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Pygeos installation doesn't work with python 3.11 #457

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Aniwax opened this issue Oct 26, 2022 · 5 comments
Closed

Pygeos installation doesn't work with python 3.11 #457

Aniwax opened this issue Oct 26, 2022 · 5 comments

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@Aniwax
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Aniwax commented Oct 26, 2022 •
edited

pip install pygeos didn't work with python 11 on Windows.
I tried pygeos version 0.10, 0.12, 0.13, all didn't work.

Here is the error message

(ibrusenv) PS C:\Users\aniwax\Documents\GitHub\iBrusCoreSim> pip install pygeos==0.12
Collecting pygeos==0.12
  Downloading pygeos-0.12.0.tar.gz (141 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 141.4/141.4 kB 8.2 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy>=1.13 in c:\users\aniwax\documents\github\ibruscoresim\ibrusenv\lib\site-packa
(from pygeos==0.12) (1.23.4)
Building wheels for collected packages: pygeos
  Building wheel for pygeos (pyproject.toml) ... error
  error: subprocess-exited-with-error

  × Building wheel for pygeos (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [65 lines of output]
      Could not find geos-config executable. Either append the path to geos-config to PATH or manually provide the ude_dirs, library_dirs, libraries and other link args for compiling against a GEOS version >=3.5.
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build\lib.win-amd64-cpython-311
      creating build\lib.win-amd64-cpython-311\pygeos
      copying pygeos\constructive.py -> build\lib.win-amd64-cpython-311\pygeos
      copying pygeos\coordinates.py -> build\lib.win-amd64-cpython-311\pygeos
      copying pygeos\creation.py -> build\lib.win-amd64-cpython-311\pygeos
      copying pygeos\decorators.py -> build\lib.win-amd64-cpython-311\pygeos
      copying pygeos\enum.py -> build\lib.win-amd64-cpython-311\pygeos
      copying pygeos\geometry.py -> build\lib.win-amd64-cpython-311\pygeos
      copying pygeos\io.py -> build\lib.win-amd64-cpython-311\pygeos
      copying pygeos\linear.py -> build\lib.win-amd64-cpython-311\pygeos
      copying pygeos\measurement.py -> build\lib.win-amd64-cpython-311\pygeos
      copying pygeos\predicates.py -> build\lib.win-amd64-cpython-311\pygeos
      copying pygeos\set_operations.py -> build\lib.win-amd64-cpython-311\pygeos
      copying pygeos\strtree.py -> build\lib.win-amd64-cpython-311\pygeos
      copying pygeos\testing.py -> build\lib.win-amd64-cpython-311\pygeos
      copying pygeos\_version.py -> build\lib.win-amd64-cpython-311\pygeos
      copying pygeos\__init__.py -> build\lib.win-amd64-cpython-311\pygeos
      creating build\lib.win-amd64-cpython-311\pygeos\tests
      copying pygeos\tests\common.py -> build\lib.win-amd64-cpython-311\pygeos\tests
      copying pygeos\tests\test_constructive.py -> build\lib.win-amd64-cpython-311\pygeos\tests
      copying pygeos\tests\test_coordinates.py -> build\lib.win-amd64-cpython-311\pygeos\tests
      copying pygeos\tests\test_creation.py -> build\lib.win-amd64-cpython-311\pygeos\tests
      copying pygeos\tests\test_creation_indices.py -> build\lib.win-amd64-cpython-311\pygeos\tests
      copying pygeos\tests\test_geometry.py -> build\lib.win-amd64-cpython-311\pygeos\tests
      copying pygeos\tests\test_io.py -> build\lib.win-amd64-cpython-311\pygeos\tests
      copying pygeos\tests\test_linear.py -> build\lib.win-amd64-cpython-311\pygeos\tests
      copying pygeos\tests\test_measurement.py -> build\lib.win-amd64-cpython-311\pygeos\tests
      copying pygeos\tests\test_misc.py -> build\lib.win-amd64-cpython-311\pygeos\tests
      copying pygeos\tests\test_predicates.py -> build\lib.win-amd64-cpython-311\pygeos\tests
      copying pygeos\tests\test_set_operations.py -> build\lib.win-amd64-cpython-311\pygeos\tests
      copying pygeos\tests\test_strtree.py -> build\lib.win-amd64-cpython-311\pygeos\tests
      copying pygeos\tests\test_testing.py -> build\lib.win-amd64-cpython-311\pygeos\tests
      copying pygeos\tests\__init__.py -> build\lib.win-amd64-cpython-311\pygeos\tests
      running egg_info
      writing pygeos.egg-info\PKG-INFO
      writing dependency_links to pygeos.egg-info\dependency_links.txt
      writing requirements to pygeos.egg-info\requires.txt
      writing top-level names to pygeos.egg-info\top_level.txt
      reading manifest file 'pygeos.egg-info\SOURCES.txt'
      adding license file 'LICENSE'
      writing manifest file 'pygeos.egg-info\SOURCES.txt'
      copying pygeos\_geometry.c -> build\lib.win-amd64-cpython-311\pygeos
      copying pygeos\_geometry.pyx -> build\lib.win-amd64-cpython-311\pygeos
      copying pygeos\_geos.c -> build\lib.win-amd64-cpython-311\pygeos
      copying pygeos\_geos.pxd -> build\lib.win-amd64-cpython-311\pygeos
      copying pygeos\_geos.pyx -> build\lib.win-amd64-cpython-311\pygeos
      copying pygeos\_pygeos_api.pxd -> build\lib.win-amd64-cpython-311\pygeos
      UPDATING build\lib.win-amd64-cpython-311\pygeos/_version.py
      set build\lib.win-amd64-cpython-311\pygeos/_version.py to '0.12.0'
      running build_ext
      building 'pygeos.lib' extension
      creating build\temp.win-amd64-cpython-311
      creating build\temp.win-amd64-cpython-311\Release
      creating build\temp.win-amd64-cpython-311\Release\src
      "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Tools\MSVC\14.28.29910\bin\HostX86\x64\cl. /c /nologo /O2 /W3 /GL /DNDEBUG /MD -IC:\Users\aniwax\Documents\GitHub\iBrusCoreSim\ibrusenv\include -IC:\Users\an\AppData\Local\Programs\Python\Python311\include -IC:\Users\aniwax\AppData\Local\Programs\Python\Python311\Include \Users\aniwax\AppData\Local\Temp\pip-build-env-qbniyqoa\overlay\Lib\site-packages\numpy\core\include "-IC:\Program s (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Tools\MSVC\14.28.29910\ATLMFC\include" "-IC:\Program Files (x86)rosoft Visual Studio\2019\Enterprise\VC\Tools\MSVC\14.28.29910\include" "-IC:\Program Files (x86)\Windows Kits\10\ide\10.0.19041.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\shared" "-IC:\Program Files (xWindows Kits\10\include\10.0.19041.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.19041.0\winrt" "-ICogram Files (x86)\Windows Kits\10\include\10.0.19041.0\cppwinrt" /Tcsrc/c_api.c /Fobuild\temp.win-amd64-cpython-311ease\src/c_api.obj
      c_api.c
      C:\Users\aniwax\AppData\Local\Temp\pip-install-_1zaabxl\pygeos_d9dff3765b834eccab5867e3e841624b\src\geos.h(13arning C4068: unknown pragma 'GCC'
      C:\Users\aniwax\AppData\Local\Temp\pip-install-_1zaabxl\pygeos_d9dff3765b834eccab5867e3e841624b\src\geos.h(14arning C4068: unknown pragma 'GCC'
      C:\Users\aniwax\AppData\Local\Temp\pip-install-_1zaabxl\pygeos_d9dff3765b834eccab5867e3e841624b\src\geos.h(15atal error C1083: Cannot open include file: 'geos_c.h': No such file or directory
      error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio\\2019\\Enterprise\\VC\\Tools\\MSVC\\14.28.29\bin\\HostX86\\x64\\cl.exe' failed with exit code 2
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for pygeos
Failed to build pygeos
ERROR: Could not build wheels for pygeos, which is required to install pyproject.toml-based projects
@Aniwax
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Aniwax commented Oct 26, 2022 •
edited

