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[BUG] Issues installing giotto-tda, python3.9 #547

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Filco306 opened this issue Dec 11, 2020 · 9 comments
Closed

[BUG] Issues installing giotto-tda, python3.9 #547

Filco306 opened this issue Dec 11, 2020 · 9 comments

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@Filco306
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Describe the bug
I am trying to install giotto-tda on my computer, but I am running into problems.

To reproduce

Reproduce:

pip3 install giotto-tda

Expected behavior

It should be installed

Actual behaviour

Versions

macOS-10.15.7-x86_64-i386-64bit
Python 3.9.0 (default, Dec  6 2020, 18:02:34) 
[Clang 12.0.0 (clang-1200.0.32.27)]
NumPy 1.19.4
SciPy 1.5.4
Joblib 0.17.0
Scikit-learn 0.23.2
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'gtda'

The last one was perhaps a bit obvious, haha.

Additional context

The output I get (which is very long) is the following.

Building wheels for collected packages: giotto-tda
  Building wheel for giotto-tda (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /Users/filipcornell/.venvs/topoaemappervenv/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/g4/2rh0j8g948b6vps252ckmk1w0000gn/T/pip-install-zrd6s0_8/giotto-tda_cbdbc0fa8687454d9d72b5e4039927b2/setup.py'"'"'; __file__='"'"'/private/var/folders/g4/2rh0j8g948b6vps252ckmk1w0000gn/T/pip-install-zrd6s0_8/giotto-tda_cbdbc0fa8687454d9d72b5e4039927b2/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/g4/2rh0j8g948b6vps252ckmk1w0000gn/T/pip-wheel-xvyqxlqi
       cwd: /private/var/folders/g4/2rh0j8g948b6vps252ckmk1w0000gn/T/pip-install-zrd6s0_8/giotto-tda_cbdbc0fa8687454d9d72b5e4039927b2/
  Complete output (194 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.macosx-10.15-x86_64-3.9
  creating build/lib.macosx-10.15-x86_64-3.9/gtda
  copying gtda/_version.py -> build/lib.macosx-10.15-x86_64-3.9/gtda
  copying gtda/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda
  copying gtda/pipeline.py -> build/lib.macosx-10.15-x86_64-3.9/gtda
  copying gtda/base.py -> build/lib.macosx-10.15-x86_64-3.9/gtda
  creating build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams
  copying gtda/diagrams/_metrics.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams
  copying gtda/diagrams/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams
  copying gtda/diagrams/features.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams
  copying gtda/diagrams/distance.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams
  copying gtda/diagrams/preprocessing.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams
  copying gtda/diagrams/_utils.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams
  creating build/lib.macosx-10.15-x86_64-3.9/gtda/externals
  copying gtda/externals/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals
  creating build/lib.macosx-10.15-x86_64-3.9/gtda/tests
  copying gtda/tests/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/tests
  copying gtda/tests/test_pipeline.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/tests
  creating build/lib.macosx-10.15-x86_64-3.9/gtda/mapper
  copying gtda/mapper/cover.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper
  copying gtda/mapper/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper
  copying gtda/mapper/visualization.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper
  copying gtda/mapper/nerve.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper
  copying gtda/mapper/cluster.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper
  copying gtda/mapper/pipeline.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper
  copying gtda/mapper/filter.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper
  creating build/lib.macosx-10.15-x86_64-3.9/gtda/utils
  copying gtda/utils/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/utils
  copying gtda/utils/_docs.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/utils
  copying gtda/utils/testing.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/utils
  copying gtda/utils/validation.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/utils
  creating build/lib.macosx-10.15-x86_64-3.9/gtda/time_series
  copying gtda/time_series/embedding.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/time_series
  copying gtda/time_series/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/time_series
  copying gtda/time_series/features.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/time_series
  copying gtda/time_series/preprocessing.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/time_series
  copying gtda/time_series/multivariate.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/time_series
  copying gtda/time_series/target.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/time_series
  creating build/lib.macosx-10.15-x86_64-3.9/gtda/meta_transformers
  copying gtda/meta_transformers/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/meta_transformers
  copying gtda/meta_transformers/features.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/meta_transformers
  creating build/lib.macosx-10.15-x86_64-3.9/gtda/graphs
