Pip & Poetry install failing

[SPlanzer]

Pip and Poetry install failure

pip install is failing (Ubuntu with a new Conda environment)

The below collapsible section has the details of the failed install. Looks to be related to compiling of the Cython code with pygeos

Installation Log: pip install vector2dggs

pip install vector2dggs
Collecting vector2dggs
  Using cached vector2dggs-0.6.0-py3-none-any.whl.metadata (9.8 kB)
Collecting click<9.0.0,>=8.1.3 (from vector2dggs)
  Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB)
Collecting click-log<0.5.0,>=0.4.0 (from vector2dggs)
  Using cached click_log-0.4.0-py2.py3-none-any.whl.metadata (1.2 kB)
Collecting dask<2024.0.0,>=2023.3.0 (from vector2dggs)
  Using cached dask-2023.12.1-py3-none-any.whl.metadata (3.7 kB)
Collecting dask-geopandas<0.4.0,>=0.3.0 (from vector2dggs)
  Using cached dask_geopandas-0.3.1-py3-none-any.whl.metadata (3.6 kB)
Collecting gdal<4.0.0,>=3.8.0 (from vector2dggs)
  Using cached gdal-3.9.1.tar.gz (840 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting geopandas<0.13.0,>=0.12.2 (from vector2dggs)
  Using cached geopandas-0.12.2-py3-none-any.whl.metadata (1.0 kB)
Collecting h3pandas<0.3.0,>=0.2.6 (from vector2dggs)
  Using cached h3pandas-0.2.6-py3-none-any.whl
Collecting psycopg2<3.0.0,>=2.9.6 (from vector2dggs)
  Using cached psycopg2-2.9.9-cp312-cp312-linux_x86_64.whl
Collecting pyarrow<15.0.0,>=14.0.1 (from vector2dggs)
  Using cached pyarrow-14.0.2-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (3.0 kB)
Collecting pygeos<0.14,>=0.13 (from vector2dggs)
  Using cached pygeos-0.13.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
  ╰─> [59 lines of output]
      <string>:8: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
      /tmp/pip-install-d4puysb_/pygeos_02aeec6a98274d01907dec1df753d816/versioneer.py:421: SyntaxWarning: invalid escape sequence '\s'
        LONG_VERSION_PY['git'] = '''
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
              self.last_error = <char *> malloc((1025) * sizeof(char))
              self.last_error[0] = 0
              self.last_warning = <char *> malloc((1025) * sizeof(char))
              self.last_warning[0] = 0
              GEOSContext_setErrorMessageHandler_r(
                  self.handle, &geos_message_handler, self.last_error
                               ^
      ------------------------------------------------------------
      
      pygeos/_geos.pyx:30:25: Cannot assign type 'void (*)(const char *, void *) except *' to 'GEOSMessageHandler_r' (alias of 'void (*)(const char *, void *) noexcept'). Exception values are incompatible. Suggest adding 'noexcept' to the type of the value being assigned.
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
              self.last_warning[0] = 0
              GEOSContext_setErrorMessageHandler_r(
                  self.handle, &geos_message_handler, self.last error
              )
              GEOSContext_setNoticeMessageHandler_r(
                  self.handle, &geos_message_handler, self last_warning
                               ^
      ------------------------------------------------------------
      
      pygeos/_geos.pyx:33:25: Cannot assign type 'void (*)(const char *, void *) except *' to 'GEOSMessageHandler_r' (alias of 'void (*)(const char *, void *) noexcept'). Exception values are incompatible. Suggest adding 'noexcept' to the type of the value being assigned.
      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 "/home/planzers/miniconda3/envs/test_v2dggs/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/home/planzers/miniconda3/envs/test_v2dggs/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 "/home/planzers/miniconda3/envs/test_v2dggs/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 "/tmp/pip-build-env-i_ujwu4p/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 327, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=[])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-i_ujwu4p/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 297, in _get_build_requires
          self.run_setup()
        File "/tmp/pip-build-env-i_ujwu4p/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 497, in run_setup
          super().run_setup(setup_script=setup_script)
        File "/tmp/pip-build-env-i_ujwu4p/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 313, in run_setup
          exec(code, locals())
        File "<string>", line 195, in <module>
        File "/tmp/pip-build-env-i_ujwu4p/overlay/lib/python3.12/site-packages/Cython/Build/Dependencies.py", line 1154, in cythonize
          cythonize_one(*args)
        File "/tmp/pip-build-env-i_ujwu4p/overlay/lib/python3.12/site-packages/Cython/Build/Dependencies.py", line 1321, in cythonize_one
          raise CompileError(None, pyx_file)
      Cython.Compiler.Errors.CompileError: pygeos/_geos.pyx
      [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.

