stable/share/proj

PYTHON DEPENDENCIES
-------------------
geopandas  : 0.10.0
pandas     : 1.3.2
fiona      : 1.8.20
numpy      : 1.21.2
shapely    : 1.7.1
rtree      : 0.9.7
pyproj     : 3.1.0
matplotlib : 3.4.3
mapclassify: 2.4.3
geopy      : None
psycopg2   : None
geoalchemy2: None
pyarrow    : None
pygeos     : 0.10.2

# packages in environment at /opt/miniconda3/envs/stable:
#
# Name                    Version                   Build  Channel
access                    1.1.3              pyhd8ed1ab_0    conda-forge
affine                    2.3.0                      py_0    conda-forge
alabaster                 0.7.12                     py_0    conda-forge
amply                     0.1.4                      py_0    conda-forge
anyio                     3.3.0            py39h6e9494a_0    conda-forge
appnope                   0.1.2            py39h6e9494a_1    conda-forge
argon2-cffi               20.1.0           py39h89e85a6_2    conda-forge
async_generator           1.10                       py_0    conda-forge
attrs                     20.3.0             pyhd3deb0d_0    conda-forge
babel                     2.9.1              pyh44b312d_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.9.3              pyhb0f4dca_0    conda-forge
bleach                    4.0.0              pyhd8ed1ab_0    conda-forge
blosc                     1.21.0               he49afe7_0    conda-forge
bokeh                     2.3.3            py39h6e9494a_0    conda-forge
boost-cpp                 1.74.0               hff03dee_4    conda-forge
branca                    0.4.2              pyhd8ed1ab_0    conda-forge
brotlipy                  0.7.0           py39h89e85a6_1001    conda-forge
bs4                       4.9.3                         0    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
c-ares                    1.17.2               h0d85af4_0    conda-forge
ca-certificates           2021.5.30            h033912b_0    conda-forge
cairo                     1.16.0            he43a7df_1008    conda-forge
certifi                   2021.5.30        py39h6e9494a_0    conda-forge
cffi                      1.14.6           py39hb71fe58_0    conda-forge
cfitsio                   3.470                h01dc385_7    conda-forge
chardet                   4.0.0            py39h6e9494a_1    conda-forge
charset-normalizer        2.0.0              pyhd8ed1ab_0    conda-forge
click                     7.1.2              pyh9f0ad1d_0    conda-forge
click-completion          0.5.2            py39h6e9494a_2    conda-forge
click-log                 0.3.2              pyh9f0ad1d_0    conda-forge
click-plugins             1.1.1                      py_0    conda-forge
cligj                     0.7.2              pyhd8ed1ab_0    conda-forge
cloudpickle               1.6.0                      py_0    conda-forge
coincbc                   2.10.5               h35dd71c_1    conda-forge
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
conda                     4.10.3           py39h6e9494a_0    conda-forge
conda-package-handling    1.7.3            py39h89e85a6_0    conda-forge
coverage                  5.5              py39h89e85a6_0    conda-forge
cryptography              3.4.7            py39ha2c9959_0    conda-forge
curl                      7.78.0               hb861fe1_0    conda-forge
cycler                    0.10.0                     py_2    conda-forge
cytoolz                   0.11.0           py39h89e85a6_3    conda-forge
dask                      2021.8.0           pyhd8ed1ab_0    conda-forge
dask-core                 2021.8.0           pyhd8ed1ab_0    conda-forge
dataclasses               0.8                pyhc8e2a94_3    conda-forge
dbus                      1.13.6               ha13b53f_2    conda-forge
debugpy                   1.4.1            py39h9fcab8e_0    conda-forge
decorator                 4.4.2                      py_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
deprecation               2.1.0              pyh9f0ad1d_0    conda-forge
descartes                 1.1.0                      py_4    conda-forge
distributed               2021.8.0         py39h6e9494a_0    conda-forge
docutils                  0.16             py39h6e9494a_3    conda-forge
entrypoints               0.3             py39hde42818_1002    conda-forge
esda                      2.4.1              pyhd8ed1ab_0    conda-forge
expat                     2.4.1                he49afe7_0    conda-forge
fiona                     1.8.20           py39h10412eb_1    conda-forge
folium                    0.12.0             pyhd8ed1ab_1    conda-forge
fontconfig                2.13.1            h10f422b_1005    conda-forge
freetype                  2.10.4               h4cff582_1    conda-forge
freexl                    1.0.6                h0d85af4_0    conda-forge
fsspec                    2021.7.0           pyhd8ed1ab_0    conda-forge
gdal                      3.3.1            py39h0530131_1    conda-forge
geopandas                 0.10.0             pyhd8ed1ab_0    conda-forge
geopandas-base            0.10.0             pyha770c72_0    conda-forge
geos                      3.9.1                he49afe7_2    conda-forge
geotiff                   1.6.0                h26421ea_6    conda-forge
gettext                   0.19.8.1          h7937167_1005    conda-forge
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gitpython                 3.1.18             pyhd8ed1ab_0    conda-forge
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hdf5                      1.10.6          nompi_hc5d9132_1114    conda-forge
heapdict                  1.0.1                      py_0    conda-forge
icu                       68.1                 h74dc148_0    conda-forge
idna                      3.1                pyhd3deb0d_0    conda-forge
imagesize                 1.2.0                      py_0    conda-forge
importlib-metadata        4.6.4            py39h6e9494a_0    conda-forge
importlib_resources       3.3.1            py39h6e9494a_0    conda-forge
inequality                1.0.0                      py_0    conda-forge
iniconfig                 1.1.1              pyh9f0ad1d_0    conda-forge
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ipython                   7.26.0           py39h71a6800_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
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joblib                    1.0.1              pyhd8ed1ab_0    conda-forge
jpeg                      9d                   hbcb3906_0    conda-forge
json-c                    0.15                 hcb556a6_0    conda-forge
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jupyter                   1.0.0            py39h6e9494a_6    conda-forge
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jupyter-cache             0.4.3              pyhd8ed1ab_0    conda-forge
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jupyter-sphinx            0.3.2                      py_0    conda-forge
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jupyter_console           6.4.0              pyhd8ed1ab_0    conda-forge
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jupyterlab_widgets        1.0.0              pyhd8ed1ab_1    conda-forge
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kiwisolver                1.3.1            py39hf018cea_1    conda-forge
krb5                      1.19.2               hcfbf3a7_0    conda-forge
latexcodec                2.0.1              pyh9f0ad1d_0    conda-forge
lcms2                     2.12                 h577c468_0    conda-forge
lerc                      2.2.1                h046ec9c_0    conda-forge
libarchive                3.5.1                h2b60450_2    conda-forge
libblas                   3.9.0           11_osx64_openblas    conda-forge
libcblas                  3.9.0           11_osx64_openblas    conda-forge
libclang                  11.1.0          default_he082bbe_1    conda-forge
libcurl                   7.78.0               hf45b732_0    conda-forge
libcxx                    12.0.1               habf9029_0    conda-forge
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libgdal                   3.3.1                hd51e85c_1    conda-forge
libgfortran               5.0.0           9_3_0_h6c81a4c_23    conda-forge
libgfortran5              9.3.0               h6c81a4c_23    conda-forge
libglib                   2.68.4               hd556434_0    conda-forge
libiconv                  1.16                 haf1e3a3_0    conda-forge
libkml                    1.3.0             h8fd9edb_1014    conda-forge
liblapack                 3.9.0           11_osx64_openblas    conda-forge
libllvm10                 10.0.1               h009f743_3    conda-forge
libllvm11                 11.1.0               hd011deb_2    conda-forge
libnetcdf                 4.8.0           nompi_hb4d10b0_103    conda-forge
libnghttp2                1.43.0               h07e645a_0    conda-forge
libopenblas               0.3.17          openmp_h3351f45_1    conda-forge
libpng                    1.6.37               h7cec526_2    conda-forge
libpq                     13.3                 hea3049e_0    conda-forge
libpysal                  4.5.1              pyhd8ed1ab_0    conda-forge
librttopo                 1.1.0                h5413771_6    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libsolv                   0.7.19               hcf210ce_5    conda-forge
libspatialindex           1.9.3                he49afe7_4    conda-forge
libspatialite             5.0.1                h035f608_5    conda-forge
libssh2                   1.9.0                h52ee1ee_6    conda-forge
libtiff                   4.3.0                h1167814_0    conda-forge
libwebp-base              1.2.1                h0d85af4_0    conda-forge
libxml2                   2.9.12               h93ec3fd_0    conda-forge
libzip                    1.8.0                h8b0c345_0    conda-forge
linkify-it-py             1.0.1              pyhd8ed1ab_0    conda-forge
llvm-openmp               12.0.1               hda6cdc1_1    conda-forge
llvmlite                  0.36.0           py39h798a4f4_0    conda-forge
locket                    0.2.0                      py_2    conda-forge
lz4-c                     1.9.3                he49afe7_1    conda-forge
lzo                       2.10              haf1e3a3_1000    conda-forge
mamba                     0.15.3           py39hb671511_0    conda-forge
mapclassify               2.4.3              pyhd8ed1ab_0    conda-forge
markdown-it-py            0.6.2              pyhd8ed1ab_0    conda-forge
markupsafe                2.0.1            py39h89e85a6_0    conda-forge
matplotlib-base           3.4.3            py39hb07454d_0    conda-forge
matplotlib-inline         0.1.2              pyhd8ed1ab_2    conda-forge
mdit-py-plugins           0.2.6              pyhd8ed1ab_0    conda-forge
mgwr                      2.1.2                      py_0    conda-forge
mistune                   0.8.4           py39h89e85a6_1004    conda-forge
mock                      4.0.3            py39h6e9494a_1    conda-forge
momepy                    0.5.0              pyhd8ed1ab_1    conda-forge
more-itertools            8.8.0              pyhd8ed1ab_0    conda-forge
mpc                       1.1.0             ha57cd0f_1009    conda-forge
mpfr                      4.1.0                h0f52abe_0    conda-forge
mpmath                    1.2.1              pyhd8ed1ab_0    conda-forge
msgpack-python            1.0.2            py39hf018cea_1    conda-forge
munch                     2.5.0                      py_0    conda-forge
