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giotto-ai / giotto-tda

A high-performance topological machine learning toolbox in Python
https://giotto-ai.github.io/gtda-docs
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[BUG]Error installing giotto-tda and pyflagser #707

Open oabawon opened 3 days ago

oabawon commented 3 days ago

I obtained the following error when I tried installing giotto-tda as described in documentation for linux computer(python -m pip install -U giotto-tda), any help on how to fix this issue will be greatly appreciated. Thank you.

Collecting giotto-tda Using cached giotto-tda-0.1.4.tar.gz (99 kB) Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done Requirement already satisfied: numpy>=1.17.0 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from giotto-tda) (2.1.2) Requirement already satisfied: scipy>=0.17.0 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from giotto-tda) (1.14.1) Requirement already satisfied: joblib>=0.11 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from giotto-tda) (1.4.2) Requirement already satisfied: scikit-learn>=0.22.0 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from giotto-tda) (1.5.2) Collecting matplotlib>=3.0.3 (from giotto-tda) Using cached matplotlib-3.9.2-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB) Requirement already satisfied: plotly>=4.4.1 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from giotto-tda) (5.24.1) Requirement already satisfied: ipywidgets>=7.5.1 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from giotto-tda) (8.1.5) Requirement already satisfied: python-igraph in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from giotto-tda) (0.11.8) Requirement already satisfied: comm>=0.1.3 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from ipywidgets>=7.5.1->giotto-tda) (0.2.2) Requirement already satisfied: ipython>=6.1.0 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from ipywidgets>=7.5.1->giotto-tda) (8.28.0) Requirement already satisfied: traitlets>=4.3.1 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from ipywidgets>=7.5.1->giotto-tda) (5.14.3) Requirement already satisfied: widgetsnbextension~=4.0.12 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from ipywidgets>=7.5.1->giotto-tda) (4.0.13) Requirement already satisfied: jupyterlab-widgets~=3.0.12 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from ipywidgets>=7.5.1->giotto-tda) (3.0.13) Collecting contourpy>=1.0.1 (from matplotlib>=3.0.3->giotto-tda) Using cached contourpy-1.3.0-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.4 kB) Collecting cycler>=0.10 (from matplotlib>=3.0.3->giotto-tda) Using cached cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB) Collecting fonttools>=4.22.0 (from matplotlib>=3.0.3->giotto-tda) Using cached fonttools-4.54.1-cp313-cp313-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (163 kB) Collecting kiwisolver>=1.3.1 (from matplotlib>=3.0.3->giotto-tda) Using cached kiwisolver-1.4.7-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.3 kB) Requirement already satisfied: packaging>=20.0 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from matplotlib>=3.0.3->giotto-tda) (24.1) Collecting pillow>=8 (from matplotlib>=3.0.3->giotto-tda) Using cached pillow-11.0.0-cp313-cp313-manylinux_2_28_x86_64.whl.metadata (9.1 kB) Collecting pyparsing>=2.3.1 (from matplotlib>=3.0.3->giotto-tda) Using cached pyparsing-3.2.0-py3-none-any.whl.metadata (5.0 kB) Requirement already satisfied: python-dateutil>=2.7 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from matplotlib>=3.0.3->giotto-tda) (2.9.0) Requirement