poetry install returns similar results

Installation Log: poetry install vector2dggs

- Installing pygeos (0.14): Failed

ChefBuildError

Backend subprocess exited when trying to invoke get_requires_for_build_wheel

<string>:8: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
/tmp/tmp8tfyojhh/pygeos-0.14/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 "/home/planzers/miniconda3/envs/test_v2dggs/lib/python3.12/site-packages/pyproject_hooks/_in_process/_in_process.py", line 373, in <module>
    main()
  File "/home/planzers/miniconda3/envs/test_v2dggs/lib/python3.12/site-packages/pyproject_hooks/_in_process/_in_process.py", line 357, in main
    json_out["return_val"] = hook(**hook_input["kwargs"])
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/planzers/miniconda3/envs/test_v2dggs/lib/python3.12/site-packages/pyproject_hooks/_in_process/_in_process.py", line 134, in get_requires_for_build_wheel
    return hook(config_settings)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpor05rulu/.venv/lib/python3.12/site-packages/setuptools/build_meta.py", line 327, in get_requires_for_build_wheel
    return self._get_build_requires(config_settings, requirements=[])
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpor05rulu/.venv/lib/python3.12/site-packages/setuptools/build_meta.py", line 297, in _get_build_requires
    self.run_setup()
  File "/tmp/tmpor05rulu/.venv/lib/python3.12/site-packages/setuptools/build_meta.py", line 313, in run_setup
    exec(code, locals())
  File "<string>", line 214, in <module>
  File "/tmp/tmp8tfyojhh/pygeos-0.14/versioneer.py", line 1480, in get_version
    return get_versions()["version"]
           ^^^^^^^^^^^^^^
  File "/tmp/tmp8tfyojhh/pygeos-0.14/versioneer.py", line 1412, in get_versions
    cfg = get_config_from_root(root)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp8tfyojhh/pygeos-0.14/versioneer.py", line 342, in get_config_from_root
    parser = configparser.SafeConfigParser()
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did  - Installing h3pandas (0.2.6)
- Installing psycopg2 (2.9.9)
- Installing pyarrow (14.0.2)
- Installing pygeos (0.14): Failed

ChefBuildError

Backend subprocess exited when trying to invoke get_requires_for_build_wheel

<string>:8: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
/tmp/tmp8tfyojhh/pygeos-0.14/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 "/home/planzers/miniconda3/envs/test_v2dggs/lib/python3.12/site-packages/pyproject_hooks/_in_process/_in_process.py", line 373, in <module>
    main()
  File "/home/planzers/miniconda3/envs/test_v2dggs/lib/python3.12/site-packages/pyproject_hooks/_in_process/_in_process.py", line 357, in main
    json_out["return_val"] = hook(**hook_input["kwargs"])
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/planzers/miniconda3/envs/test_v2dggs/lib/python3.12/site-packages/pyproject_hooks/_in_process/_in_process.py", line 134, in get_requires_for_build_wheel
    return hook(config_settings)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpor05rulu/.venv/lib/python3.12/site-packages/setuptools/build_meta.py", line 327, in get_requires_for_build_wheel
    return self._get_build_requires(config_settings, requirements=[])
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpor05rulu/.venv/lib/python3.12/site-packages/setuptools/build_meta.py", line 297, in _get_build_requires
    self.run_setup()
  File "/tmp/tmpor05rulu/.venv/lib/python3.12/site-packages/setuptools/build_meta.py", line 313, in run_setup
    exec(code, locals())
  File "<string>", line 214, in <module>
  File "/tmp/tmp8tfyojhh/pygeos-0.14/versioneer.py", line 1480, in get_version
    return get_versions()["version"]
           ^^^^^^^^^^^^^^
  File "/tmp/tmp8tfyojhh/pygeos-0.14/versioneer.py", line 1412, in get_versions
    cfg = get_config_from_root(root)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp8tfyojhh/pygeos-0.14/versioneer.py", line 342, in get_config_from_root
    parser = configparser.SafeConfigParser()
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did  - Installing gdal (3.9.1): Installing...
- Installing h3pandas (0.2.6)
- Installing psycopg2 (2.9.9)
- Installing pyarrow (14.0.2)
- Installing pygeos (0.14): Failed

