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Published 20 hours ago • verified publisher icon saketkc

Could not install pySCTransform

Open houlinyu opened this issue 1 year ago • 3 comments

  • pySCTranscform version:
  • Commit SHA:
  • Python version: 3.11.5
  • Operating System: MAC OS 13.5.2

Description

Tried to install it but failed

What I Did

pip install git+https://github.com/saketkc/pysctransform.git

-----------messages start---------- Collecting git+https://github.com/saketkc/pysctransform.git Cloning https://github.com/saketkc/pysctransform.git to /private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-req-build-5g2te194 Running command git clone --filter=blob:none --quiet https://github.com/saketkc/pysctransform.git /private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-req-build-5g2te194 Resolved https://github.com/saketkc/pysctransform.git to commit d14af48c8c1bbceb132964df202e35b7b38cc3e6 Preparing metadata (setup.py) ... error error: subprocess-exited-with-error

× python setup.py egg_info did not run successfully. │ exit code: 1 ╰─> [124 lines of output] /Users/yuhoulin/anaconda3/envs/scanpy/lib/python3.11/site-packages/setuptools/init.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !!

          ********************************************************************************
          Requirements should be satisfied by a PEP 517 installer.
          If you are using pip, you can try `pip install --use-pep517`.
          ********************************************************************************
  
  !!
    dist.fetch_build_eggs(dist.setup_requires)
    error: subprocess-exited-with-error
  
    × Getting requirements to build wheel did not run successfully.
    │ exit code: 1
    ╰─> [58 lines of output]
        <string>:19: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
        ld: library not found for -llzo2
        clang-16: error: linker command failed with exit code 1 (use -v to see invocation)
        ld: library not found for -llzo
        clang-16: error: linker command failed with exit code 1 (use -v to see invocation)
        ld: library not found for -lblosc
        clang-16: error: linker command failed with exit code 1 (use -v to see invocation)
  
        Error compiling Cython file:
        ------------------------------------------------------------
        ...
  
  
        def _dump_h5_backtrace():
            cdef object bt = []
  
            if H5Ewalk(H5E_DEFAULT, H5E_WALK_DOWNWARD, e_walk_cb, <void*>bt) < 0:
                                                       ^
        ------------------------------------------------------------
  
        tables/utilsextension.pyx:384:47: Cannot assign type 'herr_t (unsigned int, const H5E_error_t *, void *) except? -1 nogil' to 'H5E_walk_t'. Exception values are incompatible. Suggest adding 'noexcept' to type 'herr_t (unsigned int, const H5E_error_t *, void *) except? -1 nogil'.
        cpuinfo failed, assuming no CPU features: 'flags'
        * Using Python 3.11.5 | packaged by conda-forge | (main, Aug 27 2023, 03:33:12) [Clang 15.0.7 ]
        * Found cython 3.0.2
        * USE_PKGCONFIG: False
        * Found conda env: ``/Users/yuhoulin/anaconda3/envs/scanpy``
        * Found HDF5 headers at ``/Users/yuhoulin/anaconda3/envs/scanpy/include``, library at ``/Users/yuhoulin/anaconda3/envs/scanpy/lib``.
        * Could not find LZO 2 headers and library; disabling support for it.
        * Could not find LZO 1 headers and library; disabling support for it.
        * Found bzip2 headers at ``/Users/yuhoulin/anaconda3/envs/scanpy/include``, library at ``/Users/yuhoulin/anaconda3/envs/scanpy/lib``.
        * Could not find blosc headers and library; using internal sources.
        * Found blosc2 headers at ``/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-build-env-i5s241n6/overlay/include``, library at ``/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-build-env-i5s241n6/overlay/lib``.
          * Copying blosc2 runtime library to 'tables' dir because it was not found in standard locations
        Compiling tables/utilsextension.pyx because it changed.
        [1/1] Cythonizing tables/utilsextension.pyx
        Traceback (most recent call last):
          File "/Users/yuhoulin/anaconda3/envs/scanpy/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
            main()
          File "/Users/yuhoulin/anaconda3/envs/scanpy/lib/python3.11/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/yuhoulin/anaconda3/envs/scanpy/lib/python3.11/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/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-build-env-i5s241n6/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 355, in get_requires_for_build_wheel
            return self._get_build_requires(config_settings, requirements=['wheel'])
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          File "/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-build-env-i5s241n6/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 325, in _get_build_requires
            self.run_setup()
          File "/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-build-env-i5s241n6/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 341, in run_setup
            exec(code, locals())
          File "<string>", line 928, in <module>
          File "<string>", line 923, in get_cython_extfiles
          File "/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-build-env-i5s241n6/overlay/lib/python3.11/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize
            cythonize_one(*args)
          File "/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-build-env-i5s241n6/overlay/lib/python3.11/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
            raise CompileError(None, pyx_file)
        Cython.Compiler.Errors.CompileError: tables/utilsextension.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.
  Traceback (most recent call last):
    File "/Users/yuhoulin/anaconda3/envs/scanpy/lib/python3.11/site-packages/setuptools/installer.py", line 96, in _fetch_build_egg_no_warn
      subprocess.check_call(cmd)
    File "/Users/yuhoulin/anaconda3/envs/scanpy/lib/python3.11/subprocess.py", line 413, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command '['/Users/yuhoulin/anaconda3/envs/scanpy/bin/python', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/tmpga3vgp46', '--quiet', 'tables']' returned non-zero exit status 1.
  