already satisfied: tenacity>=6.2.0 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from plotly>=4.4.1->giotto-tda) (9.0.0) Requirement already satisfied: threadpoolctl>=3.1.0 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from scikit-learn>=0.22.0->giotto-tda) (3.5.0) Requirement already satisfied: igraph==0.11.8 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from python-igraph->giotto-tda) (0.11.8) Requirement already satisfied: texttable>=1.6.2 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from igraph==0.11.8->python-igraph->giotto-tda) (1.7.0) Requirement already satisfied: decorator in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from ipython>=6.1.0->ipywidgets>=7.5.1->giotto-tda) (5.1.1) Requirement already satisfied: jedi>=0.16 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from ipython>=6.1.0->ipywidgets>=7.5.1->giotto-tda) (0.19.1) Requirement already satisfied: matplotlib-inline in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from ipython>=6.1.0->ipywidgets>=7.5.1->giotto-tda) (0.1.7) Requirement already satisfied: prompt-toolkit<3.1.0,>=3.0.41 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from ipython>=6.1.0->ipywidgets>=7.5.1->giotto-tda) (3.0.48) Requirement already satisfied: pygments>=2.4.0 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from ipython>=6.1.0->ipywidgets>=7.5.1->giotto-tda) (2.18.0) Requirement already satisfied: stack-data in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from ipython>=6.1.0->ipywidgets>=7.5.1->giotto-tda) (0.6.2) Requirement already satisfied: pexpect>4.3 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from ipython>=6.1.0->ipywidgets>=7.5.1->giotto-tda) (4.9.0) Requirement already satisfied: six>=1.5 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from python-dateutil>=2.7->matplotlib>=3.0.3->giotto-tda) (1.16.0) Requirement already satisfied: parso<0.9.0,>=0.8.3 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from jedi>=0.16->ipython>=6.1.0->ipywidgets>=7.5.1->giotto-tda) (0.8.4) Requirement already satisfied: ptyprocess>=0.5 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from pexpect>4.3->ipython>=6.1.0->ipywidgets>=7.5.1->giotto-tda) (0.7.0) Requirement already satisfied: wcwidth in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from prompt-toolkit<3.1.0,>=3.0.41->ipython>=6.1.0->ipywidgets>=7.5.1->giotto-tda) (0.2.13) Requirement already satisfied: executing>=1.2.0 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from stack-data->ipython>=6.1.0->ipywidgets>=7.5.1->giotto-tda) (2.1.0) Requirement already satisfied: asttokens>=2.1.0 in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from stack-data->ipython>=6.1.0->ipywidgets>=7.5.1->giotto-tda) (2.4.1) Requirement already satisfied: pure-eval in /home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages (from stack-data->ipython>=6.1.0->ipywidgets>=7.5.1->giotto-tda) (0.2.3) Using cached matplotlib-3.9.2-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.3 MB) Using cached contourpy-1.3.0-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (319 kB) Using cached cycler-0.12.1-py3-none-any.whl (8.3 kB) Using cached fonttools-4.54.1-cp313-cp313-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.9 MB) Using cached kiwisolver-1.4.7-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.5 MB) Using cached pillow-11.0.0-cp313-cp313-manylinux_2_28_x86_64.whl (4.4 MB) Using cached pyparsing-3.2.0-py3-none-any.whl (106 kB) Building wheels for collected packages: giotto-tda Building wheel for giotto-tda (pyproject.toml) ... error error: subprocess-exited-with-error