  copying gtda/graphs/geodesic_distance.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/graphs
  copying gtda/graphs/transition.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/graphs
  copying gtda/graphs/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/graphs
  copying gtda/graphs/kneighbors.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/graphs
  creating build/lib.macosx-10.15-x86_64-3.9/gtda/homology
  copying gtda/homology/point_clouds.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/homology
  copying gtda/homology/consistent.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/homology
  copying gtda/homology/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/homology
  copying gtda/homology/_utils.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/homology
  creating build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams/tests
  copying gtda/diagrams/tests/test_features.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams/tests
  copying gtda/diagrams/tests/test_distance.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams/tests
  copying gtda/diagrams/tests/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams/tests
  copying gtda/diagrams/tests/test_preprocessing.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams/tests
  creating build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python
  copying gtda/externals/python/cubical_complex_interface.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python
  copying gtda/externals/python/simplex_tree_interface.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python
  copying gtda/externals/python/strong_witness_complex_interface.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python
  copying gtda/externals/python/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python
  copying gtda/externals/python/periodic_cubical_complex_interface.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python
  copying gtda/externals/python/witness_complex_interface.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python
  copying gtda/externals/python/rips_complex_interface.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python
  copying gtda/externals/python/ripser_interface.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python
  copying gtda/externals/python/cech_complex_interface.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python
  creating build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python/tests
  copying gtda/externals/python/tests/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python/tests
  copying gtda/externals/python/tests/test_witness.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python/tests
  copying gtda/externals/python/tests/test_rips_complex.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python/tests
  copying gtda/externals/python/tests/test_cech_complex.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python/tests
  copying gtda/externals/python/tests/test_periodic_cubical_complex.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python/tests
  creating build/lib.macosx-10.15-x86_64-3.9/gtda/mapper/utils
  copying gtda/mapper/utils/_logging.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper/utils
  copying gtda/mapper/utils/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper/utils
  copying gtda/mapper/utils/_cover.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper/utils
  copying gtda/mapper/utils/visualization.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper/utils
  copying gtda/mapper/utils/_cluster.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper/utils
  copying gtda/mapper/utils/pipeline.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper/utils
  copying gtda/mapper/utils/_list_feature_union.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper/utils
  copying gtda/mapper/utils/decorators.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper/utils
  creating build/lib.macosx-10.15-x86_64-3.9/gtda/utils/tests
  copying gtda/utils/tests/test_validation.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/utils/tests
  copying gtda/utils/tests/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/utils/tests
  creating build/lib.macosx-10.15-x86_64-3.9/gtda/time_series/tests
  copying gtda/time_series/tests/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/time_series/tests
  copying gtda/time_series/tests/test_multivariate.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/time_series/tests
  copying gtda/time_series/tests/test_embedding.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/time_series/tests
  copying gtda/time_series/tests/test_preprocessing.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/time_series/tests
  creating build/lib.macosx-10.15-x86_64-3.9/gtda/meta_transformers/tests
  copying gtda/meta_transformers/tests/test_features.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/meta_transformers/tests
  copying gtda/meta_transformers/tests/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/meta_transformers/tests
  creating build/lib.macosx-10.15-x86_64-3.9/gtda/graphs/tests
  copying gtda/graphs/tests/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/graphs/tests