ChefBuildError

Backend subprocess exited when trying to invoke get_requires_for_build_wheel

<string>:8: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
/tmp/tmp8tfyojhh/pygeos-0.14/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 "/home/planzers/miniconda3/envs/test_v2dggs/lib/python3.12/site-packages/pyproject_hooks/_in_process/_in_process.py", line 373, in <module>
    main()
  File "/home/planzers/miniconda3/envs/test_v2dggs/lib/python3.12/site-packages/pyproject_hooks/_in_process/_in_process.py", line 357, in main
    json_out["return_val"] = hook(**hook_input["kwargs"])
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/planzers/miniconda3/envs/test_v2dggs/lib/python3.12/site-packages/pyproject_hooks/_in_process/_in_process.py", line 134, in get_requires_for_build_wheel
    return hook(config_settings)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpor05rulu/.venv/lib/python3.12/site-packages/setuptools/build_meta.py", line 327, in get_requires_for_build_wheel
    return self._get_build_requires(config_settings, requirements=[])
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpor05rulu/.venv/lib/python3.12/site-packages/setuptools/build_meta.py", line 297, in _get_build_requires
    self.run_setup()
  File "/tmp/tmpor05rulu/.venv/lib/python3.12/site-packages/setuptools/build_meta.py", line 313, in run_setup
    exec(code, locals())
  File "<string>", line 214, in <module>
  File "/tmp/tmp8tfyojhh/pygeos-0.14/versioneer.py", line 1480, in get_version
    return get_versions()["version"]
           ^^^^^^^^^^^^^^
  File "/tmp/tmp8tfyojhh/pygeos-0.14/versioneer.py", line 1412, in get_versions
    cfg = get_config_from_root(root)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp8tfyojhh/pygeos-0.14/versioneer.py", line 342, in get_config_from_root
    parser = configparser.SafeConfigParser()
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did  - Installing h3pandas (0.2.6)
- Installing psycopg2 (2.9.9)
- Installing pyarrow (14.0.2)
- Installing pygeos (0.14): Failed

ChefBuildError

Backend subprocess exited when trying to invoke get_requires_for_build_wheel

<string>:8: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
/tmp/tmp8tfyojhh/pygeos-0.14/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 "/home/planzers/miniconda3/envs/test_v2dggs/lib/python3.12/site-packages/pyproject_hooks/_in_process/_in_process.py", line 373, in <module>
    main()
  File "/home/planzers/miniconda3/envs/test_v2dggs/lib/python3.12/site-packages/pyproject_hooks/_in_process/_in_process.py", line 357, in main
    json_out["return_val"] = hook(**hook_input["kwargs"])
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/planzers/miniconda3/envs/test_v2dggs/lib/python3.12/site-packages/pyproject_hooks/_in_process/_in_process.py", line 134, in get_requires_for_build_wheel
    return hook(config_settings)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpor05rulu/.venv/lib/python3.12/site-packages/setuptools/build_meta.py", line 327, in get_requires_for_build_wheel
    return self._get_build_requires(config_settings, requirements=[])
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpor05rulu/.venv/lib/python3.12/site-packages/setuptools/build_meta.py", line 297, in _get_build_requires
    self.run_setup()
  File "/tmp/tmpor05rulu/.venv/lib/python3.12/site-packages/setuptools/build_meta.py", line 313, in run_setup
    exec(code, locals())
  File "<string>", line 214, in <module>
  File "/tmp/tmp8tfyojhh/pygeos-0.14/versioneer.py", line 1480, in get_version
    return get_versions()["version"]
           ^^^^^^^^^^^^^^
  File "/tmp/tmp8tfyojhh/pygeos-0.14/versioneer.py", line 1412, in get_versions
    cfg = get_config_from_root(root)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp8tfyojhh/pygeos-0.14/versioneer.py", line 342, in get_config_from_root
    parser = configparser.SafeConfigParser()
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did  - Installing gdal (3.9.1)
- Installing h3pandas (0.2.6)
- Installing psycopg2 (2.9.9)
- Installing pyarrow (14.0.2)
- Installing pygeos (0.14): Failed