mysql-common              8.0.25               h694c41f_2    conda-forge
mysql-libs                8.0.25               h115446f_2    conda-forge
myst-nb                   0.12.3             pyhd8ed1ab_0    conda-forge
myst-parser               0.13.7             pyhd8ed1ab_0    conda-forge
nbclient                  0.5.4              pyhd8ed1ab_0    conda-forge
nbconvert                 5.6.0                      py_0    conda-forge
nbdime                    3.1.0              pyhd8ed1ab_0    conda-forge
nbformat                  5.1.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.2                  h2e338ed_4    conda-forge
nest-asyncio              1.5.1              pyhd8ed1ab_0    conda-forge
networkx                  2.6.2              pyhd8ed1ab_0    conda-forge
nose                      1.3.7                   py_1006    conda-forge
notebook                  6.4.3              pyha770c72_0    conda-forge
nspr                      4.30                 hcd9eead_0    conda-forge
nss                       3.69                 h31e2bf1_0    conda-forge
numba                     0.53.1           py39h32e38f5_1    conda-forge
numexpr                   2.7.3            py39h4d6be9b_0    conda-forge
numpy                     1.21.2           py39h7eed0ac_0    conda-forge
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openjpeg                  2.4.0                h6e7aa92_1    conda-forge
openssl                   1.1.1l               h0d85af4_0    conda-forge
packaging                 21.0               pyhd8ed1ab_0    conda-forge
pandas                    1.3.2            py39h4d6be9b_0    conda-forge
pandoc                    2.14.1               h0d85af4_0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
parso                     0.8.2              pyhd8ed1ab_0    conda-forge
partd                     1.2.0              pyhd8ed1ab_0    conda-forge
patsy                     0.5.1                      py_0    conda-forge
pcre                      8.45                 he49afe7_0    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5           py39hde42818_1002    conda-forge
pillow                    8.3.1            py39he9bb72f_0    conda-forge
pip                       21.2.4             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               hbcb3906_0    conda-forge
pluggy                    0.13.1           py39h6e9494a_4    conda-forge
pointpats                 2.2.0                      py_0    conda-forge
poppler                   21.03.0              h640f9a4_0    conda-forge
poppler-data              0.4.10                        0    conda-forge
postgresql                13.3                 he8fe76e_0    conda-forge
proj                      8.0.1                h1512c50_0    conda-forge
prometheus_client         0.11.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.19             pyha770c72_0    conda-forge
prompt_toolkit            3.0.19               hd8ed1ab_0    conda-forge
psutil                    5.8.0            py39h89e85a6_1    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pulp                      2.5.0            py39h6e9494a_0    conda-forge
py                        1.10.0             pyhd3deb0d_0    conda-forge
pybtex                    0.24.0           py39h6e9494a_0    conda-forge
pybtex-docutils           1.0.1            py39h6e9494a_0    conda-forge
pycosat                   0.6.3           py39h89e85a6_1006    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pydata-sphinx-theme       0.6.3              pyhd8ed1ab_0    conda-forge
pygeos                    0.10.2a2                  dev_0    <develop>
pygments                  2.10.0             pyhd8ed1ab_0    conda-forge
pyopenssl                 20.0.1             pyhd8ed1ab_0    conda-forge
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
pypdf2                    1.26.0                     py_2    conda-forge
pyproj                    3.1.0            py39h7b8b08e_4    conda-forge
pyqt                      5.12.3           py39h6e9494a_7    conda-forge
pyqt-impl                 5.12.3           py39hef7122c_7    conda-forge
pyqt5-sip                 4.19.18          py39hd8f94c5_7    conda-forge
pyqtchart                 5.12             py39hef7122c_7    conda-forge
pyqtwebengine             5.12.1           py39hef7122c_7    conda-forge
pyrsistent                0.17.3           py39h89e85a6_2    conda-forge
pysal                     2.5.0              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1            py39h6e9494a_3    conda-forge
pytables                  3.6.1            py39hd07922a_3    conda-forge
pytest                    6.2.4            py39h6e9494a_0    conda-forge
pytest-cov                2.12.1             pyhd8ed1ab_0    conda-forge
python                    3.9.6           hd187cdc_1_cpython    conda-forge
python-dateutil           2.8.0                      py_0    conda-forge
python_abi                3.9                      2_cp39    conda-forge
pytz                      2021.1             pyhd8ed1ab_0    conda-forge
pyyaml                    5.4.1            py39h89e85a6_1    conda-forge
pyzmq                     22.2.1           py39h7fec2f1_0    conda-forge
qt                        5.12.9               h126340a_4    conda-forge
qtconsole                 5.1.1              pyhd8ed1ab_0    conda-forge
qtpy                      1.10.0             pyhd8ed1ab_0    conda-forge
quantecon                 0.5.1            py39h6e9494a_0    conda-forge
rasterio                  1.2.6            py39h906574e_2    conda-forge
rasterstats               0.15.0             pyhd8ed1ab_0    conda-forge
readline                  8.1                  h05e3726_0    conda-forge
reproc                    14.2.1               hbcb3906_0    conda-forge
reproc-cpp                14.2.1               h2e338ed_0    conda-forge
requests                  2.26.0             pyhd8ed1ab_0    conda-forge
requests-unixsocket       0.2.0                      py_0    conda-forge
rtree                     0.9.7            py39h7d0d40a_2    conda-forge
ruamel_yaml               0.15.80         py39h89e85a6_1004    conda-forge
rvlib                     0.0.5            py39hc89836e_0    conda-forge
scikit-learn              0.24.2           py39hd4eea88_1    conda-forge
scipy                     1.7.1            py39h056f1c0_0    conda-forge
seaborn                   0.11.2               hd8ed1ab_0    conda-forge
seaborn-base              0.11.2             pyhd8ed1ab_0    conda-forge
segregation               2.1.0              pyhd8ed1ab_0    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                57.4.0           py39h6e9494a_0    conda-forge
shapely                   1.7.1            py39h1d9c377_5    conda-forge
shellingham               1.4.0              pyh44b312d_0    conda-forge
simplejson                3.17.3           py39h89e85a6_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
smmap                     3.0.5              pyh44b312d_0    conda-forge
snakeviz                  2.1.0              pyh9f0ad1d_0    conda-forge
sniffio                   1.2.0            py39h6e9494a_1    conda-forge
snowballstemmer           2.1.0              pyhd8ed1ab_0    conda-forge
snuggs                    1.4.7                      py_0    conda-forge
sortedcontainers          2.4.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.0.1                      py_1    conda-forge
spaghetti                 1.6.2              pyhd8ed1ab_0    conda-forge
spglm                     1.0.8                      py_0    conda-forge
sphinx                    3.5.4              pyh44b312d_0    conda-forge
sphinx-book-theme         0.1.3              pyhd8ed1ab_0    conda-forge
sphinx-comments           0.0.3              pyh9f0ad1d_0    conda-forge
sphinx-copybutton         0.4.0              pyhd8ed1ab_0    conda-forge
sphinx-external-toc       0.2.3              pyhd8ed1ab_0    conda-forge
sphinx-jupyterbook-latex  0.4.2              pyhd8ed1ab_1    conda-forge
sphinx-multitoc-numbering 0.1.3              pyhd8ed1ab_0    conda-forge
sphinx-panels             0.5.2              pyhd3deb0d_0    conda-forge
sphinx-thebe              0.0.10             pyhd8ed1ab_0    conda-forge
sphinx-togglebutton       0.2.3              pyhd3deb0d_0    conda-forge
sphinxcontrib-applehelp   1.0.2                      py_0    conda-forge
sphinxcontrib-bibtex      2.2.1              pyhd8ed1ab_0    conda-forge
sphinxcontrib-devhelp     1.0.2                      py_0    conda-forge
sphinxcontrib-htmlhelp    2.0.0              pyhd8ed1ab_0    conda-forge
sphinxcontrib-jsmath      1.0.1                      py_0    conda-forge
sphinxcontrib-qthelp      1.0.3                      py_0    conda-forge
sphinxcontrib-serializinghtml 1.1.5              pyhd8ed1ab_0    conda-forge
spint                     1.0.7              pyhd8ed1ab_0    conda-forge
splot                     1.1.4              pyhd8ed1ab_0    conda-forge
spopt                     0.1.2              pyhd8ed1ab_0    conda-forge
spreg                     1.2.4              pyhd8ed1ab_0    conda-forge
spvcm                     0.3.0                      py_0    conda-forge
sqlalchemy                1.3.23           py39h4b0b724_0    conda-forge
sqlite                    3.36.0               h23a322b_0    conda-forge
statsmodels               0.12.2           py39h329c335_0    conda-forge
sympy                     1.8              py39h6e9494a_0    conda-forge
tblib                     1.7.0              pyhd8ed1ab_0    conda-forge
terminado                 0.11.1           py39h6e9494a_0    conda-forge
testpath                  0.5.0              pyhd8ed1ab_0    conda-forge
threadpoolctl             2.2.0              pyh8a188c0_0    conda-forge
tiledb                    2.3.3                h8370e7a_0    conda-forge
tk                        8.6.10               h0419947_1    conda-forge
tobler                    0.8.2              pyhd8ed1ab_0    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
toolz                     0.11.1                     py_0    conda-forge
tornado                   6.1              py39h89e85a6_1    conda-forge
tqdm                      4.62.1             pyhd8ed1ab_0    conda-forge
traitlets                 5.0.5                      py_0    conda-forge
typing_extensions         3.10.0.0           pyha770c72_0    conda-forge
tzcode                    2021a                h0d85af4_2    conda-forge
tzdata                    2021a                he74cb21_1    conda-forge
uc-micro-py               1.0.1              pyhd8ed1ab_0    conda-forge
urllib3                   1.25.11                    py_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          0.57.0           py39h6e9494a_4    conda-forge
wheel                     0.37.0             pyhd8ed1ab_1    conda-forge
widgetsnbextension        3.5.1            py39h6e9494a_4    conda-forge
xarray                    0.19.0             pyhd8ed1ab_1    conda-forge
xerces-c                  3.2.3                h379762d_2    conda-forge
xyzservices               2021.9.1           pyhd8ed1ab_0    conda-forge
xz                        5.2.5                haf1e3a3_1    conda-forge
yaml                      0.2.5                haf1e3a3_0    conda-forge
zeromq                    4.3.4                h1c7c35f_0    conda-forge
zict                      2.0.0                      py_0    conda-forge
zipp                      3.5.0              pyhd8ed1ab_0    conda-forge
zlib                      1.2.11            h7795811_1010    conda-forge
zstd                      1.5.0                h582d3a0_0    conda-forge

