fix(bootstrap): remap stdlib sys.path entries to runfiles during site init

python/private/py_executable.bzl

@@ -594,6 +594,7 @@ def _create_venv(ctx, output_prefix, imports, runtime_details, add_runfiles_root
             "%add_runfiles_root_to_sys_path%": add_runfiles_root_to_sys_path,
             "%coverage_tool%": _get_coverage_tool_runfiles_path(ctx, runtime),
             "%import_all%": "True" if read_possibly_native_flag(ctx, "python_import_all_repositories") else "False",
+            "%interpreter_actual_path%": interpreter_actual_path,
             "%site_init_runfiles_path%": runfiles_root_path(ctx, site_init.short_path),
             "%workspace_name%": ctx.workspace_name,
         },

python/private/site_init_template.py

@@ -29,6 +29,7 @@
 _COVERAGE_TOOL = "%coverage_tool%"
 # True if the runfiles root should be added to sys.path
 _ADD_RUNFILES_ROOT_TO_SYS_PATH = "%add_runfiles_root_to_sys_path%" == "1"
+_INTERPRETER_ACTUAL_PATH = "%interpreter_actual_path%"
 
 
 def _is_verbose():
@@ -52,6 +53,7 @@ def _print_verbose(*args, mapping=None, values=None):
 _print_verbose("workspace_name:", _WORKSPACE_NAME)
 _print_verbose("self_runfiles_path:", _SELF_RUNFILES_RELATIVE_PATH)
 _print_verbose("coverage_tool:", _COVERAGE_TOOL)
+_print_verbose("interpreter_actual_path:", _INTERPRETER_ACTUAL_PATH)
 
 
 def _find_runfiles_root():
@@ -238,7 +240,96 @@ def _fixup_sys_base_executable():
     sys._base_executable = exe
 
 
+def _fixup_stdlib_paths():
+    """Remap non-runfiles runtime paths to their runfiles locations.
+
+    Replaces non-runfiles sys prefix roots (e.g. sys.base_prefix) with the
+    runtime root inside runfiles across sys.path, sys prefixes, and
+    site.PREFIXES.
+    """
+    if not _INTERPRETER_ACTUAL_PATH or os.path.isabs(_INTERPRETER_ACTUAL_PATH):
+        return
+    if not _RUNFILES_ROOT:
+        return
+
+    abs_interpreter = os.path.join(_RUNFILES_ROOT, _INTERPRETER_ACTUAL_PATH)
+    parent = os.path.dirname(abs_interpreter)
+    if os.path.basename(parent).lower() in ("bin", "scripts"):
+        runtime_root = os.path.dirname(parent)
+    else:
+        runtime_root = parent
+
+    def _norm_path(path_str):
+        return os.path.normcase(path_str).replace("\\", "/").rstrip("/")
+
+    runfiles_norm = _norm_path(_RUNFILES_ROOT)
+    runfiles_prefix = runfiles_norm + "/"
+
+    def _in_runfiles(path_str):
+        norm = _norm_path(path_str)
+        return norm == runfiles_norm or norm.startswith(runfiles_prefix)
+
+    # Fast path: only remap if runtime_root in runfiles actually contains a
+    # standard library (avoiding remapping system/platform Python runtimes).
+    has_stdlib = False
+    for entry in ("lib", "lib64", "Lib", "DLLs"):
+        if os.path.exists(os.path.join(runtime_root, entry)):
+            has_stdlib = True
+            break
+    if not has_stdlib:
+        return
+
+    target_root = _get_windows_path_with_unc_prefix(runtime_root)
+    if _is_windows():
+        target_root = target_root.replace("/", os.sep)
+
+    # When running in a virtual environment (sys.prefix != sys.base_prefix),
+    # sys.prefix points to the .venv directory (which on Windows may reside
+    # outside the runfiles tree). Never overwrite sys.prefix / sys.exec_prefix
+    # with the base Python stdlib root in a venv.
+    in_venv = sys.prefix != sys.base_prefix
+    attrs = (
+        ("base_prefix", "base_exec_prefix")
+        if in_venv
+        else ("base_prefix", "base_exec_prefix", "prefix", "exec_prefix")
+    )
+    old_prefixes = set()
+    for attr in attrs:
+        old_prefix = getattr(sys, attr)
+        if _in_runfiles(old_prefix):
+            continue
+
+        old_prefixes.add(old_prefix)
+
+        _print_verbose(f"remap sys.{attr}:", old_prefix, "->", target_root)
+        setattr(sys, attr, target_root)
+
+    # Fast path: if no runtime prefixes were replaced, no paths leaked outside
+    # the tree and no further remapping is needed.
+    if not old_prefixes:
+        return
+
+    for i, p in enumerate(sys.path):
+        norm_p = _norm_path(p)
+        for old_prefix in old_prefixes:
+            norm_old = _norm_path(old_prefix)
+            if norm_p == norm_old or norm_p.startswith(norm_old + "/"):
+                new_path = target_root + p[len(old_prefix) :]
+                _print_verbose("remap stdlib sys.path:", p, "->", new_path)
+                sys.path[i] = new_path
+                break
+
+    import site
+
+    if hasattr(site, "PREFIXES"):
+        for i, prefix in enumerate(site.PREFIXES):
+            if not _in_runfiles(prefix):
+                _print_verbose("remap site.PREFIXES:", prefix, "->", target_root)
+                site.PREFIXES[i] = target_root
+
+
 _fixup_sys_base_executable()
+_fixup_stdlib_paths()
 