  The above exception was the direct cause of the following exception:
  
  Traceback (most recent call last):
    File "<string>", line 2, in <module>
    File "<pip-setuptools-caller>", line 34, in <module>
    File "/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-req-build-5g2te194/setup.py", line 18, in <module>
      setup(
    File "/Users/yuhoulin/anaconda3/envs/scanpy/lib/python3.11/site-packages/setuptools/__init__.py", line 106, in setup
      _install_setup_requires(attrs)
    File "/Users/yuhoulin/anaconda3/envs/scanpy/lib/python3.11/site-packages/setuptools/__init__.py", line 79, in _install_setup_requires
      _fetch_build_eggs(dist)
    File "/Users/yuhoulin/anaconda3/envs/scanpy/lib/python3.11/site-packages/setuptools/__init__.py", line 84, in _fetch_build_eggs
      dist.fetch_build_eggs(dist.setup_requires)
    File "/Users/yuhoulin/anaconda3/envs/scanpy/lib/python3.11/site-packages/setuptools/dist.py", line 907, in fetch_build_eggs
      return _fetch_build_eggs(self, requires)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/yuhoulin/anaconda3/envs/scanpy/lib/python3.11/site-packages/setuptools/installer.py", line 38, in _fetch_build_eggs
      resolved_dists = pkg_resources.working_set.resolve(
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/yuhoulin/anaconda3/envs/scanpy/lib/python3.11/site-packages/pkg_resources/__init__.py", line 829, in resolve
      dist = self._resolve_dist(
             ^^^^^^^^^^^^^^^^^^^
    File "/Users/yuhoulin/anaconda3/envs/scanpy/lib/python3.11/site-packages/pkg_resources/__init__.py", line 865, in _resolve_dist
      dist = best[req.key] = env.best_match(
                             ^^^^^^^^^^^^^^^
    File "/Users/yuhoulin/anaconda3/envs/scanpy/lib/python3.11/site-packages/pkg_resources/__init__.py", line 1135, in best_match
      return self.obtain(req, installer)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/yuhoulin/anaconda3/envs/scanpy/lib/python3.11/site-packages/pkg_resources/__init__.py", line 1147, in obtain
      return installer(requirement)
             ^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/yuhoulin/anaconda3/envs/scanpy/lib/python3.11/site-packages/setuptools/installer.py", line 98, in _fetch_build_egg_no_warn
      raise DistutilsError(str(e)) from e
  distutils.errors.DistutilsError: Command '['/Users/yuhoulin/anaconda3/envs/scanpy/bin/python', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/tmpga3vgp46', '--quiet', 'tables']' returned non-zero exit status 1.
  [end of output]

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

× Encountered error while generating package metadata. ╰─> See above for output.

note: This is an issue with the package mentioned above, not pip. hint: See above for details. -------------------message end-----------------

I then tried: pip install git+https://github.com/saketkc/pysctransform.git --use-pep517

-------------------message start------------------

Collecting git+https://github.com/saketkc/pysctransform.git Cloning https://github.com/saketkc/pysctransform.git to /private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-req-build-oy2horsc Running command git clone --filter=blob:none --quiet https://github.com/saketkc/pysctransform.git /private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-req-build-oy2horsc Resolved https://github.com/saketkc/pysctransform.git to commit d14af48c8c1bbceb132964df202e35b7b38cc3e6 Installing build dependencies ... done Getting requirements to build wheel ... done Installing backend dependencies ... error error: subprocess-exited-with-error