Ubuntu environment:

SYSTEM INFO
-----------
python     : 3.8.8 | packaged by conda-forge | (default, Feb 20 2021, 16:22:27)  [GCC 9.3.0]
executable : /opt/conda/bin/python
machine    : Linux-5.4.0-88-generic-x86_64-with-glibc2.10

GEOS, GDAL, PROJ INFO
---------------------
GEOS       : 3.9.0
GEOS lib   : /usr/lib/x86_64-linux-gnu/libgeos_c.so
GDAL       : 3.3.2
GDAL data dir: /opt/conda/share/gdal
PROJ       : 8.1.1
PROJ data dir: /opt/conda/share/proj

PYTHON DEPENDENCIES
-------------------
geopandas  : 0.10.0
pandas     : 1.3.3
fiona      : 1.8.20
numpy      : 1.20.3
shapely    : 1.7.1
rtree      : 0.9.7
pyproj     : 3.2.1
matplotlib : 3.4.3
mapclassify: 2.4.3
geopy      : 2.2.0
psycopg2   : 2.9.1 (dt dec pq3 ext lo64)
geoalchemy2: 0.8.4
pyarrow    : 5.0.0
pygeos     : 0.10.2

# packages in environment at /opt/conda:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                      1_llvm    conda-forge
ablog                     0.10.17                  pypi_0    pypi
abseil-cpp                20210324.2           h9c3ff4c_0    conda-forge
access                    1.1.3              pyhd8ed1ab_0    conda-forge
adal                      1.2.7              pyhd8ed1ab_0    conda-forge
affine                    2.3.0                      py_0    conda-forge
aiohttp                   3.7.4.post0      py38h497a2fe_0    conda-forge
alabaster                 0.7.12                   pypi_0    pypi
alembic                   1.7.3              pyhd8ed1ab_0    conda-forge
amply                     0.1.4                      py_0    conda-forge
amqp                      5.0.6              pyhd8ed1ab_0    conda-forge
anyio                     3.3.2            py38h578d9bd_0    conda-forge
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
argon2-cffi               20.1.0           py38h497a2fe_2    conda-forge
arrow-cpp                 5.0.0           py38h94c96a7_8_cpu    conda-forge
asciitree                 0.3.3                      py_2    conda-forge
async-timeout             3.0.1                   py_1000    conda-forge
async_generator           1.10                       py_0    conda-forge
attrs                     21.2.0             pyhd8ed1ab_0    conda-forge
aws-c-cal                 0.5.11               h95a6274_0    conda-forge
aws-c-common              0.6.2                h7f98852_0    conda-forge
aws-c-event-stream        0.2.7               h3541f99_13    conda-forge
aws-c-io                  0.10.5               hfb6a706_0    conda-forge
aws-checksums             0.1.11               ha31a3da_7    conda-forge
aws-sdk-cpp               1.8.186              hb4091e7_3    conda-forge
babel                     2.9.1              pyh44b312d_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
bcrypt                    3.2.0            py38h497a2fe_1    conda-forge
beautifulsoup4            4.10.0             pyha770c72_0    conda-forge
billiard                  3.6.4.0          py38h497a2fe_0    conda-forge
black                     21.9b0             pyhd8ed1ab_0    conda-forge
blas                      2.111                  openblas    conda-forge
blas-devel                3.9.0           11_linux64_openblas    conda-forge
bleach                    4.1.0              pyhd8ed1ab_0    conda-forge
blinker                   1.4                        py_1    conda-forge
blosc                     1.21.0               h9c3ff4c_0    conda-forge
bokeh                     2.4.0            py38h578d9bd_0    conda-forge
boost-cpp                 1.74.0               h312852a_4    conda-forge
boto3                     1.18.53            pyhd8ed1ab_0    conda-forge
botocore                  1.21.53            pyhd8ed1ab_0    conda-forge
bottleneck                1.3.2            py38h6c62de6_4    conda-forge
branca                    0.4.2              pyhd8ed1ab_0    conda-forge
brotli                    1.0.9                h7f98852_5    conda-forge
brotli-bin                1.0.9                h7f98852_5    conda-forge
brotlipy                  0.7.0           py38h497a2fe_1001    conda-forge
brunsli                   0.1                  he1b5a44_0    conda-forge
bs4                       4.10.0               hd8ed1ab_0    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.17.2               h7f98852_0    conda-forge
ca-certificates           2021.5.30            ha878542_0    conda-forge
cachetools                4.2.4              pyhd8ed1ab_0    conda-forge
cairo                     1.16.0            h6cf1ce9_1008    conda-forge
celery                    5.1.2              pyhd8ed1ab_0    conda-forge
cenpy                     1.0.0.post4                py_0    conda-forge
certifi                   2021.5.30        py38h578d9bd_0    conda-forge
certipy                   0.1.3                      py_0    conda-forge
cffi                      1.14.6           py38ha65f79e_0    conda-forge
cfitsio                   3.470                hb418390_7    conda-forge
cftime                    1.5.1            py38h6c62de6_0    conda-forge
chardet                   4.0.0            py38h578d9bd_1    conda-forge
charls                    2.2.0                h9c3ff4c_0    conda-forge
charset-normalizer        2.0.0              pyhd8ed1ab_0    conda-forge
click                     7.1.2              pyh9f0ad1d_0    conda-forge
click-didyoumean          0.0.3              pyh8c360ce_0    conda-forge
click-plugins             1.1.1                      py_0    conda-forge
click-repl                0.2.0              pyhd8ed1ab_0    conda-forge
cligj                     0.7.2              pyhd8ed1ab_0    conda-forge
cloudpickle               2.0.0              pyhd8ed1ab_0    conda-forge
clustergram               0.5.1              pyhd8ed1ab_0    conda-forge
coincbc                   2.10.5               hcee13e7_1    conda-forge
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
colorcet                  2.0.6              pyhd8ed1ab_0    conda-forge
conda                     4.9.2            py38h578d9bd_0    conda-forge
conda-package-handling    1.7.3            py38h497a2fe_0    conda-forge
configurable-http-proxy   4.5.0           node15_he6ea98c_0    conda-forge
contextily                1.1.0              pyhd8ed1ab_0    conda-forge
coverage                  6.0              py38h497a2fe_0    conda-forge
cryptography              3.4.7            py38ha5dfef3_0    conda-forge
curl                      7.79.1               h2574ce0_1    conda-forge
cycler                    0.10.0                     py_2    conda-forge
cykhash                   1.0.2            py38h950e882_2    conda-forge
cython                    0.29.24          py38h709712a_0    conda-forge
cytoolz                   0.11.0           py38h497a2fe_3    conda-forge
dask                      2021.9.1           pyhd8ed1ab_0    conda-forge
dask-core                 2021.9.1           pyhd8ed1ab_0    conda-forge
dask-geopandas            0.1.0a2                  pypi_0    pypi
dask-glm                  0.2.0                      py_1    conda-forge
dask-kubernetes           2021.3.1           pyhd8ed1ab_0    conda-forge
dask-ml                   1.9.0              pyhd8ed1ab_0    conda-forge
dataclasses               0.8                pyhc8e2a94_3    conda-forge
datacube                  1.8.6              pyhd8ed1ab_0    conda-forge
datashader                0.13.0             pyh6c4a22f_0    conda-forge
datashape                 0.5.4                      py_1    conda-forge
debugpy                   1.4.1            py38h709712a_0    conda-forge
decorator                 5.1.0              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
deprecation               2.1.0              pyh9f0ad1d_0    conda-forge
descartes                 1.1.0                      py_4    conda-forge
distributed               2021.9.1         py38h578d9bd_0    conda-forge
docutils                  0.17.1           py38h578d9bd_0    conda-forge
download                  0.3.5                    pypi_0    pypi
entrypoints               0.3             py38h32f6830_1002    conda-forge
esda                      2.4.1              pyhd8ed1ab_0    conda-forge
et_xmlfile                1.0.1                   py_1001    conda-forge
expat                     2.4.1                h9c3ff4c_0    conda-forge
fasteners                 0.16               pyhd8ed1ab_0    conda-forge
feather-format            0.4.1              pyh9f0ad1d_0    conda-forge
feedgen                   0.9.0                    pypi_0    pypi
fiona                     1.8.20           py38hbb147eb_1    conda-forge
flake8                    3.9.2              pyhd8ed1ab_0    conda-forge
folium                    0.12.0             pyhd8ed1ab_1    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.13.1            hba837de_1005    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
freexl                    1.0.6                h7f98852_0    conda-forge
fsspec                    2021.10.0          pyhd8ed1ab_0    conda-forge
fuzzywuzzy                0.18.0             pyhd8ed1ab_0    conda-forge
gdal                      3.3.2            py38h81a01a0_4    conda-forge
geoalchemy2               0.8.4                    pypi_0    pypi
geocube                   0.0.17             pyhd8ed1ab_0    conda-forge
geographiclib             1.52               pyhd8ed1ab_0    conda-forge
geopandas                 0.10.0             pyhd8ed1ab_0    conda-forge
geopandas-base            0.10.0             pyha770c72_0    conda-forge
geopandas-view            0.0.1                    pypi_0    pypi
geopy                     2.2.0              pyhd8ed1ab_0    conda-forge
geos                      3.9.1                h9c3ff4c_2    conda-forge
geotiff                   1.7.0                hcfb7246_3    conda-forge
gettext                   0.19.8.1          h0b5b191_1005    conda-forge
gflags                    2.2.2             he1b5a44_1004    conda-forge
giddy                     2.3.3                      py_0    conda-forge
giflib                    5.2.1                h516909a_2    conda-forge
gitdb                     4.0.7              pyhd8ed1ab_0    conda-forge
gitpython                 3.1.24             pyhd8ed1ab_0    conda-forge
glog                      0.5.0                h48cff8f_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
gmpy2                     2.1.0b5          py38h8384b0a_0    conda-forge
google-auth               2.2.1              pyh6c4a22f_0    conda-forge
greenlet                  1.1.2            py38h709712a_0    conda-forge
grpc-cpp                  1.40.0               h05f19cf_2    conda-forge
h3-py                     3.7.3            py38h709712a_1    conda-forge
hdbscan                   0.8.27           py38h5c078b8_0    conda-forge
hdf4                      4.2.15               h10796ff_3    conda-forge
hdf5                      1.12.1          nompi_h2750804_100    conda-forge
heapdict                  1.0.1                      py_0    conda-forge
icu                       68.1                 h58526e2_0    conda-forge
idna                      3.1                pyhd3deb0d_0    conda-forge
imagecodecs               2021.7.30        py38hb5ce8f7_1    conda-forge
imageio                   2.9.0                      py_0    conda-forge
imagesize                 1.2.0                    pypi_0    pypi
importlib-metadata        4.8.1            py38h578d9bd_0    conda-forge
importlib_resources       5.2.2              pyhd8ed1ab_0    conda-forge
inequality                1.0.0                      py_0    conda-forge
iniconfig                 1.1.1              pyh9f0ad1d_0    conda-forge
intake                    0.6.3              pyhd8ed1ab_0    conda-forge
intake-stac               0.3.0                      py_0    conda-forge
intake-xarray             0.5.0              pyhd8ed1ab_0    conda-forge
invoke                    1.5.0                    pypi_0    pypi
ipykernel                 6.4.1            py38he5a9106_0    conda-forge
ipyleaflet                0.14.0             pyhd8ed1ab_1    conda-forge
ipympl                    0.8.0              pyhd8ed1ab_0    conda-forge
ipyparallel               7.1.0              pyhd8ed1ab_0    conda-forge
ipyspin                   0.1.5              pyhd8ed1ab_0    conda-forge
ipython                   7.28.0           py38he5a9106_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipyurl                    0.1.2              pyhc268e32_1    conda-forge
ipywidgets                7.6.5              pyhd8ed1ab_0    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
jdcal                     1.4.1                      py_0    conda-forge
jedi                      0.18.0           py38h578d9bd_2    conda-forge
jinja2                    3.0.1              pyhd8ed1ab_0    conda-forge
