Installation issues: building wheel

[alexlenail]

It's not much of an issue, since ultimately, setup.py works, but worth mentioning:

Building wheels for collected packages: pysctransform
  Building wheel for pysctransform (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [30 lines of output]
      /Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/setuptools/installer.py:27: SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer.
        warnings.warn(
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/private/var/folders/mq/yzq45gh52xn7zz498z7cjtkw0000gn/T/pip-req-build-rfkb9ihn/setup.py", line 18, in <module>
          setup(
        File "/Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/setuptools/__init__.py", line 86, in setup
          _install_setup_requires(attrs)
        File "/Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/setuptools/__init__.py", line 80, in _install_setup_requires
          dist.fetch_build_eggs(dist.setup_requires)
        File "/Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/setuptools/dist.py", line 875, in fetch_build_eggs
          resolved_dists = pkg_resources.working_set.resolve(
        File "/Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/pkg_resources/__init__.py", line 789, in resolve
          dist = best[req.key] = env.best_match(
        File "/Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/pkg_resources/__init__.py", line 1075, in best_match
          return self.obtain(req, installer)
        File "/Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/pkg_resources/__init__.py", line 1087, in obtain
          return installer(requirement)
        File "/Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/setuptools/dist.py", line 945, in fetch_build_egg
          return fetch_build_egg(self, req)
        File "/Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/setuptools/installer.py", line 87, in fetch_build_egg
          wheel.install_as_egg(dist_location)
        File "/Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/setuptools/wheel.py", line 96, in install_as_egg
          self._install_as_egg(destination_eggdir, zf)
        File "/Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/setuptools/wheel.py", line 104, in _install_as_egg
          self._convert_metadata(zf, destination_eggdir, dist_info, egg_info)
        File "/Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/setuptools/wheel.py", line 148, in _convert_metadata
          os.rename(dist_info, egg_info)
      OSError: [Errno 66] Directory not empty: '/private/var/folders/mq/yzq45gh52xn7zz498z7cjtkw0000gn/T/pip-req-build-rfkb9ihn/.eggs/KDEpy-1.1.0-py3.10-macosx-10.9-x86_64.egg/KDEpy-1.1.0.dist-info' -> '/private/var/folders/mq/yzq45gh52xn7zz498z7cjtkw0000gn/T/pip-req-build-rfkb9ihn/.eggs/KDEpy-1.1.0-py3.10-macosx-10.9-x86_64.egg/EGG-INFO'
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for pysctransform
  Running setup.py clean for pysctransform
  error: subprocess-exited-with-error

  × python setup.py clean did not run successfully.
  │ exit code: 1
  ╰─> [30 lines of output]
      /Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/setuptools/installer.py:27: SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer.
        warnings.warn(
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/private/var/folders/mq/yzq45gh52xn7zz498z7cjtkw0000gn/T/pip-req-build-rfkb9ihn/setup.py", line 18, in <module>
          setup(
        File "/Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/setuptools/__init__.py", line 86, in setup
          _install_setup_requires(attrs)
        File "/Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/setuptools/__init__.py", line 80, in _install_setup_requires
          dist.fetch_build_eggs(dist.setup_requires)
        File "/Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/setuptools/dist.py", line 875, in fetch_build_eggs
          resolved_dists = pkg_resources.working_set.resolve(
        File "/Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/pkg_resources/__init__.py", line 789, in resolve
          dist = best[req.key] = env.best_match(
        File "/Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/pkg_resources/__init__.py", line 1075, in best_match
          return self.obtain(req, installer)
        File "/Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/pkg_resources/__init__.py", line 1087, in obtain
          return installer(requirement)
        File "/Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/setuptools/dist.py", line 945, in fetch_build_egg
          return fetch_build_egg(self, req)
        File "/Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/setuptools/installer.py", line 87, in fetch_build_egg
          wheel.install_as_egg(dist_location)
        File "/Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/setuptools/wheel.py", line 96, in install_as_egg
          self._install_as_egg(destination_eggdir, zf)
        File "/Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/setuptools/wheel.py", line 104, in _install_as_egg
          self._convert_metadata(zf, destination_eggdir, dist_info, egg_info)
        File "/Users/alex/miniconda3/envs/pysct/lib/python3.10/site-packages/setuptools/wheel.py", line 148, in _convert_metadata
          os.rename(dist_info, egg_info)
      OSError: [Errno 66] Directory not empty: '/private/var/folders/mq/yzq45gh52xn7zz498z7cjtkw0000gn/T/pip-req-build-rfkb9ihn/.eggs/KDEpy-1.1.0-py3.10-macosx-10.9-x86_64.egg/KDEpy-1.1.0.dist-info' -> '/private/var/folders/mq/yzq45gh52xn7zz498z7cjtkw0000gn/T/pip-req-build-rfkb9ihn/.eggs/KDEpy-1.1.0-py3.10-macosx-10.9-x86_64.egg/EGG-INFO'
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed cleaning build dir for pysctransform
Failed to build pysctransform
Installing collected packages: sinfo, numexpr, dunamai, tables, KDEpy, get-version, adjustText, legacy-api-wrap, scanpy, pysctransform
  Attempting uninstall: scanpy
    Found existing installation: scanpy 1.9.1
    Uninstalling scanpy-1.9.1:
      Successfully uninstalled scanpy-1.9.1
  Running setup.py install for pysctransform ... done
  DEPRECATION: pysctransform was installed using the legacy 'setup.py install' method, because a wheel could not be built for it. A possible replacement is to fix the wheel build issue reported above. Discussion can be found at https://github.com/pypa/pip/issues/8368
Successfully installed KDEpy-1.1.0 adjustText-0.7.3 dunamai-1.12.0 get-version-3.5.4 legacy-api-wrap-1.2 numexpr-2.8.3 pysctransform-0.1.1 scanpy-1.7.2 sinfo-0.3.4 tables-3.7.0