× pip subprocess to install backend dependencies did not run successfully. │ exit code: 1 ╰─> [115 lines of output] Collecting KDEpy>=1.1.0 Using cached KDEpy-1.1.5-cp311-cp311-macosx_11_0_arm64.whl Collecting patsy>=0.5.1 Using cached patsy-0.5.3-py2.py3-none-any.whl (233 kB) Collecting pandas>=1.3.0 Obtaining dependency information for pandas>=1.3.0 from https://files.pythonhosted.org/packages/e5/cd/c941b51e95992968e3e8abc7180f33b952478abd6943062051517a808db7/pandas-2.1.0-cp311-cp311-macosx_11_0_arm64.whl.metadata Using cached pandas-2.1.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (18 kB) Collecting matplotlib>=3.4.2 Obtaining dependency information for matplotlib>=3.4.2 from https://files.pythonhosted.org/packages/f6/22/9c31044ff7339c63727a135872e5cb59564f11625372a81c3eebf148f4af/matplotlib-3.7.2-cp311-cp311-macosx_11_0_arm64.whl.metadata Using cached matplotlib-3.7.2-cp311-cp311-macosx_11_0_arm64.whl.metadata (5.6 kB) Collecting numpy>=1.21.0 Obtaining dependency information for numpy>=1.21.0 from https://files.pythonhosted.org/packages/86/a1/b8ef999c32f26a97b5f714887e21f96c12ae99a38583a0a96e65283ac0a1/numpy-1.25.2-cp311-cp311-macosx_11_0_arm64.whl.metadata Using cached numpy-1.25.2-cp311-cp311-macosx_11_0_arm64.whl.metadata (5.6 kB) Collecting adjustText>=0.7.3 Using cached adjustText-0.8-py3-none-any.whl (9.1 kB) Collecting scipy>=1.7.0 Obtaining dependency information for scipy>=1.7.0 from https://files.pythonhosted.org/packages/2a/12/62804d63514ecd9d2ecb73497c3e38094f9139bc60b0353b653253d106bb/scipy-1.11.2-cp311-cp311-macosx_12_0_arm64.whl.metadata Using cached scipy-1.11.2-cp311-cp311-macosx_12_0_arm64.whl.metadata (146 kB) Collecting scikit-learn>=0.24 Obtaining dependency information for scikit-learn>=0.24 from https://files.pythonhosted.org/packages/18/36/60b58b6199547b7b46be03e05508d053162fbce146639bfc65609fa49b23/scikit_learn-1.3.0-cp311-cp311-macosx_12_0_arm64.whl.metadata Using cached scikit_learn-1.3.0-cp311-cp311-macosx_12_0_arm64.whl.metadata (11 kB) Collecting tqdm>=4.61.2 Obtaining dependency information for tqdm>=4.61.2 from https://files.pythonhosted.org/packages/00/e5/f12a80907d0884e6dff9c16d0c0114d81b8cd07dc3ae54c5e962cc83037e/tqdm-4.66.1-py3-none-any.whl.metadata Using cached tqdm-4.66.1-py3-none-any.whl.metadata (57 kB) Collecting statsmodels>=0.12.2 Using cached statsmodels-0.14.0-cp311-cp311-macosx_11_0_arm64.whl (9.4 MB) Collecting scanpy==1.7.2 Using cached scanpy-1.7.2-py3-none-any.whl (10.3 MB) Collecting anndata>=0.7.4 (from scanpy==1.7.2) Obtaining dependency information for anndata>=0.7.4 from https://files.pythonhosted.org/packages/a7/ee/767a05c299d95b438ef9c8ab6dbc15896cfb9121cf4327fe1da160a45343/anndata-0.9.2-py3-none-any.whl.metadata Using cached anndata-0.9.2-py3-none-any.whl.metadata (6.1 kB) Collecting seaborn (from scanpy==1.7.2) Using cached seaborn-0.12.2-py3-none-any.whl (293 kB) Collecting h5py>=2.10.0 (from scanpy==1.7.2) Obtaining dependency information for h5py>=2.10.0 from https://files.pythonhosted.org/packages/37/82/859d9fc800a316e692bd040437d45613512b43d49fb0435c5bbab9e71511/h5py-3.9.0-cp311-cp311-macosx_11_0_arm64.whl.metadata Using cached h5py-3.9.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.5 kB) Collecting tables (from scanpy==1.7.2) Using cached tables-3.8.0.tar.gz (8.0 MB) Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'error' error: subprocess-exited-with-error

    × Getting requirements to build wheel did not run successfully.
    │ exit code: 1
    ╰─> [58 lines of output]
        <string>:19: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
        ld: library not found for -llzo2
        clang-16: error: linker command failed with exit code 1 (use -v to see invocation)
        ld: library not found for -llzo
        clang-16: error: linker command failed with exit code 1 (use -v to see invocation)
        ld: library not found for -lblosc
        clang-16: error: linker command failed with exit code 1 (use -v to see invocation)
  
        Error compiling Cython file:
        ------------------------------------------------------------
        ...
  
