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Unable to install tslearn on MacOS due to Numpy headers #196

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dfontenot opened this issue Mar 10, 2020 · 10 comments
Closed

Unable to install tslearn on MacOS due to Numpy headers #196

dfontenot opened this issue Mar 10, 2020 · 10 comments
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bug

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@dfontenot
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Describe the bug
pip3 install tslearn fails with the following error:

Building wheels for collected packages: tslearn
  Building wheel for tslearn (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /usr/local/opt/python/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/fl/5t7gh9md4jn83nrmhcph3r9m0000gn/T/pip-install-qc_jggl7/tslearn/setup.py'"'"'; __file__='"'"'/private/var/folders/fl/5t7gh9md4jn83nrmhcph3r9m0000gn/T/pip-install-qc_jggl7/tslearn/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/fl/5t7gh9md4jn83nrmhcph3r9m0000gn/T/pip-wheel-9sqz_lji --python-tag cp37
       cwd: /private/var/folders/fl/5t7gh9md4jn83nrmhcph3r9m0000gn/T/pip-install-qc_jggl7/tslearn/
  Complete output (46 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.macosx-10.12-x86_64-3.7
  creating build/lib.macosx-10.12-x86_64-3.7/tslearn
  copying tslearn/__init__.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
  copying tslearn/barycenters.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
  copying tslearn/bases.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
  copying tslearn/clustering.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
  copying tslearn/datasets.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
  copying tslearn/deprecated.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
  copying tslearn/generators.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
  copying tslearn/hdftools.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
  copying tslearn/metrics.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
  copying tslearn/neighbors.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
  copying tslearn/piecewise.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
  copying tslearn/preprocessing.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
  copying tslearn/shapelets.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
  copying tslearn/svm.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
  copying tslearn/utils.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
  creating build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
  copying tslearn/tests/__init__.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
  copying tslearn/tests/sklearn_patches.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
  copying tslearn/tests/test_barycenters.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
  copying tslearn/tests/test_clustering.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
  copying tslearn/tests/test_estimators.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
  copying tslearn/tests/test_metrics.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
  copying tslearn/tests/test_neighbors.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
  copying tslearn/tests/test_piecewise.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
  copying tslearn/tests/test_serialize_models.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
  copying tslearn/tests/test_shapelets.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
  copying tslearn/tests/test_utils.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
  copying tslearn/tests/test_variablelength.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
  creating build/lib.macosx-10.12-x86_64-3.7/tslearn/.cached_datasets
  copying tslearn/.cached_datasets/Trace.npz -> build/lib.macosx-10.12-x86_64-3.7/tslearn/.cached_datasets
  running build_ext
  building 'tslearn.cycc' extension
  creating build/temp.macosx-10.12-x86_64-3.7
  creating build/temp.macosx-10.12-x86_64-3.7/tslearn
  clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/usr/local/include -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.6_1/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c tslearn/cycc.c -o build/temp.macosx-10.12-x86_64-3.7/tslearn/cycc.o
  tslearn/cycc.c:611:10: fatal error: 'numpy/arrayobject.h' file not found
  #include "numpy/arrayobject.h"
           ^~~~~~~~~~~~~~~~~~~~~
  1 error generated.
  error: command 'clang' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for tslearn
  Running setup.py clean for tslearn
