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site.getsitepackages() broken on debian #2105

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freundTech opened this issue May 4, 2021 · 8 comments · Fixed by #2108
Closed

site.getsitepackages() broken on debian #2105

freundTech opened this issue May 4, 2021 · 8 comments · Fixed by #2108
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@freundTech
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freundTech commented May 4, 2021

Issue

Debian and it's derivatives patch site.getsitepackages() to use dist-packages directories instead of site-packages directories. See https://salsa.debian.org/cpython-team/python2/-/blob/master/debian/patches/site-locations.diff

This causes site.getsitepackages() to not point to the correct directory inside virtualenvs.

I discovered this bug while looking into why virtualenv>=20 broke some mypy tests: python/mypy#10407

I'm currently preparing a PR to fix this.

Environment

  • OS: debian derivatives. Tested on Ubuntu 18.04.3 LTS
  • pip list of the host python where virtualenv is installed:
apipkg (1.5)
appdirs (1.4.4)
attrs (20.3.0)
coverage (5.5)
distlib (0.3.1)
execnet (1.8.0)
filelock (3.0.12)
flake8 (3.9.1)
flake8-bugbear (21.4.3)
flake8-pyi (20.10.0)
importlib-metadata (0.20)
importlib-resources (5.1.2)
iniconfig (1.1.1)
lxml (4.6.3)
mccabe (0.6.1)
mypy-extensions (0.4.3)
packaging (20.9)
pip (9.0.1)
pkg-resources (0.0.0)
pluggy (0.13.1)
psutil (5.8.0)
py (1.10.0)
pycodestyle (2.7.0)
pyflakes (2.3.1)
pyparsing (2.4.7)
pytest (6.1.2)
pytest-cov (2.11.1)
pytest-forked (1.3.0)
pytest-xdist (1.34.0)
setuptools (56.0.0)
six (1.15.0)
toml (0.10.2)
typed-ast (1.4.3)
types-mypy-extensions (0.4.3)
types-toml (0.1.1)
types-typed-ast (1.4.1)
typing-extensions (3.10.0.0)
virtualenv (20.4.4)
zipp (3.4.1)

Output of the virtual environment creation

Make sure to run the creation with -vvv --with-traceback:

