pygeos dependency causing installation to fail

[PatBall1]

Pygeos causes installation to fail on macOS 15 as reported by Fei Qi:

But when I ran “pip install git+https://github.com/PatBall1/detectree2.git”,Error happened to me,I really need your help, thx a lot

The result is:

Collecting git+https://github.com/PatBall1/detectree2.git

  Cloning https://github.com/PatBall1/detectree2.git to /private/var/folders/y4/y6253cy573xf2dc3n2437q6m0000gn/T/pip-req-build-5eraprcl

  Running command git clone --filter=blob:none --quiet https://github.com/PatBall1/detectree2.git /private/var/folders/y4/y6253cy573xf2dc3n2437q6m0000gn/T/pip-req-build-5eraprcl

  Resolved https://github.com/PatBall1/detectree2.git to commit c983eda802daa7286d8f7eb37dbaf1751254c68d

  Preparing metadata (setup.py) ... done

Collecting detectron2@ git+https://github.com/facebookresearch/detectron2.git (from detectree2==1.1.0)

  Cloning https://github.com/facebookresearch/detectron2.git to /private/var/folders/y4/y6253cy573xf2dc3n2437q6m0000gn/T/pip-install-w1hdjfjg/detectron2_2a90086c30ad400fb9d870d88eb03909

  Running command git clone --filter=blob:none --quiet https://github.com/facebookresearch/detectron2.git /private/var/folders/y4/y6253cy573xf2dc3n2437q6m0000gn/T/pip-install-w1hdjfjg/detectron2_2a90086c30ad400fb9d870d88eb03909

  Resolved https://github.com/facebookresearch/detectron2.git to commit c69939aa85460e8135f40bce908a6cddaa73065f

  Preparing metadata (setup.py) ... done

Collecting pyyaml>=5.1 (from detectree2==1.1.0)

  Using cached PyYAML-6.0.2-cp312-cp312-macosx_11_0_arm64.whl.metadata (2.1 kB)

Collecting GDAL>=1.11 (from detectree2==1.1.0)

  Using cached gdal-3.10.tar.gz (848 kB)

  Installing build dependencies ... done

  Getting requirements to build wheel ... done

  Preparing metadata (pyproject.toml) ... done

Requirement already satisfied: numpy in ./venv/lib/python3.12/site-packages (from detectree2==1.1.0) (2.1.3)

Collecting rtree (from detectree2==1.1.0)

  Using cached Rtree-1.3.0-py3-none-macosx_11_0_arm64.whl.metadata (2.1 kB)

Collecting proj (from detectree2==1.1.0)

  Using cached proj-0.2.0-py2.py3-none-any.whl.metadata (3.3 kB)

Collecting geos (from detectree2==1.1.0)

  Using cached geos-0.2.3-py3-none-any.whl.metadata (480 bytes)

Collecting pypng (from detectree2==1.1.0)

  Using cached pypng-0.20220715.0-py3-none-any.whl.metadata (13 kB)

Collecting pygeos (from detectree2==1.1.0)

  Using cached pygeos-0.14.tar.gz (141 kB)

  Installing build dependencies ... done

  Getting requirements to build wheel ... error

  error: subprocess-exited-with-error

  

  × Getting requirements to build wheel did not run successfully.

  │ exit code: 1

  ╰─> [34 lines of output]

      <string>:8: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html

      /private/var/folders/y4/y6253cy573xf2dc3n2437q6m0000gn/T/pip-install-w1hdjfjg/pygeos_1e70e5e9d2af48c7819e9f91d96a22e2/versioneer.py:421: SyntaxWarning: invalid escape sequence '\s'

        LONG_VERSION_PY['git'] = '''

      Compiling pygeos/_geometry.pyx because it changed.

      Compiling pygeos/_geos.pyx because it changed.

      [1/2] Cythonizing pygeos/_geometry.pyx

      [2/2] Cythonizing pygeos/_geos.pyx

      Traceback (most recent call last):

        File "/Users/lemon/Documents/detectree/venv/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>

          main()

        File "/Users/lemon/Documents/detectree/venv/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main

          json_out['return_val'] = hook(**hook_input['kwargs'])

                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

        File "/Users/lemon/Documents/detectree/venv/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel

          return hook(config_settings)

                 ^^^^^^^^^^^^^^^^^^^^^

        File "/private/var/folders/y4/y6253cy573xf2dc3n2437q6m0000gn/T/pip-build-env-9phgd3xo/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 334, in get_requires_for_build_wheel

          return self._get_build_requires(config_settings, requirements=[])

                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

        File "/private/var/folders/y4/y6253cy573xf2dc3n2437q6m0000gn/T/pip-build-env-9phgd3xo/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 304, in _get_build_requires

          self.run_setup()

        File "/private/var/folders/y4/y6253cy573xf2dc3n2437q6m0000gn/T/pip-build-env-9phgd3xo/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 320, in run_setup

          exec(code, locals())

        File "<string>", line 214, in <module>

        File "/private/var/folders/y4/y6253cy573xf2dc3n2437q6m0000gn/T/pip-install-w1hdjfjg/pygeos_1e70e5e9d2af48c7819e9f91d96a22e2/versioneer.py", line 1480, in get_version

          return get_versions()["version"]

                 ^^^^^^^^^^^^^^

        File "/private/var/folders/y4/y6253cy573xf2dc3n2437q6m0000gn/T/pip-install-w1hdjfjg/pygeos_1e70e5e9d2af48c7819e9f91d96a22e2/versioneer.py", line 1412, in get_versions

          cfg = get_config_from_root(root)

                ^^^^^^^^^^^^^^^^^^^^^^^^^^

        File "/private/var/folders/y4/y6253cy573xf2dc3n2437q6m0000gn/T/pip-install-w1hdjfjg/pygeos_1e70e5e9d2af48c7819e9f91d96a22e2/versioneer.py", line 342, in get_config_from_root

          parser = configparser.SafeConfigParser()

                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

      AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did you mean: 'RawConfigParser'?