Failed to build tslearn
Installing collected packages: tslearn
    Running setup.py install for tslearn ... error
    ERROR: Command errored out with exit status 1:
     command: /usr/local/opt/python/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/fl/5t7gh9md4jn83nrmhcph3r9m0000gn/T/pip-install-qc_jggl7/tslearn/setup.py'"'"'; __file__='"'"'/private/var/folders/fl/5t7gh9md4jn83nrmhcph3r9m0000gn/T/pip-install-qc_jggl7/tslearn/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/fl/5t7gh9md4jn83nrmhcph3r9m0000gn/T/pip-record-s2w_imf2/install-record.txt --single-version-externally-managed --compile
         cwd: /private/var/folders/fl/5t7gh9md4jn83nrmhcph3r9m0000gn/T/pip-install-qc_jggl7/tslearn/
    Complete output (46 lines):
    running install
    running build
    running build_py
    creating build
    creating build/lib.macosx-10.12-x86_64-3.7
    creating build/lib.macosx-10.12-x86_64-3.7/tslearn
    copying tslearn/__init__.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
    copying tslearn/barycenters.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
    copying tslearn/bases.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
    copying tslearn/clustering.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
    copying tslearn/datasets.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
    copying tslearn/deprecated.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
    copying tslearn/generators.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
    copying tslearn/hdftools.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
    copying tslearn/metrics.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
    copying tslearn/neighbors.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
    copying tslearn/piecewise.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
    copying tslearn/preprocessing.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
    copying tslearn/shapelets.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
    copying tslearn/svm.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
    copying tslearn/utils.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn
    creating build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
    copying tslearn/tests/__init__.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
    copying tslearn/tests/sklearn_patches.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
    copying tslearn/tests/test_barycenters.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
    copying tslearn/tests/test_clustering.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
    copying tslearn/tests/test_estimators.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
    copying tslearn/tests/test_metrics.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
    copying tslearn/tests/test_neighbors.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
    copying tslearn/tests/test_piecewise.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
    copying tslearn/tests/test_serialize_models.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
    copying tslearn/tests/test_shapelets.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
    copying tslearn/tests/test_utils.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
    copying tslearn/tests/test_variablelength.py -> build/lib.macosx-10.12-x86_64-3.7/tslearn/tests
    creating build/lib.macosx-10.12-x86_64-3.7/tslearn/.cached_datasets
    copying tslearn/.cached_datasets/Trace.npz -> build/lib.macosx-10.12-x86_64-3.7/tslearn/.cached_datasets
    running build_ext
    building 'tslearn.cycc' extension
    creating build/temp.macosx-10.12-x86_64-3.7
    creating build/temp.macosx-10.12-x86_64-3.7/tslearn
    clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/usr/local/include -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.6_1/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c tslearn/cycc.c -o build/temp.macosx-10.12-x86_64-3.7/tslearn/cycc.o
    tslearn/cycc.c:611:10: fatal error: 'numpy/arrayobject.h' file not found
    #include "numpy/arrayobject.h"
             ^~~~~~~~~~~~~~~~~~~~~
    1 error generated.
    error: command 'clang' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/local/opt/python/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/fl/5t7gh9md4jn83nrmhcph3r9m0000gn/T/pip-install-qc_jggl7/tslearn/setup.py'"'"'; __file__='"'"'/private/var/folders/fl/5t7gh9md4jn83nrmhcph3r9m0000gn/T/pip-install-qc_jggl7/tslearn/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/fl/5t7gh9md4jn83nrmhcph3r9m0000gn/T/pip-record-s2w_imf2/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.