  
        def _dump_h5_backtrace():
            cdef object bt = []
  
            if H5Ewalk(H5E_DEFAULT, H5E_WALK_DOWNWARD, e_walk_cb, <void*>bt) < 0:
                                                       ^
        ------------------------------------------------------------
  
        tables/utilsextension.pyx:384:47: Cannot assign type 'herr_t (unsigned int, const H5E_error_t *, void *) except? -1 nogil' to 'H5E_walk_t'. Exception values are incompatible. Suggest adding 'noexcept' to type 'herr_t (unsigned int, const H5E_error_t *, void *) except? -1 nogil'.
        cpuinfo failed, assuming no CPU features: 'flags'
        * Using Python 3.11.5 | packaged by conda-forge | (main, Aug 27 2023, 03:33:12) [Clang 15.0.7 ]
        * Found cython 3.0.2
        * USE_PKGCONFIG: False
        * Found conda env: ``/Users/yuhoulin/anaconda3/envs/scanpy``
        * Found HDF5 headers at ``/Users/yuhoulin/anaconda3/envs/scanpy/include``, library at ``/Users/yuhoulin/anaconda3/envs/scanpy/lib``.
        * Could not find LZO 2 headers and library; disabling support for it.
        * Could not find LZO 1 headers and library; disabling support for it.
        * Found bzip2 headers at ``/Users/yuhoulin/anaconda3/envs/scanpy/include``, library at ``/Users/yuhoulin/anaconda3/envs/scanpy/lib``.
        * Could not find blosc headers and library; using internal sources.
        * Found blosc2 headers at ``/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-build-env-45b10jwy/overlay/include``, library at ``/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-build-env-45b10jwy/overlay/lib``.
          * Copying blosc2 runtime library to 'tables' dir because it was not found in standard locations
        Compiling tables/utilsextension.pyx because it changed.
        [1/1] Cythonizing tables/utilsextension.pyx
        Traceback (most recent call last):
          File "/Users/yuhoulin/anaconda3/envs/scanpy/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
            main()
          File "/Users/yuhoulin/anaconda3/envs/scanpy/lib/python3.11/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/yuhoulin/anaconda3/envs/scanpy/lib/python3.11/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/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-build-env-45b10jwy/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 355, in get_requires_for_build_wheel
            return self._get_build_requires(config_settings, requirements=['wheel'])
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          File "/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-build-env-45b10jwy/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 325, in _get_build_requires
            self.run_setup()
          File "/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-build-env-45b10jwy/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 341, in run_setup
            exec(code, locals())
          File "<string>", line 928, in <module>
          File "<string>", line 923, in get_cython_extfiles
          File "/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-build-env-45b10jwy/overlay/lib/python3.11/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize
            cythonize_one(*args)
          File "/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-build-env-45b10jwy/overlay/lib/python3.11/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
            raise CompileError(None, pyx_file)
        Cython.Compiler.Errors.CompileError: tables/utilsextension.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.
  [end of output]

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

× pip subprocess to install backend dependencies 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.

-------------------message end-----------------

houlinyu avatar Sep 10 '23 23:09 houlinyu

I would recommend creating a conda environment for pysctransform. The rest of the install instructions remain the same.

saketkc avatar Sep 11 '23 00:09 saketkc

I created a new conda env called pysct, and installed both scanpy (installed together with the creation of conda env) and louvain (conda install failed so I installed using pip install louvain after activating the pysct conda env). And did both pip install git+https://github.com/saketkc/pysctransform.git and. pip install git+https://github.com/saketkc/pysctransform.git --use-pep517. The message I got seems to be the same as before. Appreciate it if you could help me further.

---------message------------- (pysct) xxx ~ % pip install git+https://github.com/saketkc/pysctransform.git

