Fix installed package discovery

- Exclude python when searching virtualenvs created using nested
  virtualenv interpreters (via `lib-dynload` library directory)

Signed-off-by: Dan Ryan <dan@danryan.co>

pipenv/cli/command.py

@@ -630,7 +630,8 @@ def sync(
 def clean(ctx, state, dry_run=False, bare=False, user=False):
     """Uninstalls all packages not specified in Pipfile.lock."""
     from ..core import do_clean
-    do_clean(ctx=ctx, three=state.three, python=state.python, dry_run=dry_run)
+    do_clean(ctx=ctx, three=state.three, python=state.python, dry_run=dry_run,
+             system=state.system)
 
 
 # Only invoke the "did you mean" when an argument wasn't passed (it breaks those).

pipenv/core.py

@@ -2714,7 +2714,10 @@ def do_sync(
         click.echo(crayons.green("All dependencies are now up-to-date!"))
 
 
-def do_clean(ctx, three=None, python=None, dry_run=False, bare=False, pypi_mirror=None):
+def do_clean(
+    ctx, three=None, python=None, dry_run=False, bare=False, pypi_mirror=None,
+    system=False
+):
     # Ensure that virtualenv is available.
     from packaging.utils import canonicalize_name
     ensure_project(three=three, python=python, validate=False, pypi_mirror=pypi_mirror)
@@ -2736,6 +2739,7 @@ def do_clean(ctx, three=None, python=None, dry_run=False, bare=False, pypi_mirro
         if used_package in installed_package_names:
             installed_package_names.remove(used_package)
     failure = False
+    cmd = [which_pip(allow_global=system), "uninstall", "-y", "-qq"]
     for apparent_bad_package in installed_package_names:
         if dry_run and not bare:
             click.echo(apparent_bad_package)
@@ -2747,12 +2751,8 @@ def do_clean(ctx, three=None, python=None, dry_run=False, bare=False, pypi_mirro
                     )
                 )
             # Uninstall the package.
-            c = delegator.run(
-                "{0} uninstall {1} -y".format(
-                    escape_grouped_arguments(which_pip()),
-                    apparent_bad_package
-                )
-            )
+            cmd_str = Script.parse(cmd + [apparent_bad_package]).cmdify()
+            c = delegator.run(cmd_str, block=True)
             if c.return_code != 0:
                 failure = True
     sys.exit(int(failure))

pipenv/environment.py

@@ -244,7 +244,7 @@ class Environment(object):
         """
 
         pkg_resources = self.safe_import("pkg_resources")
-        return pkg_resources.find_distributions(self.paths["PYTHONPATH"])
+        return pkg_resources.find_distributions(self.paths["libdirs"])
 
     def find_egg(self, egg_dist):
         """Find an egg by name in the given environment"""
@@ -271,16 +271,22 @@ class Environment(object):
     def dist_is_in_project(self, dist):
         """Determine whether the supplied distribution is in the environment."""
         from .project import _normalized
-        prefix = _normalized(self.base_paths["prefix"])
+        prefixes = [
+            _normalized(prefix) for prefix in self.base_paths["libdirs"]
+            if _normalized(self.prefix).startswith(_normalized(prefix))
+        ]
         location = self.locate_dist(dist)
         if not location:
             return False
-        return _normalized(location).startswith(prefix)
+        return any(_normalized(location).startswith(prefix) for prefix in prefixes)
 
     def get_installed_packages(self):
         """Returns all of the installed packages in a given environment"""
         workingset = self.get_working_set()
-        packages = [pkg for pkg in workingset if self.dist_is_in_project(pkg)]
+        packages = [
+            pkg for pkg in workingset
+            if self.dist_is_in_project(pkg) and pkg.key != "python"
+        ]
         return packages
 
     @contextlib.contextmanager

tests/integration/test_pipenv.py

@@ -100,7 +100,6 @@ def test_directory_with_leading_dash(PipenvInstance):
         return mkdtemp(suffix, prefix, dir)
 
     with mock.patch('pipenv.vendor.vistir.compat.mkdtemp', side_effect=mocked_mkdtemp):
-        del os.environ['PIPENV_VENV_IN_PROJECT']
         with temp_environ(), PipenvInstance(chdir=True) as p:
             if "PIPENV_VENV_IN_PROJECT" in os.environ:
                 del os.environ['PIPENV_VENV_IN_PROJECT']