To Reproduce
Python version: 3.7.6, pip version 19.3.1. I have installed cython as well as numpy via pip.

Expected behavior
tslearn to install

Environment (please complete the following information):

  • OS: MacOS 10.12.6
  • tslearn version 0.3.0

Additional context

>>> np.get_include()
'/usr/local/lib/python3.7/site-packages/numpy/core/include'
@dfontenot dfontenot added the bug label Mar 10, 2020
@johannfaouzi
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Looking at this issue from hmmlearn, could you try the solution that they proposed?

export CFLAGS="-I /usr/local/lib/python3.7/site-packages/numpy/core/include $CFLAGS"

@rtavenar
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@dfontenot : could you try @johannfaouzi 's trick and tell us if it works? If so, I could implement the solution suggested there as a fix.

@dfontenot
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@rtavenar I believe that worked. At the end of pip3 install tslearn, after having exported that CFLAGS var:

ERROR: Could not install packages due to an EnvironmentError: [Errno 13] Permission denied: '/usr/local/LICENSE'
Consider using the `--user` option or check the permissions.

A subsequent pip3 install -user tslearn stated the tslearn was already installed, and I could import tslearn in python3.

@mustafadgr
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mustafadgr commented Apr 13, 2020 •
edited

i also have similar one:

 tslearn/cycc.c:613:10: fatal error: 'numpy/arrayobject.h' file not found
#include "numpy/arrayobject.h"
         ^~~~~~~~~~~~~~~~~~~~~
1 error generated.
error: command 'clang' failed with exit status 1

none of the proposed methods worked for me. i tried to include these paths both to my environment as well as global path. couldn't install!!!! neither globally nor in local env.
also in setup.py np.get_include() is already present. so i don't think this method would help anyway.

@rtavenar
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Hi @mustafadgr

Could you provide the same information @dfontenot did in his original post (os, python version, full error trace) so that we can try to figure out what is happening ?

@mustafadgr
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Collecting tslearn
  Downloading tslearn-0.3.1.tar.gz (548 kB)
     |████████████████████████████████| 548 kB 412 kB/s 
Requirement already satisfied: numpy in ./project_env/lib/python3.7/site-packages (from tslearn) (1.18.1)
Requirement already satisfied: scipy in ./project_env/lib/python3.7/site-packages (from tslearn) (1.4.1)
Requirement already satisfied: scikit-learn in ./project_env/lib/python3.7/site-packages (from tslearn) (0.22.2.post1)
Requirement already satisfied: Cython in ./project_env/lib/python3.7/site-packages (from tslearn) (0.29.16)
Requirement already satisfied: numba in ./project_env/lib/python3.7/site-packages (from tslearn) (0.48.0)
Requirement already satisfied: joblib in ./project_env/lib/python3.7/site-packages (from tslearn) (0.14.1)
Requirement already satisfied: setuptools in ./project_env/lib/python3.7/site-packages (from numba->tslearn) (41.2.0)
Requirement already satisfied: llvmlite<0.32.0,>=0.31.0dev0 in ./project_env/lib/python3.7/site-packages (from numba->tslearn) (0.31.0)
Installing collected packages: tslearn
    Running setup.py install for tslearn ... error
    ERROR: Command errored out with exit status 1:
     command: /Users/mustafadoeger/491/python/project_env/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/tmp/pip-install-0c6eopd_/tslearn/setup.py'"'"'; __file__='"'"'/private/tmp/pip-install-0c6eopd_/tslearn/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/tmp/pip-record-og9816i3/install-record.txt --single-version-externally-managed --compile --install-headers /Users/mustafadoeger/491/python/project_env/include/site/python3.7/tslearn
         cwd: /private/tmp/pip-install-0c6eopd_/tslearn/
    Complete output (47 lines):
    running install
    running build
    running build_py
    creating build
    creating build/lib.macosx-10.15-x86_64-3.7
    creating build/lib.macosx-10.15-x86_64-3.7/tslearn
    copying tslearn/metrics.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn
    copying tslearn/barycenters.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn
    copying tslearn/clustering.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn
    copying tslearn/hdftools.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn
    copying tslearn/neighbors.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn
    copying tslearn/deprecated.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn
    copying tslearn/datasets.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn
    copying tslearn/__init__.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn
    copying tslearn/shapelets.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn
    copying tslearn/generators.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn
    copying tslearn/utils.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn
    copying tslearn/preprocessing.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn
    copying tslearn/piecewise.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn
    copying tslearn/svm.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn
    copying tslearn/bases.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn
    creating build/lib.macosx-10.15-x86_64-3.7/tslearn/tests
    copying tslearn/tests/test_utils.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn/tests
    copying tslearn/tests/test_estimators.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn/tests
    copying tslearn/tests/test_metrics.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn/tests
    copying tslearn/tests/test_barycenters.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn/tests
    copying tslearn/tests/__init__.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn/tests
    copying tslearn/tests/test_piecewise.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn/tests
    copying tslearn/tests/test_variablelength.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn/tests
    copying tslearn/tests/test_svm.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn/tests
    copying tslearn/tests/test_serialize_models.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn/tests
    copying tslearn/tests/sklearn_patches.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn/tests
    copying tslearn/tests/test_shapelets.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn/tests
    copying tslearn/tests/test_neighbors.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn/tests
    copying tslearn/tests/test_clustering.py -> build/lib.macosx-10.15-x86_64-3.7/tslearn/tests
    creating build/lib.macosx-10.15-x86_64-3.7/tslearn/.cached_datasets
    copying tslearn/.cached_datasets/Trace.npz -> build/lib.macosx-10.15-x86_64-3.7/tslearn/.cached_datasets
    running build_ext
    building 'tslearn.cycc' extension
    creating build/temp.macosx-10.15-x86_64-3.7
    creating build/temp.macosx-10.15-x86_64-3.7/tslearn
    clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/include -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/sqlite/include -I/Users/mustafadoeger/491/python/project_env/include -I/usr/local/Cellar/python/3.7.6_1/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c tslearn/cycc.c -o build/temp.macosx-10.15-x86_64-3.7/tslearn/cycc.o
    tslearn/cycc.c:613:10: fatal error: 'numpy/arrayobject.h' file not found
    #include "numpy/arrayobject.h"
             ^~~~~~~~~~~~~~~~~~~~~
    1 error generated.
    error: command 'clang' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /Users/mustafadoeger/491/python/project_env/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/tmp/pip-install-0c6eopd_/tslearn/setup.py'"'"'; __file__='"'"'/private/tmp/pip-install-0c6eopd_/tslearn/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/tmp/pip-record-og9816i3/install-record.txt --single-version-externally-managed --compile --install-headers /Users/mustafadoeger/491/python/project_env/include/site/python3.7/tslearn Check the logs for full command output.