61 setup logging to NOTSET [DEBUG report:43]
78 find interpreter for spec PythonSpec(implementation=CPython, major=2) [INFO builtin:62]
78 discover exe for PythonInfo(spec=CPython3.6.9.final.0-64, exe=/home/vagrant/mypy/.venv/bin/python, platform=linux, version='3.6.9 (default, Jan 26 2021, 15:33:00) \n[GCC 8.4.0]', encoding_fs_io=utf-8-UTF-8) in /usr [DEBUG py_info:372]
79 filesystem is case-sensitive [DEBUG info:28]
80 Attempting to acquire lock 139857009658960 on /home/vagrant/.local/share/virtualenv/py_info/1/30295c5bec572e859485b1ffa5e89b8b3e2022ef6e3e739c1ac40f143a557caf.lock [DEBUG filelock:270]
80 Lock 139857009658960 acquired on /home/vagrant/.local/share/virtualenv/py_info/1/30295c5bec572e859485b1ffa5e89b8b3e2022ef6e3e739c1ac40f143a557caf.lock [INFO filelock:274]
81 got python info of /usr/bin/python3.6 from /home/vagrant/.local/share/virtualenv/py_info/1/30295c5bec572e859485b1ffa5e89b8b3e2022ef6e3e739c1ac40f143a557caf.json [DEBUG via_disk_folder:135]
81 Attempting to release lock 139857009658960 on /home/vagrant/.local/share/virtualenv/py_info/1/30295c5bec572e859485b1ffa5e89b8b3e2022ef6e3e739c1ac40f143a557caf.lock [DEBUG filelock:315]
82 Lock 139857009658960 released on /home/vagrant/.local/share/virtualenv/py_info/1/30295c5bec572e859485b1ffa5e89b8b3e2022ef6e3e739c1ac40f143a557caf.lock [INFO filelock:318]
82 proposed PythonInfo(spec=CPython3.6.9.final.0-64, system=/usr/bin/python3.6, exe=/home/vagrant/mypy/.venv/bin/python, platform=linux, version='3.6.9 (default, Jan 26 2021, 15:33:00) \n[GCC 8.4.0]', encoding_fs_io=utf-8-UTF-8) [INFO builtin:69]
82 discover PATH[0]=/home/vagrant/mypy/.venv/bin [DEBUG builtin:114]
83 discover exe from cache /usr - exact False: PythonInfo({'architecture': 64, 'base_exec_prefix': '/usr', 'base_prefix': '/usr', 'distutils_install': {'data': '', 'headers': 'include/python3.6m/UNKNOWN', 'platlib': 'lib/python3.6/site-packages', 'purelib': 'lib/python3.6/site-packages', 'scripts': 'bin'}, 'exec_prefix': '/usr', 'executable': '/home/vagrant/mypy/.venv/bin/python', 'file_system_encoding': 'utf-8', 'has_venv': True, 'implementation': 'CPython', 'max_size': 9223372036854775807, 'original_executable': '/usr/bin/python3.6', 'os': 'posix', 'path': ['/home/vagrant/mypy/.venv/lib/python3.6/site-packages/virtualenv/discovery', '/usr/lib/python36.zip', '/usr/lib/python3.6', '/usr/lib/python3.6/lib-dynload', '/usr/local/lib/python3.6/dist-packages', '/usr/lib/python3/dist-packages'], 'platform': 'linux', 'prefix': '/usr', 'real_prefix': None, 'stdout_encoding': 'UTF-8', 'sysconfig': {'makefile_filename': '/usr/lib/python3.6/config-3.6m-x86_64-linux-gnu/Makefile'}, 'sysconfig_paths': {'data': '{base}', 'include': '{installed_base}/include/python{py_version_short}{abiflags}', 'platlib': '{platbase}/lib/python{py_version_short}/site-packages', 'platstdlib': '{platbase}/lib/python{py_version_short}', 'purelib': '{base}/lib/python{py_version_short}/site-packages', 'scripts': '{base}/bin', 'stdlib': '{installed_base}/lib/python{py_version_short}'}, 'sysconfig_vars': {'PYTHONFRAMEWORK': '', 'abiflags': 'm', 'base': '/usr', 'installed_base': '/usr', 'platbase': '/usr', 'py_version_short': '3.6'}, 'system_executable': '/usr/bin/python3.6', 'system_stdlib': '/usr/lib/python3.6', 'system_stdlib_platform': '/usr/lib/python3.6', 'version': '3.6.9 (default, Jan 26 2021, 15:33:00) \n[GCC 8.4.0]', 'version_info': VersionInfo(major=3, minor=6, micro=9, releaselevel='final', serial=0)}) [DEBUG py_info:370]
83 discover PATH[1]=/usr/local/sbin [DEBUG builtin:114]
84 discover PATH[2]=/usr/local/bin [DEBUG builtin:114]
84 discover PATH[3]=/usr/sbin [DEBUG builtin:114]
84 discover PATH[4]=/usr/bin [DEBUG builtin:114]
85 Attempting to acquire lock 139857009612280 on /home/vagrant/.local/share/virtualenv/py_info/1/f92b2924b84ff19c1c3dc485f7644d4486f64738191026bf8e6de303969141b5.lock [DEBUG filelock:270]
85 Lock 139857009612280 acquired on /home/vagrant/.local/share/virtualenv/py_info/1/f92b2924b84ff19c1c3dc485f7644d4486f64738191026bf8e6de303969141b5.lock [INFO filelock:274]
85 got python info of /usr/bin/python2 from /home/vagrant/.local/share/virtualenv/py_info/1/f92b2924b84ff19c1c3dc485f7644d4486f64738191026bf8e6de303969141b5.json [DEBUG via_disk_folder:135]
86 Attempting to release lock 139857009612280 on /home/vagrant/.local/share/virtualenv/py_info/1/f92b2924b84ff19c1c3dc485f7644d4486f64738191026bf8e6de303969141b5.lock [DEBUG filelock:315]
86 Lock 139857009612280 released on /home/vagrant/.local/share/virtualenv/py_info/1/f92b2924b84ff19c1c3dc485f7644d4486f64738191026bf8e6de303969141b5.lock [INFO filelock:318]
86 proposed PathPythonInfo(spec=CPython2.7.15.final.0-64, exe=/usr/bin/python2, platform=linux2, version='2.7.15+ (default, Nov 27 2018, 23:36:35) \n[GCC 7.3.0]', encoding_fs_io=UTF-8-None) [INFO builtin:69]
87 accepted PathPythonInfo(spec=CPython2.7.15.final.0-64, exe=/usr/bin/python2, platform=linux2, version='2.7.15+ (default, Nov 27 2018, 23:36:35) \n[GCC 7.3.0]', encoding_fs_io=UTF-8-None) [DEBUG builtin:71]