× Building wheel for giotto-tda (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [286 lines of output] /tmp/pip-build-env-8cg72kel/overlay/lib/python3.13/site-packages/setuptools/dist.py:495: SetuptoolsDeprecationWarning: Invalid dash-separated options !!

          ********************************************************************************
          Usage of dash-separated 'description-file' will not be supported in future
          versions. Please use the underscore name 'description_file' instead.

          By 2025-Mar-03, you need to update your project and remove deprecated calls
          or your builds will no longer be supported.

          See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
          ********************************************************************************

  !!
    opt = self.warn_dash_deprecation(opt, section)
  running bdist_wheel
  running build
  running build_py
  creating build/lib.linux-x86_64-cpython-313/gtda
  copying gtda/pipeline.py -> build/lib.linux-x86_64-cpython-313/gtda
  copying gtda/_version.py -> build/lib.linux-x86_64-cpython-313/gtda
  copying gtda/base.py -> build/lib.linux-x86_64-cpython-313/gtda
  copying gtda/__init__.py -> build/lib.linux-x86_64-cpython-313/gtda
  creating build/lib.linux-x86_64-cpython-313/gtda/time_series
  copying gtda/time_series/multivariate.py -> build/lib.linux-x86_64-cpython-313/gtda/time_series
  copying gtda/time_series/target.py -> build/lib.linux-x86_64-cpython-313/gtda/time_series
  copying gtda/time_series/features.py -> build/lib.linux-x86_64-cpython-313/gtda/time_series
  copying gtda/time_series/embedding.py -> build/lib.linux-x86_64-cpython-313/gtda/time_series
  copying gtda/time_series/preprocessing.py -> build/lib.linux-x86_64-cpython-313/gtda/time_series
  copying gtda/time_series/__init__.py -> build/lib.linux-x86_64-cpython-313/gtda/time_series
  creating build/lib.linux-x86_64-cpython-313/gtda/diagrams
  copying gtda/diagrams/_metrics.py -> build/lib.linux-x86_64-cpython-313/gtda/diagrams
  copying gtda/diagrams/features.py -> build/lib.linux-x86_64-cpython-313/gtda/diagrams
  copying gtda/diagrams/_utils.py -> build/lib.linux-x86_64-cpython-313/gtda/diagrams
  copying gtda/diagrams/distance.py -> build/lib.linux-x86_64-cpython-313/gtda/diagrams
  copying gtda/diagrams/preprocessing.py -> build/lib.linux-x86_64-cpython-313/gtda/diagrams
  copying gtda/diagrams/__init__.py -> build/lib.linux-x86_64-cpython-313/gtda/diagrams
  creating build/lib.linux-x86_64-cpython-313/gtda/externals
  copying gtda/externals/__init__.py -> build/lib.linux-x86_64-cpython-313/gtda/externals
  creating build/lib.linux-x86_64-cpython-313/gtda/graphs
  copying gtda/graphs/kneighbors.py -> build/lib.linux-x86_64-cpython-313/gtda/graphs
  copying gtda/graphs/transition.py -> build/lib.linux-x86_64-cpython-313/gtda/graphs
  copying gtda/graphs/geodesic_distance.py -> build/lib.linux-x86_64-cpython-313/gtda/graphs
  copying gtda/graphs/__init__.py -> build/lib.linux-x86_64-cpython-313/gtda/graphs
  creating build/lib.linux-x86_64-cpython-313/gtda/meta_transformers
  copying gtda/meta_transformers/features.py -> build/lib.linux-x86_64-cpython-313/gtda/meta_transformers
  copying gtda/meta_transformers/__init__.py -> build/lib.linux-x86_64-cpython-313/gtda/meta_transformers
  creating build/lib.linux-x86_64-cpython-313/gtda/mapper
  copying gtda/mapper/cluster.py -> build/lib.linux-x86_64-cpython-313/gtda/mapper
  copying gtda/mapper/pipeline.py -> build/lib.linux-x86_64-cpython-313/gtda/mapper
  copying gtda/mapper/visualization.py -> build/lib.linux-x86_64-cpython-313/gtda/mapper
  copying gtda/mapper/cover.py -> build/lib.linux-x86_64-cpython-313/gtda/mapper