  copying gtda/graphs/tests/test_transition.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/graphs/tests
  copying gtda/graphs/tests/test_geodesic_distance.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/graphs/tests
  copying gtda/graphs/tests/test_kneighbors.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/graphs/tests
  creating build/lib.macosx-10.15-x86_64-3.9/gtda/homology/tests
  copying gtda/homology/tests/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/homology/tests
  copying gtda/homology/tests/test_consistent.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/homology/tests
  copying gtda/homology/tests/test_point_clouds.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/homology/tests
  running build_ext
  Cloning into '/private/var/folders/g4/2rh0j8g948b6vps252ckmk1w0000gn/T/pip-install-zrd6s0_8/giotto-tda_cbdbc0fa8687454d9d72b5e4039927b2/gtda/externals/pybind11'...
  -- The CXX compiler identification is AppleClang 12.0.0.12000032
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  -- pybind11 v2.6.2 dev1
  -- CMake 3.18.4
  -- Found PythonInterp: /Users/filipcornell/.venvs/topoaemappervenv/bin/python (found version "3.9")
  -- Found PythonLibs: /usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/lib/libpython3.9.dylib
  -- PYTHON 3.9.0
  -- Performing Test HAS_FLTO
  -- Performing Test HAS_FLTO - Success
  -- pybind11::lto enabled
  -- Performing Test HAS_FLTO_THIN
  -- Performing Test HAS_FLTO_THIN - Success
  -- pybind11::thin_lto enabled
  -- Configuring done
  -- Generating done
  -- Build files have been written to: /private/var/folders/g4/2rh0j8g948b6vps252ckmk1w0000gn/T/pip-install-zrd6s0_8/giotto-tda_cbdbc0fa8687454d9d72b5e4039927b2/gtda/externals/pybind11/build
  Install the project...
  -- Install configuration: ""
  -- Up-to-date: /usr/local/include/pybind11
  -- Installing: /usr/local/include/pybind11/attr.h
  -- Installing: /usr/local/include/pybind11/embed.h
  -- Installing: /usr/local/include/pybind11/numpy.h
  -- Installing: /usr/local/include/pybind11/pybind11.h
  -- Installing: /usr/local/include/pybind11/operators.h
  -- Installing: /usr/local/include/pybind11/iostream.h
  -- Installing: /usr/local/include/pybind11/chrono.h
  -- Installing: /usr/local/include/pybind11/stl_bind.h
  -- Installing: /usr/local/include/pybind11/buffer_info.h
  -- Installing: /usr/local/include/pybind11/options.h
  -- Installing: /usr/local/include/pybind11/functional.h
  -- Installing: /usr/local/include/pybind11/stl.h
  -- Up-to-date: /usr/local/include/pybind11/detail
  -- Installing: /usr/local/include/pybind11/detail/typeid.h
  -- Installing: /usr/local/include/pybind11/detail/descr.h
  -- Installing: /usr/local/include/pybind11/detail/internals.h
  -- Installing: /usr/local/include/pybind11/detail/common.h
  -- Installing: /usr/local/include/pybind11/detail/class.h
  -- Installing: /usr/local/include/pybind11/detail/init.h
  -- Installing: /usr/local/include/pybind11/common.h
  -- Installing: /usr/local/include/pybind11/eval.h
  -- Installing: /usr/local/include/pybind11/cast.h
  -- Installing: /usr/local/include/pybind11/eigen.h
  -- Installing: /usr/local/include/pybind11/pytypes.h
  -- Installing: /usr/local/include/pybind11/complex.h
  -- Installing: /usr/local/share/cmake/pybind11/pybind11Config.cmake
  -- Installing: /usr/local/share/cmake/pybind11/pybind11ConfigVersion.cmake
  -- Installing: /usr/local/share/cmake/pybind11/FindPythonLibsNew.cmake
  -- Installing: /usr/local/share/cmake/pybind11/pybind11Common.cmake
  -- Installing: /usr/local/share/cmake/pybind11/pybind11Tools.cmake
  -- Installing: /usr/local/share/cmake/pybind11/pybind11NewTools.cmake
  -- Installing: /usr/local/share/cmake/pybind11/pybind11Targets.cmake
  fatal: not a git repository (or any of the parent directories): .git
  Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "/private/var/folders/g4/2rh0j8g948b6vps252ckmk1w0000gn/T/pip-install-zrd6s0_8/giotto-tda_cbdbc0fa8687454d9d72b5e4039927b2/setup.py", line 183, in <module>
      setup(name=DISTNAME,
    File "/Users/filipcornell/.venvs/topoaemappervenv/lib/python3.9/site-packages/setuptools/__init__.py", line 153, in setup
      return distutils.core.setup(**attrs)
    File "/usr/local/Cellar/[email protected]/3.9.0_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/core.py", line 148, in setup
      dist.run_commands()
    File "/usr/local/Cellar/[email protected]/3.9.0_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py", line 966, in run_commands
      self.run_command(cmd)
    File "/usr/local/Cellar/[email protected]/3.9.0_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "/Users/filipcornell/.venvs/topoaemappervenv/lib/python3.9/site-packages/wheel/bdist_wheel.py", line 299, in run
      self.run_command('build')
    File "/usr/local/Cellar/[email protected]/3.9.0_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/cmd.py", line 313, in run_command
      self.distribution.run_command(command)
    File "/usr/local/Cellar/[email protected]/3.9.0_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "/usr/local/Cellar/[email protected]/3.9.0_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/command/build.py", line 135, in run
      self.run_command(cmd_name)