 COVERAGE_SETUP = _setup_sys_path()
 _print_verbose("DONE")

tests/bootstrap_impls/BUILD.bazel

@@ -17,6 +17,7 @@ load("//python:py_test.bzl", "py_test")
 load("//tests/support:py_reconfig.bzl", "py_reconfig_binary", "py_reconfig_test")
 load("//tests/support:sh_py_run_test.bzl", "sh_py_run_test")
 load("//tests/support:support.bzl", "SUPPORTS_BOOTSTRAP_SCRIPT")
+load("//tests/support/pytest_test:pytest_test.bzl", "pytest_test")
 load(":venv_relative_path_tests.bzl", "relative_path_test_suite")
 
 py_reconfig_binary(
@@ -127,6 +128,18 @@ py_reconfig_test(
     target_compatible_with = SUPPORTS_BOOTSTRAP_SCRIPT,
 )
 
+pytest_test(
+    name = "stdlib_symlink_syspath_bootstrap_script_test",
+    srcs = ["stdlib_symlink_syspath_test.py"],
+    config_settings = {
+        "//python/config_settings:bootstrap_impl": "script",
+    },
+    target_compatible_with = SUPPORTS_BOOTSTRAP_SCRIPT,
+    deps = [
+        "//python/runfiles",
+    ],
+)
+
 py_reconfig_test(
     name = "sys_path_order_bootstrap_system_python_test",
     srcs = ["sys_path_order_test.py"],

tests/bootstrap_impls/stdlib_symlink_syspath_test.py

@@ -0,0 +1,53 @@
+"""Tests that stdlib entries in sys.path point to runfiles locations.
+
+Verifies stdlib is not added from the underlying repository location.
+"""
+
+from __future__ import annotations
+
+import os
+import pathlib
+import re
+import sys
+
+from python.runfiles import runfiles
+
+
+def _is_stdlib_path(path_str: str) -> bool:
+    norm = path_str.replace("\\", "/").rstrip("/")
+    base = norm.split("/")[-1].lower()
+    if base.endswith("-packages"):
+        return False
+    if re.match(r"^python\d*\.zip$", base):
+        return True
+    if base in ("lib-dynload", "dlls", "lib"):
+        return True
+    if re.match(r"^python3\.\d+$", base):
+        return True
+    return False
+
+
+def test_stdlib_sys_path_in_runfiles() -> None:
+    rf = runfiles.CreateOrRaise()
+    runfiles_root = rf.root()
+
+    stdlib_paths = [p for p in sys.path if _is_stdlib_path(p)]
+    assert stdlib_paths, (
+        "Expected to find at least one stdlib path in sys.path:\n" + "\n".join(sys.path)
+    )
+
+    norm_root = pathlib.Path(os.path.normcase(runfiles_root))
+    violations = []
+    for p in stdlib_paths:
+        norm_p = pathlib.Path(os.path.normcase(p))
+        if not norm_p.is_relative_to(norm_root):
+            violations.append(p)
+
+    assert not violations, (
+        "Expected stdlib sys.path entries to be located within "
+        f"runfiles tree ({runfiles_root}), but got underlying "
+        "repository locations:\n"
+        + "\n".join(f"  {v}" for v in violations)
+        + "\nFull sys.path:\n"
+        + "\n".join(f"  {p}" for p in sys.path)
+    )