[Bug]: interpreted classes cannot inherit from compiled traits

jamesbraza commented 1 year ago

Has your issue already been fixed?

[X] Have you checked to see if your issue still exists on the master branch? See the docs for instructions on how to setup a local build of Refurb.
[X] Have you looked at the open/closed issues to see if anyone has already reported your issue?

The Bug

Running refurb like so emits a strange error:

> mypy dir1 file.py
# nothing
> refurb dir1 file.py
interpreted classes cannot inherit from compiled traits

I tried running refurb --verbose --verbose --verbose dir1 file.py, and it doesn't add anything meaningful to the output. I am at the root causing level of this issue, I am not even sure why this message is being emitted.

My package is internal, so I can't share the source code. Can you help me figure out how to add verbosity to refurb so I can properly root cause this issue?

Version Info

Refurb: v1.22.2
Mypy: v1.7.0

Python Version

Python 3.11.5

Config File

[tool.mypy]
check_untyped_defs = true
error_summary = false
platform = "linux"
pretty = true
show_column_numbers = true
show_error_codes = true
show_error_context = true
warn_redundant_casts = true
warn_unreachable = true
warn_unused_configs = true
warn_unused_ignores = true

[[tool.mypy.overrides]]
ignore_missing_imports = true
module = [
    "fastapi_socketio",  # SEE: https://github.com/pyropy/fastapi-socketio/issues/27
    "fsspec",  # SEE: https://github.com/fsspec/filesystem_spec/issues/625
    "huggingface_hub",  # SEE: https://github.com/huggingface/huggingface_hub/issues/1662
    "rapidjson",  # SEE: https://github.com/python-rapidjson/python-rapidjson/issues/190
    "s3fs",  # SEE: https://github.com/fsspec/s3fs/issues/383
    "setuptools_scm",  # SEE: https://github.com/pypa/setuptools_scm/issues/501
    "socketio.*",  # SEE: https://github.com/miguelgrinberg/python-socketio/issues/1276
    "streamlit_pydantic",
    "transformers",
]

[tool.refurb]
enable_all = true
ignore = [
    "FURB103",
    "FURB141",
    "FURB144",
    "FURB147",
    "FURB150",
    "FURB155",
]

Extra Info

This issue is a continuation of the saga after https://github.com/dosisod/refurb/issues/302

I found https://github.com/python/mypy/issues/6706 with a related message, but it was fixed a long time ago so I am not sure what the issue is here.

anpr commented 1 year ago

We have the same problem. Interestingly, I cannot reproduce it on my local machine, it happens only in the CI. So there must be some environment-specific cause.

jamesbraza commented 1 year ago

@anpr originally that was the case for me (CI is GitHub Action's ubuntu-latest runner) too. However, when I updated to yesterday's refurb release of 1.22.2, the error started showing up on my macOS. Possibly related is, in my mypy config, I also specify platform = "linux".

Yeah the error is interesting, I think it is emitted to stderr by mypy's internals, not by refurb. However, it doesn't show up when invoking mypy directly.

refurb dir1 file.py -- --verbose --verbose >> logs 2>&1

Will output a ton of build logs to a logs file, which ends with:

LOG:  No fresh SCCs left in queue
LOG:  Build finished in 16.285 seconds with 2138 modules, and 0 errors
interpreted classes cannot inherit from compiled traits

So it's some error at runtime after mypy internal's build step

dosisod commented 1 year ago

Thank you for reporting this, this seems to be an issue with the latest 1.7.0 release of Mypy. I'm currently investigating, but downgrading/pinning Mypy to version 1.6.1 should fix it for the time being.

jamesbraza commented 1 year ago

I just confirmed downgrading mypy<1.7 resolves this issue, thanks for sharing that. Also, https://github.com/python/mypy/issues/14736 is possibly related

apoclyps commented 1 year ago

I was able to reproduce the following error: interpreted classes cannot inherit from compiled traits using the example provided within by mypy:

https://github.com/python/mypy/blob/023eb4101347dd151a2ce5bf7baf5a60d2de4145/mypyc/test-data/run-traits.test#L401

from native import Trait, create
from testutil import assertRaises

with assertRaises(TypeError, "traits may not be directly created"):
    Trait()

with assertRaises(TypeError, "traits may not be directly created"):
    create()

class Sub(Trait):
    pass

with assertRaises(TypeError, "interpreted classes cannot inherit from compiled traits"):
    Sub()

similiar to:

https://github.com/python/mypy/issues/6706

francesco086 commented 1 year ago

I am also encountering this problem. But for me it's very weird. On my master the CI pipeline was successful few days ago. Today, without any change, it fails. What is strange, is that I have mypy pinned to 1.6.1.

