setuptools 3.5 breaks numpy/scipy install with Python 2.7 on Mac OS X

[ghost]

Originally reported by: Anonymous

---

After update to setup tools 3.5 numpy and scipy fail to install on Mac OS X 10.9.2 with system Python 2.7. This is a regression from 3.4.4. (Rolling back to this version successfully installs numpy and scipy).

Here is the output with setuptools 3.5 when installing scipy:

 Running from scipy source directory.
    Splitting linalg.interpolative Fortran source files
    non-existing path in 'scipy/sparse': 'sparsetools/sparsetools_impl.h'
    non-existing path in 'scipy/sparse': 'sparsetools/bsr_impl.h'
    non-existing path in 'scipy/sparse': 'sparsetools/csc_impl.h'
    non-existing path in 'scipy/sparse': 'sparsetools/csr_impl.h'
    non-existing path in 'scipy/sparse': 'sparsetools/other_impl.h'
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/private/tmp/pip_build_root/scipy/setup.py", line 237, in <module>
        setup_package()
      File "/private/tmp/pip_build_root/scipy/setup.py", line 234, in setup_package
        setup(**metadata)
      File "/Library/Python/2.7/site-packages/numpy-1.8.1-py2.7-macosx-10.9-intel.egg/numpy/distutils/core.py", line 135, in setup
        config = configuration()
      File "/private/tmp/pip_build_root/scipy/setup.py", line 173, in configuration
        config.add_subpackage('scipy')
      File "/Library/Python/2.7/site-packages/numpy-1.8.1-py2.7-macosx-10.9-intel.egg/numpy/distutils/misc_util.py", line 966, in add_subpackage
        caller_level = 2)
      File "/Library/Python/2.7/site-packages/numpy-1.8.1-py2.7-macosx-10.9-intel.egg/numpy/distutils/misc_util.py", line 935, in get_subpackage
        caller_level = caller_level + 1)
      File "/Library/Python/2.7/site-packages/numpy-1.8.1-py2.7-macosx-10.9-intel.egg/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py
        config = setup_module.configuration(*args)
      File "scipy/setup.py", line 23, in configuration
        config.add_subpackage('special')
      File "/Library/Python/2.7/site-packages/numpy-1.8.1-py2.7-macosx-10.9-intel.egg/numpy/distutils/misc_util.py", line 966, in add_subpackage
        caller_level = 2)
      File "/Library/Python/2.7/site-packages/numpy-1.8.1-py2.7-macosx-10.9-intel.egg/numpy/distutils/misc_util.py", line 935, in get_subpackage
        caller_level = caller_level + 1)
      File "/Library/Python/2.7/site-packages/numpy-1.8.1-py2.7-macosx-10.9-intel.egg/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py
        config = setup_module.configuration(*args)
      File "scipy/special/setup.py", line 83, in configuration
        extra_info=get_info("npymath"))
      File "/Library/Python/2.7/site-packages/numpy-1.8.1-py2.7-macosx-10.9-intel.egg/numpy/distutils/misc_util.py", line 2138, in get_info
        pkg_info = get_pkg_info(pkgname, dirs)
      File "/Library/Python/2.7/site-packages/numpy-1.8.1-py2.7-macosx-10.9-intel.egg/numpy/distutils/misc_util.py", line 2090, in get_pkg_info
        return read_config(pkgname, dirs)
      File "/Library/Python/2.7/site-packages/numpy-1.8.1-py2.7-macosx-10.9-intel.egg/numpy/distutils/npy_pkg_config.py", line 393, in read_config
        v = _read_config_imp(pkg_to_filename(pkgname), dirs)
      File "/Library/Python/2.7/site-packages/numpy-1.8.1-py2.7-macosx-10.9-intel.egg/numpy/distutils/npy_pkg_config.py", line 329, in _read_config_imp
        meta, vars, sections, reqs = _read_config(filenames)
      File "/Library/Python/2.7/site-packages/numpy-1.8.1-py2.7-macosx-10.9-intel.egg/numpy/distutils/npy_pkg_config.py", line 312, in _read_config
        meta, vars, sections, reqs = parse_config(f, dirs)
      File "/Library/Python/2.7/site-packages/numpy-1.8.1-py2.7-macosx-10.9-intel.egg/numpy/distutils/npy_pkg_config.py", line 284, in parse_config
        raise PkgNotFound("Could not find file(s) %s" % str(filenames))
    numpy.distutils.npy_pkg_config.PkgNotFound: Could not find file(s) ['/Library/Python/2.7/site-packages/numpy-1.8.1-py2.7-macosx-10.9-intel.egg/numpy/core/lib/npy-pkg-config/npymath.ini']
    Complete output from command /usr/bin/python -c "import setuptools, tokenize;__file__='/private/tmp/pip_build_root/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-TyVdHj-record/install-record.txt --single-version-externally-managed --compile:
    blas_opt_info:

---

• Bitbucket: https://bitbucket.org/pypa/setuptools/issue/199

[ghost]

Original comment by jaraco (Bitbucket: jaraco, GitHub: jaraco):

---

Ref scipy/scipy#3608

[ghost]

Original comment by jaraco (Bitbucket: jaraco, GitHub: jaraco):

---

53f0c01ff5cd is almost certainly implicated. I suspect numpy is relying on internal implementation details of setuptools prior to the 3.5 release.

[ghost]

Original comment by jaraco (Bitbucket: jaraco, GitHub: jaraco):

---

Ref numpy/numpy#4664

[ghost]

Original comment by jaraco (Bitbucket: jaraco, GitHub: jaraco):

---

Restore install._install with a comment to capture its requirement on earlier NumPy versions. Fixes #199.

[ghost]

Original comment by jaraco (Bitbucket: jaraco, GitHub: jaraco):

---

Released with 3.5.1