    File "/usr/local/Cellar/[email protected]/3.9.0_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/cmd.py", line 313, in run_command
      self.distribution.run_command(command)
    File "/usr/local/Cellar/[email protected]/3.9.0_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "/private/var/folders/g4/2rh0j8g948b6vps252ckmk1w0000gn/T/pip-install-zrd6s0_8/giotto-tda_cbdbc0fa8687454d9d72b5e4039927b2/setup.py", line 116, in run
      self.install_dependencies()
    File "/private/var/folders/g4/2rh0j8g948b6vps252ckmk1w0000gn/T/pip-install-zrd6s0_8/giotto-tda_cbdbc0fa8687454d9d72b5e4039927b2/setup.py", line 150, in install_dependencies
      subprocess.check_call(['git', 'submodule', 'update',
    File "/usr/local/Cellar/[email protected]/3.9.0_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 373, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command '['git', 'submodule', 'update', '--init', '--recursive']' returned non-zero exit status 128.
  ----------------------------------------
  ERROR: Failed building wheel for giotto-tda
  Running setup.py clean for giotto-tda
Failed to build giotto-tda
Installing collected packages: giotto-tda
    Running setup.py install for giotto-tda ... error
    ERROR: Command errored out with exit status 1:
     command: /Users/filipcornell/.venvs/topoaemappervenv/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/g4/2rh0j8g948b6vps252ckmk1w0000gn/T/pip-install-zrd6s0_8/giotto-tda_cbdbc0fa8687454d9d72b5e4039927b2/setup.py'"'"'; __file__='"'"'/private/var/folders/g4/2rh0j8g948b6vps252ckmk1w0000gn/T/pip-install-zrd6s0_8/giotto-tda_cbdbc0fa8687454d9d72b5e4039927b2/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/g4/2rh0j8g948b6vps252ckmk1w0000gn/T/pip-record-b18rt_yk/install-record.txt --single-version-externally-managed --compile --install-headers /Users/filipcornell/.venvs/topoaemappervenv/include/site/python3.9/giotto-tda
         cwd: /private/var/folders/g4/2rh0j8g948b6vps252ckmk1w0000gn/T/pip-install-zrd6s0_8/giotto-tda_cbdbc0fa8687454d9d72b5e4039927b2/
    Complete output (141 lines):
    running install
    running build
    running build_py
    creating build
    creating build/lib.macosx-10.15-x86_64-3.9
    creating build/lib.macosx-10.15-x86_64-3.9/gtda
    copying gtda/_version.py -> build/lib.macosx-10.15-x86_64-3.9/gtda
    copying gtda/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda
    copying gtda/pipeline.py -> build/lib.macosx-10.15-x86_64-3.9/gtda
    copying gtda/base.py -> build/lib.macosx-10.15-x86_64-3.9/gtda
    creating build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams
    copying gtda/diagrams/_metrics.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams
    copying gtda/diagrams/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams
    copying gtda/diagrams/features.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams
    copying gtda/diagrams/distance.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams
    copying gtda/diagrams/preprocessing.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams
    copying gtda/diagrams/_utils.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams
    creating build/lib.macosx-10.15-x86_64-3.9/gtda/externals
    copying gtda/externals/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals
    creating build/lib.macosx-10.15-x86_64-3.9/gtda/tests
    copying gtda/tests/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/tests
    copying gtda/tests/test_pipeline.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/tests
    creating build/lib.macosx-10.15-x86_64-3.9/gtda/mapper
    copying gtda/mapper/cover.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper
    copying gtda/mapper/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper
    copying gtda/mapper/visualization.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper
    copying gtda/mapper/nerve.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper
    copying gtda/mapper/cluster.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper
    copying gtda/mapper/pipeline.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper
    copying gtda/mapper/filter.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper
    creating build/lib.macosx-10.15-x86_64-3.9/gtda/utils
    copying gtda/utils/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/utils
    copying gtda/utils/_docs.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/utils
    copying gtda/utils/testing.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/utils
    copying gtda/utils/validation.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/utils
    creating build/lib.macosx-10.15-x86_64-3.9/gtda/time_series
    copying gtda/time_series/embedding.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/time_series
    copying gtda/time_series/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/time_series
    copying gtda/time_series/features.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/time_series
    copying gtda/time_series/preprocessing.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/time_series
    copying gtda/time_series/multivariate.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/time_series