On my local, where it was also successful, today I got the same error after running

pre-commit run --all-files

Some more details

.pre-commit-config.yaml:

default_language_version:
  python: python3
repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.5.0
    hooks:
      - id: check-added-large-files
      - id: check-ast
      - id: trailing-whitespace
      - id: end-of-file-fixer
      - id: check-json
      - id: check-toml
      - id: check-yaml
  - repo: https://github.com/psf/black
    rev: 23.10.0
    hooks:
      - id: black
  - repo: https://github.com/pre-commit/mirrors-mypy
    rev: v1.6.1
    hooks:
      - id: mypy
        additional_dependencies: [types-requests]
  - repo: https://github.com/dosisod/refurb
    rev: v1.22.1
    hooks:
      - id: refurb
  - repo: https://github.com/charliermarsh/ruff-pre-commit
    rev: "v0.1.0"
    hooks:
      - id: ruff
        args: [--fix, --exit-non-zero-on-fix]

.gitlab-ci.yml

style:
  stage: test
  image: python:3.12
  before_script:
    - pip install -U pip wheel setuptools pre-commit
    - pre-commit install
  script:
    - pre-commit run --all-files

Failing log (today):

$ pip install -U pip wheel setuptools pre-commit
Requirement already satisfied: pip in /usr/local/lib/python3.12/site-packages (23.2.1)
Collecting pip
  Obtaining dependency information for pip from https://files.pythonhosted.org/packages/47/6a/453160888fab7c6a432a6e25f8afe6256d0d9f2cbd25971021da6491d899/pip-23.3.1-py3-none-any.whl.metadata
  Downloading pip-23.3.1-py3-none-any.whl.metadata (3.5 kB)
Requirement already satisfied: wheel in /usr/local/lib/python3.12/site-packages (0.41.3)
Requirement already satisfied: setuptools in /usr/local/lib/python3.12/site-packages (68.2.2)
Collecting pre-commit
  Obtaining dependency information for pre-commit from https://files.pythonhosted.org/packages/6c/75/526915fedf462e05eeb1c75ceaf7e3f9cde7b5ce6f62740fe5f7f19a0050/pre_commit-3.5.0-py2.py3-none-any.whl.metadata
  Downloading pre_commit-3.5.0-py2.py3-none-any.whl.metadata (1.3 kB)
Collecting cfgv>=2.0.0 (from pre-commit)
  Obtaining dependency information for cfgv>=2.0.0 from https://files.pythonhosted.org/packages/c5/55/51844dd50c4fc7a33b653bfaba4c2456f06955289ca770a5dbd5fd267374/cfgv-3.4.0-py2.py3-none-any.whl.metadata
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Collecting identify>=1.0.0 (from pre-commit)
  Obtaining dependency information for identify>=1.0.0 from https://files.pythonhosted.org/packages/46/02/2581c37256119d65e6f1f47b62dd51dd3136d6b[20](https://gitlab.com/the-munchkins/self-paced-course/on-registration-send-invoice/-/jobs/5523912904#L20)7bb49a8885a0d45c41a/identify-2.5.31-py2.py3-none-any.whl.metadata
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Collecting nodeenv>=0.11.1 (from pre-commit)
  Obtaining dependency information for nodeenv>=0.11.1 from https://files.pythonhosted.org/packages/1a/e6/6d2ead760a9ddb35e65740fd5a57e46aadd7b0c49861ab24f94812797a1c/nodeenv-1.8.0-py2.py3-none-any.whl.metadata
  Downloading nodeenv-1.8.0-py2.py3-none-any.whl.metadata ([21](https://gitlab.com/the-munchkins/self-paced-course/on-registration-send-invoice/-/jobs/5523912904#L21) kB)
Collecting pyyaml>=5.1 (from pre-commit)
  Obtaining dependency information for pyyaml>=5.1 from https://files.pythonhosted.org/packages/b4/33/720548182ffa8344418126017aa1d4ab4aeec9a[22](https://gitlab.com/the-munchkins/self-paced-course/on-registration-send-invoice/-/jobs/5523912904#L22)75f04ce3f3573d8ace8/PyYAML-6.0.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
  Downloading PyYAML-6.0.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
Collecting virtualenv>=20.10.0 (from pre-commit)
  Obtaining dependency information for virtualenv>=20.10.0 from https://files.pythonhosted.org/packages/7f/19/1f0eddcb9acf00a95793ce83417f69e0fd106c192121360af499cd6fde39/virtualenv-20.24.6-py3-none-any.whl.metadata
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Collecting distlib<1,>=0.3.7 (from virtualenv>=20.10.0->pre-commit)