ChefBuildError

Backend subprocess exited when trying to invoke get_requires_for_build_wheel

<string>:8: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
/tmp/tmp8tfyojhh/pygeos-0.14/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 "/home/planzers/miniconda3/envs/test_v2dggs/lib/python3.12/site-packages/pyproject_hooks/_in_process/_in_process.py", line 373, in <module>
    main()
  File "/home/planzers/miniconda3/envs/test_v2dggs/lib/python3.12/site-packages/pyproject_hooks/_in_process/_in_process.py", line 357, in main
    json_out["return_val"] = hook(**hook_input["kwargs"])
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/planzers/miniconda3/envs/test_v2dggs/lib/python3.12/site-packages/pyproject_hooks/_in_process/_in_process.py", line 134, in get_requires_for_build_wheel
    return hook(config_settings)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpor05rulu/.venv/lib/python3.12/site-packages/setuptools/build_meta.py", line 327, in get_requires_for_build_wheel
    return self._get_build_requires(config_settings, requirements=[])
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpor05rulu/.venv/lib/python3.12/site-packages/setuptools/build_meta.py", line 297, in _get_build_requires
    self.run_setup()
  File "/tmp/tmpor05rulu/.venv/lib/python3.12/site-packages/setuptools/build_meta.py", line 313, in run_setup
    exec(code, locals())
  File "<string>", line 214, in <module>
  File "/tmp/tmp8tfyojhh/pygeos-0.14/versioneer.py", line 1480, in get_version
    return get_versions()["version"]
           ^^^^^^^^^^^^^^
  File "/tmp/tmp8tfyojhh/pygeos-0.14/versioneer.py", line 1412, in get_versions
    cfg = get_config_from_root(root)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp8tfyojhh/pygeos-0.14/versioneer.py", line 342, in get_config_from_root
    parser = configparser.SafeConfigParser()
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did you mean: 'RawConfigParser'?


at ~/miniconda3/envs/test_v2dggs/lib/python3.12/site-packages/poetry/installation/chef.py:164 in _prepare
    160│ 
    161│                 error = ChefBuildError("\n\n".join(message_parts))
    162│ 
    163│             if error is not None:
  → 164│                 raise error from None
    165│ 
    166│             return path
    167│ 
    168│     def _prepare_sdist(self, archive: Path, destination: Path | None = None) -> Path:

Note: This error originates from the build backend, and is likely not a problem with poetry but with pygeos (0.14) not supporting PEP 517 builds. You can verify this by running 'pip wheel --no-cache-dir --use-pep517 "pygeos (==0.14)"'.

- Installing pytest (7.4.4)

For Now

I was successful in install this with the below

git clone [email protected]:manaakiwhenua/vector2dggs.git
cd vector2dggs
mamba create -n vector2dggs python=3.11
mamba install gdal geopandas h3pandas dask-geopandas dask click tqdm click-log pyarrow pygeos pyproj sqlalchemy psycopg2
pip install -e .

[alpha-beta-soup]

I can't even get your workaround to work.

What I have been using is a conda environment file (which still uses pip to install vector2dggs):

name: vector2dggs
channels:
  - conda-forge
  - defaults
dependencies:
  - python=3.11
  - pip
  - gdal=3.9.1
  - pip:
    - vector2dggs>=0.5.4

If you save this to env.yml and run conda env create --name v2d --file env.yml... well, it still fails. (However, it definitely has worked in the past.)

However here's my new workaround:

conda create --name v2d python=3.11 gdal=3.9.1 -c conda-forge
pip install vector2dggs==0.5.4

Installing 0.6.0 (current release) does not work even with this method. This is probably due to an upgrade in the gdal dependency introduced in c61b7db

Since it seems to matter, my system has libgeos-dev on Ubuntu 22.04 LTS at 3.12.1-1.

[alpha-beta-soup]

name: vector2dggs
channels:
  - conda-forge
  - defaults
dependencies:
  - python=3.11
  - pip
  - gdal=3.9.1
  - pip:
    - vector2dggs==0.5.4

Works. So this is ultimately associated with upgrading the python GDAL dependency; perhaps some conflict with system-installed GEOS. I'll see if we even need the upgrade to GDAL for v0.6; I don't think it's necesssary.

[alpha-beta-soup]

With latest release (0.6.1) I can now do a bare pip install vector2dggs successfully.

@SPlanzer if you can do this too, please close the issue.