Is the solution similar to this issue, #358 ?

This solution didn't work for me atm. I set GEOS_INCLUDE_PATH == ./OSGEO4W/include, GEOS_LIBRARY_PATH==./OSGEO4W/lib or GEOS_INCLUDE_PATH == ./OSGEO4W/include, GEOS_LIBRARY_PATH==./OSGEO4W/bin

both solution worked for installation. But then when I run a simulation, I get error from pygeos/__init__.py that
from .lib import GEOS_EXCEPTION, dll couldn't find the corresponding file. So I guess this means the path setting was not correct.

from .lib import GEOSException # NOQA ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: DLL load failed while importing lib: The specified module could not be found.

@John-P John-P mentioned this issue Nov 4, 2022
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@Erotemic
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Erotemic commented Dec 3, 2022

Any updates on when pygeos wheels for 3.11 will be released?

@caspervdw
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Sorry for the late reply, there is now a PR up over here: #458

@caspervdw
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@Aniwax @Erotemic Version 0.14 release has started, it should be up (with Py3.11 wheels) within an hour.

@jorisvandenbossche
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@caspervdw thanks for the release!

shaneahmed added a commit to TissueImageAnalytics/tiatoolbox that referenced this issue May 5, 2023
@John-P @shaneahmed
🐍 Update Supported Python Versions (add 3.11 ) (#500)
591482c 
Adds support for Python 3.11 (beta)

- [x] Add 3.11 to the GitHub Actions CI workflow.
- [x] Add 3.11 to setup.py
- [x] Update pip install workflow.
- [x] Update conda requirements python versions.


Waiting on some dependencies to update:

- [x] Shapely (closed) shapely/shapely#1584
  - PyGeos pygeos/pygeos#457
- [x] PyTorch pytorch/pytorch#86566 
    - [x] PyTorch 2.0 supports Python 3.11 
    - [ ] `torch.compile` is not fully supported yet.
- [x] Scipy 1.9.2 not supported by Scikit-image scikit-image/scikit-image#6773
- [x] numba numba/numba#8304 support https://github.com/numba/numba/milestone/63
  - [x] numba/numba#8841
- [x] OpenSlide support for Python 3.11 openslide/openslide-python#189 
  - [ ] openslide/openslide-python#188

---------

Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
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4 participants
@jorisvandenbossche @Erotemic @caspervdw @Aniwax