123 create virtual environment via CPython2Posix(dest=/home/vagrant/mypy/testenv2, clear=False, no_vcs_ignore=False, global=False) [INFO session:52]
123 no include folders as can't find include marker /usr/local/include/python2.7/Python.h [DEBUG cpython2:53]
124 create folder /home/vagrant/mypy/testenv2/bin [DEBUG _sync:25]
124 create folder /home/vagrant/mypy/testenv2/lib/python2.7/site-packages [DEBUG _sync:25]
125 write /home/vagrant/mypy/testenv2/pyvenv.cfg [DEBUG pyenv_cfg:34]
125     home = /usr [DEBUG pyenv_cfg:38]
125     implementation = CPython [DEBUG pyenv_cfg:38]
126     version_info = 2.7.15.final.0 [DEBUG pyenv_cfg:38]
126     virtualenv = 20.4.4 [DEBUG pyenv_cfg:38]
126     include-system-site-packages = false [DEBUG pyenv_cfg:38]
127     base-prefix = /usr [DEBUG pyenv_cfg:38]
127     base-exec-prefix = /usr [DEBUG pyenv_cfg:38]
127     base-executable = /usr/bin/python2 [DEBUG pyenv_cfg:38]
128 copy /usr/bin/python2 to /home/vagrant/mypy/testenv2/bin/python [DEBUG _sync:52]
131 symlink /usr/lib/python2.7/os.py to /home/vagrant/mypy/testenv2/lib/python2.7/os.py [DEBUG _sync:44]
132 symlink /usr/lib/python2.7/os.pyc to /home/vagrant/mypy/testenv2/lib/python2.7/os.pyc [DEBUG _sync:44]
132 symlink directory /usr/lib/python2.7/lib-dynload to /home/vagrant/mypy/testenv2/lib/python2.7/lib-dynload [DEBUG _sync:44]
132 create virtualenv import hook file /home/vagrant/mypy/testenv2/lib/python2.7/site-packages/_virtualenv.pth [DEBUG api:95]
133 create /home/vagrant/mypy/testenv2/lib/python2.7/site-packages/_virtualenv.py [DEBUG api:98]
134 ============================== target debug ============================== [DEBUG session:54]
134 debug via /home/vagrant/mypy/testenv2/bin/python /home/vagrant/mypy/.venv/lib/python3.6/site-packages/virtualenv/create/debug.py [DEBUG creator:224]
134 {
  "sys": {
    "executable": "/home/vagrant/mypy/testenv2/bin/python",
    "_base_executable": null,
    "prefix": "/home/vagrant/mypy/testenv2",
    "base_prefix": "/usr",
    "real_prefix": "/usr",
    "exec_prefix": "/home/vagrant/mypy/testenv2",
    "base_exec_prefix": "/usr",
    "path": [
      "/usr/lib/python2.7",
      "/usr/lib/python2.7/plat-x86_64-linux-gnu",
      "/usr/lib/python2.7/lib-tk",
      "/usr/lib/python2.7/lib-old",
      "/usr/lib/python2.7/lib-dynload",
      "/home/vagrant/mypy/testenv2/lib/python2.7/site-packages"
    ],
    "meta_path": [
      "<class '_virtualenv._VirtualenvImporter'>"
    ],
    "fs_encoding": "UTF-8",
    "io_encoding": null
  },
  "version": "2.7.15+ (default, Nov 27 2018, 23:36:35) \n[GCC 7.3.0]",
  "makefile_filename": "/usr/lib/python2.7/config-x86_64-linux-gnu/Makefile",
  "os": "<module 'os' from '/usr/lib/python2.7/os.pyc'>",
  "site": "<module 'site' from '/usr/lib/python2.7/site.pyc'>",
  "datetime": "<module 'datetime' (built-in)>",
  "math": "<module 'math' (built-in)>",
  "json": "<module 'json' from '/usr/lib/python2.7/json/__init__.pyc'>"
} [DEBUG session:55]
150 add seed packages via FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/vagrant/.local/share/virtualenv) [INFO session:59]
152 got embed update of distribution pip from /home/vagrant/.local/share/virtualenv/wheel/2.7/embed/1/pip.json [DEBUG via_disk_folder:135]
154 got embed update of distribution pip from /home/vagrant/.local/share/virtualenv/wheel/2.7/embed/1/pip.json [DEBUG via_disk_folder:135]
155 got embed update of distribution setuptools from /home/vagrant/.local/share/virtualenv/wheel/2.7/embed/1/setuptools.json [DEBUG via_disk_folder:135]
156 got embed update of distribution setuptools from /home/vagrant/.local/share/virtualenv/wheel/2.7/embed/1/setuptools.json [DEBUG via_disk_folder:135]
157 got embed update of distribution wheel from /home/vagrant/.local/share/virtualenv/wheel/2.7/embed/1/wheel.json [DEBUG via_disk_folder:135]
158 got embed update of distribution wheel from /home/vagrant/.local/share/virtualenv/wheel/2.7/embed/1/wheel.json [DEBUG via_disk_folder:135]
158 install pip from wheel /home/vagrant/mypy/.venv/lib/python3.6/site-packages/virtualenv/seed/wheels/embed/pip-20.3.4-py2.py3-none-any.whl via CopyPipInstall [DEBUG via_app_data:49]
159 Attempting to acquire lock 139857002467224 on /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/pip-20.3.4-py2.py3-none-any.lock [DEBUG filelock:270]
159 Lock 139857002467224 acquired on /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/pip-20.3.4-py2.py3-none-any.lock [INFO filelock:274]
159 Attempting to release lock 139857002467224 on /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/pip-20.3.4-py2.py3-none-any.lock [DEBUG filelock:315]
160 Lock 139857002467224 released on /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/pip-20.3.4-py2.py3-none-any.lock [INFO filelock:318]
160 copy directory /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/pip-20.3.4-py2.py3-none-any/pip to /home/vagrant/mypy/testenv2/lib/python2.7/site-packages/pip [DEBUG _sync:52]
172 install setuptools from wheel /home/vagrant/mypy/.venv/lib/python3.6/site-packages/virtualenv/seed/wheels/embed/setuptools-44.1.1-py2.py3-none-any.whl via CopyPipInstall [DEBUG via_app_data:49]