      [end of output]

  

  note: This error originates from a subprocess, and is likely not a problem with pip.

error: subprocess-exited-with-error



× Getting requirements to build wheel did not run successfully.

│ exit code: 1

╰─> See above for output.



note: This error originates from a subprocess, and is likely not a problem with pip.```


The requirement pygeos fails to install with python 3.12 with the error described here: [pygeos/pygeos#463](https://github.com/pygeos/pygeos/issues/463)

The maintainer explains that pygeos is no longer maintained and has been merged into the shapley 2.0 dependency of geopandas. Since version 0.14, geopandas uses shapley instead of pygeos: https://geopandas.org/en/stable/docs/user_guide/pygeos_to_shapely.html

Therefore, the PR drops the unmaintained pygeos and requires geopandas >= 0.14 to ensure the default shapley version is used

[PatBall1]

Pygeos installation still fails, and I try to find the reason in GitHub:

The requirement pygeos fails to install with python 3.12 with the error described here: pygeos/pygeos#463

The maintainer explains that pygeos is no longer maintained and has been merged into the shapley 2.0 dependency of geopandas. Since version 0.14, geopandas uses shapley instead of pygeos: https://geopandas.org/en/stable/docs/user_guide/pygeos_to_shapely.html

Therefore, the PR drops the unmaintained pygeos and requires geopandas >= 0.14 to ensure the default shapley version is used instead.

[PatBall1]

Wow,
I just edit setup.py, commented out pygeos ,
And edit requirements.txt,commented out pygeos ,and replaced shapely==1.18 with shapely==2.0

Then it seemed installation successful ? And how verify it will work?

Successfully built rasterio GDAL detectron2 pycrs fvcore antlr4-python3-runtime

Installing collected packages: pytz, pypng, pycrs, antlr4-python3-runtime, tzdata, types-python-dateutil, tqdm, termcolor, tensorboard-data-server, tabulate, six, shapely, rtree, pyyaml, pyparsing, protobuf, portalocker, platformdirs, pathspec, packaging, mypy-extensions, markdown, kiwisolver, grpcio, GDAL, fonttools, cycler, contourpy, cloudpickle, cligj, click-plugins, certifi, attrs, affine, absl-py, yacs, tensorboard, snuggs, python-dateutil, pyproj, pyogrio, omegaconf, iopath, fiona, black, rasterio, pandas, matplotlib, hydra-core, fvcore, arrow, pycocotools, proj, geopandas, descartes, detectron2, detectree2

  DEPRECATION: Legacy editable install of detectree2==1.1.0 from file:///Users/lemon/Documents/detectree/detectree2 (setup.py develop) is deprecated. pip 25.0 will enforce this behaviour change. A possible replacement is to add a pyproject.toml or enable --use-pep517, and use setuptools >= 64. If the resulting installation is not behaving as expected, try using --config-settings editable_mode=compat. Please consult the setuptools documentation for more information. Discussion can be found at https://github.com/pypa/pip/issues/11457

  Running setup.py develop for detectree2

Successfully installed GDAL-3.10.0 absl-py-2.1.0 affine-2.4.0 antlr4-python3-runtime-4.9.3 arrow-1.3.0 attrs-24.2.0 black-24.10.0 certifi-2024.8.30 click-plugins-1.1.1 cligj-0.7.2 cloudpickle-3.1.0 contourpy-1.3.1 cycler-0.12.1 descartes-1.1.0 detectree2-1.1.0 detectron2-0.6 fiona-1.9.6 fonttools-4.55.0 fvcore-0.1.5.post20221221 geopandas-1.0.1 grpcio-1.68.0 hydra-core-1.3.2 iopath-0.1.9 kiwisolver-1.4.7 markdown-3.7 matplotlib-3.9.2 mypy-extensions-1.0.0 omegaconf-2.3.0 packaging-24.2 pandas-2.2.3 pathspec-0.12.1 platformdirs-4.3.6 portalocker-3.0.0 proj-0.2.0 protobuf-5.28.3 pycocotools-2.0.8 pycrs-1.0.2 pyogrio-0.10.0 pyparsing-3.2.0 pypng-0.20220715.0 pyproj-3.7.0 python-dateutil-2.9.0.post0 pytz-2024.2 pyyaml-6.0.2 rasterio-1.3a3 rtree-1.3.0 shapely-2.0.6 six-1.16.0 snuggs-1.4.7 tabulate-0.9.0 tensorboard-2.18.0 tensorboard-data-server-0.7.2 termcolor-2.5.0 tqdm-4.67.1 types-python-dateutil-2.9.0.20241003 tzdata-2024.2 yacs-0.1.8```