    copying gtda/time_series/target.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/time_series
    creating build/lib.macosx-10.15-x86_64-3.9/gtda/meta_transformers
    copying gtda/meta_transformers/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/meta_transformers
    copying gtda/meta_transformers/features.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/meta_transformers
    creating build/lib.macosx-10.15-x86_64-3.9/gtda/graphs
    copying gtda/graphs/geodesic_distance.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/graphs
    copying gtda/graphs/transition.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/graphs
    copying gtda/graphs/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/graphs
    copying gtda/graphs/kneighbors.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/graphs
    creating build/lib.macosx-10.15-x86_64-3.9/gtda/homology
    copying gtda/homology/point_clouds.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/homology
    copying gtda/homology/consistent.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/homology
    copying gtda/homology/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/homology
    copying gtda/homology/_utils.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/homology
    creating build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams/tests
    copying gtda/diagrams/tests/test_features.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams/tests
    copying gtda/diagrams/tests/test_distance.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams/tests
    copying gtda/diagrams/tests/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams/tests
    copying gtda/diagrams/tests/test_preprocessing.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/diagrams/tests
    creating build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python
    copying gtda/externals/python/cubical_complex_interface.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python
    copying gtda/externals/python/simplex_tree_interface.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python
    copying gtda/externals/python/strong_witness_complex_interface.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python
    copying gtda/externals/python/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python
    copying gtda/externals/python/periodic_cubical_complex_interface.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python
    copying gtda/externals/python/witness_complex_interface.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python
    copying gtda/externals/python/rips_complex_interface.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python
    copying gtda/externals/python/ripser_interface.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python
    copying gtda/externals/python/cech_complex_interface.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python
    creating build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python/tests
    copying gtda/externals/python/tests/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python/tests
    copying gtda/externals/python/tests/test_witness.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python/tests
    copying gtda/externals/python/tests/test_rips_complex.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python/tests
    copying gtda/externals/python/tests/test_cech_complex.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python/tests
    copying gtda/externals/python/tests/test_periodic_cubical_complex.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/externals/python/tests
    creating build/lib.macosx-10.15-x86_64-3.9/gtda/mapper/utils
    copying gtda/mapper/utils/_logging.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper/utils
    copying gtda/mapper/utils/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper/utils
    copying gtda/mapper/utils/_cover.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper/utils
    copying gtda/mapper/utils/visualization.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper/utils
    copying gtda/mapper/utils/_cluster.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper/utils
    copying gtda/mapper/utils/pipeline.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper/utils
    copying gtda/mapper/utils/_list_feature_union.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper/utils
    copying gtda/mapper/utils/decorators.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/mapper/utils
    creating build/lib.macosx-10.15-x86_64-3.9/gtda/utils/tests
    copying gtda/utils/tests/test_validation.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/utils/tests
    copying gtda/utils/tests/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/utils/tests
    creating build/lib.macosx-10.15-x86_64-3.9/gtda/time_series/tests
    copying gtda/time_series/tests/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/time_series/tests
    copying gtda/time_series/tests/test_multivariate.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/time_series/tests
    copying gtda/time_series/tests/test_embedding.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/time_series/tests