Collecting git+https://github.com/saketkc/pysctransform.git Cloning https://github.com/saketkc/pysctransform.git to /private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-req-build-f99zsvb4 Running command git clone --filter=blob:none --quiet https://github.com/saketkc/pysctransform.git /private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-req-build-f99zsvb4 Resolved https://github.com/saketkc/pysctransform.git to commit d14af48c8c1bbceb132964df202e35b7b38cc3e6 Preparing metadata (setup.py) ... done Collecting adjustText>=0.7.3 (from pysctransform==0.1.1) Using cached adjustText-0.8-py3-none-any.whl (9.1 kB) Collecting KDEpy>=1.1.0 (from pysctransform==0.1.1) Using cached KDEpy-1.1.5-cp311-cp311-macosx_11_0_arm64.whl Requirement already satisfied: matplotlib>=3.4.2 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from pysctransform==0.1.1) (3.7.2) Requirement already satisfied: numpy>=1.21.0 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from pysctransform==0.1.1) (1.23.5) Requirement already satisfied: pandas>=1.3.0 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from pysctransform==0.1.1) (2.0.3) Requirement already satisfied: patsy>=0.5.1 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from pysctransform==0.1.1) (0.5.3) Requirement already satisfied: scipy>=1.7.0 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from pysctransform==0.1.1) (1.10.1) Requirement already satisfied: scikit-learn>=0.24 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from pysctransform==0.1.1) (1.3.0) Requirement already satisfied: scanpy==1.7.2 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from pysctransform==0.1.1) (1.7.2) Requirement already satisfied: statsmodels>=0.12.2 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from pysctransform==0.1.1) (0.14.0) Requirement already satisfied: tqdm>=4.61.2 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from pysctransform==0.1.1) (4.65.0) Requirement already satisfied: anndata>=0.7.4 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from scanpy==1.7.2->pysctransform==0.1.1) (0.9.2) Requirement already satisfied: seaborn in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from scanpy==1.7.2->pysctransform==0.1.1) (0.12.2) Requirement already satisfied: h5py>=2.10.0 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from scanpy==1.7.2->pysctransform==0.1.1) (3.9.0) Requirement already satisfied: tables in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from scanpy==1.7.2->pysctransform==0.1.1) (3.8.0) Requirement already satisfied: networkx>=2.3 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from scanpy==1.7.2->pysctransform==0.1.1) (3.1) Requirement already satisfied: natsort in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from scanpy==1.7.2->pysctransform==0.1.1) (7.1.1) Requirement already satisfied: joblib in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from scanpy==1.7.2->pysctransform==0.1.1) (1.2.0) Requirement already satisfied: numba>=0.41.0 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from scanpy==1.7.2->pysctransform==0.1.1) (0.57.1) Requirement already satisfied: umap-learn>=0.3.10 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from scanpy==1.7.2->pysctransform==0.1.1) (0.5.3) Requirement already satisfied: legacy-api-wrap in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from scanpy==1.7.2->pysctransform==0.1.1) (0.0.0) Requirement already satisfied: packaging in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from scanpy==1.7.2->pysctransform==0.1.1) (23.1) Requirement already satisfied: sinfo in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from scanpy==1.7.2->pysctransform==0.1.1) (0.3.1) Requirement already satisfied: contourpy>=1.0.1 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from matplotlib>=3.4.2->pysctransform==0.1.1) (1.0.5) Requirement already satisfied: cycler>=0.10 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from matplotlib>=3.4.2->pysctransform==0.1.1) (0.11.0) Requirement already satisfied: fonttools>=4.22.0 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from matplotlib>=3.4.2->pysctransform==0.1.1) (4.25.0) Requirement already satisfied: kiwisolver>=1.0.1 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from matplotlib>=3.4.2->pysctransform==0.1.1) (1.4.4) Requirement already satisfied: pillow>=6.2.0 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from matplotlib>=3.4.2->pysctransform==0.1.1) (9.4.0) Requirement already satisfied: pyparsing<3.1,>=2.3.1 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from matplotlib>=3.4.2->pysctransform==0.1.1) (3.0.9) Requirement already satisfied: python-dateutil>=2.7 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from matplotlib>=3.4.2->pysctransform==0.1.1) (2.8.2) Requirement already satisfied: pytz>=2020.1 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from pandas>=1.3.0->pysctransform==0.1.1) (2022.7) Requirement already satisfied: tzdata>=2022.1 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from pandas>=1.3.0->pysctransform==0.1.1) (2023.3) Requirement already satisfied: six in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from patsy>=0.5.1->pysctransform==0.1.1) (1.16.0) Requirement already satisfied: threadpoolctl>=2.0.0 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from scikit-learn>=0.24->pysctransform==0.1.1) (2.2.0) Requirement already satisfied: llvmlite<0.41,>=0.40.0dev0 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from numba>=0.41.0->scanpy==1.7.2->pysctransform==0.1.1) (0.40.0) Requirement already satisfied: pynndescent>=0.5 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from umap-learn>=0.3.10->scanpy==1.7.2->pysctransform==0.1.1) (0.5.10) Requirement already satisfied: get-version>=2.0.4 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from legacy-api-wrap->scanpy==1.7.2->pysctransform==0.1.1) (3.5.4) Requirement already satisfied: setuptools in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from legacy-api-wrap->scanpy==1.7.2->pysctransform==0.1.1) (68.0.0) Requirement already satisfied: stdlib-list in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from sinfo->scanpy==1.7.2->pysctransform==0.1.1) (0.8.0) Collecting cython>=0.29.21 (from tables->scanpy==1.7.2->pysctransform==0.1.1) Obtaining dependency information for cython>=0.29.21 from https://files.pythonhosted.org/packages/03/e9/9cc0c4f0d8a566089d096254cd25168a0db02dd047863a7f995d8d3eefa7/Cython-3.0.2-py2.py3-none-any.whl.metadata Using cached Cython-3.0.2-py2.py3-none-any.whl.metadata (3.1 kB) Requirement already satisfied: numexpr>=2.6.2 in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from tables->scanpy==1.7.2->pysctransform==0.1.1) (2.8.4) Collecting blosc2~=2.0.0 (from tables->scanpy==1.7.2->pysctransform==0.1.1) Using cached blosc2-2.0.0-cp311-cp311-macosx_11_0_arm64.whl (3.1 MB) Requirement already satisfied: py-cpuinfo in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from tables->scanpy==1.7.2->pysctransform==0.1.1) (8.0.0) Collecting msgpack (from blosc2~=2.0.0->tables->scanpy==1.7.2->pysctransform==0.1.1) Using cached msgpack-1.0.5-cp311-cp311-macosx_11_0_arm64.whl (69 kB) Requirement already satisfied: dunamai in ./anaconda3/envs/pysct/lib/python3.11/site-packages (from get-version>=2.0.4->legacy-api-wrap->scanpy==1.7.2->pysctransform==0.1.1) (1.17.0) Using cached Cython-3.0.2-py2.py3-none-any.whl (1.2 MB) 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 ╰─> [48 lines of output] /Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/setuptools/init.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !!

