Build Issue on OS X 10.11.6

dbl001 commented 4 years ago

I got this error trying to install 'tutorial_mapper' on OS X 10.11.6 in a conda 3.6 virtual enviornment (it worked on Ubuntu 16.06 LTS):

$ pip install -r requirements.txt
Collecting giotto-learn-nightly
  Using cached https://files.pythonhosted.org/packages/06/3f/2a4cd22ad2488650e7b955ea0268b3c772f80873d80872dd5e2bf9fa06af/giotto-learn-nightly-20191220.25.tar.gz
Collecting python-igraph>=0.7.1.post6
  Using cached https://files.pythonhosted.org/packages/0f/a0/4e7134f803737aa6eebb4e5250565ace0e2599659e22be7f7eba520ff017/python-igraph-0.7.1.post6.tar.gz
Requirement already satisfied: pandas>=0.25.1 in /Users/davidlaxer/anaconda/envs/ai/lib/python3.6/site-packages (from -r requirements.txt (line 3)) (0.25.3)
Requirement already satisfied: numpy>=1.17.2 in /Users/davidlaxer/anaconda/envs/ai/lib/python3.6/site-packages (from -r requirements.txt (line 4)) (1.17.3)
Collecting plotly>=4.4.1
  Using cached https://files.pythonhosted.org/packages/8e/ce/6ea5683c47b682bffad39ad41d10913141b560b1b875a90dbc6abe3f4fa9/plotly-4.4.1-py2.py3-none-any.whl
Requirement already satisfied: scikit-learn>=0.22 in /Users/davidlaxer/anaconda/envs/ai/lib/python3.6/site-packages (from -r requirements.txt (line 6)) (0.22)
Requirement already satisfied: scipy>=0.17.0 in /Users/davidlaxer/anaconda/envs/ai/lib/python3.6/site-packages (from giotto-learn-nightly->-r requirements.txt (line 1)) (1.4.1)
Requirement already satisfied: joblib>=0.11 in /Users/davidlaxer/anaconda/envs/ai/lib/python3.6/site-packages (from giotto-learn-nightly->-r requirements.txt (line 1)) (0.14.1)
Collecting networkx>=2.4
  Using cached https://files.pythonhosted.org/packages/41/8f/dd6a8e85946def36e4f2c69c84219af0fa5e832b018c970e92f2ad337e45/networkx-2.4-py3-none-any.whl
Requirement already satisfied: matplotlib in /Users/davidlaxer/anaconda/envs/ai/lib/python3.6/site-packages (from giotto-learn-nightly->-r requirements.txt (line 1)) (3.1.2)
Requirement already satisfied: pytz>=2017.2 in /Users/davidlaxer/anaconda/envs/ai/lib/python3.6/site-packages (from pandas>=0.25.1->-r requirements.txt (line 3)) (2019.3)
Requirement already satisfied: python-dateutil>=2.6.1 in /Users/davidlaxer/anaconda/envs/ai/lib/python3.6/site-packages (from pandas>=0.25.1->-r requirements.txt (line 3)) (2.8.1)
Collecting retrying>=1.3.3
  Using cached https://files.pythonhosted.org/packages/44/ef/beae4b4ef80902f22e3af073397f079c96969c69b2c7d52a57ea9ae61c9d/retrying-1.3.3.tar.gz
Requirement already satisfied: six in /Users/davidlaxer/anaconda/envs/ai/lib/python3.6/site-packages (from plotly>=4.4.1->-r requirements.txt (line 5)) (1.13.0)
Requirement already satisfied: decorator>=4.3.0 in /Users/davidlaxer/anaconda/envs/ai/lib/python3.6/site-packages (from networkx>=2.4->giotto-learn-nightly->-r requirements.txt (line 1)) (4.4.1)
Requirement already satisfied: cycler>=0.10 in /Users/davidlaxer/anaconda/envs/ai/lib/python3.6/site-packages (from matplotlib->giotto-learn-nightly->-r requirements.txt (line 1)) (0.10.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /Users/davidlaxer/anaconda/envs/ai/lib/python3.6/site-packages (from matplotlib->giotto-learn-nightly->-r requirements.txt (line 1)) (1.1.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /Users/davidlaxer/anaconda/envs/ai/lib/python3.6/site-packages (from matplotlib->giotto-learn-nightly->-r requirements.txt (line 1)) (2.4.6)
Requirement already satisfied: setuptools in /Users/davidlaxer/anaconda/envs/ai/lib/python3.6/site-packages (from kiwisolver>=1.0.1->matplotlib->giotto-learn-nightly->-r requirements.txt (line 1)) (42.0.2.post20191201)
Building wheels for collected packages: giotto-learn-nightly, python-igraph, retrying
  Building wheel for giotto-learn-nightly (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /Users/davidlaxer/anaconda/envs/ai/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/nj/nphdkhyj6s1dttb0pd9zb2wc0000gn/T/pip-install-nmpr6cqa/giotto-learn-nightly/setup.py'"'"'; __file__='"'"'/private/var/folders/nj/nphdkhyj6s1dttb0pd9zb2wc0000gn/T/pip-install-nmpr6cqa/giotto-learn-nightly/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/nj/nphdkhyj6s1dttb0pd9zb2wc0000gn/T/pip-wheel-lrdd6hwi --python-tag cp36
       cwd: /private/var/folders/nj/nphdkhyj6s1dttb0pd9zb2wc0000gn/T/pip-install-nmpr6cqa/giotto-learn-nightly/
  Complete output (181 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.macosx-10.7-x86_64-3.6
  creating build/lib.macosx-10.7-x86_64-3.6/giotto
  copying giotto/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto
  copying giotto/_version.py -> build/lib.macosx-10.7-x86_64-3.6/giotto
  copying giotto/base.py -> build/lib.macosx-10.7-x86_64-3.6/giotto
  copying giotto/pipeline.py -> build/lib.macosx-10.7-x86_64-3.6/giotto
  creating build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams
  copying giotto/diagrams/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams
  copying giotto/diagrams/_metrics.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams
  copying giotto/diagrams/_utils.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams
  copying giotto/diagrams/distance.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams
  copying giotto/diagrams/features.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams
  copying giotto/diagrams/preprocessing.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams
  creating build/lib.macosx-10.7-x86_64-3.6/giotto/externals
  copying giotto/externals/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/externals
  creating build/lib.macosx-10.7-x86_64-3.6/giotto/graphs
  copying giotto/graphs/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs
  copying giotto/graphs/create_clique_complex.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs
  copying giotto/graphs/geodesic_distance.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs
  copying giotto/graphs/graph_entropy.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs
  copying giotto/graphs/heat_diffusion.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs
  copying giotto/graphs/kneighbors.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs
  copying giotto/graphs/transition.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs
  creating build/lib.macosx-10.7-x86_64-3.6/giotto/homology
  copying giotto/homology/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/homology
  copying giotto/homology/_utils.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/homology
  copying giotto/homology/consistent.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/homology
  copying giotto/homology/point_clouds.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/homology
  creating build/lib.macosx-10.7-x86_64-3.6/giotto/mapper
  copying giotto/mapper/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper
  copying giotto/mapper/cluster.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper
  copying giotto/mapper/cover.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper
  copying giotto/mapper/filter.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper
  copying giotto/mapper/nerve.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper
  copying giotto/mapper/pipeline.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper
  copying giotto/mapper/visualization.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper
  creating build/lib.macosx-10.7-x86_64-3.6/giotto/meta_transformers
  copying giotto/meta_transformers/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/meta_transformers
  copying giotto/meta_transformers/features.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/meta_transformers
  creating build/lib.macosx-10.7-x86_64-3.6/giotto/tests
  copying giotto/tests/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/tests
  copying giotto/tests/test_pipeline.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/tests
  creating build/lib.macosx-10.7-x86_64-3.6/giotto/time_series
  copying giotto/time_series/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/time_series
  copying giotto/time_series/embedding.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/time_series
  copying giotto/time_series/features.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/time_series
  copying giotto/time_series/multivariate.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/time_series
  copying giotto/time_series/preprocessing.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/time_series
  copying giotto/time_series/target.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/time_series
  creating build/lib.macosx-10.7-x86_64-3.6/giotto/utils
  copying giotto/utils/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/utils
  copying giotto/utils/testing.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/utils
  copying giotto/utils/validation.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/utils
  creating build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams/tests
  copying giotto/diagrams/tests/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams/tests
  copying giotto/diagrams/tests/test_distance.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams/tests
  copying giotto/diagrams/tests/test_features.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams/tests
  copying giotto/diagrams/tests/test_preprocessing.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams/tests
  creating build/lib.macosx-10.7-x86_64-3.6/giotto/externals/python
  copying giotto/externals/python/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/externals/python
  copying giotto/externals/python/cubical_complex_interface.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/externals/python
  copying giotto/externals/python/ripser_interface.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/externals/python
  copying giotto/externals/python/simplex_tree_interface.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/externals/python
  creating build/lib.macosx-10.7-x86_64-3.6/giotto/graphs/tests
  copying giotto/graphs/tests/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs/tests
  copying giotto/graphs/tests/test_create_complex.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs/tests
  copying giotto/graphs/tests/test_geodesic_distance.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs/tests
  copying giotto/graphs/tests/test_graph_entropy.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs/tests