jmespath                  0.10.0             pyh9f0ad1d_0    conda-forge
joblib                    1.0.1              pyhd8ed1ab_0    conda-forge
jpeg                      9d                   h516909a_0    conda-forge
json-c                    0.15                 h98cffda_0    conda-forge
json5                     0.9.5              pyh9f0ad1d_0    conda-forge
jsonschema                4.0.1              pyhd8ed1ab_0    conda-forge
jupyter-book              0.10.1                   pypi_0    pypi
jupyter-cache             0.4.2                    pypi_0    pypi
jupyter-packaging         0.10.6             pyhd8ed1ab_0    conda-forge
jupyter-server-mathjax    0.2.3              pyhd8ed1ab_0    conda-forge
jupyter-server-proxy      3.1.0              pyhd8ed1ab_0    conda-forge
jupyter-sphinx            0.3.1                    pypi_0    pypi
jupyter_bokeh             3.0.2              pyhd8ed1ab_0    conda-forge
jupyter_client            7.0.5              pyhd8ed1ab_0    conda-forge
jupyter_core              4.8.1            py38h578d9bd_0    conda-forge
jupyter_server            1.11.0             pyhd8ed1ab_0    conda-forge
jupyter_telemetry         0.1.0              pyhd8ed1ab_1    conda-forge
jupyterhub                1.4.2            py38h578d9bd_0    conda-forge
jupyterhub-base           1.4.2            py38h578d9bd_0    conda-forge
jupyterlab                3.1.14             pyhd8ed1ab_0    conda-forge
jupyterlab-geojson        3.1.2                    pypi_0    pypi
jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge
jupyterlab_server         2.8.2              pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        1.0.2              pyhd8ed1ab_0    conda-forge
jupytext                  1.13.0             pyhd0ecf6b_0    conda-forge
jxrlib                    1.1                  h516909a_2    conda-forge
kealib                    1.4.14               h87e4c3c_3    conda-forge
kiwisolver                1.3.2            py38h1fd1430_0    conda-forge
kombu                     5.1.0            py38h578d9bd_0    conda-forge
krb5                      1.19.2               hcc1bbae_2    conda-forge
kubernetes_asyncio        18.20.0            pyhd8ed1ab_0    conda-forge
lark-parser               0.12.0             pyhd8ed1ab_0    conda-forge
latexcodec                2.0.1                    pypi_0    pypi
lckr-jupyterlab-variableinspector 3.0.6                    pypi_0    pypi
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
legendgram                0.0.3                      py_1    conda-forge
lerc                      2.2.1                h9c3ff4c_0    conda-forge
libaec                    1.0.6                h9c3ff4c_0    conda-forge
libarchive                3.5.2                hccf745f_1    conda-forge
libblas                   3.9.0           11_linux64_openblas    conda-forge
libbrotlicommon           1.0.9                h7f98852_5    conda-forge
libbrotlidec              1.0.9                h7f98852_5    conda-forge
libbrotlienc              1.0.9                h7f98852_5    conda-forge
libcblas                  3.9.0           11_linux64_openblas    conda-forge
libcurl                   7.79.1               h2574ce0_1    conda-forge
libdap4                   3.20.6               hd7c4107_2    conda-forge
libdeflate                1.7                  h7f98852_5    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.10               hcdb4288_3    conda-forge
libffi                    3.3                  h58526e2_2    conda-forge
libgcc-ng                 11.2.0               h1d223b6_9    conda-forge
libgdal                   3.3.2                h9c9eb65_4    conda-forge
libgfortran-ng            11.2.0               h69a702a_9    conda-forge
libgfortran5              11.2.0               h5c6108e_9    conda-forge
libglib                   2.68.4               h3e27bee_0    conda-forge
libgomp                   11.2.0               h1d223b6_9    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
libkml                    1.3.0             h238a007_1014    conda-forge
liblapack                 3.9.0           11_linux64_openblas    conda-forge
liblapacke                3.9.0           11_linux64_openblas    conda-forge
libllvm10                 10.0.1               he513fc3_3    conda-forge
libllvm11                 11.1.0               hf817b99_2    conda-forge
libnetcdf                 4.8.1           nompi_hb3fd0d9_101    conda-forge
libnghttp2                1.43.0               h812cca2_1    conda-forge
libopenblas               0.3.17          pthreads_h8fe5266_1    conda-forge
libpng                    1.6.37               hed695b0_2    conda-forge
libpq                     13.3                 hd57d9b9_0    conda-forge
libprotobuf               3.18.0               h780b84a_1    conda-forge
libpysal                  4.5.1              pyhd8ed1ab_0    conda-forge
librttopo                 1.1.0                h1185371_6    conda-forge
libsodium                 1.0.18               h516909a_1    conda-forge
libsolv                   0.7.19               h780b84a_5    conda-forge
libspatialindex           1.9.3                h9c3ff4c_4    conda-forge
libspatialite             5.0.1                h8796b1e_9    conda-forge
libssh2                   1.10.0               ha56f1ee_2    conda-forge
libstdcxx-ng              11.2.0               he4da1e4_9    conda-forge
libthrift                 0.15.0               he6d91bd_0    conda-forge
libtiff                   4.3.0                hf544144_1    conda-forge
libutf8proc               2.6.1                h7f98852_0    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libuv                     1.41.1               h7f98852_0    conda-forge
libwebp-base              1.2.1                h7f98852_0    conda-forge
libxcb                    1.13              h7f98852_1003    conda-forge
libxml2                   2.9.12               h72842e0_0    conda-forge
libxslt                   1.1.33               h15afd5d_2    conda-forge
libzip                    1.8.0                h4de3113_1    conda-forge
libzlib                   1.2.11            h36c2ea0_1013    conda-forge
libzopfli                 1.0.3                he1b5a44_0    conda-forge
linkify-it-py             1.0.1                    pypi_0    pypi
llvm-openmp               12.0.1               h4bd325d_1    conda-forge
llvmlite                  0.37.0           py38h4630a5e_0    conda-forge
locket                    0.2.0                      py_2    conda-forge
lxml                      4.6.3            py38hf1fe3a4_0    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
mako                      1.1.5              pyhd8ed1ab_0    conda-forge
mamba                     0.16.0           py38h2aa5da1_0    conda-forge
mapclassify               2.4.3              pyhd8ed1ab_0    conda-forge
markdown-it-py            1.1.0              pyhd8ed1ab_0    conda-forge
markupsafe                2.0.1            py38h497a2fe_0    conda-forge
matplotlib-base           3.4.3            py38hf4fb855_1    conda-forge
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
matplotlib-scalebar       0.7.2                    pypi_0    pypi
mccabe                    0.6.1                      py_1    conda-forge
mdit-py-plugins           0.2.8              pyhd8ed1ab_0    conda-forge
mercantile                1.2.1              pyhd8ed1ab_0    conda-forge
mgwr                      2.1.2                      py_0    conda-forge
mistune                   0.8.4           py38h497a2fe_1004    conda-forge
mock                      4.0.3            py38h578d9bd_1    conda-forge
momepy                    0.5.0              pyhd8ed1ab_1    conda-forge
monotonic                 1.5                        py_0    conda-forge
more-itertools            8.10.0             pyhd8ed1ab_0    conda-forge
morecantile               3.0.0              pyhd8ed1ab_0    conda-forge
mpc                       1.2.1                h9f54685_0    conda-forge
mpfr                      4.1.0                h9202a9a_1    conda-forge
mpmath                    1.2.1              pyhd8ed1ab_0    conda-forge
msgpack-python            1.0.2            py38h1fd1430_1    conda-forge
multidict                 5.2.0            py38h497a2fe_0    conda-forge
multipledispatch          0.6.0                      py_0    conda-forge
munch                     2.5.0                      py_0    conda-forge
mypy_extensions           0.4.3            py38h578d9bd_3    conda-forge
myst-nb                   0.12.0                   pypi_0    pypi
myst-parser               0.13.5                   pypi_0    pypi
nbclassic                 0.3.2              pyhd8ed1ab_0    conda-forge
nbclient                  0.5.4              pyhd8ed1ab_0    conda-forge
nbconvert                 6.2.0            py38h578d9bd_0    conda-forge
nbdime                    3.1.0              pyhd8ed1ab_0    conda-forge
nbformat                  5.1.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
nest-asyncio              1.5.1              pyhd8ed1ab_0    conda-forge
nested-lookup             0.2.22                   pypi_0    pypi
netcdf4                   1.5.7           nompi_py38h2823cc8_103    conda-forge
networkx                  2.5                        py_0    conda-forge
nodejs                    15.14.0              h92b4a50_0    conda-forge
nose                      1.3.7           py38h32f6830_1004    conda-forge
notebook                  6.4.4              pyha770c72_0    conda-forge
nspr                      4.30                 h9c3ff4c_0    conda-forge
nss                       3.69                 hb5efdd6_1    conda-forge
numba                     0.54.0           py38h4bf6c61_0    conda-forge
numcodecs                 0.9.1            py38h709712a_0    conda-forge
numexpr                   2.7.3            py38h51da96c_0    conda-forge
numpy                     1.20.3           py38h9894fe3_1    conda-forge
oauthlib                  3.1.1              pyhd8ed1ab_0    conda-forge
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openblas                  0.3.17          pthreads_h4748800_1    conda-forge
openjpeg                  2.4.0                hb52868f_1    conda-forge
openpyxl                  3.0.9              pyhd8ed1ab_0    conda-forge
openssl                   1.1.1l               h7f98852_0    conda-forge
orc                       1.7.0                h68e2c4e_0    conda-forge
osmnet                    0.1.6                      py_0    conda-forge
osmnx                     1.1.1              pyhd8ed1ab_0    conda-forge
packaging                 21.0               pyhd8ed1ab_0    conda-forge
palettable                3.3.0                      py_0    conda-forge
pamela                    1.0.0                      py_0    conda-forge
pandana                   0.6.1            py38h1abd341_0    conda-forge
pandas                    1.3.3            py38h43a58ef_0    conda-forge
pandas-bokeh              0.5.4                    pypi_0    pypi
pandoc                    2.14.2               h7f98852_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
param                     1.11.1             pyh6c4a22f_0    conda-forge
paramiko                  2.7.2              pyh9f0ad1d_0    conda-forge
parquet-cpp               1.5.1                         1    conda-forge
parso                     0.8.2              pyhd8ed1ab_0    conda-forge
partd                     1.2.0              pyhd8ed1ab_0    conda-forge
pathspec                  0.9.0              pyhd8ed1ab_0    conda-forge
patsy                     0.5.2              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
pexpect                   4.8.0            py38h32f6830_1    conda-forge
pickleshare               0.7.5           py38h32f6830_1002    conda-forge
pillow                    8.3.2            py38h8e6f84c_0    conda-forge
pip                       21.2.4             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
platformdirs              2.3.0              pyhd8ed1ab_0    conda-forge
pluggy                    1.0.0            py38h578d9bd_1    conda-forge
pointpats                 2.2.0                      py_0    conda-forge
polyline                  1.4.0                      py_0    conda-forge
pooch                     1.5.1              pyhd8ed1ab_0    conda-forge
poppler                   21.09.0              ha39eefc_3    conda-forge
poppler-data              0.4.11               hd8ed1ab_0    conda-forge
postgresql                13.3                 h2510834_0    conda-forge
proj                      8.1.1                h277dcde_2    conda-forge
prometheus_client         0.11.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.20             pyha770c72_0    conda-forge
