MacOS & Python 3.8.9 gets error when running pip install

[martincpt]

Hi there,

I get error when trying to install the package. I'm on MacOS Big Sur running Python 3.8.9 in a virtualenv.

I cloned your repo, activated my virtualenv and ran pip install ./TVD_Condat2013

Processing /Users/martin/Desktop/TVD_Condat2013
Requirement already satisfied: pybind11>=2.0.1 in /Users/martin/.virtualenvs/myenv/lib/python3.8/site-packages (from TVDCondat2013==0.0.1) (2.9.0)
Requirement already satisfied: numpy in /Users/martin/.virtualenvs/myenv/lib/python3.8/site-packages (from TVDCondat2013==0.0.1) (1.19.5)
Building wheels for collected packages: TVDCondat2013
  Building wheel for TVDCondat2013 (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /Users/martin/.virtualenvs/myenv/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/pip-req-build-65bjutj_/setup.py'"'"'; __file__='"'"'/private/var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/pip-req-build-65bjutj_/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/49/k84c0vjd0394sk846jmjrt9h0000gn/T/pip-wheel-wr43e01q
       cwd: /private/var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/pip-req-build-65bjutj_/
  Complete output (20 lines):
  running bdist_wheel
  running build
  running build_ext
  creating var
  creating var/folders
  creating var/folders/49
  creating var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn
  creating var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T
  clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -iwithsysroot/System/Library/Frameworks/System.framework/PrivateHeaders -iwithsysroot/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/Headers -arch arm64 -arch x86_64 -Werror=implicit-function-declaration -I/Users/martin/.virtualenvs/myenv/include -I/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/include/python3.8 -c /var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/tmpo7e5_93b.cpp -o var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/tmpo7e5_93b.o -std=c++14
  clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -iwithsysroot/System/Library/Frameworks/System.framework/PrivateHeaders -iwithsysroot/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/Headers -arch arm64 -arch x86_64 -Werror=implicit-function-declaration -I/Users/martin/.virtualenvs/myenv/include -I/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/include/python3.8 -c /var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/tmpifqhogfs.cpp -o var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/tmpifqhogfs.o -fvisibility=hidden
  building 'TVDCondat2013' extension
  creating build
  creating build/temp.macosx-10.14-x86_64-3.8
  creating build/temp.macosx-10.14-x86_64-3.8/src
  clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -iwithsysroot/System/Library/Frameworks/System.framework/PrivateHeaders -iwithsysroot/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/Headers -arch arm64 -arch x86_64 -Werror=implicit-function-declaration -I/Users/martin/.virtualenvs/myenv/lib/python3.8/site-packages/pybind11/include -I/Users/martin/.virtualenvs/myenv/lib/python3.8/site-packages/pybind11/include -I/Users/martin/.virtualenvs/myenv/lib/python3.8/site-packages/numpy/core/include -I/Users/martin/.virtualenvs/myenv/include -I/Users/martin/.virtualenvs/myenv/Library/include -I/Users/martin/.virtualenvs/myenv/include -I/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/include/python3.8 -c src/main.cpp -o build/temp.macosx-10.14-x86_64-3.8/src/main.o -stdlib=libc++ -mmacosx-version-min=10.7 -DVERSION_INFO="0.0.1" -std=c++14 -fvisibility=hidden
  src/main.cpp:3:10: fatal error: 'xtensor/xmath.hpp' file not found
  #include "xtensor/xmath.hpp"
           ^~~~~~~~~~~~~~~~~~~
  1 error generated.
  error: command 'clang' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for TVDCondat2013
  Running setup.py clean for TVDCondat2013
Failed to build TVDCondat2013
Installing collected packages: TVDCondat2013
    Running setup.py install for TVDCondat2013 ... error
    ERROR: Command errored out with exit status 1:
     command: /Users/martin/.virtualenvs/myenv/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/pip-req-build-65bjutj_/setup.py'"'"'; __file__='"'"'/private/var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/pip-req-build-65bjutj_/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/49/k84c0vjd0394sk846jmjrt9h0000gn/T/pip-record-4d_79p_e/install-record.txt --single-version-externally-managed --compile --install-headers /Users/martin/.virtualenvs/myenv/include/site/python3.8/TVDCondat2013
         cwd: /private/var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/pip-req-build-65bjutj_/
    Complete output (15 lines):
    running install
    running build
    running build_ext
    clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -iwithsysroot/System/Library/Frameworks/System.framework/PrivateHeaders -iwithsysroot/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/Headers -arch arm64 -arch x86_64 -Werror=implicit-function-declaration -I/Users/martin/.virtualenvs/myenv/include -I/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/include/python3.8 -c /var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/tmp9fwt3sy7.cpp -o var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/tmp9fwt3sy7.o -std=c++14
    clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -iwithsysroot/System/Library/Frameworks/System.framework/PrivateHeaders -iwithsysroot/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/Headers -arch arm64 -arch x86_64 -Werror=implicit-function-declaration -I/Users/martin/.virtualenvs/myenv/include -I/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/include/python3.8 -c /var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/tmpeyanws0z.cpp -o var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/tmpeyanws0z.o -fvisibility=hidden
    building 'TVDCondat2013' extension
    creating build
    creating build/temp.macosx-10.14-x86_64-3.8
    creating build/temp.macosx-10.14-x86_64-3.8/src
    clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -iwithsysroot/System/Library/Frameworks/System.framework/PrivateHeaders -iwithsysroot/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/Headers -arch arm64 -arch x86_64 -Werror=implicit-function-declaration -I/Users/martin/.virtualenvs/myenv/lib/python3.8/site-packages/pybind11/include -I/Users/martin/.virtualenvs/myenv/lib/python3.8/site-packages/pybind11/include -I/Users/martin/.virtualenvs/myenv/lib/python3.8/site-packages/numpy/core/include -I/Users/martin/.virtualenvs/myenv/include -I/Users/martin/.virtualenvs/myenv/Library/include -I/Users/martin/.virtualenvs/myenv/include -I/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/include/python3.8 -c src/main.cpp -o build/temp.macosx-10.14-x86_64-3.8/src/main.o -stdlib=libc++ -mmacosx-version-min=10.7 -DVERSION_INFO="0.0.1" -std=c++14 -fvisibility=hidden
    src/main.cpp:3:10: fatal error: 'xtensor/xmath.hpp' file not found
    #include "xtensor/xmath.hpp"
             ^~~~~~~~~~~~~~~~~~~
    1 error generated.
    error: command 'clang' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /Users/martin/.virtualenvs/myenv/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/pip-req-build-65bjutj_/setup.py'"'"'; __file__='"'"'/private/var/folders/49/k84c0vjd0394sk846jmjrt9h0000gn/T/pip-req-build-65bjutj_/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/49/k84c0vjd0394sk846jmjrt9h0000gn/T/pip-record-4d_79p_e/install-record.txt --single-version-externally-managed --compile --install-headers /Users/martin/.virtualenvs/myenv/include/site/python3.8/TVDCondat2013 Check the logs for full command output.

Any idea how to resolve?

Regards,
Martin

[bgailleton]

Hi Martin,
Apologies for the late reply, I forgot to add notifications for this project.
One of the dependencies is missing: xtensor (and probably xtensor-python), these are the backend I am using to convert results between numpy and c++.

Are you using any sort of anaconda (e.g. miniconda, mambaforge, ...)? if so you can install them with conda install -c conda-forge xtensor-python otherwise you can have a look on their repo.

It's not optimal as I did not carried on working on this small project, but at some points I'll try to upload binaries and a conda-forge package.

Let me know if it solves your issue.
Boris