  copying giotto/graphs/tests/test_heat_diffusion.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs/tests
  copying giotto/graphs/tests/test_kneighbors.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs/tests
  copying giotto/graphs/tests/test_transition.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs/tests
  creating build/lib.macosx-10.7-x86_64-3.6/giotto/homology/tests
  copying giotto/homology/tests/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/homology/tests
  copying giotto/homology/tests/test_consistent.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/homology/tests
  copying giotto/homology/tests/test_point_clouds.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/homology/tests
  creating build/lib.macosx-10.7-x86_64-3.6/giotto/mapper/utils
  copying giotto/mapper/utils/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper/utils
  copying giotto/mapper/utils/_cluster.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper/utils
  copying giotto/mapper/utils/_cover.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper/utils
  copying giotto/mapper/utils/_list_feature_union.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper/utils
  copying giotto/mapper/utils/_logging.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper/utils
  copying giotto/mapper/utils/decorators.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper/utils
  copying giotto/mapper/utils/pipeline.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper/utils
  copying giotto/mapper/utils/visualization.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper/utils
  creating build/lib.macosx-10.7-x86_64-3.6/giotto/meta_transformers/tests
  copying giotto/meta_transformers/tests/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/meta_transformers/tests
  copying giotto/meta_transformers/tests/test_features.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/meta_transformers/tests
  creating build/lib.macosx-10.7-x86_64-3.6/giotto/time_series/tests
  copying giotto/time_series/tests/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/time_series/tests
  copying giotto/time_series/tests/test_embedding.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/time_series/tests
  copying giotto/time_series/tests/test_multivariate.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/time_series/tests
  copying giotto/time_series/tests/test_preprocessing.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/time_series/tests
  creating build/lib.macosx-10.7-x86_64-3.6/giotto/utils/tests
  copying giotto/utils/tests/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/utils/tests
  copying giotto/utils/tests/test_validation.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/utils/tests
  running build_ext
  Cloning into '/private/var/folders/nj/nphdkhyj6s1dttb0pd9zb2wc0000gn/T/pip-install-nmpr6cqa/giotto-learn-nightly/giotto/externals/pybind11'...
  -- The CXX compiler identification is AppleClang 8.0.0.8000042
  -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
  -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  -- Found PythonInterp: /opt/local/bin/python3.7 (found version "3.7.6")
  -- Found PythonLibs: /opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/libpython3.7m.dylib
  -- Performing Test HAS_CPP14_FLAG
  -- Performing Test HAS_CPP14_FLAG - Success
  -- pybind11 v2.4.dev4
  -- Configuring done
  -- Generating done
  -- Build files have been written to: /private/var/folders/nj/nphdkhyj6s1dttb0pd9zb2wc0000gn/T/pip-install-nmpr6cqa/giotto-learn-nightly/giotto/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/buffer_info.h
  -- Installing: /usr/local/include/pybind11/cast.h
  -- Installing: /usr/local/include/pybind11/chrono.h
  -- Installing: /usr/local/include/pybind11/common.h
  -- Installing: /usr/local/include/pybind11/complex.h
  -- Up-to-date: /usr/local/include/pybind11/detail
  -- Installing: /usr/local/include/pybind11/detail/class.h
  -- Installing: /usr/local/include/pybind11/detail/common.h
  -- Installing: /usr/local/include/pybind11/detail/descr.h
  -- Installing: /usr/local/include/pybind11/detail/init.h
  -- Installing: /usr/local/include/pybind11/detail/internals.h
  -- Installing: /usr/local/include/pybind11/detail/typeid.h
  -- Installing: /usr/local/include/pybind11/eigen.h
  -- Installing: /usr/local/include/pybind11/embed.h
  -- Installing: /usr/local/include/pybind11/eval.h
  -- Installing: /usr/local/include/pybind11/functional.h
  -- Installing: /usr/local/include/pybind11/iostream.h
  -- Installing: /usr/local/include/pybind11/numpy.h
  -- Installing: /usr/local/include/pybind11/operators.h
  -- Installing: /usr/local/include/pybind11/options.h
  -- Installing: /usr/local/include/pybind11/pybind11.h
  -- Installing: /usr/local/include/pybind11/pytypes.h
  -- Installing: /usr/local/include/pybind11/stl.h
  -- Installing: /usr/local/include/pybind11/stl_bind.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/pybind11Tools.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/nj/nphdkhyj6s1dttb0pd9zb2wc0000gn/T/pip-install-nmpr6cqa/giotto-learn-nightly/setup.py", line 177, in <module>
      cmdclass=dict(build_ext=CMakeBuild))
    File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/site-packages/setuptools/__init__.py", line 145, in setup