prompt_toolkit            3.0.20               hd8ed1ab_0    conda-forge
psutil                    5.8.0            py38h497a2fe_1    conda-forge
psycopg2                  2.9.1            py38h497a2fe_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pulp                      2.5.0            py38h578d9bd_0    conda-forge
py                        1.10.0             pyhd3deb0d_0    conda-forge
pyarrow                   5.0.0           py38h1bc9799_8_cpu    conda-forge
pyasn1                    0.4.8                      py_0    conda-forge
pyasn1-modules            0.2.7                      py_0    conda-forge
pybtex                    0.24.0                   pypi_0    pypi
pybtex-docutils           1.0.0                    pypi_0    pypi
pycodestyle               2.7.0              pyhd8ed1ab_0    conda-forge
pycosat                   0.6.3           py38h497a2fe_1006    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pyct                      0.4.8                      py_0    pyviz
pyct-core                 0.4.8                      py_0    pyviz
pycurl                    7.44.1           py38h996a351_0    conda-forge
pydantic                  1.8.2            py38h497a2fe_0    conda-forge
pydata-sphinx-theme       0.4.3                    pypi_0    pypi
pyee                      8.1.0              pyh9f0ad1d_0    conda-forge
pyflakes                  2.3.1              pyhd8ed1ab_0    conda-forge
pygeoda                   0.0.8                    pypi_0    pypi
pygeos                    0.10.2           py38hb7fe4a8_0    conda-forge
pygments                  2.10.0             pyhd8ed1ab_0    conda-forge
pyjwt                     2.1.0              pyhd8ed1ab_0    conda-forge
pynacl                    1.4.0            py38h497a2fe_2    conda-forge
pyopenssl                 21.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
pyppeteer                 0.2.6              pyhd8ed1ab_0    conda-forge
pyproj                    3.2.1            py38h80797bf_2    conda-forge
pyrobuf                   0.9.3            py38h709712a_2    conda-forge
pyrosm                    0.6.0            py38hadf7658_0    conda-forge
pyrsistent                0.17.3           py38h497a2fe_2    conda-forge
pysal                     2.5.0              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1            py38h578d9bd_3    conda-forge
pytables                  3.6.1            py38hdb04529_4    conda-forge
pytest                    6.2.5            py38h578d9bd_0    conda-forge
pytest-cov                3.0.0              pyhd8ed1ab_0    conda-forge
pytest-tornasync          0.6.0.post2              pypi_0    pypi
python                    3.8.8           hffdb5ce_0_cpython    conda-forge
python-dateutil           2.7.5                      py_0    conda-forge
python-editor             1.0.4                      py_0    conda-forge
python-json-logger        2.0.1              pyh9f0ad1d_0    conda-forge
python-kubernetes         18.20.0            pyhd8ed1ab_0    conda-forge
python-levenshtein        0.12.2           py38h497a2fe_0    conda-forge
python-rapidjson          1.4              py38h709712a_0    conda-forge
python-snappy             0.6.0            py38h49bdff1_0    conda-forge
python_abi                3.8                      2_cp38    conda-forge
pytz                      2021.1             pyhd8ed1ab_0    conda-forge
pyu2f                     0.1.5              pyhd8ed1ab_0    conda-forge
pywavelets                1.1.1            py38hab2c0dc_3    conda-forge
pyyaml                    5.4.1            py38h497a2fe_1    conda-forge
pyzmq                     22.3.0           py38h2035c66_0    conda-forge
quantecon                 0.5.1            py38h578d9bd_0    conda-forge
rasterio                  1.2.9            py38hfd64e68_2    conda-forge
rasterstats               0.15.0             pyhd8ed1ab_0    conda-forge
re2                       2021.09.01           h9c3ff4c_0    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
redis-py                  3.5.3              pyh9f0ad1d_0    conda-forge
regex                     2021.9.30        py38h497a2fe_0    conda-forge
reproc                    14.2.3               h7f98852_0    conda-forge
reproc-cpp                14.2.3               h9c3ff4c_0    conda-forge
requests                  2.26.0             pyhd8ed1ab_0    conda-forge
requests-oauthlib         1.3.0              pyh9f0ad1d_0    conda-forge
requests-unixsocket       0.2.0                      py_0    conda-forge
retrying                  1.3.3                      py_2    conda-forge
rio-cogeo                 3.0.0              pyhd8ed1ab_0    conda-forge
rioxarray                 0.7.1              pyhd8ed1ab_0    conda-forge
rpy2                      3.4.3                    pypi_0    pypi
rsa                       4.7.2              pyh44b312d_0    conda-forge
rtree                     0.9.7            py38h02d302b_2    conda-forge
ruamel.yaml               0.17.16          py38h497a2fe_0    conda-forge
ruamel.yaml.clib          0.2.2            py38h497a2fe_2    conda-forge
ruamel_yaml               0.15.80         py38h497a2fe_1004    conda-forge
rvlib                     0.0.5            py38h6c62de6_0    conda-forge
s2n                       1.0.10               h9b69904_0    conda-forge
s3transfer                0.5.0              pyhd8ed1ab_0    conda-forge
sat-stac                  0.4.1              pyh44b312d_0    conda-forge
scikit-image              0.18.3           py38h43a58ef_0    conda-forge
scikit-learn              1.0              py38hacb3eff_1    conda-forge
scipy                     1.7.1            py38h56a6a73_0    conda-forge
seaborn                   0.11.2               hd8ed1ab_0    conda-forge
seaborn-base              0.11.2             pyhd8ed1ab_0    conda-forge
segregation               2.1.0              pyhd8ed1ab_0    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                58.0.4           py38h578d9bd_2    conda-forge
shapely                   1.7.1            py38hb7fe4a8_5    conda-forge
simpervisor               0.4                pyhd8ed1ab_0    conda-forge
simplejson                3.17.5           py38h497a2fe_0    conda-forge
simplification            0.5.12                   pypi_0    pypi
six                       1.16.0             pyh6c4a22f_0    conda-forge
smmap                     3.0.5              pyh44b312d_0    conda-forge
snappy                    1.1.8                he1b5a44_3    conda-forge
sniffio                   1.2.0            py38h578d9bd_1    conda-forge
snowballstemmer           2.1.0                    pypi_0    pypi
snuggs                    1.4.7                      py_0    conda-forge
sortedcontainers          2.4.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.0.1            py38h32f6830_0    conda-forge
spaghetti                 1.6.4              pyhd8ed1ab_0    conda-forge
spatialpandas             0.4.3              pyhd8ed1ab_0    conda-forge
spglm                     1.0.8                      py_0    conda-forge
sphinx                    3.5.3                    pypi_0    pypi
sphinx-book-theme         0.0.42                   pypi_0    pypi
sphinx-comments           0.0.3                    pypi_0    pypi
sphinx-copybutton         0.3.1                    pypi_0    pypi
sphinx-panels             0.5.2                    pypi_0    pypi
sphinx-thebe              0.0.8                    pypi_0    pypi
sphinx-togglebutton       0.2.3                    pypi_0    pypi
sphinxcontrib-applehelp   1.0.2                    pypi_0    pypi
sphinxcontrib-bibtex      2.1.4                    pypi_0    pypi
sphinxcontrib-devhelp     1.0.2                    pypi_0    pypi
sphinxcontrib-htmlhelp    1.0.3                    pypi_0    pypi
sphinxcontrib-jsmath      1.0.1                    pypi_0    pypi
sphinxcontrib-qthelp      1.0.3                    pypi_0    pypi
sphinxcontrib-serializinghtml 1.1.4                    pypi_0    pypi
spint                     1.0.7              pyhd8ed1ab_0    conda-forge
splot                     1.1.4              pyhd8ed1ab_0    conda-forge
spopt                     0.1.2              pyhd8ed1ab_0    conda-forge
spreg                     1.2.4              pyhd8ed1ab_0    conda-forge
spvcm                     0.3.0                      py_0    conda-forge
sqlalchemy                1.4.25           py38h497a2fe_0    conda-forge
sqlite                    3.36.0               h9cd32fc_2    conda-forge
sshtunnel                 0.3.1              pyhd8ed1ab_0    conda-forge
statsmodels               0.13.0           py38h6c62de6_0    conda-forge
supermercado              0.2.0              pyh9f0ad1d_0    conda-forge
sympy                     1.8              py38h578d9bd_0    conda-forge
tabulate                  0.8.9              pyhd8ed1ab_0    conda-forge
tblib                     1.7.0              pyhd8ed1ab_0    conda-forge
terminado                 0.12.1           py38h578d9bd_0    conda-forge
testpath                  0.5.0              pyhd8ed1ab_0    conda-forge
threadpoolctl             3.0.0              pyh8a188c0_0    conda-forge
tifffile                  2021.8.30          pyhd8ed1ab_0    conda-forge
tiledb                    2.3.4                he87e0bf_0    conda-forge
tini                      0.18.0            h14c3975_1001    conda-forge
tk                        8.6.11               h27826a3_1    conda-forge
tobler                    0.7.0                    pypi_0    pypi
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     1.2.1              pyhd8ed1ab_0    conda-forge
tomlkit                   0.7.2            py38h578d9bd_0    conda-forge
toolz                     0.11.1                     py_0    conda-forge
topojson                  1.0                      pypi_0    pypi
tornado                   6.1              py38h497a2fe_1    conda-forge
tqdm                      4.62.3             pyhd8ed1ab_0    conda-forge
traitlets                 5.1.0              pyhd8ed1ab_0    conda-forge
traittypes                0.2.1              pyh9f0ad1d_2    conda-forge
typed-ast                 1.4.3            py38h497a2fe_0    conda-forge
typing-extensions         3.10.0.2             hd8ed1ab_0    conda-forge
typing_extensions         3.10.0.2           pyha770c72_0    conda-forge
tzcode                    2021a                h7f98852_2    conda-forge
tzdata                    2021b                he74cb21_0    conda-forge
uc-micro-py               1.0.1                    pypi_0    pypi
urbanaccess               0.2.2              pyhd3deb0d_0    conda-forge
urbangrammar-graphics     1.2.2                    pypi_0    pypi
urllib3                   1.25.11                    py_0    conda-forge
vine                      5.0.0              pyhd8ed1ab_1    conda-forge
watchdog                  2.0.2                    pypi_0    pypi
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          0.57.0           py38h578d9bd_4    conda-forge
websockets                9.1              py38h497a2fe_0    conda-forge
wheel                     0.37.0             pyhd8ed1ab_1    conda-forge
widgetsnbextension        3.5.1            py38h578d9bd_4    conda-forge
xarray                    0.19.0             pyhd8ed1ab_1    conda-forge
xarray-spatial            0.1.8              pyhd8ed1ab_0    conda-forge
xarray_leaflet            0.1.15             pyhd8ed1ab_0    conda-forge
xerces-c                  3.2.3                h9d8b166_2    conda-forge
xlrd                      2.0.1              pyhd8ed1ab_3    conda-forge
xlsxwriter                3.0.1              pyhd8ed1ab_0    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.10               h516909a_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.7.2                h7f98852_0    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
xorg-libxext              1.3.4                h7f98852_1    conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xyzservices               2021.9.1           pyhd8ed1ab_0    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
yaml                      0.2.5                h516909a_0    conda-forge
yarl                      1.6.3            py38h497a2fe_2    conda-forge
zarr                      2.10.1             pyhd8ed1ab_0    conda-forge
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zfp                       0.5.5                h9c3ff4c_7    conda-forge
zict                      2.0.0                      py_0    conda-forge
zipp                      3.6.0              pyhd8ed1ab_0    conda-forge
zlib                      1.2.11            h36c2ea0_1013    conda-forge
zstd                      1.5.0                ha95c52a_0    conda-forge

