[Python-modules-team] Bug#813431: python-numpy: Debian adds include dir symlinks that break virtualenvs

[Pauli Virtanen]

Package: python-numpy
Version: 1:1.8.2-2
Severity: normal

Dear Maintainer,

Debian python-numpy packaging adds the following symlinks not contained
in upstream:

    /usr/include/numpy
    /usr/include/pythonX.Y/numpy

Their presence causes the following to fail:

$ virtualenv env
$ ./env/bin/pip install numpy==1.7.2
$ ./env/bin/pip install scipy nose
$ ./env/bin/python -c 'import scipy; scipy.test()'

The problem is that some modules are compiled with

-I/usr/include/python2.7
-I$PWD/env/lib/python2.7/site-packages/numpy/core/include

and so apparently end up picking the Numpy headers from the system-wide
python-numpy package, rather than from the older 1.7.2 version in the
virtualenv, resulting to binaries incompatible with the version
installed in the virtualenv.

Typical failure mode is getting "numpy.ufunc has the wrong size, try
recompiling" error message.

One workaround is 'sudo rm /usr/include/numpy
/usr/include/python*/numpy' --- it might be possible to work around this
by changing the package setup.py files, by trying to ensure the correct
order of the include directories. However, this is something that is
needed only on Debian-based systems.

Python packages using Numpy in general get the header locations via
numpy.distutils --- I would expect there are no Python packages that
assume headers are under /usr/include or /usr/include/pythonX.Y/, as
this is a Debian-only feature AFAIK.

Best regards,
Pauli Virtanen

PS. It appears some other python packages in Debian also add such
symlinks. If this is a Debian Python policy, it might be good to
consider the present issue.

-- System Information:
Debian Release: 8.3
  APT prefers stable
  APT policy: (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 3.16.0-4-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/bash
Init: systemd (via /run/systemd/system)

Versions of packages python-numpy depends on:
ii  libblas3 [libblas.so.3]            1.2.20110419-10
ii  libc6                              2.19-18+deb8u2
ii  libgcc1                            1:4.9.2-10
ii  libgfortran3                       4.9.2-10
ii  liblapack3 [liblapack.so.3]        3.5.0-4
ii  libopenblas-base [liblapack.so.3]  0.2.12-1
ii  libquadmath0                       4.9.2-10
ii  python                             2.7.9-1
pn  python2.7:any                      <none>

python-numpy recommends no packages.

Versions of packages python-numpy suggests:
ii  gcc               4:4.9.2-2
ii  gfortran          4:4.9.2-2
ii  python-dev        2.7.9-1
ii  python-nose       1.3.4-1
pn  python-numpy-dbg  <none>
pn  python-numpy-doc  <none>

-- no debconf information