      return distutils.core.setup(**attrs)
    File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/distutils/core.py", line 148, in setup
      dist.run_commands()
    File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/distutils/dist.py", line 955, in run_commands
      self.run_command(cmd)
    File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/distutils/dist.py", line 974, in run_command
      cmd_obj.run()
    File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/site-packages/wheel/bdist_wheel.py", line 192, in run
      self.run_command('build')
    File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/distutils/cmd.py", line 313, in run_command
      self.distribution.run_command(command)
    File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/distutils/dist.py", line 974, in run_command
      cmd_obj.run()
    File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/distutils/command/build.py", line 135, in run
      self.run_command(cmd_name)
    File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/distutils/cmd.py", line 313, in run_command
      self.distribution.run_command(command)
    File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/distutils/dist.py", line 974, in run_command
      cmd_obj.run()
    File "/private/var/folders/nj/nphdkhyj6s1dttb0pd9zb2wc0000gn/T/pip-install-nmpr6cqa/giotto-learn-nightly/setup.py", line 93, in run
      self.install_dependencies()
    File "/private/var/folders/nj/nphdkhyj6s1dttb0pd9zb2wc0000gn/T/pip-install-nmpr6cqa/giotto-learn-nightly/setup.py", line 128, in install_dependencies
      '--init', '--recursive'])
    File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/subprocess.py", line 291, 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-learn-nightly
  Running setup.py clean for giotto-learn-nightly
  Building wheel for python-igraph (setup.py) ... done
  Created wheel for python-igraph: filename=python_igraph-0.7.1.post6-cp36-cp36m-macosx_10_7_x86_64.whl size=2008913 sha256=c7fc64f10cc0c2cae6d1e5d53395425cfd9e83e66d014af64fed35182dc7aff1
  Stored in directory: /Users/davidlaxer/Library/Caches/pip/wheels/41/d6/02/34eebae97e25f5b87d60f4c0687e00523e3f244fa41bc3f4a7
  Building wheel for retrying (setup.py) ... done
  Created wheel for retrying: filename=retrying-1.3.3-cp36-none-any.whl size=11429 sha256=23bc9a7a1b37f6f049e1a05853cd96dfdb0fa4c98646f1d598a9a55732772cad
  Stored in directory: /Users/davidlaxer/Library/Caches/pip/wheels/d7/a9/33/acc7b709e2a35caa7d4cae442f6fe6fbf2c43f80823d46460c
Successfully built python-igraph retrying
Failed to build giotto-learn-nightly
Installing collected packages: networkx, retrying, plotly, giotto-learn-nightly, python-igraph
    Running setup.py install for giotto-learn-nightly ... error
    ERROR: Command errored out with exit status 1:
     command: /Users/davidlaxer/anaconda/envs/ai/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/nj/nphdkhyj6s1dttb0pd9zb2wc0000gn/T/pip-install-nmpr6cqa/giotto-learn-nightly/setup.py'"'"'; __file__='"'"'/private/var/folders/nj/nphdkhyj6s1dttb0pd9zb2wc0000gn/T/pip-install-nmpr6cqa/giotto-learn-nightly/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/nj/nphdkhyj6s1dttb0pd9zb2wc0000gn/T/pip-record-4m2bna6u/install-record.txt --single-version-externally-managed --compile
         cwd: /private/var/folders/nj/nphdkhyj6s1dttb0pd9zb2wc0000gn/T/pip-install-nmpr6cqa/giotto-learn-nightly/
    Complete output (135 lines):
    running install
    running build
    running build_py
    creating build
    creating build/lib.macosx-10.7-x86_64-3.6
    creating build/lib.macosx-10.7-x86_64-3.6/giotto
    copying giotto/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto
    copying giotto/_version.py -> build/lib.macosx-10.7-x86_64-3.6/giotto
    copying giotto/base.py -> build/lib.macosx-10.7-x86_64-3.6/giotto
    copying giotto/pipeline.py -> build/lib.macosx-10.7-x86_64-3.6/giotto
    creating build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams
    copying giotto/diagrams/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams
    copying giotto/diagrams/_metrics.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams
    copying giotto/diagrams/_utils.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams
    copying giotto/diagrams/distance.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams
    copying giotto/diagrams/features.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams
    copying giotto/diagrams/preprocessing.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams
    creating build/lib.macosx-10.7-x86_64-3.6/giotto/externals
    copying giotto/externals/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/externals
    creating build/lib.macosx-10.7-x86_64-3.6/giotto/graphs
    copying giotto/graphs/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs
    copying giotto/graphs/create_clique_complex.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs
    copying giotto/graphs/geodesic_distance.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs
    copying giotto/graphs/graph_entropy.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs
    copying giotto/graphs/heat_diffusion.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs
    copying giotto/graphs/kneighbors.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs
    copying giotto/graphs/transition.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs
    creating build/lib.macosx-10.7-x86_64-3.6/giotto/homology
    copying giotto/homology/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/homology
    copying giotto/homology/_utils.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/homology
    copying giotto/homology/consistent.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/homology
    copying giotto/homology/point_clouds.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/homology
    creating build/lib.macosx-10.7-x86_64-3.6/giotto/mapper
    copying giotto/mapper/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper
    copying giotto/mapper/cluster.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper
    copying giotto/mapper/cover.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper
    copying giotto/mapper/filter.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper
    copying giotto/mapper/nerve.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper
    copying giotto/mapper/pipeline.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper
    copying giotto/mapper/visualization.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper
    creating build/lib.macosx-10.7-x86_64-3.6/giotto/meta_transformers
    copying giotto/meta_transformers/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/meta_transformers
    copying giotto/meta_transformers/features.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/meta_transformers
    creating build/lib.macosx-10.7-x86_64-3.6/giotto/tests
    copying giotto/tests/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/tests
    copying giotto/tests/test_pipeline.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/tests
    creating build/lib.macosx-10.7-x86_64-3.6/giotto/time_series
    copying giotto/time_series/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/time_series
    copying giotto/time_series/embedding.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/time_series
    copying giotto/time_series/features.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/time_series
    copying giotto/time_series/multivariate.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/time_series
    copying giotto/time_series/preprocessing.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/time_series
    copying giotto/time_series/target.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/time_series
    creating build/lib.macosx-10.7-x86_64-3.6/giotto/utils
    copying giotto/utils/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/utils
    copying giotto/utils/testing.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/utils
    copying giotto/utils/validation.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/utils
    creating build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams/tests
    copying giotto/diagrams/tests/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams/tests
    copying giotto/diagrams/tests/test_distance.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams/tests
    copying giotto/diagrams/tests/test_features.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams/tests
    copying giotto/diagrams/tests/test_preprocessing.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/diagrams/tests
    creating build/lib.macosx-10.7-x86_64-3.6/giotto/externals/python
    copying giotto/externals/python/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/externals/python
    copying giotto/externals/python/cubical_complex_interface.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/externals/python
    copying giotto/externals/python/ripser_interface.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/externals/python
    copying giotto/externals/python/simplex_tree_interface.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/externals/python
    creating build/lib.macosx-10.7-x86_64-3.6/giotto/graphs/tests
    copying giotto/graphs/tests/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs/tests
    copying giotto/graphs/tests/test_create_complex.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs/tests
    copying giotto/graphs/tests/test_geodesic_distance.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs/tests
    copying giotto/graphs/tests/test_graph_entropy.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs/tests
    copying giotto/graphs/tests/test_heat_diffusion.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs/tests
    copying giotto/graphs/tests/test_kneighbors.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs/tests
    copying giotto/graphs/tests/test_transition.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/graphs/tests
    creating build/lib.macosx-10.7-x86_64-3.6/giotto/homology/tests
    copying giotto/homology/tests/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/homology/tests
    copying giotto/homology/tests/test_consistent.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/homology/tests
    copying giotto/homology/tests/test_point_clouds.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/homology/tests
    creating build/lib.macosx-10.7-x86_64-3.6/giotto/mapper/utils