  Obtaining dependency information for distlib<1,>=0.3.7 from https://files.pythonhosted.org/packages/43/a0/9ba967fdbd55293bacfc1507f58e316f740a3b[23](https://gitlab.com/the-munchkins/self-paced-course/on-registration-send-invoice/-/jobs/5523912904#L23)1fc00e3d86dc39bc185a/distlib-0.3.7-py2.py3-none-any.whl.metadata
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  Obtaining dependency information for filelock<4,>=3.12.2 from https://files.pythonhosted.org/packages/81/54/84d42a0bee35edba99dee7b59a8d4970eccdd44b99fe728ed912106fc781/filelock-3.13.1-py3-none-any.whl.metadata
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Downloading pre_commit-3.5.0-py2.py3-none-any.whl (203 kB)
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Downloading PyYAML-6.0.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7[24](https://gitlab.com/the-munchkins/self-paced-course/on-registration-send-invoice/-/jobs/5523912904#L24) kB)
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Downloading virtualenv-20.24.6-py3-none-any.whl (3.8 MB)
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Downloading distlib-0.3.7-py2.py3-none-any.whl (468 kB)
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Downloading filelock-3.13.1-py3-none-any.whl (11 kB)
Downloading platformdirs-3.11.0-py3-none-any.whl (17 kB)
Installing collected packages: distlib, pyyaml, platformdirs, pip, nodeenv, identify, filelock, cfgv, virtualenv, pre-commit
  Attempting uninstall: pip
    Found existing installation: pip 23.2.1
    Uninstalling pip-23.2.1:
      Successfully uninstalled pip-23.2.1
Successfully installed cfgv-3.4.0 distlib-0.3.7 filelock-3.13.1 identify-2.5.[31](https://gitlab.com/the-munchkins/self-paced-course/on-registration-send-invoice/-/jobs/5523912904#L31) nodeenv-1.8.0 pip-23.3.1 platformdirs-3.11.0 pre-commit-3.5.0 pyyaml-6.0.1 virtualenv-20.24.6
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
$ pre-commit install
pre-commit installed at .git/hooks/pre-commit
$ pre-commit run --all-files
[INFO] Initializing environment for https://github.com/pre-commit/pre-commit-hooks.
[INFO] Initializing environment for https://github.com/psf/black.
[INFO] Initializing environment for https://github.com/pre-commit/mirrors-mypy.
[INFO] Initializing environment for https://github.com/pre-commit/mirrors-mypy:types-requests.
[INFO] Initializing environment for https://github.com/dosisod/refurb.
[INFO] Initializing environment for https://github.com/charliermarsh/ruff-pre-commit.
[INFO] Installing environment for https://github.com/pre-commit/pre-commit-hooks.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
[INFO] Installing environment for https://github.com/psf/black.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
[INFO] Installing environment for https://github.com/pre-commit/mirrors-mypy.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
[INFO] Installing environment for https://github.com/dosisod/refurb.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
[INFO] Installing environment for https://github.com/charliermarsh/ruff-pre-commit.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
check for added large files..............................................Passed
check python ast.........................................................Passed
trim trailing whitespace.................................................Passed
fix end of files.........................................................Passed
check json...............................................................Passed
check toml...............................................................Passed
check yaml...............................................................Passed
black....................................................................Passed
mypy.....................................................................Passed
refurb...................................................................Failed
- hook id: refurb
- exit code: 1
interpreted classes cannot inherit from compiled traits
ruff.....................................................................Passed
Cleaning up project directory and file based variables
00:00
ERROR: Job failed: exit code 1