          ********************************************************************************
          Requirements should be satisfied by a PEP 517 installer.
          If you are using pip, you can try `pip install --use-pep517`.
          ********************************************************************************
  
  !!
    dist.fetch_build_eggs(dist.setup_requires)
  Traceback (most recent call last):
    File "<string>", line 2, in <module>
    File "<pip-setuptools-caller>", line 34, in <module>
    File "/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-req-build-f99zsvb4/setup.py", line 18, in <module>
      setup(
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/setuptools/__init__.py", line 106, in setup
      _install_setup_requires(attrs)
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/setuptools/__init__.py", line 79, in _install_setup_requires
      _fetch_build_eggs(dist)
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/setuptools/__init__.py", line 84, in _fetch_build_eggs
      dist.fetch_build_eggs(dist.setup_requires)
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/setuptools/dist.py", line 907, in fetch_build_eggs
      return _fetch_build_eggs(self, requires)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/setuptools/installer.py", line 38, in _fetch_build_eggs
      resolved_dists = pkg_resources.working_set.resolve(
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/pkg_resources/__init__.py", line 829, in resolve
      dist = self._resolve_dist(
             ^^^^^^^^^^^^^^^^^^^
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/pkg_resources/__init__.py", line 865, in _resolve_dist
      dist = best[req.key] = env.best_match(
                             ^^^^^^^^^^^^^^^
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/pkg_resources/__init__.py", line 1135, in best_match
      return self.obtain(req, installer)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/pkg_resources/__init__.py", line 1147, in obtain
      return installer(requirement)
             ^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/setuptools/installer.py", line 101, in _fetch_build_egg_no_warn
      wheel.install_as_egg(dist_location)
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/setuptools/wheel.py", line 117, in install_as_egg
      self._install_as_egg(destination_eggdir, zf)
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/setuptools/wheel.py", line 125, in _install_as_egg
      self._convert_metadata(zf, destination_eggdir, dist_info, egg_info)
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/setuptools/wheel.py", line 171, in _convert_metadata
      os.rename(dist_info, egg_info)
  OSError: [Errno 66] Directory not empty: '/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-req-build-f99zsvb4/.eggs/KDEpy-1.1.5-py3.11-macosx-11.0-arm64.egg/KDEpy-1.1.5.dist-info' -> '/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-req-build-f99zsvb4/.eggs/KDEpy-1.1.5-py3.11-macosx-11.0-arm64.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 ╰─> [48 lines of output] /Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/setuptools/init.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !!

          ********************************************************************************
          Requirements should be satisfied by a PEP 517 installer.
          If you are using pip, you can try `pip install --use-pep517`.
          ********************************************************************************
  
  !!
    dist.fetch_build_eggs(dist.setup_requires)
  Traceback (most recent call last):
    File "<string>", line 2, in <module>
    File "<pip-setuptools-caller>", line 34, in <module>
    File "/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-req-build-f99zsvb4/setup.py", line 18, in <module>
      setup(
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/setuptools/__init__.py", line 106, in setup
      _install_setup_requires(attrs)
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/setuptools/__init__.py", line 79, in _install_setup_requires
      _fetch_build_eggs(dist)
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/setuptools/__init__.py", line 84, in _fetch_build_eggs
      dist.fetch_build_eggs(dist.setup_requires)
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/setuptools/dist.py", line 907, in fetch_build_eggs
      return _fetch_build_eggs(self, requires)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/setuptools/installer.py", line 38, in _fetch_build_eggs
      resolved_dists = pkg_resources.working_set.resolve(
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/pkg_resources/__init__.py", line 829, in resolve
      dist = self._resolve_dist(
             ^^^^^^^^^^^^^^^^^^^
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/pkg_resources/__init__.py", line 865, in _resolve_dist
      dist = best[req.key] = env.best_match(
                             ^^^^^^^^^^^^^^^
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/pkg_resources/__init__.py", line 1135, in best_match
      return self.obtain(req, installer)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/pkg_resources/__init__.py", line 1147, in obtain
      return installer(requirement)
             ^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/setuptools/installer.py", line 101, in _fetch_build_egg_no_warn
      wheel.install_as_egg(dist_location)
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/setuptools/wheel.py", line 117, in install_as_egg
      self._install_as_egg(destination_eggdir, zf)
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/setuptools/wheel.py", line 125, in _install_as_egg
      self._convert_metadata(zf, destination_eggdir, dist_info, egg_info)
    File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/setuptools/wheel.py", line 171, in _convert_metadata
      os.rename(dist_info, egg_info)
  OSError: [Errno 66] Directory not empty: '/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-req-build-f99zsvb4/.eggs/KDEpy-1.1.5-py3.11-macosx-11.0-arm64.egg/KDEpy-1.1.5.dist-info' -> '/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-req-build-f99zsvb4/.eggs/KDEpy-1.1.5-py3.11-macosx-11.0-arm64.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 ERROR: Could not build wheels for pysctransform, which is required to install pyproject.toml-based projects