    copying giotto/mapper/utils/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper/utils
    copying giotto/mapper/utils/_cluster.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper/utils
    copying giotto/mapper/utils/_cover.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper/utils
    copying giotto/mapper/utils/_list_feature_union.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper/utils
    copying giotto/mapper/utils/_logging.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper/utils
    copying giotto/mapper/utils/decorators.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper/utils
    copying giotto/mapper/utils/pipeline.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper/utils
    copying giotto/mapper/utils/visualization.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/mapper/utils
    creating build/lib.macosx-10.7-x86_64-3.6/giotto/meta_transformers/tests
    copying giotto/meta_transformers/tests/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/meta_transformers/tests
    copying giotto/meta_transformers/tests/test_features.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/meta_transformers/tests
    creating build/lib.macosx-10.7-x86_64-3.6/giotto/time_series/tests
    copying giotto/time_series/tests/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/time_series/tests
    copying giotto/time_series/tests/test_embedding.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/time_series/tests
    copying giotto/time_series/tests/test_multivariate.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/time_series/tests
    copying giotto/time_series/tests/test_preprocessing.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/time_series/tests
    creating build/lib.macosx-10.7-x86_64-3.6/giotto/utils/tests
    copying giotto/utils/tests/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/utils/tests
    copying giotto/utils/tests/test_validation.py -> build/lib.macosx-10.7-x86_64-3.6/giotto/utils/tests
    running build_ext
    CMake Error: The source directory "/private/var/folders/nj/nphdkhyj6s1dttb0pd9zb2wc0000gn/T/pip-install-nmpr6cqa/giotto-learn-nightly" 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/nj/nphdkhyj6s1dttb0pd9zb2wc0000gn/T/pip-install-nmpr6cqa/giotto-learn-nightly/setup.py", line 177, in <module>
        cmdclass=dict(build_ext=CMakeBuild))
      File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/site-packages/setuptools/__init__.py", line 145, in setup
        return distutils.core.setup(**attrs)
      File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/distutils/core.py", line 148, in setup
        dist.run_commands()
      File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/distutils/dist.py", line 955, in run_commands
        self.run_command(cmd)
      File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/distutils/dist.py", line 974, in run_command
        cmd_obj.run()
      File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/site-packages/setuptools/command/install.py", line 61, in run
        return orig.install.run(self)
      File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/distutils/command/install.py", line 545, in run
        self.run_command('build')
      File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/distutils/dist.py", line 974, in run_command
        cmd_obj.run()
      File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/distutils/command/build.py", line 135, in run
        self.run_command(cmd_name)
      File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/distutils/dist.py", line 974, in run_command
        cmd_obj.run()
      File "/private/var/folders/nj/nphdkhyj6s1dttb0pd9zb2wc0000gn/T/pip-install-nmpr6cqa/giotto-learn-nightly/setup.py", line 96, in run
        self.build_extension(ext)
      File "/private/var/folders/nj/nphdkhyj6s1dttb0pd9zb2wc0000gn/T/pip-install-nmpr6cqa/giotto-learn-nightly/setup.py", line 155, in build_extension
        cwd=self.build_temp, env=env)
      File "/Users/davidlaxer/anaconda/envs/ai/lib/python3.6/subprocess.py", line 291, in check_call
        raise CalledProcessError(retcode, cmd)
    subprocess.CalledProcessError: Command '['cmake', '/private/var/folders/nj/nphdkhyj6s1dttb0pd9zb2wc0000gn/T/pip-install-nmpr6cqa/giotto-learn-nightly', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/private/var/folders/nj/nphdkhyj6s1dttb0pd9zb2wc0000gn/T/pip-install-nmpr6cqa/giotto-learn-nightly/build/lib.macosx-10.7-x86_64-3.6', '-DPYTHON_EXECUTABLE=/Users/davidlaxer/anaconda/envs/ai/bin/python', '-DCMAKE_BUILD_TYPE=Release']' returned non-zero exit status 1.
    ----------------------------------------
ERROR: Command errored out with exit status 1: /Users/davidlaxer/anaconda/envs/ai/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/nj/nphdkhyj6s1dttb0pd9zb2wc0000gn/T/pip-install-nmpr6cqa/giotto-learn-nightly/setup.py'"'"'; __file__='"'"'/private/var/folders/nj/nphdkhyj6s1dttb0pd9zb2wc0000gn/T/pip-install-nmpr6cqa/giotto-learn-nightly/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/nj/nphdkhyj6s1dttb0pd9zb2wc0000gn/T/pip-record-4m2bna6u/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.
(ai) MacBook-Pro:tutorial_mapper davidlaxer$

