[Bug]: ModuleNotFoundError: No module named 'encodings'

[Shamsidinkhon]

What happened?

Upgrading rules_py from 1.3.2 to 1.6.6 version breaks Python extension (https://open-vsx.org/extension/ms-python/python) in IDE (Cursor and Vscode) with the following error:

~/shams/.python3-bazel.venv/bin/python -I ~/.cursor-server/extensions/ms-python.python-2025.6.1-linux-x64/python_files/get_output_via_markers.py ~/.cursor-server/extensions/ms-python.python-2025.6.1-linux-x64/python_files/interpreterInfo.py
Could not find platform independent libraries <prefix>
Could not find platform dependent libraries <exec_prefix>
Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
Python path configuration:
  PYTHONHOME = (not set)
  PYTHONPATH = (not set)
  program name = '/home/user/.cache/bazel/_bazel_shams/2d66f777601ac4cdc56880586b3f83ab/execroot/_main/bazel-out/k8-fastbuild/bin/venv.runfiles/_main/.venv/bin/python3'
  isolated = 1
  environment = 0
  user site = 0
  import site = 1
  sys._base_executable = '/home/user/.cache/bazel/_bazel_shams/2d66f777601ac4cdc56880586b3f83ab/execroot/_main/bazel-out/k8-fastbuild/bin/venv.runfiles/_main/.venv/bin/python3'
  sys.base_prefix = '/install'
  sys.base_exec_prefix = '/install'
  sys.platlibdir = 'lib'
  sys.executable = '/home/user/.cache/bazel/_bazel_shams/2d66f777601ac4cdc56880586b3f83ab/execroot/_main/bazel-out/k8-fastbuild/bin/venv.runfiles/_main/.venv/bin/python3'
  sys.prefix = '/install'
  sys.exec_prefix = '/install'
  sys.path = [
    '/install/lib/python39.zip',
    '/install/lib/python3.9',
    '/install/lib/lib-dynload',
  ]
Fatal Python error: init_fs_encoding: failed to get the Python codec of the filesystem encoding
Python runtime state: core initialized
ModuleNotFoundError: No module named 'encodings'

Current thread 0x000078e3c60dd740 (most recent call first):
<no Python frame>

I can see sys.path starts from the root, shouldn't it point to /home/user/.cache/bazel/_bazel_shams/2d66f777601ac4cdc56880586b3f83ab/execroot/_main/bazel-out/k8-fastbuild/bin/venv.runfiles/_main/.venv/lib ?

Version

Development (host) and target OS/architectures: Debian GNU/Linux 12 (bookworm) / x86_64

Output of bazel --version: 8.4.1

Version of the Aspect rules, or other relevant rules from your
WORKSPACE or MODULE.bazel file:

Language(s) and/or frameworks involved:

How to reproduce

Install Python extension https://open-vsx.org/extension/ms-python/python (2025.6.1 version) in Vscode or Cursor. Check "Output" of "Python" for errors.

Any other information?

py_venv(
    name = "venv",
    package_collisions = "ignore",
    venv_name = ".python3-bazel.venv",
    deps = VENV_DEPS_3_9,
)

[arrdem]

Missing encodings indicates that the interpreter did not have $PYTHONHOME set and was not able to auto-discover it. The interpreter ship we ship as .venv/bin/python is supposed to provide that discovery, seems it did not here. Need to dig into why.

[arrdem]

Hey @Shamsidinkhon, looking a bit more carefully at this your editor plugin is explicitly setting the -I flag, which our venv shim is incompatible with.

The Python interpreter shim exists to play a shell game with PYTHONEXECUTABLE and PYTHONHOME, allowing the venv to activate without requiring a constant path from the venv to the interpreter it's aimed at.

When the -I flag is set, the shim does the right thing but then the interpreter it delegates to disregards the key PYTHONHOME parameter which the shim has provided and breaks. Which we can't do anything about besides either 1) remove that flag on the caller side 2) add more machinery in the shim to disregard that flag.

Is there a short path in IDE configuration to not setting that flag?

[Shamsidinkhon]

@arrdem Thanks for checking! I don't see any easy way to fix it on the caller side. Would it be possible to adjust logic in the shim to ignore this flag? I think this would align with python command line and environment flags https://docs.python.org/3/using/cmdline.html?utm_source=chatgpt.com#cmdoption-I and prevents breaking it with other extensions as well.

[arrdem]

Yeah that's a possibility I poked at some last night. We could at least convert -I (which implies -E and -S) to -S. I'd want to build out a real flags parser for doing this for fear of creating other problems with quick work.