opened by martinfleis 16

Test new binary wheels
The new binary wheels are distributed under version 0.10.2a2! I'd like to spot-test some of them before tagging the release.

Please try it out:

$ pip install --pre pygeos[test] $ pytest --pyargs pygeos.tests

And report back the exact wheel version you used + if tests passed.

For me: pygeos-0.10.2a2-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl works.

@jorisvandenbossche @mwtoews @brendan-ward
opened by caspervdw 16
Release the GIL for geometry-creating operations

This addresses #155 , now only for the geometry-to-geometry operations (like envelope and convex_hull)

The same pattern could be repeated for all other geometry-creating operations.

opened by caspervdw 16
ENH: add STRtree nearest neighbor(s) function

Replaces #111, resolves #110.

Note: this builds on top of #265, which should be reviewed and merged first.

Based on the feedback in #111, this provides a nearest neighbor function on the tree that overcomes some of the limitations of the GEOS API. Specifically, the GEOS API returns a single, nondeterministic geometry from a set of intersected or equidistant tree geometries, which causes problems with downstream usage.

This provides an index-oriented results (input indexes, target indexes) similar to query_bulk, with an optional distance array.

This implementation should return all intersected or equidistant tree geometries for each input geometry. To do this, it leverages the userdata parameter of the tree's distance callback function to pass in a data structure that allows us to accumulate pairs of nearby geometries, track the minimum distance observed, and slightly modify (read: lie about) the distance returned to the GEOS function to force investigation of tree geometries in adjacent tree nodes. Without this modification, the algorithm stops before visiting additional equidistant or intersected geometries in adjacent tree nodes, producing an incomplete result set.