  copying gtda/mapper/filter.py -> build/lib.linux-x86_64-cpython-313/gtda/mapper
  copying gtda/mapper/nerve.py -> build/lib.linux-x86_64-cpython-313/gtda/mapper
  copying gtda/mapper/__init__.py -> build/lib.linux-x86_64-cpython-313/gtda/mapper
  creating build/lib.linux-x86_64-cpython-313/gtda/tests
  copying gtda/tests/__init__.py -> build/lib.linux-x86_64-cpython-313/gtda/tests
  copying gtda/tests/test_pipeline.py -> build/lib.linux-x86_64-cpython-313/gtda/tests
  creating build/lib.linux-x86_64-cpython-313/gtda/utils
  copying gtda/utils/validation.py -> build/lib.linux-x86_64-cpython-313/gtda/utils
  copying gtda/utils/testing.py -> build/lib.linux-x86_64-cpython-313/gtda/utils
  copying gtda/utils/_docs.py -> build/lib.linux-x86_64-cpython-313/gtda/utils
  copying gtda/utils/__init__.py -> build/lib.linux-x86_64-cpython-313/gtda/utils
  creating build/lib.linux-x86_64-cpython-313/gtda/homology
  copying gtda/homology/point_clouds.py -> build/lib.linux-x86_64-cpython-313/gtda/homology
  copying gtda/homology/consistent.py -> build/lib.linux-x86_64-cpython-313/gtda/homology
  copying gtda/homology/_utils.py -> build/lib.linux-x86_64-cpython-313/gtda/homology
  copying gtda/homology/__init__.py -> build/lib.linux-x86_64-cpython-313/gtda/homology
  creating build/lib.linux-x86_64-cpython-313/gtda/time_series/tests
  copying gtda/time_series/tests/test_embedding.py -> build/lib.linux-x86_64-cpython-313/gtda/time_series/tests
  copying gtda/time_series/tests/__init__.py -> build/lib.linux-x86_64-cpython-313/gtda/time_series/tests
  copying gtda/time_series/tests/test_preprocessing.py -> build/lib.linux-x86_64-cpython-313/gtda/time_series/tests
  copying gtda/time_series/tests/test_multivariate.py -> build/lib.linux-x86_64-cpython-313/gtda/time_series/tests
  creating build/lib.linux-x86_64-cpython-313/gtda/diagrams/tests
  copying gtda/diagrams/tests/test_features.py -> build/lib.linux-x86_64-cpython-313/gtda/diagrams/tests
  copying gtda/diagrams/tests/__init__.py -> build/lib.linux-x86_64-cpython-313/gtda/diagrams/tests
  copying gtda/diagrams/tests/test_distance.py -> build/lib.linux-x86_64-cpython-313/gtda/diagrams/tests
  copying gtda/diagrams/tests/test_preprocessing.py -> build/lib.linux-x86_64-cpython-313/gtda/diagrams/tests
  creating build/lib.linux-x86_64-cpython-313/gtda/externals/python
  copying gtda/externals/python/strong_witness_complex_interface.py -> build/lib.linux-x86_64-cpython-313/gtda/externals/python
  copying gtda/externals/python/cubical_complex_interface.py -> build/lib.linux-x86_64-cpython-313/gtda/externals/python
  copying gtda/externals/python/witness_complex_interface.py -> build/lib.linux-x86_64-cpython-313/gtda/externals/python
  copying gtda/externals/python/cech_complex_interface.py -> build/lib.linux-x86_64-cpython-313/gtda/externals/python
  copying gtda/externals/python/ripser_interface.py -> build/lib.linux-x86_64-cpython-313/gtda/externals/python
  copying gtda/externals/python/simplex_tree_interface.py -> build/lib.linux-x86_64-cpython-313/gtda/externals/python
  copying gtda/externals/python/rips_complex_interface.py -> build/lib.linux-x86_64-cpython-313/gtda/externals/python
  copying gtda/externals/python/__init__.py -> build/lib.linux-x86_64-cpython-313/gtda/externals/python
  copying gtda/externals/python/periodic_cubical_complex_interface.py -> build/lib.linux-x86_64-cpython-313/gtda/externals/python
  creating build/lib.linux-x86_64-cpython-313/gtda/externals/python/tests
  copying gtda/externals/python/tests/test_witness.py -> build/lib.linux-x86_64-cpython-313/gtda/externals/python/tests
  copying gtda/externals/python/tests/test_rips_complex.py -> build/lib.linux-x86_64-cpython-313/gtda/externals/python/tests