173 Attempting to acquire lock 139857002509032 on /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/setuptools-44.1.1-py2.py3-none-any.lock [DEBUG filelock:270]
173 Lock 139857002509032 acquired on /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/setuptools-44.1.1-py2.py3-none-any.lock [INFO filelock:274]
173 Attempting to release lock 139857002509032 on /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/setuptools-44.1.1-py2.py3-none-any.lock [DEBUG filelock:315]
174 Lock 139857002509032 released on /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/setuptools-44.1.1-py2.py3-none-any.lock [INFO filelock:318]
174 copy /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/setuptools-44.1.1-py2.py3-none-any/easy_install.py to /home/vagrant/mypy/testenv2/lib/python2.7/site-packages/easy_install.py [DEBUG _sync:52]
174 copy directory /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/setuptools-44.1.1-py2.py3-none-any/setuptools-44.1.1.dist-info to /home/vagrant/mypy/testenv2/lib/python2.7/site-packages/setuptools-44.1.1.dist-info [DEBUG _sync:52]
176 copy directory /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/setuptools-44.1.1-py2.py3-none-any/setuptools to /home/vagrant/mypy/testenv2/lib/python2.7/site-packages/setuptools [DEBUG _sync:52]
183 copy directory /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/setuptools-44.1.1-py2.py3-none-any/pkg_resources to /home/vagrant/mypy/testenv2/lib/python2.7/site-packages/pkg_resources [DEBUG _sync:52]
176 install wheel from wheel /home/vagrant/mypy/.venv/lib/python3.6/site-packages/virtualenv/seed/wheels/embed/wheel-0.36.2-py2.py3-none-any.whl via CopyPipInstall [DEBUG via_app_data:49]
184 Attempting to acquire lock 139857002509312 on /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/wheel-0.36.2-py2.py3-none-any.lock [DEBUG filelock:270]
184 Lock 139857002509312 acquired on /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/wheel-0.36.2-py2.py3-none-any.lock [INFO filelock:274]
184 Attempting to release lock 139857002509312 on /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/wheel-0.36.2-py2.py3-none-any.lock [DEBUG filelock:315]
185 Lock 139857002509312 released on /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/wheel-0.36.2-py2.py3-none-any.lock [INFO filelock:318]
185 copy /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/wheel-0.36.2-py2.py3-none-any/wheel-0.36.2.virtualenv to /home/vagrant/mypy/testenv2/lib/python2.7/site-packages/wheel-0.36.2.virtualenv [DEBUG _sync:52]
185 copy directory /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/wheel-0.36.2-py2.py3-none-any/wheel-0.36.2.dist-info to /home/vagrant/mypy/testenv2/lib/python2.7/site-packages/wheel-0.36.2.dist-info [DEBUG _sync:52]
186 copy directory /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/wheel-0.36.2-py2.py3-none-any/wheel to /home/vagrant/mypy/testenv2/lib/python2.7/site-packages/wheel [DEBUG _sync:52]
189 generated console scripts wheel2 wheel wheel-2.7 wheel2.7 [DEBUG base:48]
192 copy /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/setuptools-44.1.1-py2.py3-none-any/setuptools-44.1.1.virtualenv to /home/vagrant/mypy/testenv2/lib/python2.7/site-packages/setuptools-44.1.1.virtualenv [DEBUG _sync:52]
207 generated console scripts easy_install-2.7 easy_install2.7 easy_install easy_install2 [DEBUG base:48]
216 copy /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/pip-20.3.4-py2.py3-none-any/pip-20.3.4.virtualenv to /home/vagrant/mypy/testenv2/lib/python2.7/site-packages/pip-20.3.4.virtualenv [DEBUG _sync:52]
217 copy directory /home/vagrant/.local/share/virtualenv/wheel/2.7/image/1/CopyPipInstall/pip-20.3.4-py2.py3-none-any/pip-20.3.4.dist-info to /home/vagrant/mypy/testenv2/lib/python2.7/site-packages/pip-20.3.4.dist-info [DEBUG _sync:52]
218 generated console scripts pip pip2 pip-2.7 pip2.7 [DEBUG base:48]
219 add activators for Bash, CShell, Fish, PowerShell, Python [INFO session:66]
220 write /home/vagrant/mypy/testenv2/pyvenv.cfg [DEBUG pyenv_cfg:34]
220     home = /usr [DEBUG pyenv_cfg:38]
221     implementation = CPython [DEBUG pyenv_cfg:38]
221     version_info = 2.7.15.final.0 [DEBUG pyenv_cfg:38]
221     virtualenv = 20.4.4 [DEBUG pyenv_cfg:38]
222     include-system-site-packages = false [DEBUG pyenv_cfg:38]
222     base-prefix = /usr [DEBUG pyenv_cfg:38]
223     base-exec-prefix = /usr [DEBUG pyenv_cfg:38]
223     base-executable = /usr/bin/python2 [DEBUG pyenv_cfg:38]
223 created virtual environment CPython2.7.15.final.0-64 in 164ms
  creator CPython2Posix(dest=/home/vagrant/mypy/testenv2, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/vagrant/.local/share/virtualenv)
    added seed packages: pip==20.3.4, setuptools==44.1.1, wheel==0.36.2
  activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator [WARNING __main__:19]
@freundTech freundTech added the bug label May 4, 2021
@gaborbernat
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The patch only applies to the system python, not the created virtual environments.