    copying gtda/time_series/tests/test_preprocessing.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/time_series/tests
    creating build/lib.macosx-10.15-x86_64-3.9/gtda/meta_transformers/tests
    copying gtda/meta_transformers/tests/test_features.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/meta_transformers/tests
    copying gtda/meta_transformers/tests/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/meta_transformers/tests
    creating build/lib.macosx-10.15-x86_64-3.9/gtda/graphs/tests
    copying gtda/graphs/tests/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/graphs/tests
    copying gtda/graphs/tests/test_transition.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/graphs/tests
    copying gtda/graphs/tests/test_geodesic_distance.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/graphs/tests
    copying gtda/graphs/tests/test_kneighbors.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/graphs/tests
    creating build/lib.macosx-10.15-x86_64-3.9/gtda/homology/tests
    copying gtda/homology/tests/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/homology/tests
    copying gtda/homology/tests/test_consistent.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/homology/tests
    copying gtda/homology/tests/test_point_clouds.py -> build/lib.macosx-10.15-x86_64-3.9/gtda/homology/tests
    running build_ext
    CMake Error: The source directory "/private/var/folders/g4/2rh0j8g948b6vps252ckmk1w0000gn/T/pip-install-zrd6s0_8/giotto-tda_cbdbc0fa8687454d9d72b5e4039927b2" does not appear to contain CMakeLists.txt.
    Specify --help for usage, or press the help button on the CMake GUI.
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/private/var/folders/g4/2rh0j8g948b6vps252ckmk1w0000gn/T/pip-install-zrd6s0_8/giotto-tda_cbdbc0fa8687454d9d72b5e4039927b2/setup.py", line 183, in <module>
        setup(name=DISTNAME,
      File "/Users/filipcornell/.venvs/topoaemappervenv/lib/python3.9/site-packages/setuptools/__init__.py", line 153, in setup
        return distutils.core.setup(**attrs)
      File "/usr/local/Cellar/[email protected]/3.9.0_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/core.py", line 148, in setup
        dist.run_commands()
      File "/usr/local/Cellar/[email protected]/3.9.0_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py", line 966, in run_commands
        self.run_command(cmd)
      File "/usr/local/Cellar/[email protected]/3.9.0_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/Users/filipcornell/.venvs/topoaemappervenv/lib/python3.9/site-packages/setuptools/command/install.py", line 61, in run
        return orig.install.run(self)
      File "/usr/local/Cellar/[email protected]/3.9.0_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/command/install.py", line 546, in run
        self.run_command('build')
      File "/usr/local/Cellar/[email protected]/3.9.0_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "/usr/local/Cellar/[email protected]/3.9.0_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/usr/local/Cellar/[email protected]/3.9.0_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/command/build.py", line 135, in run
        self.run_command(cmd_name)
      File "/usr/local/Cellar/[email protected]/3.9.0_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "/usr/local/Cellar/[email protected]/3.9.0_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/private/var/folders/g4/2rh0j8g948b6vps252ckmk1w0000gn/T/pip-install-zrd6s0_8/giotto-tda_cbdbc0fa8687454d9d72b5e4039927b2/setup.py", line 119, in run
        self.build_extension(ext)
      File "/private/var/folders/g4/2rh0j8g948b6vps252ckmk1w0000gn/T/pip-install-zrd6s0_8/giotto-tda_cbdbc0fa8687454d9d72b5e4039927b2/setup.py", line 177, in build_extension
        subprocess.check_call(['cmake', ext.sourcedir] + cmake_args,
      File "/usr/local/Cellar/[email protected]/3.9.0_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 373, in check_call
        raise CalledProcessError(retcode, cmd)
    subprocess.CalledProcessError: Command '['cmake', '/private/var/folders/g4/2rh0j8g948b6vps252ckmk1w0000gn/T/pip-install-zrd6s0_8/giotto-tda_cbdbc0fa8687454d9d72b5e4039927b2', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/private/var/folders/g4/2rh0j8g948b6vps252ckmk1w0000gn/T/pip-install-zrd6s0_8/giotto-tda_cbdbc0fa8687454d9d72b5e4039927b2/build/lib.macosx-10.15-x86_64-3.9', '-DPYTHON_EXECUTABLE=/Users/filipcornell/.venvs/topoaemappervenv/bin/python', '-DCMAKE_BUILD_TYPE=Release']' returned non-zero exit status 1.
    ----------------------------------------
ERROR: Command errored out with exit status 1: /Users/filipcornell/.venvs/topoaemappervenv/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/g4/2rh0j8g948b6vps252ckmk1w0000gn/T/pip-install-zrd6s0_8/giotto-tda_cbdbc0fa8687454d9d72b5e4039927b2/setup.py'"'"'; __file__='"'"'/private/var/folders/g4/2rh0j8g948b6vps252ckmk1w0000gn/T/pip-install-zrd6s0_8/giotto-tda_cbdbc0fa8687454d9d72b5e4039927b2/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/g4/2rh0j8g948b6vps252ckmk1w0000gn/T/pip-record-b18rt_yk/install-record.txt --single-version-externally-managed --compile --install-headers /Users/filipcornell/.venvs/topoaemappervenv/include/site/python3.9/giotto-tda Check the logs for full command output.