macos version: 10.15.4
python version: 3.7.6
tslearn 0.3.1

numpy.include()
'/Users/mustafadoeger/491/python/project_env/lib/python3.7/site-packages/numpy/core/include'

ps: this is virtual env, but as i said same error pops up in global environment

@johannfaouzi
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Another related issue from another Python package: andersbll/cudarray#25

Could you try the proposed solutions there please? You may also have less trouble installing tslearn using conda (if you use conda of course).

@mustafadgr
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i don't use conda. i already saw this thread and tried them.
when i try to change
ext_modules=cythonize("tslearn/*.pyx", include_path=[numpy.get_include()]),
to:
ext_modules=cythonize("tslearn/*.pyx", include_dirs=[numpy.get_include()]),
i get an error saying remove include_dirs.
meanwhile when i try to change include_dirs in line 24 in setup.py, to include_pat i get numpy header error.

@johannfaouzi
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Contributor

According to this issue on Cython project, include_path doesn't do anything.

Looking at the documentation of Cython, and more specifically to the cythonize function, you can use the aliases parameter if you want to use include_dirs in cythonize. I really don't much about Cython, so I don't know if this can be useful or not.

Another proposed solution in the issue is to give an Extension object to the cynthonize function. It would like this I guess:

from setuptools import setup, Extension
from Cython.Build import cythonize

setup(
    ...,
    ext_modules=cythonize(Extension("tslearn", sources=["tslearn/*.pyx"], include_dirs=[numpyp.get_include()])),
    ...
)

So you would have to change line 1 to import Extension and line 31 to use an Extension inside cythonize.

I hope that it helps you a bit.

@mustafadgr
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it worked great!!! thanks

@mustafadgr mustafadgr mentioned this issue Apr 26, 2020
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@dfontenot @johannfaouzi @rtavenar @mustafadgr