@freundTech
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freundTech commented May 4, 2021

The patch applies to virtual environments. Virtualenv>=20 on python2 has it's own site.py, which loads the system site.py and fixes up sys.path. It does however not fix site.getsitepackages().

python -m virtualenv -ppython2 testenv2
. testenv2/bin/activate
python -c "import site; print(site.getsitepackages())"
['/home/vagrant/mypy/testenv2/local/lib/python2.7/dist-packages', '/home/vagrant/mypy/testenv2/lib/python2.7/dist-packages']

virtualenv 20.4.4 on Ubuntu 18.04.3 LTS

I already wrote a patch to fix this and am currently preparing a PR.

@gaborbernat
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What does happen in venv?

@gaborbernat gaborbernat reopened this May 4, 2021
@freundTech
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This issue only affects python2.
On python3 both venv and virtualenv output ['/home/vagrant/mypy/testenv3/lib/python3.6/site-packages', '/home/vagrant/mypy/testenv3/local/lib/python3.6/dist-packages', '/home/vagrant/mypy/testenv3/lib/python3/dist-packages', '/home/vagrant/mypy/testenv3/lib/python3.6/dist-packages'], which also contain a few dist-packages paths, but also contain the correct site-packages path.

@gaborbernat
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Ah, python 2 my old friend.

not miss you

@freundTech
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freundTech commented May 4, 2021

I just checked the debian patches for python3 and there they work around virtual environments by checking for the VIRTUAL_ENV environment variable: https://salsa.debian.org/cpython-team/python3/-/blob/master/debian/patches/distutils-install-layout.diff#L197

Debian doesn't do that for python2

@freundTech
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The fix I came up with just replaces occurences of 'dist-packages' with 'site-packages' in getsitepackages. It's probably not the cleanest fix, but it works.
freundTech@0044510

A cleaner fix could be reimplementing getsitepackages in virtualenv and patching it into site.

@gaborbernat
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Ugh, seems an ugly hack for Debian lacking proper patching, but can't come up with better.

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