This implementation also enables pre-screening of input geometries by a max_distance parameter. This is used to create an envelope around the geometry to query against the tree which is used to make sure that there are tree geometries within that distance. Depending on the configuration of the geometry and the distance used, this either incurs extra overhead or it can dramatically reduce the time needed to find nearest items within that distance (vs finding all nearest then filtering later).

This involved adding helper functions to calculate bounds and create a box; these were derived from similar functions in the ufuncs (and could be consolidated later).

Note: this is not intended to be used for kNN functionality; that will require a separate algorithm implemented within GEOS first. The only time this will return multiple neighbors for an input geometry is when there are multiple equidistant or intersected tree geometries.

The doctests for nearest are marked to skip them completely; I could not find a way to conditionally skip them for GEOS < 3.6.

/cc @adriangb
enhancement

opened by brendan-ward 15
Pygeos exception:"non-noded intersection" encountered under python 3.11

Hey guys, I just tried running the pygeso 0.14 with python 3.11 on one of our regular scripts. The following two exceptions are encountered.

pygeos.GEOSException is encountered, retrying union_all with 1E-3 grid size. Traceback (most recent call last): File "C:\Users\aniwax\Documents\GitHub\iBrusCoreSim\SimulationToolbox\Geometry\geometric_objects.py", line 431, in to_area2D pygeos.set_operations.union_all(polygons), tolerance=wp_slice_precision) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\aniwax\Documents\GitHub\iBrusCoreSim\ibrusenv3_11\Lib\site-packages\pygeos\decorators.py", line 80, in wrapped return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\aniwax\Documents\GitHub\iBrusCoreSim\ibrusenv3_11\Lib\site-packages\pygeos\set_operations.py", line 388, in union_all result = lib.unary_union(collections, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ pygeos.GEOSException: TopologyException: found non-noded intersection between LINESTRING (-0.0627738 -0.559665, -0.0627738 -0.559665) and LINESTRING (-0.0627738 -0.559665, -0.0627738 -0.559665) at -0.062773768781892267 -0.55966495759925516

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "", line 198, in _run_module_as_main File "", line 88, in _run_code File "C:\Users\aniwax\AppData\Local\Programs\Python\Python311\Lib\cProfile.py", line 190, in main() File "C:\Users\aniwax\AppData\Local\Programs\Python\Python311\Lib\cProfile.py", line 179, in main runctx(code, globs, None, options.outfile, options.sort) File "C:\Users\aniwax\AppData\Local\Programs\Python\Python311\Lib\cProfile.py", line 19, in runctx return _pyprofile._Utils(Profile).runctx(statement, globals, locals, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\aniwax\AppData\Local\Programs\Python\Python311\Lib\profile.py", line 62, in runctx prof.runctx(statement, globals, locals) File "C:\Users\aniwax\AppData\Local\Programs\Python\Python311\Lib\cProfile.py", line 100, in runctx exec(cmd, globals, locals) File ".\PerformanceOptimisation\runtime_optimisation_railgrinding.py", line 148, in optimization_run(True) File ".\PerformanceOptimisation\runtime_optimisation_railgrinding.py", line 107, in optimization_run apply_attritious_wear(wear_model_result, tool, File "C:\Users\aniwax\Documents\GitHub\iBrusCoreSim\SimulationToolbox\Simulation\wear_models.py", line 195, in apply_attritious_wear modify_reduced_grains(tool, mat_remover_result) File "C:\Users\aniwax\Documents\GitHub\iBrusCoreSim\SimulationToolbox\Simulation\wear_models.py", line 165, in modify_reduced_grains projected_fm = projected_mesh.to_flatmanifold( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\aniwax\Documents\GitHub\iBrusCoreSim\SimulationToolbox\Geometry\geometric_objects.py", line 387, in to_flatmanifold flatManifold = FlatManifold(self.to_area2D(precision), self.pose) ^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\aniwax\Documents\GitHub\iBrusCoreSim\SimulationToolbox\Geometry\geometric_objects.py", line 455, in to_area2D area2d = Area2D.from_pygeos_polygon(pygeos.polygons( ^^^^^^^^^^^^^^^^ File "C:\Users\aniwax\Documents\GitHub\iBrusCoreSim\ibrusenv3_11\Lib\site-packages\pygeos\decorators.py", line 80, in wrapped return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\aniwax\Documents\GitHub\iBrusCoreSim\ibrusenv3_11\Lib\site-packages\pygeos\creation.py", line 250, in polygons geometries = linearrings(geometries) ^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\aniwax\Documents\GitHub\iBrusCoreSim\ibrusenv3_11\Lib\site-packages\pygeos\decorators.py", line 80, in wrapped return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\aniwax\Documents\GitHub\iBrusCoreSim\ibrusenv3_11\Lib\site-packages\pygeos\creation.py", line 172, in linearrings return lib.linearrings(coords, out=out, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ValueError: linearrings: Input operand 0 does not have enough dimensions (has 1, gufunc core with signature (i, d)->() requires 2)

opened by Aniwax 0
Please raise issues at https://github.com/shapely/shapely

PyGEOS was merged with shapely in December 2021 and will be released as part of Shapely 2.0.

The development will take place at the Shapely repository. Please raise issues or create pull request over there. PyGEOS itself will receive updates (by backporting from the Shapely repository) until Shapely 2.0 is actually released.

opened by caspervdw 0
Add “offsets” as an alternative to “indices”

In #436 @jorisvandenbossche found that the “indices” argument takes significant part of the processing time of the “simple geometries from indices” routine.

It seems that using offsets instead (for example [4, 6, 11] instead of [0,0,0,0,1,1,2,2,2,2,2] gives better performance. This is exactly what numpy.ufuncs.reduceat takes; we might even implement this as a ufunc? https://numpy.org/doc/stable/reference/generated/numpy.ufunc.reduceat.html
enhancement to-shapely

opened by caspervdw 4
ENH: release GIL during STRtree creation

We aren't currently releasing the GIL during the creation of STRtree; this might be possible and could yield potential performance improvements in a multi-threaded environment.

In particular, the initial query against the tree after construction toward the end of STRtree_new should not need to hold the GIL.
enhancement to-shapely

opened by brendan-ward 1
TST: add high level integration test suite

From @caspervdw at https://github.com/pygeos/pygeos/issues/362#issuecomment-874013431:

maybe we could bundle these kind of high level tests (integration tests could be the word, not sure) at some point and also resurrect the test I did when implementing the GIL release.

testing to-shapely

opened by jorisvandenbossche 0
ENH: Exclude same input geometry from output of nearest_all

In this issue in Shapely, there is a need to find the nearest items in a tree constructed of the same geometries that are being used to query the tree, but return the non-self nearest neighbor(s).

One way to approach this would be to provide a new function that does not take new geometry inputs, but instead uses the underlying tree geometries in such a way that we can compare addresses of a geometry to the results returned within the nearest callback function, so as to avoid a more expensive test for equality. We would then return an arbitrarily large distance for the self-pair, to force the tree to look for the next nearest neighbor.

/cc @liunx7594
enhancement to-shapely

opened by brendan-ward 6

Releases(0.14)

0.14(Dec 12, 2022)

Source code(tar.gz)
Source code(zip)
pygeos-0.14.tar.gz(138.01 KB)
0.13(Aug 25, 2022)

Source code(tar.gz)
Source code(zip)
pygeos-0.13.tar.gz(137.83 KB)
0.12.0(Dec 3, 2021)

Source code(tar.gz)
Source code(zip)
pygeos-0.12.0.tar.gz(138.07 KB)
0.11.1(Oct 30, 2021)

Source code(tar.gz)
Source code(zip)
pygeos-0.11.1.tar.gz(132.40 KB)
0.10.2(Aug 23, 2021)

Source code(tar.gz)
Source code(zip)
pygeos-0.10.2.tar.gz(124.33 KB)
0.10.2a2(Aug 19, 2021)

Source code(tar.gz)
Source code(zip)
pygeos-0.10.2a2.tar.gz(124.12 KB)
0.10.2a1(Aug 19, 2021)

Source code(tar.gz)
Source code(zip)
pygeos-0.10.2a1.tar.gz(124.13 KB)
0.10.1(Jul 6, 2021)
Version 0.10.1 (2021-07-06)

Bug fixes

Fixed the box and set_precision functions with numpy 1.21 (#367).

Fixed STRtree creation to allow querying the tree in a multi-threaded context (#361).

Acknowledgements

Thanks to everyone who contributed to this release! People with a "+" by their names contributed a patch for the first time.

Brendan Ward

Casper van der Wel

Joris Van den Bossche

Source code(tar.gz)
Source code(zip)
pygeos-0.10.1.tar.gz(104.35 KB)
0.10(May 18, 2021)
Version 0.10 (2021-05-18)

Major enhancements

Addition of nearest and nearest_all functions to STRtree for GEOS >= 3.6 to find the nearest neighbors (#272).

Enable bulk construction of geometries with different number of coordinates by optionally taking index arrays in all creation functions (#230, #322, #326, #346).

Released the GIL in all geometry creation functions (#310, #326).

Added the option to return the geometry index in get_coordinates (#318).

Added the get_rings function, similar as get_parts but specifically to extract the rings of Polygon geometries (#342).

Updated box ufunc to use internal C function for creating polygon (about 2x faster) and added ccw parameter to create polygon in counterclockwise (default) or clockwise direction (#308).

Added to_shapely and improved performance of from_shapely in the case GEOS versions are different (#312).

