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plotly displays empty graphs in Jupyter lab notebook on Ubuntu 16.06LTS
The plots are empty white space.
Could this issue be related?
plotly/plotly.py#452
Build Issue on OS X 10.11.6
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$
KeyError
Thanks for your repo
when I use this code
""""
configure Mapper pipeline
pipeline = make_mapper_pipeline(
filter_func=None,
cover=CubicalCover(),
clusterer=DBSCAN())
plot the graph arising from applying the pipeline
fig = plot_mapper_graph_from_pipeline(pipeline)
""""
it return error
KeyError Traceback (most recent call last)
Cell In [9], line 8
2 pipeline = make_mapper_pipeline(
3 filter_func=None,
4 cover=CubicalCover(),
5 clusterer=DBSCAN())
7 # plot the graph arising from applying the pipeline
----> 8 fig = plot_mapper_graph_from_pipeline(pipeline)
Cell In [7], line 13, in plot_mapper_graph_from_pipeline(pipe)
10 graph = pipeline.fit_transform(coords)
12 # get cluster member indices
---> 13 node_elements = graph["node_metadata"]["node_elements"]
15 # configure choice of layout (x,z values)
16 layout = np.array([np.mean(coords[el], axis=0)[[0,2]] for el in node_elements])
KeyError: 'Attribute does not exist'
error importing sklearn.cluster._hierarchical
Hi all,
I tried to run the notebook myself and noticed a really minor thing: in cluster.py on line 7 it says
from sklearn.cluster._hierarchical import _TREE_BUILDERS, _hc_cut
That threw an exception, but when I removed the leading underscore on hierarchical, to read
from sklearn.cluster.hierarchical import _TREE_BUILDERS, _hc_cut
everything works beautifully.
Does this need to be changed in general, or is that just a hack that happens to work on my machine?
Thanks,
Philip
Adapt notebook to new API
Update the notebook to run with new API. #8 does not have the updated plot_static_mapper_graph despite history saying so.
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