matteocao commented 4 years ago

Dear @dbl001 ,

The reason for this error is that you are using an old version of the macOS system for which we have not built the wheels. Therefore, your conda environment is trying to compile the library from scratch. You have two options:

One quick fix (if it works), is to go here https://pypi.org/project/giotto-learn-nightly/#files and download the macOS version for python 3.6, rename it to giotto_learn_nightly-20191220.25-cp36-cp36m-macosx_10_11_x86_64.whland pip install the wheel file directly (i.e. put the renamed file in the PWD and simply type pip install giotto_learn_nightly-20191220.25-cp36-cp36m-macosx_10_11_x86_64.whl).

then, do the installation procedure again.

You have first to git clone the giotto-learn repository in your PWD. If boost and make are not installed (which seems to be the case given your errors), please also type conda install boost and conda install cmake . After the two programs have been installed, type cd giotto-learn and then pip install -e .. In this case, you will have to remove the giotto-learn-nightly from the requirements.txt file before proceeding with the installation.

@lewtun : please do not hesitate to improve on my comment.

dbl001 commented 4 years ago

I opted for your second option. Everything built properly, I needed to add ipywidgets to my conda environment. plotly is displaying empty space on OS X 10.11.6.

On Dec 25, 2019, at 12:33 PM, matteocao notifications@github.com wrote:

Dear @dbl001 https://github.com/dbl001 ,

The reason for this error is that you are using an old version of the macOS system for which we have not built the wheels. Therefore, your conda environment is trying to compile the library from scratch. You have two options:

One quick fix (if it works), is to go here https://pypi.org/project/giotto-learn-nightly/#files https://pypi.org/project/giotto-learn-nightly/#files and download the macOS version for python 3.6, rename it to giotto_learn_nightly-20191220.25-cp36-cp36m-macosx_10_11_x86_64.whland pip install the wheel file directly (i.e. put the renamed file in the PWD and simply type pip install giotto_learn_nightly-20191220.25-cp36-cp36m-macosx_10_11_x86_64.whl). then, do the installation procedure again.

You have first to git clone the giotto-learn repository in your PWD. If boost and make are not installed (which seems to be the case given your errors), please also type conda install boost and conda install cmake . After the two programs have been installed, type cd giotto-learn and then pip install -e .. In this case, you will have to remove the giotto-learn-nightly from the requirements.txt file before proceeding with the installation. @lewtun https://github.com/lewtun : please do not hesitate to improve on my comment.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/giotto-ai/tutorial_mapper/issues/4?email_source=notifications&email_token=AAXWFWYJQTRHM7QDGTT7R33Q2O7RFA5CNFSM4J7GLBLKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEHUTATA#issuecomment-568930380, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAXWFW64LSL57SSSL7VRGTLQ2O7RFANCNFSM4J7GLBLA.

lewtun commented 4 years ago

@dbl001 thanks for raising this issue - i've now added ipywidgets to the requirements file. i've also suggested a fix to your empty space issue on issue #5

dbl001 commented 4 years ago

I followed these steps in my Anaconda 3.6 virtual environment on Ubuntu 16.06 LTS as well as on my Mac running OS X 10.11.6

conda install -c plotly plotly=4.4.1 conda install jupyterlab=1.2 conda install "ipywidgets=7.5" Still no plot displayed (and no error messages).