-------message end------------

-------new message------------ (pysct) xxx ~ % pip install git+https://github.com/saketkc/pysctransform.git --use-pep517

Collecting git+https://github.com/saketkc/pysctransform.git Cloning https://github.com/saketkc/pysctransform.git to /private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-req-build-j_tkn5y2 Running command git clone --filter=blob:none --quiet https://github.com/saketkc/pysctransform.git /private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-req-build-j_tkn5y2 Resolved https://github.com/saketkc/pysctransform.git to commit d14af48c8c1bbceb132964df202e35b7b38cc3e6 Installing build dependencies ... done Getting requirements to build wheel ... done Installing backend dependencies ... error error: subprocess-exited-with-error

× pip subprocess to install backend dependencies did not run successfully. │ exit code: 1 ╰─> [108 lines of output] Collecting KDEpy>=1.1.0 Using cached KDEpy-1.1.5-cp311-cp311-macosx_11_0_arm64.whl Collecting scikit-learn>=0.24 Obtaining dependency information for scikit-learn>=0.24 from https://files.pythonhosted.org/packages/18/36/60b58b6199547b7b46be03e05508d053162fbce146639bfc65609fa49b23/scikit_learn-1.3.0-cp311-cp311-macosx_12_0_arm64.whl.metadata Using cached scikit_learn-1.3.0-cp311-cp311-macosx_12_0_arm64.whl.metadata (11 kB) Collecting tqdm>=4.61.2 Obtaining dependency information for tqdm>=4.61.2 from https://files.pythonhosted.org/packages/00/e5/f12a80907d0884e6dff9c16d0c0114d81b8cd07dc3ae54c5e962cc83037e/tqdm-4.66.1-py3-none-any.whl.metadata Using cached tqdm-4.66.1-py3-none-any.whl.metadata (57 kB) Collecting numpy>=1.21.0 Obtaining dependency information for numpy>=1.21.0 from https://files.pythonhosted.org/packages/86/a1/b8ef999c32f26a97b5f714887e21f96c12ae99a38583a0a96e65283ac0a1/numpy-1.25.2-cp311-cp311-macosx_11_0_arm64.whl.metadata Using cached numpy-1.25.2-cp311-cp311-macosx_11_0_arm64.whl.metadata (5.6 kB) Collecting scipy>=1.7.0 Obtaining dependency information for scipy>=1.7.0 from https://files.pythonhosted.org/packages/2a/12/62804d63514ecd9d2ecb73497c3e38094f9139bc60b0353b653253d106bb/scipy-1.11.2-cp311-cp311-macosx_12_0_arm64.whl.metadata Using cached scipy-1.11.2-cp311-cp311-macosx_12_0_arm64.whl.metadata (146 kB) Collecting statsmodels>=0.12.2 Using cached statsmodels-0.14.0-cp311-cp311-macosx_11_0_arm64.whl (9.4 MB) Collecting adjustText>=0.7.3 Using cached adjustText-0.8-py3-none-any.whl (9.1 kB) Collecting pandas>=1.3.0 Obtaining dependency information for pandas>=1.3.0 from https://files.pythonhosted.org/packages/e5/cd/c941b51e95992968e3e8abc7180f33b952478abd6943062051517a808db7/pandas-2.1.0-cp311-cp311-macosx_11_0_arm64.whl.metadata Using cached pandas-2.1.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (18 kB) Collecting patsy>=0.5.1 Using cached patsy-0.5.3-py2.py3-none-any.whl (233 kB) Collecting scanpy==1.7.2 Using cached scanpy-1.7.2-py3-none-any.whl (10.3 MB) Collecting matplotlib>=3.4.2 Obtaining dependency information for matplotlib>=3.4.2 from https://files.pythonhosted.org/packages/f6/22/9c31044ff7339c63727a135872e5cb59564f11625372a81c3eebf148f4af/matplotlib-3.7.2-cp311-cp311-macosx_11_0_arm64.whl.metadata Using cached matplotlib-3.7.2-cp311-cp311-macosx_11_0_arm64.whl.metadata (5.6 kB) Collecting anndata>=0.7.4 (from scanpy==1.7.2) Obtaining dependency information for anndata>=0.7.4 from https://files.pythonhosted.org/packages/a7/ee/767a05c299d95b438ef9c8ab6dbc15896cfb9121cf4327fe1da160a45343/anndata-0.9.2-py3-none-any.whl.metadata Using cached anndata-0.9.2-py3-none-any.whl.metadata (6.1 kB) Collecting seaborn (from scanpy==1.7.2) Using cached seaborn-0.12.2-py3-none-any.whl (293 kB) Collecting h5py>=2.10.0 (from scanpy==1.7.2) Obtaining dependency information for h5py>=2.10.0 from https://files.pythonhosted.org/packages/37/82/859d9fc800a316e692bd040437d45613512b43d49fb0435c5bbab9e71511/h5py-3.9.0-cp311-cp311-macosx_11_0_arm64.whl.metadata Using cached h5py-3.9.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.5 kB) Collecting tables (from scanpy==1.7.2) Using cached tables-3.8.0.tar.gz (8.0 MB) Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'error' error: subprocess-exited-with-error