Successful log (4 days ago)

$ pip install -U pip wheel setuptools pre-commit
Requirement already satisfied: pip in /usr/local/lib/python3.12/site-packages (23.2.1)
Collecting pip
  Obtaining dependency information for pip from https://files.pythonhosted.org/packages/47/6a/453160888fab7c6a432a6e25f8afe6256d0d9f2cbd25971021da6491d899/pip-23.3.1-py3-none-any.whl.metadata
  Downloading pip-23.3.1-py3-none-any.whl.metadata (3.5 kB)
Requirement already satisfied: wheel in /usr/local/lib/python3.12/site-packages (0.41.3)
Requirement already satisfied: setuptools in /usr/local/lib/python3.12/site-packages (68.2.2)
Collecting pre-commit
  Obtaining dependency information for pre-commit from https://files.pythonhosted.org/packages/6c/75/526915fedf462e05eeb1c75ceaf7e3f9cde7b5ce6f62740fe5f7f19a0050/pre_commit-3.5.0-py2.py3-none-any.whl.metadata
  Downloading pre_commit-3.5.0-py2.py3-none-any.whl.metadata (1.3 kB)
Collecting cfgv>=2.0.0 (from pre-commit)
  Obtaining dependency information for cfgv>=2.0.0 from https://files.pythonhosted.org/packages/c5/55/51844dd50c4fc7a33b653bfaba4c2456f06955289ca770a5dbd5fd267374/cfgv-3.4.0-py2.py3-none-any.whl.metadata
  Downloading cfgv-3.4.0-py2.py3-none-any.whl.metadata (8.5 kB)
Collecting identify>=1.0.0 (from pre-commit)
  Obtaining dependency information for identify>=1.0.0 from https://files.pythonhosted.org/packages/46/02/2581c37256119d65e6f1f47b62dd51dd3136d6b[20](https://gitlab.com/the-munchkins/self-paced-course/on-registration-send-invoice/-/jobs/5495274980#L20)7bb49a8885a0d45c41a/identify-2.5.31-py2.py3-none-any.whl.metadata
  Downloading identify-2.5.31-py2.py3-none-any.whl.metadata (4.4 kB)
Collecting nodeenv>=0.11.1 (from pre-commit)
  Obtaining dependency information for nodeenv>=0.11.1 from https://files.pythonhosted.org/packages/1a/e6/6d2ead760a9ddb35e65740fd5a57e46aadd7b0c49861ab24f94812797a1c/nodeenv-1.8.0-py2.py3-none-any.whl.metadata
  Downloading nodeenv-1.8.0-py2.py3-none-any.whl.metadata ([21](https://gitlab.com/the-munchkins/self-paced-course/on-registration-send-invoice/-/jobs/5495274980#L21) kB)
Collecting pyyaml>=5.1 (from pre-commit)
  Obtaining dependency information for pyyaml>=5.1 from https://files.pythonhosted.org/packages/b4/33/720548182ffa8344418126017aa1d4ab4aeec9a[22](https://gitlab.com/the-munchkins/self-paced-course/on-registration-send-invoice/-/jobs/5495274980#L22)75f04ce3f3573d8ace8/PyYAML-6.0.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
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Collecting virtualenv>=20.10.0 (from pre-commit)
  Obtaining dependency information for virtualenv>=20.10.0 from https://files.pythonhosted.org/packages/7f/19/1f0eddcb9acf00a95793ce83417f69e0fd106c192121360af499cd6fde39/virtualenv-20.24.6-py3-none-any.whl.metadata
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Collecting distlib<1,>=0.3.7 (from virtualenv>=20.10.0->pre-commit)
  Obtaining dependency information for distlib<1,>=0.3.7 from https://files.pythonhosted.org/packages/43/a0/9ba967fdbd55293bacfc1507f58e316f740a3b[23](https://gitlab.com/the-munchkins/self-paced-course/on-registration-send-invoice/-/jobs/5495274980#L23)1fc00e3d86dc39bc185a/distlib-0.3.7-py2.py3-none-any.whl.metadata
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Collecting platformdirs<4,>=3.9.1 (from virtualenv>=20.10.0->pre-commit)
  Obtaining dependency information for platformdirs<4,>=3.9.1 from https://files.pythonhosted.org/packages/56/29/3ec311dc18804409ecf0d2b09caa976f3ae6215559306b5b530004e11156/platformdirs-3.11.0-py3-none-any.whl.metadata
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Downloading distlib-0.3.7-py2.py3-none-any.whl (468 kB)
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Downloading filelock-3.13.1-py3-none-any.whl (11 kB)
Downloading platformdirs-3.11.0-py3-none-any.whl (17 kB)
Installing collected packages: distlib, pyyaml, platformdirs, pip, nodeenv, identify, filelock, cfgv, virtualenv, pre-commit
  Attempting uninstall: pip
    Found existing installation: pip 23.2.1
    Uninstalling pip-23.2.1:
      Successfully uninstalled pip-23.2.1
Successfully installed cfgv-3.4.0 distlib-0.3.7 filelock-3.13.1 identify-2.5.[31](https://gitlab.com/the-munchkins/self-paced-course/on-registration-send-invoice/-/jobs/5495274980#L31) nodeenv-1.8.0 pip-23.3.1 platformdirs-3.11.0 pre-commit-3.5.0 pyyaml-6.0.1 virtualenv-20.24.6
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
$ pre-commit install
pre-commit installed at .git/hooks/pre-commit
$ pre-commit run --all-files
[INFO] Initializing environment for https://github.com/pre-commit/pre-commit-hooks.
[INFO] Initializing environment for https://github.com/psf/black.
[INFO] Initializing environment for https://github.com/pre-commit/mirrors-mypy.
[INFO] Initializing environment for https://github.com/pre-commit/mirrors-mypy:types-requests.
[INFO] Initializing environment for https://github.com/dosisod/refurb.
[INFO] Initializing environment for https://github.com/charliermarsh/ruff-pre-commit.
[INFO] Installing environment for https://github.com/pre-commit/pre-commit-hooks.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
[INFO] Installing environment for https://github.com/psf/black.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
[INFO] Installing environment for https://github.com/pre-commit/mirrors-mypy.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
[INFO] Installing environment for https://github.com/dosisod/refurb.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
[INFO] Installing environment for https://github.com/charliermarsh/ruff-pre-commit.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
check for added large files..............................................Passed
check python ast.........................................................Passed
trim trailing whitespace.................................................Passed
fix end of files.........................................................Passed
check json...............................................................Passed
check toml...............................................................Passed
check yaml...............................................................Passed
black....................................................................Passed
mypy.....................................................................Passed
refurb...................................................................Passed
ruff.....................................................................Passed
Cleaning up project directory and file based variables
00:01
Job succeeded