Would anyone know what the problem is?

Thank you!
@Filco306 Filco306 added the bug Something isn't working label Dec 11, 2020
@wreise
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wreise commented Dec 11, 2020

Hey! Thank you for reporting this!
I was wondering whether you are trying to install the package from pypi or from source - the log would point to the fact that the latter, but the source is not included on pypi.

@Filco306
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Thank you for your quick reply! I run pip3 install giotto-tda, so I assume pypi?

@wreise
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wreise commented Dec 11, 2020

Actually, we do not officially support python 3.9 just yet, and it seems that the wheels for it are not yet out. You should be able to install the package from source anyway, following the instructions in the documentation. You can also use an environment with python 3.8, if you insist on installing from pypi.
Good news is that python 3.9 should be supported as of the next release though.

@ulupo ulupo removed the bug Something isn't working label Dec 11, 2020
@ulupo
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ulupo commented Dec 11, 2020

Indeed, wheels for python 3.9 are hopefully a couple of days away... For now, you will need to resort to the developer installation, which is a little bit more involved (but not exactly hard): https://giotto-ai.github.io/gtda-docs/0.3.1/installation.html#developer-installation

@Filco306
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It worked! Wohoo!!

@ulupo
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ulupo commented Dec 11, 2020

@Filco306 great! This is the best way to go to start developing your own code ;)

@muditsharma1234
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Dear All,
I am facing similar issue. My python version is 3.11. My guess is the error is at the following stage:
Install the project...
-- Install configuration: ""
-- Up-to-date: /usr/local/include/pybind11
CMake Error at cmake_install.cmake:41 (file):
file INSTALL cannot set permissions on "/usr/local/include/pybind11":
Operation not permitted.

I am not sure how to resolve this. I have tried most of the things on this thread, if anyone can help I will be grateful.

@raphaelreinauer
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@muditsharma1234 You could either run the install with sudo or change the permissions of the /usr/local/include/ folder.

@nwaniek
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nwaniek commented Jan 25, 2024 •
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@raphaelreinauer both are remarkable absurd recommendations. If you need to ask a user to 'sudo pip install' something or to change file permissions outside their home directory, there's something fundamentally wrong.

During the installation of giotto-tda via pip on a python 3.11 installation, pybind11 gets pulled in. This is odd insofar as the giotto-tda documentation (readme file) explicitly says that it ships with precompiled parts and "does not require any C++ dependencies". I might be misinterpreting the documentation, however, and it only refers to the nightly build. The issue might also be that giotto-tda doesn't ship a prebuilt python 3.11 wheel. The developer installation won't work because the latest giotto-tda depends on giotto-ph. In turn, giotto-ph fails during installation on a python 3.11 system. While there is a corresponding issue for this (see giotto-ai/giotto-ph#71 and giotto-ai/giotto-ph#72), the "solutions" don't resolve the problem.

I might update this comment if I find a way to install both successfully on a python3.11 system.
Update (although this issue is closed): I ended up doing almost the same as @alibayeh, whose repositories I discovered afterwards. I successfully tested their repositories in a fresh virtual environment. I'd recommend to adopt their changes (see https://github.com/alibayeh/giotto-ph and https://github.com/alibayeh/giotto-tda).

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6 participants
@nwaniek @Filco306 @raphaelreinauer @muditsharma1234 @wreise @ulupo