  copying gtda/externals/python/tests/__init__.py -> build/lib.linux-x86_64-cpython-313/gtda/externals/python/tests
  copying gtda/externals/python/tests/test_cech_complex.py -> build/lib.linux-x86_64-cpython-313/gtda/externals/python/tests
  copying gtda/externals/python/tests/test_periodic_cubical_complex.py -> build/lib.linux-x86_64-cpython-313/gtda/externals/python/tests
  creating build/lib.linux-x86_64-cpython-313/gtda/graphs/tests
  copying gtda/graphs/tests/test_geodesic_distance.py -> build/lib.linux-x86_64-cpython-313/gtda/graphs/tests
  copying gtda/graphs/tests/test_kneighbors.py -> build/lib.linux-x86_64-cpython-313/gtda/graphs/tests
  copying gtda/graphs/tests/__init__.py -> build/lib.linux-x86_64-cpython-313/gtda/graphs/tests
  copying gtda/graphs/tests/test_transition.py -> build/lib.linux-x86_64-cpython-313/gtda/graphs/tests
  creating build/lib.linux-x86_64-cpython-313/gtda/meta_transformers/tests
  copying gtda/meta_transformers/tests/test_features.py -> build/lib.linux-x86_64-cpython-313/gtda/meta_transformers/tests
  copying gtda/meta_transformers/tests/__init__.py -> build/lib.linux-x86_64-cpython-313/gtda/meta_transformers/tests
  creating build/lib.linux-x86_64-cpython-313/gtda/mapper/utils
  copying gtda/mapper/utils/pipeline.py -> build/lib.linux-x86_64-cpython-313/gtda/mapper/utils
  copying gtda/mapper/utils/visualization.py -> build/lib.linux-x86_64-cpython-313/gtda/mapper/utils
  copying gtda/mapper/utils/_logging.py -> build/lib.linux-x86_64-cpython-313/gtda/mapper/utils
  copying gtda/mapper/utils/_cover.py -> build/lib.linux-x86_64-cpython-313/gtda/mapper/utils
  copying gtda/mapper/utils/_list_feature_union.py -> build/lib.linux-x86_64-cpython-313/gtda/mapper/utils
  copying gtda/mapper/utils/decorators.py -> build/lib.linux-x86_64-cpython-313/gtda/mapper/utils
  copying gtda/mapper/utils/__init__.py -> build/lib.linux-x86_64-cpython-313/gtda/mapper/utils
  copying gtda/mapper/utils/_cluster.py -> build/lib.linux-x86_64-cpython-313/gtda/mapper/utils
  creating build/lib.linux-x86_64-cpython-313/gtda/utils/tests
  copying gtda/utils/tests/test_validation.py -> build/lib.linux-x86_64-cpython-313/gtda/utils/tests
  copying gtda/utils/tests/__init__.py -> build/lib.linux-x86_64-cpython-313/gtda/utils/tests
  creating build/lib.linux-x86_64-cpython-313/gtda/homology/tests
  copying gtda/homology/tests/test_point_clouds.py -> build/lib.linux-x86_64-cpython-313/gtda/homology/tests
  copying gtda/homology/tests/test_consistent.py -> build/lib.linux-x86_64-cpython-313/gtda/homology/tests
  copying gtda/homology/tests/__init__.py -> build/lib.linux-x86_64-cpython-313/gtda/homology/tests
  running build_ext
  Cloning into '/tmp/pip-install-_4_3_8m7/giotto-tda_a6a685f6819c4166b8fe0e29d7869b55/gtda/externals/pybind11'...
  -- The CXX compiler identification is GNU 9.4.0
  -- Check for working CXX compiler: /usr/bin/c++
  -- Check for working CXX compiler: /usr/bin/c++ -- works
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  -- pybind11 v2.14.0 dev1
  -- CMake 3.16.3
  -- Found PythonInterp: /home/olakunle/anaconda3/envs/new_env/bin/python (found suitable version "3.13", minimum required is "3.8")
  -- Found PythonLibs: /home/olakunle/anaconda3/envs/new_env/lib/libpython3.13.so
  -- PYTHON 3.13.0
  -- Performing Test HAS_FLTO
  -- Performing Test HAS_FLTO - Success
  -- pybind11::lto enabled
  -- pybind11::thin_lto enabled
  -- Configuring done
  -- Generating done
  -- Build files have been written to: /tmp/pip-install-_4_3_8m7/giotto-tda_a6a685f6819c4166b8fe0e29d7869b55/gtda/externals/pybind11/build
  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.

