Problem with compiling pymatgen on macOS due to C++ extensions

[mkhorton]

User report:

  Running setup.py develop for pymatgen
    ERROR: Command errored out with exit status 1:
     command: /Users/.../miniconda3/envs/pmg/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/Users/.../uw/pymatgen/setup.py'"'"'; __file__='"'"'/Users/.../uw/pymatgen/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps
         cwd: /Users/.../uw/pymatgen/
    Complete output (18 lines):
    running develop
    running egg_info
    writing pymatgen.egg-info/PKG-INFO
    writing dependency_links to pymatgen.egg-info/dependency_links.txt
    writing entry points to pymatgen.egg-info/entry_points.txt
    writing requirements to pymatgen.egg-info/requires.txt
    writing top-level names to pymatgen.egg-info/top_level.txt
    reading manifest file 'pymatgen.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    writing manifest file 'pymatgen.egg-info/SOURCES.txt'
    running build_ext
    building 'pymatgen.optimization.neighbors' extension
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/.../miniconda3/envs/pmg/include -arch x86_64 -I/Users/.../miniconda3/envs/pmg/include -arch x86_64 -I/Users/.../miniconda3/envs/pmg/include/python3.6m -I/Users/.../miniconda3/envs/pmg/lib/python3.6/site-packages/numpy/core/include -c pymatgen/optimization/neighbors.cpp -o build/temp.macosx-10.7-x86_64-3.6/pymatgen/optimization/neighbors.o -Wno-cpp -Wno-unused-function -O2 -march=native -std=c++11 -stdlib=libc++
    g++ -bundle -undefined dynamic_lookup -L/Users/.../miniconda3/envs/pmg/lib -arch x86_64 -L/Users/.../miniconda3/envs/pmg/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/pymatgen/optimization/neighbors.o -o build/lib.macosx-10.7-x86_64-3.6/pymatgen/optimization/neighbors.cpython-36m-darwin.so
    clang: warning: libstdc++ is deprecated; move to libc++ with a minimum deployment target of OS X 10.9 [-Wdeprecated]
    ld: library not found for -lstdc++
    clang: error: linker command failed with exit code 1 (use -v to see invocation)
    error: command 'g++' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /Users/.../miniconda3/envs/pmg/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/Users/.../uw/pymatgen/setup.py'"'"'; __file__='"'"'/Users/.../uw/pymatgen/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps Check the logs for full command output.

@chc273 This shouldn't be too hard to fix, you have to link to libc++ on macOS instead since libstdc++ is not supported anymore. There are a few other Python codes that have had similar issues (including BoltzTraP I think?)

[shyuep]

Just tell user to use conda install -c conda-forge pymatgen.

[shyuep]

Also, the current dev version of pymatgen actually does link libc++. It seems this user's Xcode is out of date.

[mkhorton]

To clarify, python setup.py develop is broken on macOS for development purposes. This is not just an end user issue.

[shyuep]

@chc273 Just pushed a fix.

[mkhorton]

Thanks ! I'll let them know to update their Xcode also