Hope this can help... I have no clue what it could be.

jamesbraza commented 1 year ago

@francesco086 for now, we need to add an additional_dependencies to pre-commit configs:

    - repo: https://github.com/dosisod/refurb
      rev: v1.22.2
      hooks:
          - id: refurb
            additional_dependencies:
                - mypy<1.7 # SEE: https://github.com/dosisod/refurb/issues/305

Or alternately, the mypy dependency range here could have mypy<1.7 for now: https://github.com/dosisod/refurb/blob/v1.22.2/pyproject.toml#L20

francesco086 commented 1 year ago

@francesco086 you need to add an additional_dependencies for now:

Oh, got it! Many thanks! It works now :)

dosisod commented 1 year ago

@jamesbraza I'm considering capping Mypy to <1.7.0 since I can't seem to find any viable work-arounds. If I can't find a solution in the next few hours I'll cap it until I can find a better solution (or it gets fixed upstream).

jamesbraza commented 1 year ago

Okay sounds good 👍.

In general, I am wondering if mypy minor version bumps have backwards compatible internals. It may make sense for refurb to always pin the minor version, and have some CI automation that, upon new mypy release, bumps the minor version if all tests pass. Tho that sounds like a pain in the butt to implement 😆

dosisod commented 1 year ago

Didn't mean to close this. I still consider this an issue, #306 is a bandaid fix until I find a better workaround.

dosisod commented 1 year ago

Closed by #309

dosisod / refurb