  make: *** [Makefile:86: install] Error 1
  Install the project...
  -- Install configuration: ""
  -- Up-to-date: /usr/local/include/pybind11
  -- Installing: /usr/local/include/pybind11/chrono.h
  -- Installing: /usr/local/include/pybind11/iostream.h
  -- Up-to-date: /usr/local/include/pybind11/eigen
  -- Installing: /usr/local/include/pybind11/eigen/matrix.h
  -- Installing: /usr/local/include/pybind11/eigen/common.h
  -- Installing: /usr/local/include/pybind11/eigen/tensor.h
  -- Installing: /usr/local/include/pybind11/stl_bind.h
  -- Installing: /usr/local/include/pybind11/options.h
  -- Up-to-date: /usr/local/include/pybind11/stl
  -- Installing: /usr/local/include/pybind11/stl/filesystem.h
  -- Installing: /usr/local/include/pybind11/cast.h
  -- Installing: /usr/local/include/pybind11/embed.h
  -- Installing: /usr/local/include/pybind11/functional.h
  -- Installing: /usr/local/include/pybind11/type_caster_pyobject_ptr.h
  -- Installing: /usr/local/include/pybind11/pybind11.h
  -- Installing: /usr/local/include/pybind11/common.h
  -- Installing: /usr/local/include/pybind11/attr.h
  -- Installing: /usr/local/include/pybind11/buffer_info.h
  -- Installing: /usr/local/include/pybind11/gil_safe_call_once.h
  -- Up-to-date: /usr/local/include/pybind11/conduit
  -- Installing: /usr/local/include/pybind11/conduit/pybind11_conduit_v1.h
  -- Installing: /usr/local/include/pybind11/conduit/README.txt
  -- Installing: /usr/local/include/pybind11/conduit/pybind11_platform_abi_id.h
  -- Installing: /usr/local/include/pybind11/conduit/wrap_include_python_h.h
  -- Installing: /usr/local/include/pybind11/eigen.h
  -- Installing: /usr/local/include/pybind11/numpy.h
  -- Installing: /usr/local/include/pybind11/complex.h
  -- Up-to-date: /usr/local/include/pybind11/detail
  -- Installing: /usr/local/include/pybind11/detail/value_and_holder.h
  -- Installing: /usr/local/include/pybind11/detail/exception_translation.h
  -- Installing: /usr/local/include/pybind11/detail/typeid.h
  -- Installing: /usr/local/include/pybind11/detail/common.h
  -- Installing: /usr/local/include/pybind11/detail/init.h
  -- Installing: /usr/local/include/pybind11/detail/class.h
  -- Installing: /usr/local/include/pybind11/detail/type_caster_base.h
  -- Installing: /usr/local/include/pybind11/detail/descr.h
  -- Installing: /usr/local/include/pybind11/detail/cpp_conduit.h
  -- Installing: /usr/local/include/pybind11/detail/internals.h
  -- Installing: /usr/local/include/pybind11/stl.h
  -- Installing: /usr/local/include/pybind11/gil.h
  -- Installing: /usr/local/include/pybind11/typing.h
  -- Installing: /usr/local/include/pybind11/warnings.h
  -- Installing: /usr/local/include/pybind11/operators.h
  -- Installing: /usr/local/include/pybind11/eval.h
  -- Installing: /usr/local/include/pybind11/pytypes.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/pybind11GuessPythonExtSuffix.cmake
  -- Installing: /usr/local/share/cmake/pybind11/pybind11Targets.cmake
  -- Installing: /usr/local/share/pkgconfig/pybind11.pc
  fatal: not a git repository (or any of the parent directories): .git
  Traceback (most recent call last):
    File "/home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
      main()
      ~~~~^^
    File "/home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
                               ~~~~^^^^^^^^^^^^^^^^^^^^^^^^
    File "/home/olakunle/anaconda3/envs/new_env/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
      return _build_backend().build_wheel(wheel_directory, config_settings,
             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                                          metadata_directory)
                                          ^^^^^^^^^^^^^^^^^^^
    File "/tmp/pip-build-env-8cg72kel/overlay/lib/python3.13/site-packages/setuptools/build_meta.py", line 437, in build_wheel
      return _build(['bdist_wheel', '--dist-info-dir', str(metadata_directory)])
    File "/tmp/pip-build-env-8cg72kel/overlay/lib/python3.13/site-packages/setuptools/build_meta.py", line 425, in _build
      return self._build_with_temp_dir(
             ~~~~~~~~~~~~~~~~~~~~~~~~~^
          cmd,
          ^^^^
      ...<3 lines>...
          self._arbitrary_args(config_settings),
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      )
      ^
    File "/tmp/pip-build-env-8cg72kel/overlay/lib/python3.13/site-packages/setuptools/build_meta.py", line 406, in _build_with_temp_dir
      self.run_setup()
      ~~~~~~~~~~~~~~^^
    File "/tmp/pip-build-env-8cg72kel/overlay/lib/python3.13/site-packages/setuptools/build_meta.py", line 521, in run_setup