    × Getting requirements to build wheel did not run successfully.
    │ exit code: 1
    ╰─> [51 lines of output]
        <string>:19: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  
        Error compiling Cython file:
        ------------------------------------------------------------
        ...
  
  
        def _dump_h5_backtrace():
            cdef object bt = []
  
            if H5Ewalk(H5E_DEFAULT, H5E_WALK_DOWNWARD, e_walk_cb, <void*>bt) < 0:
                                                       ^
        ------------------------------------------------------------
  
        tables/utilsextension.pyx:384:47: Cannot assign type 'herr_t (unsigned int, const H5E_error_t *, void *) except? -1 nogil' to 'H5E_walk_t'. Exception values are incompatible. Suggest adding 'noexcept' to type 'herr_t (unsigned int, const H5E_error_t *, void *) except? -1 nogil'.
        cpuinfo failed, assuming no CPU features: 'flags'
        * Using Python 3.11.5 | packaged by conda-forge | (main, Aug 27 2023, 03:33:12) [Clang 15.0.7 ]
        * Found cython 3.0.2
        * USE_PKGCONFIG: False
        * Found conda env: ``/Users/yuhoulin/anaconda3/envs/pysct``
        * Found HDF5 headers at ``/Users/yuhoulin/anaconda3/envs/pysct/include``, library at ``/Users/yuhoulin/anaconda3/envs/pysct/lib``.
        * Found LZO 2 headers at ``/Users/yuhoulin/anaconda3/envs/pysct/include``, library at ``/Users/yuhoulin/anaconda3/envs/pysct/lib``.
        * Skipping detection of LZO 1 since LZO 2 has already been found.
        * Found bzip2 headers at ``/Users/yuhoulin/anaconda3/envs/pysct/include``, library at ``/Users/yuhoulin/anaconda3/envs/pysct/lib``.
        * Found blosc headers at ``/Users/yuhoulin/anaconda3/envs/pysct/include``, library at ``/Users/yuhoulin/anaconda3/envs/pysct/lib``.
        * Found blosc2 headers at ``/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-build-env-mnlokc3w/overlay/include``, library at ``/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-build-env-mnlokc3w/overlay/lib``.
        Compiling tables/utilsextension.pyx because it changed.
        [1/1] Cythonizing tables/utilsextension.pyx
        Traceback (most recent call last):
          File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
            main()
          File "/Users/yuhoulin/anaconda3/envs/pysct/lib/python3.11/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/yuhoulin/anaconda3/envs/pysct/lib/python3.11/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/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-build-env-mnlokc3w/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 355, in get_requires_for_build_wheel
            return self._get_build_requires(config_settings, requirements=['wheel'])
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          File "/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-build-env-mnlokc3w/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 325, in _get_build_requires
            self.run_setup()
          File "/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-build-env-mnlokc3w/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 341, in run_setup
            exec(code, locals())
          File "<string>", line 928, in <module>
          File "<string>", line 923, in get_cython_extfiles
          File "/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-build-env-mnlokc3w/overlay/lib/python3.11/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize
            cythonize_one(*args)
          File "/private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-build-env-mnlokc3w/overlay/lib/python3.11/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
            raise CompileError(None, pyx_file)
        Cython.Compiler.Errors.CompileError: tables/utilsextension.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.
  [end of output]

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

× pip subprocess to install backend dependencies 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.

-------message end------------

houlinyu avatar Sep 11 '23 02:09 houlinyu

I was able to install this using conda:

$ conda create -n pysct scipy numpy kdepy matplotlib
$ conda activate pysct
$ pip install git+https://github.com/saketkc/pysctransform.git --use-pep517

saketkc avatar Sep 11 '23 13:09 saketkc