On Dec 25, 2019, at 1:31 PM, lewtun notifications@github.com wrote:

@dbl001 https://github.com/dbl001 thanks for raising this issue - i've now added ipywidgets to the requirements file. i've also suggested a fix to your empty space issue on issue #5 https://github.com/giotto-ai/tutorial_mapper/issues/5 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/giotto-ai/tutorial_mapper/issues/4?email_source=notifications&email_token=AAXWFW553Q2LONXYSMTOCULQ2PGLBA5CNFSM4J7GLBLKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEHUTUUQ#issuecomment-568932946, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAXWFWZVEMRZ6BUME7TMAATQ2PGLBANCNFSM4J7GLBLA.

lewtun commented 4 years ago

i've found that with jupyterlab, one usually needs to run the following extra steps:

# Avoid "JavaScript heap out of memory" errors during extension installation
export NODE_OPTIONS=--max-old-space-size=4096

# Jupyter widgets extension
jupyter labextension install @jupyter-widgets/jupyterlab-manager@1.1 --no-build

# FigureWidget support
jupyter labextension install plotlywidget@1.4.0 --no-build

# and jupyterlab renderer support
jupyter labextension install jupyterlab-plotly@1.4.0 --no-build

# Build extensions (must be done to activate extensions since --no-build is used above)
jupyter lab build

# Unset NODE_OPTIONS environment variable
unset NODE_OPTIONS

after running these steps, deactivate and reactivate your conda env and hopefully that solves the blank canvas problem.

dbl001 commented 4 years ago

Thank You! It’s now working on both platforms (e.g. - OS X 10.11.6, Ubuntu 16.06LTS).

Has anyone tries this with Google CoLab?

On Dec 26, 2019, at 12:58 AM, lewtun notifications@github.com wrote:

i've found that with jupyterlab, one usually needs to run the following extra steps:

Avoid "JavaScript heap out of memory" errors during extension installation

export NODE_OPTIONS=--max-old-space-size=4096

Jupyter widgets extension

jupyter labextension install @jupyter-widgets/jupyterlab-manager@1.1 --no-build

FigureWidget support

jupyter labextension install plotlywidget@1.4.0 --no-build

and jupyterlab renderer support

jupyter labextension install jupyterlab-plotly@1.4.0 --no-build

Build extensions (must be done to activate extensions since --no-build is used above)

jupyter lab build

Unset NODE_OPTIONS environment variable

unset NODE_OPTIONS after running these steps, deactivate and reactivate your conda env and hopefully that solves the blank canvas problem.

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lewtun commented 4 years ago

great to hear it is working @dbl001 😄

we have not tested this on google colab, but that would likely be an interesting experiment to perform.

i'm closing this issue and #5 since it seems to have been solved.

dbl001 commented 4 years ago

Has anyone tried using the mapper on high dimensional word vector embeddings (e.g. wor2vec, GloVe, BERT, ElMo, GPT-2)?

On Dec 26, 2019, at 11:50 AM, lewtun notifications@github.com wrote:

great to hear it is working @dbl001 https://github.com/dbl001 😄

we have not tested this on google colab, but that would likely be an interesting experiment to perform.

i'm closing this issue and #5 https://github.com/giotto-ai/tutorial_mapper/issues/5 since it seems to have been solved.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/giotto-ai/tutorial_mapper/issues/4?email_source=notifications&email_token=AAXWFW56RF5ADOIJNTEETK3Q2UDJLA5CNFSM4J7GLBLKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEHWCDMQ#issuecomment-569123250, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAXWFWZ5ZHDTQXXCKCHGER3Q2UDJLANCNFSM4J7GLBLA.

lewtun commented 4 years ago

@dbl001 I'm not aware of any works on applying Mapper directly to word embeddings (especially on those from transformer models). A better place to discuss this than a GitHub issue would be on Slack:

giotto: https://slack.giotto.ai/
TDA in ML: https://t.co/szhJxcMQuA?amp=1

giotto-ai / tutorial_mapper

Build Issue on OS X 10.11.6 #4

Avoid "JavaScript heap out of memory" errors during extension installation

Jupyter widgets extension

FigureWidget support

and jupyterlab renderer support

Build extensions (must be done to activate extensions since --no-build is used above)

Unset NODE_OPTIONS environment variable