commit b6d5da6796801862eb751a93d507c343af0604d6

Author: Victor Stinner <vstinner@redhat.com>

Date:   Tue Sep 18 17:13:51 2018 +0200

    Subject: Prevent removing of the system packages installed under /usr/lib

    when pip install -U is executed.

    Resolves: rhbz#1550368

    Co-Authored-By: Michal Cyprian <m.cyprian@gmail.com>

diff --git a/src/pip/_internal/legacy_resolve.py b/src/pip/_internal/legacy_resolve.py

index 1d9229cb..3088d22d 100644

--- a/src/pip/_internal/legacy_resolve.py

+++ b/src/pip/_internal/legacy_resolve.py

@@ -24,7 +24,7 @@ from pip._internal.exceptions import (

 from pip._internal.req.constructors import install_req_from_req_string

 from pip._internal.utils.logging import indent_log

 from pip._internal.utils.misc import (

-    dist_in_usersite, ensure_dir, normalize_version_info,

+    dist_in_install_path, dist_in_usersite, ensure_dir, normalize_version_info,

 )

 from pip._internal.utils.packaging import (

     check_requires_python, get_requires_python,

@@ -219,7 +219,9 @@ class Resolver(object):

         """

         # Don't uninstall the conflict if doing a user install and the

         # conflict is not a user install.

-        if not self.use_user_site or dist_in_usersite(req.satisfied_by):

+        if ((not self.use_user_site

+                or dist_in_usersite(req.satisfied_by))

+                and dist_in_install_path(req.satisfied_by)):

             req.conflicts_with = req.satisfied_by

         req.satisfied_by = None

diff --git a/src/pip/_internal/req/req_install.py b/src/pip/_internal/req/req_install.py

index f5c93504..1096c397 100644

--- a/src/pip/_internal/req/req_install.py

+++ b/src/pip/_internal/req/req_install.py

@@ -27,7 +27,7 @@ from pip._internal.utils.logging import indent_log

 from pip._internal.utils.marker_files import PIP_DELETE_MARKER_FILENAME

 from pip._internal.utils.misc import (

     _make_build_dir, ask_path_exists, backup_dir, call_subprocess,

-    display_path, dist_in_site_packages, dist_in_usersite, ensure_dir,

+    display_path, dist_in_install_path, dist_in_site_packages, dist_in_usersite, ensure_dir,

     get_installed_version, redact_password_from_url, rmtree,

 )

 from pip._internal.utils.packaging import get_metadata

@@ -427,7 +427,7 @@ class InstallRequirement(object):

                         "lack sys.path precedence to %s in %s" %

                         (existing_dist.project_name, existing_dist.location)

                     )

-            else:

+            elif dist_in_install_path(existing_dist):

                 self.conflicts_with = existing_dist

         return True

diff --git a/src/pip/_internal/utils/misc.py b/src/pip/_internal/utils/misc.py

index 61f74dc8..ffa8042c 100644

--- a/src/pip/_internal/utils/misc.py

+++ b/src/pip/_internal/utils/misc.py

@@ -30,7 +30,7 @@ from pip._vendor.six.moves.urllib.parse import unquote as urllib_unquote

 from pip import __version__

 from pip._internal.exceptions import CommandError, InstallationError

-from pip._internal.locations import site_packages, user_site

+from pip._internal.locations import distutils_scheme, site_packages, user_site

 from pip._internal.utils.compat import (

     WINDOWS, console_to_str, expanduser, stdlib_pkgs, str_to_display,

 )

@@ -454,6 +454,16 @@ def dist_in_site_packages(dist):

     ).startswith(normalize_path(site_packages))

+def dist_in_install_path(dist):

+    """

+    Return True if given Distribution is installed in

+    path matching distutils_scheme layout.

+    """

+    norm_path = normalize_path(dist_location(dist))

+    return norm_path.startswith(normalize_path(

+        distutils_scheme("")['purelib'].split('python')[0]))

+

+

 def dist_is_editable(dist):

     # type: (Distribution) -> bool

     """