fix packages loading

README.md

@@ -143,8 +143,7 @@ the outside, the PDM's installer has already injected the package path to the `s
 
 ### 3. What site-packages will be loaded when using PDM?
 
-Only packages in the local `__pypackages__` directory will be loaded. `site-packages` of Python interpreter isn't loaded.
-It is fully isolated.
+Packages in the local `__pypackages__` directory will be loaded before the system-level `site-packages` for islation.
 
 ### 4. Can I relocate or move the `__pypackages__` folder for deployment?
 

README_zh.md

@@ -131,7 +131,7 @@ PEP 582 尚处于草案阶段，还需要补充很多细节，比如提案中并
 
 ### 3. 使用 PDM 时会载入哪些三方库路径?
 
-只有本项目的 `__pypackages__` 中的包会被载入，也就是说，Python 的 `site-packages` 目录不会被载入，完全项目隔离。
+本项目的 `__pypackages__` 中的包会在系统的`site-packages`之前被载入，这样能更好地隔离包的环境。
 
 ### 4. 我能把 `__pypackages__` 保存下来用来部署到别的机器上吗?
 

docs/docs/project.md

@@ -277,13 +277,6 @@ test_shell  shell echo $FOO        shell command
 
 You can add an `help` option with the description of the script, and it will be displayed in the `Description` column in the above output.
 
-### Include system site-packages in the isolated environment
-
-By default, system-level site-packages will be excluded from the `sys.path` when PEP 582 is enabled, unless:
-
-- Run `pdm run` with `-s/--site-packages` flag.
-- With environment variable `PDM_WITH_SITE_PACKAGES=1`.
-
 ## How we make PEP 582 packages available to the Python interpreter
 
 Thanks to the [site packages loading](https://docs.python.org/3/library/site.html) on Python startup. It is possible to patch the `sys.path`

pdm/cli/commands/run.py

@@ -27,12 +27,6 @@ class Command(BaseCommand):
             action="store_true",
             help="Show all available scripts defined in pyproject.toml",
         )
-        parser.add_argument(
-            "-s",
-            "--site-packages",
-            action="store_true",
-            help="Load site-packages from system interpreter",
-        )
         parser.add_argument("command", nargs="?", help="The command to run")
         parser.add_argument(
             "args",
@@ -163,8 +157,6 @@ class Command(BaseCommand):
         if options.list:
             return self._show_list(project)
         global_env_options = project.scripts.get("_", {}) if project.scripts else {}
-        if options.site_packages:
-            os.environ.update({"PDM_WITH_SITE_PACKAGES": "1"})
         if project.scripts and options.command in project.scripts:
             self._run_script(project, options.command, options.args, global_env_options)
         else:

pdm/pep582/sitecustomize.py

 import os
 import site
 import sys
-import warnings
 
 
 def get_pypackages_path(maxdepth=5):
@@ -37,49 +36,27 @@ def main():
     self_path = os.path.normcase(os.path.dirname(os.path.abspath(__file__)))
     sys.path[:] = [path for path in sys.path if os.path.normcase(path) != self_path]
 
-    with_site_packages = os.getenv("PDM_WITH_SITE_PACKAGES")
-    needs_user_site = False
-    needs_site_packages = False
-    script_path = None
-
-    if getattr(sys, "argv", None) is None:
-        warnings.warn(
-            "PEP 582 can't be loaded based on the script path. "
-            "As Python 2.7 reached the end of life on 2020/01/01, "
-            "please upgrade to Python 3.",
-        )
-    else:
-        script_path = os.path.normcase(os.path.realpath(sys.argv[0]))
-        needs_user_site = script_path.startswith(os.path.normcase(site.USER_BASE))
-        needs_site_packages = any(
-            script_path.startswith(os.path.normcase(p)) for p in site.PREFIXES
-        )
     libpath = get_pypackages_path()
     if not libpath:
         return
-    pypackages = os.path.dirname(os.path.dirname(libpath))
+
     # First, drop site related paths.
     original_sys_path = sys.path[:]
-    paths_to_remove = set()
-    if not (with_site_packages or needs_user_site):
-        site.addusersitepackages(paths_to_remove)
-    if not (
-        with_site_packages
-        or needs_site_packages
-        or script_path
-        and not script_path.startswith(os.path.normcase(os.path.dirname(pypackages)))
-    ):
-        site.addsitepackages(paths_to_remove)
-    paths_to_remove = set(os.path.normcase(path) for path in paths_to_remove)
+    known_paths = set()
+    site.addusersitepackages(known_paths)
+    site.addsitepackages(known_paths)
+    known_paths = set(os.path.normcase(path) for path in known_paths)
     original_sys_path = [
-        path
-        for path in original_sys_path
-        if os.path.normcase(path) not in paths_to_remove
+        path for path in original_sys_path if os.path.normcase(path) not in known_paths
     ]
     sys.path[:] = original_sys_path
 
     # Second, add lib directories, ensuring .pth file are processed.
     site.addsitedir(libpath)
+    # Then add the removed path to the tail of the paths
+    known_paths.clear()
+    site.addusersitepackages(known_paths)
+    site.addsitepackages(known_paths)
 
 
 main()

tests/cli/test_run.py

-import json
 import os
 import subprocess
 import textwrap
@@ -9,18 +8,6 @@ from pdm.cli.actions import PEP582_PATH
 from pdm.utils import cd, temp_environ
 
 
-def test_pep582_not_loading_site_packages(project, invoke, capfd):
-    with cd(project.root):
-        invoke(["install"], obj=project)
-        invoke(
-            ["run", "python", "-c", "import sys,json;print(json.dumps(sys.path))"],
-            obj=project,
-        )
-    sys_path = json.loads(capfd.readouterr()[0])
-    assert not any("site-packages" in p for p in sys_path)
-    assert str(project.environment.packages_path / "lib") in sys_path
-
-
 @pytest.mark.pypi
 def test_pep582_launcher_for_python_interpreter(project, invoke):
     project.meta["requires-python"] = ">=3.6"
@@ -38,16 +25,6 @@ def test_pep582_launcher_for_python_interpreter(project, invoke):
     assert output.decode().strip() == "2.24.0"
 
 
-def test_pep582_launcher_with_system_site_packages(project, invoke):
-    with cd(project.root):
-        invoke(["install"], obj=project)
-        result = invoke(["run", "python", "-c", "import resolvelib"], obj=project)
-        assert result.exit_code != 0
-
-        result = invoke(["run", "-s", "python", "-c", "import resolvelib"], obj=project)
-        assert result.exit_code == 0
-
-
 def test_run_command_not_found(invoke):
     result = invoke(["run", "foobar"])
     assert "Command 'foobar' is not found on your PATH." in result.stderr