      super().run_setup(setup_script=setup_script)
      ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/tmp/pip-build-env-8cg72kel/overlay/lib/python3.13/site-packages/setuptools/build_meta.py", line 319, in run_setup
      exec(code, locals())
      ~~~~^^^^^^^^^^^^^^^^
    File "<string>", line 183, in <module>
    File "/tmp/pip-build-env-8cg72kel/overlay/lib/python3.13/site-packages/setuptools/__init__.py", line 117, in setup
      return distutils.core.setup(**attrs)
             ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
    File "/tmp/pip-build-env-8cg72kel/overlay/lib/python3.13/site-packages/setuptools/_distutils/core.py", line 183, in setup
      return run_commands(dist)
    File "/tmp/pip-build-env-8cg72kel/overlay/lib/python3.13/site-packages/setuptools/_distutils/core.py", line 199, in run_commands
      dist.run_commands()
      ~~~~~~~~~~~~~~~~~^^
    File "/tmp/pip-build-env-8cg72kel/overlay/lib/python3.13/site-packages/setuptools/_distutils/dist.py", line 954, in run_commands
      self.run_command(cmd)
      ~~~~~~~~~~~~~~~~^^^^^
    File "/tmp/pip-build-env-8cg72kel/overlay/lib/python3.13/site-packages/setuptools/dist.py", line 999, in run_command
      super().run_command(command)
      ~~~~~~~~~~~~~~~~~~~^^^^^^^^^
    File "/tmp/pip-build-env-8cg72kel/overlay/lib/python3.13/site-packages/setuptools/_distutils/dist.py", line 973, in run_command
      cmd_obj.run()
      ~~~~~~~~~~~^^
    File "/tmp/pip-build-env-8cg72kel/overlay/lib/python3.13/site-packages/setuptools/command/bdist_wheel.py", line 410, in run
      self.run_command("build")
      ~~~~~~~~~~~~~~~~^^^^^^^^^
    File "/tmp/pip-build-env-8cg72kel/overlay/lib/python3.13/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command
      self.distribution.run_command(command)
      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
    File "/tmp/pip-build-env-8cg72kel/overlay/lib/python3.13/site-packages/setuptools/dist.py", line 999, in run_command
      super().run_command(command)
      ~~~~~~~~~~~~~~~~~~~^^^^^^^^^
    File "/tmp/pip-build-env-8cg72kel/overlay/lib/python3.13/site-packages/setuptools/_distutils/dist.py", line 973, in run_command
      cmd_obj.run()
      ~~~~~~~~~~~^^
    File "/tmp/pip-build-env-8cg72kel/overlay/lib/python3.13/site-packages/setuptools/_distutils/command/build.py", line 135, in run
      self.run_command(cmd_name)
      ~~~~~~~~~~~~~~~~^^^^^^^^^^
    File "/tmp/pip-build-env-8cg72kel/overlay/lib/python3.13/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command
      self.distribution.run_command(command)
      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
    File "/tmp/pip-build-env-8cg72kel/overlay/lib/python3.13/site-packages/setuptools/dist.py", line 999, in run_command
      super().run_command(command)
      ~~~~~~~~~~~~~~~~~~~^^^^^^^^^
    File "/tmp/pip-build-env-8cg72kel/overlay/lib/python3.13/site-packages/setuptools/_distutils/dist.py", line 973, in run_command
      cmd_obj.run()
      ~~~~~~~~~~~^^
    File "<string>", line 116, in run
    File "<string>", line 150, in install_dependencies
    File "/home/olakunle/anaconda3/envs/new_env/lib/python3.13/subprocess.py", line 419, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command '['git', 'submodule', 'update', '--init', '--recursive']' returned non-zero exit status 128.
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for giotto-tda Failed to build giotto-tda ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (giotto-tda)

matteocao commented 2 days ago

Dear @oabawon ,

It seems that you are trying to build the giotto-tda wheels rather than pip installing the pre-compiled version.

My suggestion is to use one of these wheel files that have already been pre-compiled for different operative systems. You can find them here: https://pypi.org/project/giotto-tda/#files

You should find and download the file most appropriate for your environment (it depends on the python version and whether you are on win, macos or linux.).

For example this file

giotto_tda-0.6.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

is to be selected in case you are using python 3.11 on a linux distro.

In theory, if you do something like pip install giotto-tda --force-reinstall , it should automatically get the right file for you. If not, you can try to force your system to install the wheel directly: place the file if the cwd and simply run pip install <name_of_the_file.whl>.

If it does not works, please let us know the python version you are using and the operative system as well.

Good luck!