API Changes

STRtree default leaf size is now 10 instead of 5, for somewhat better performance under normal conditions (#286)

Deprecated VALID_PREDICATES set from pygeos.strtree package; these can be constructed in downstream libraries using the pygeos.strtree.BinaryPredicate enum. This will be removed in a future release.

points, linestrings, linearrings, and polygons now return a GEOSException instead of a ValueError or TypeError for invalid input (#310, #326).

Addition of on_invalid parameter to from_wkb and from_wkt to optionally return invalid WKB geometries as None.

Removed the (internal) function lib.polygons_without_holes and renamed lib.polygons_with_holes to lib.polygons (#326).

polygons will now return an empty polygon for None inputs (#346).

Removed compatibility with Python 3.5 (#341).

Added GEOS functions

Addition of a contains_properly function (#267)

Addition of a polygonize function (#275)

Addition of a polygonize_full function (#298)

Addition of a segmentize function for GEOS >= 3.10 (#299)

Addition of oriented_envelope and minimum_rotated_rectangle functions (#314)

Addition of minimum_bounding_circle and minimum_bounding_radius functions for GEOS >= 3.8 (#315)

Addition of a shortest_line ("nearest points") function (#334)

Bug fixes

Fixed portability issue for ARM architecture (#293)

Fixed segfault in linearrings and box when constructing a geometry with nan coordinates (#310).

Fixed segfault in polygons (with holes) when None was provided.

Fixed memory leak in polygons when non-linearring input was provided.

Acknowledgments

Thanks to everyone who contributed to this release! People with a "+" by their names contributed a patch for the first time.

Brendan Ward

Casper van der Wel

Joris Van den Bossche

Martin Fleischmann

Mike Taves

Tanguy Ophoff +

James Myatt +

Source code(tar.gz)
Source code(zip)
pygeos-0.10.tar.gz(104.11 KB)
0.9(Jan 23, 2021)
Version 0.9 (2021-01-23)

Major enhancements

Addition of prepare function that generates a GEOS prepared geometry which is stored on the Geometry object itself. All binary predicates (except equals) make use of this. Helper functions destroy_prepared and is_prepared are also available. (#92, #252)

Use previously prepared geometries within STRtree query and query_bulk functions if available (#246)

Official support for Python 3.9 and numpy 1.20 (#278, #279)

Drop support for Python 3.5 (#211)

Added support for pickling to Geometry objects (#190)

The apply function for coordinate transformations and the set_coordinates function now support geometries with z-coordinates (#131)

Addition of Cython and internal PyGEOS C API to enable easier development of internal functions (previously all significant internal functions were developed in C). Added a Cython-implemented get_parts function (#51)

API Changes

Geometry and counting functions (get_num_coordinates, get_num_geometries, get_num_interior_rings, get_num_points) now return 0 for None input values instead of -1 (#218)

intersection_all and symmetric_difference_all now ignore None values instead of returning None if any value is None (#249)

union_all now returns None (instead of GEOMETRYCOLLECTION EMPTY) if all input values are None (#249)

The default axis of union_all, intersection_all, symmetric_difference_all, and coverage_union_all can now reduce over multiple axes. The default changed from the first axis (0) to all axes (None) (#266)

Argument in line_interpolate_point and line_locate_point was renamed from normalize to normalized (#209)

Addition of grid_size parameter to specify fixed-precision grid for difference, intersection, symmetric_difference, union, and union_all operations for GEOS >= 3.9 (#276)

Added GEOS functions

Release the GIL for is_geometry(), is_missing(), and is_valid_input() (#207)

Addition of a is_ccw() function for GEOS >= 3.7 (#201)

Addition of a minimum_clearance function for GEOS >= 3.6.0 (#223)

Addition of a offset_curve function (#229)

Addition of a relate_pattern function (#245)

Addition of a clip_by_rect function (#273)

Addition of a reverse function for GEOS >= 3.7 (#254)

Addition of get_precision to get precision of a geometry and set_precision to set the precision of a geometry (may round and reduce coordinates) (#257)

Bug fixes

Fixed internal GEOS error code detection for get_dimensions and get_srid (#218)

Limited the length of geometry repr to 80 characters (#189)

Fixed error handling in line_locate_point for incorrect geometry types, now actually requiring line and point geometries (#216)

Addition of get_parts function to get individual parts of an array of multipart geometries (#197)

Ensure that python setup.py clean removes all previously Cythonized and compiled files (#239)

Handle GEOS beta versions (#262)

Acknowledgments

Thanks to everyone who contributed to this release! People with a "+" by their names contributed a patch for the first time.

Brendan Ward

Casper van der Wel

Joris Van den Bossche

Mike Taves

Source code(tar.gz)
Source code(zip)
pygeos-0.9.tar.gz(87.65 KB)
0.8(Sep 6, 2020)
Highlights of this release

Handle multi geometries in boundary (#188)

Handle empty points in to_wkb by conversion to POINT (nan, nan) (#179)

Prevent segfault in to_wkt (and repr) with empty points in multipoints (#171)

Fixed bug in multilinestrings(), it now accepts linearrings again (#168)

Release the GIL to allow for multithreading in functions that do not create geometries (#144) and in the STRtree query_bulk() method (#174)

Addition of a frechet_distance() function for GEOS >= 3.7 (#144)

Addition of coverage_union() and coverage_union_all() functions for GEOS >= 3.8 (#142)

Fixed segfaults when adding empty geometries to the STRtree (#147)

Addition of include_z=True keyword in the get_coordinates() function to get 3D coordinates (#178)

Addition of a build_area() function for GEOS >= 3.8 (#141)

Addition of a normalize() function (#136)

Addition of a make_valid() function for GEOS >= 3.8 (#107)

Addition of a get_z() function for GEOS >= 3.7 (#175)

Addition of a relate() function (#186)

The get_coordinate_dimensions() function was renamed to get_coordinate_dimension() for consistency with GEOS (#176)

Addition of covers, covered_by, contains_properly predicates to STRtree query and query_bulk (#157)

Acknowledgments

Thanks to everyone who contributed to this release! People with a "+" by their names contributed a patch for the first time.

Brendan Ward

Casper van der Wel

Joris Van den Bossche

Krishna Chaitanya +

Martin Fleischmann +

Tom Clancy +

Source code(tar.gz)
Source code(zip)
pygeos-0.8.tar.gz(72.77 KB)
0.7(Mar 18, 2020)
Highlights of this release

STRtree improvements for spatial indexing:

Directly include predicate evaluation in STRtree.query() (#87)

Query multiple input geometries (spatial join style) with STRtree.query_bulk (#108)

Addition of a total_bounds() function (#107)

Geometries are now hashable, and can be compared with == or != (#102)

Fixed bug in create_collections() with wrong types (#86)

Fixed a reference counting bug in STRtree (#97, #100)

Start of a benchmarking suite using ASV (#96)

This is the first release that will provide wheels!

Acknowledgments

Thanks to everyone who contributed to this release! People with a "+" by their names contributed a patch for the first time.

Brendan Ward +

Casper van der Wel

Joris Van den Bossche

Mike Taves +

Source code(tar.gz)
Source code(zip)
pygeos-0.7.tar.gz(58.03 KB)
0.6(Jan 31, 2020)
Highlights of this release:

Addition of the STRtree class for spatial indexing (#58)

Addition of a bounds function (#69)

A new from_shapely function to convert Shapely geometries to pygeos.Geometry (#61)

Reintroduction of the shared_paths function (#77)

Source code(tar.gz)
Source code(zip)
pygeos-0.6.tar.gz(55.03 KB)
0.5(Oct 25, 2019)
Highlights of this release:

Moved to the pygeos GitHub organization.

Addition of functionality to get and transform all coordinates (eg for reprojections or affine transformations) [#44]

Ufuncs for converting to and from the WKT and WKB formats [#45]

equals_exact has been added [PR #57]

Source code(tar.gz)
Source code(zip)
pygeos-0.5.tar.gz(48.51 KB)
0.4(Sep 16, 2019)
This is a major release of PyGEOS and the first one with actual release notes. Most important features of this release are:

buffer and haussdorff_distance were completed [#15]

voronoi_polygons and delaunay_triangles have been added [#17]

The PyGEOS documentation is now mostly complete and available on http://pygeos.readthedocs.io .

The concepts of "empty" and "missing" geometries have been separated. The pygeos.Empty and pygeos.NaG objects has been removed. Empty geometries are handled the same as normal geometries. Missing geometries are denoted by None and are handled by every pygeos function. NaN values cannot be used anymore to denote missing geometries. [PR #36]

Added pygeos.__version__ and pygeos.geos_version. [PR #43]

Source code(tar.gz)
Source code(zip)
pygeos-0.4.tar.gz(41.92 KB)

Wraps GEOS geometry functions in numpy ufuncs.

Related tags

Overview

PyGEOS

What is a ufunc?

Multithreading

Examples

Relationship to Shapely

References

Copyright & License

Comments

Releases(0.14)

0.14(Dec 12, 2022)

0.13(Aug 25, 2022)

0.12.0(Dec 3, 2021)

0.11.1(Oct 30, 2021)

0.10.2(Aug 23, 2021)

0.10.2a2(Aug 19, 2021)

0.10.2a1(Aug 19, 2021)

0.10.1(Jul 6, 2021)

Version 0.10.1 (2021-07-06)

0.10(May 18, 2021)

Version 0.10 (2021-05-18)

0.9(Jan 23, 2021)

Version 0.9 (2021-01-23)

0.8(Sep 6, 2020)

0.7(Mar 18, 2020)

0.6(Jan 31, 2020)

0.5(Oct 25, 2019)

0.4(Sep 16, 2019)

Owner

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