Pyrefly Cannot Correctly Figure Out Dependencies in Non-VSCode Editors

[Notenlish]

Describe the Bug

(.venv) noten@noten:~/Documents/GitHub/hukuksuzlugun-bedeli$ ls
backend.sh  frontend.sh  pyproject.toml      README.md
backend   frontend    LICENSE      pyrightconfig.json

In my project, the backend module contains python code. Pyrefly cannot detect that I am using a virtualenv and therefore gives an error when I run pyrefly check, as it thinks I haven't installed those modules. My venv directory is .venv/.

I already have a pyproject.toml setup:

[tool.pyrefly]
search_path = ["backend/"]  # analyze these directories
#python_executable = ".venv/bin/python3"
# site_package_path=[".venv/lib/python3.12/site-packages"]
# python_interpreter=".venv/bin/python3"

I tried commenting and uncommenting the site_package_path and python_interpreter, it still doesn't work.
I am guessing I am missing something, what am I doing wrong?

(.venv) noten@noten:~/Documents/GitHub/hukuksuzlugun-bedeli$ pyrefly check
 INFO Checking project configured at `/home/noten/Documents/GitHub/hukuksuzlugun-bedeli/pyproject.toml`
ERROR /home/noten/Documents/GitHub/hukuksuzlugun-bedeli/backend/actions.py:2:21-27: Could not import `bcrypt` from `passlib` [missing-module-attribute]
ERROR /home/noten/Documents/GitHub/hukuksuzlugun-bedeli/backend/evdsclient.py:10:25-42: No attribute `adapters` in module `requests` [missing-attribute]
ERROR /home/noten/Documents/GitHub/hukuksuzlugun-bedeli/backend/evdsclient.py:17:14-25: Attribute `poolmanager` is implicitly defined by assignment in method `init_poolmanager`, which is not a constructor [implicitly-defined-attribute]
ERROR /home/noten/Documents/GitHub/hukuksuzlugun-bedeli/backend/evdsclient.py:55:14-21: Attribute `session` is implicitly defined by assignment in method `__create_session`, which is not a constructor [implicitly-defined-attribute]
ERROR /home/noten/Documents/GitHub/hukuksuzlugun-bedeli/backend/evdsclient.py:78:13-46: Item assignment is not supported on `DataFrame | Series | Unknown`
  Expected `__setitem__` to be a callable, got BoundMethod[DataFrame, (self: Self@DataFrame, key: Unknown, value: Unknown) -> None] | BoundMethod[Series, (self: Self@Series, key: Unknown, value: Unknown) -> None] | Unknown [not-callable]
ERROR /home/noten/Documents/GitHub/hukuksuzlugun-bedeli/backend/evdsclient.py:103:33-76: Object of class `ndarray` has no attribute `to_list` [missing-attribute]
ERROR /home/noten/Documents/GitHub/hukuksuzlugun-bedeli/backend/fetcher.py:208:27-58: Expected 0 type arguments for `FrequencyEVDS`, got 1 [bad-specialization]
ERROR /home/noten/Documents/GitHub/hukuksuzlugun-bedeli/backend/fetcher.py:208:41-57: Expected a type form, got instance of `FrequencyEnum` [not-a-type]
ERROR /home/noten/Documents/GitHub/hukuksuzlugun-bedeli/backend/main.py:53:5-23: Missing argument `self` in function `functools._Wrapped.__call__` [missing-argument]
ERROR /home/noten/Documents/GitHub/hukuksuzlugun-bedeli/backend/main.py:60:1-19: Expected `Ellipsis` to be a ParamSpec value in function `starlette.applications.Starlette.add_middleware` [bad-argument-type]
ERROR /home/noten/Documents/GitHub/hukuksuzlugun-bedeli/backend/main.py:61:5-19: Argument `type[CORSMiddleware]` is not assignable to parameter with type `_MiddlewareFactory[@_]` in function `starlette.applications.Starlette.add_middleware` [bad-argument-type]
ERROR /home/noten/Documents/GitHub/hukuksuzlugun-bedeli/backend/main.py:227:33-56: Item assignment is not supported on `dict[str, str]`
  Argument `list[@_]` is not assignable to parameter with type `str` in function `dict.__setitem__` [bad-argument-type]
ERROR /home/noten/Documents/GitHub/hukuksuzlugun-bedeli/backend/main.py:240:21-48: Item assignment is not supported on `dict[str, dict[str, list[Unknown]]]`
  Argument `dict[str, str]` is not assignable to parameter with type `dict[str, list[Unknown]]` in function `dict.__setitem__` [bad-argument-type]
ERROR /home/noten/Documents/GitHub/hukuksuzlugun-bedeli/backend/models.py:89:11-15: Class member `MetricDataPoint.Meta` overrides parent class `Model` in an inconsistent manner [bad-override]
 INFO 14 errors shown, 1 errors ignored, 15 modules, 1,610 transitive dependencies, 753,673 lines, took 1.76s (checking 1.06s; listing 0.69s), peak memory physical 494.4 MiB

If it helps, I am on Linux Mint 22.1 with Zed editor, however I don't think it's something related to Zed.

Sandbox Link

No response

(Only applicable for extension issues) IDE Information

No response

[anzhi0708]

Same issue here when tesing on Windows 11 with a uv created project

[connernilsen]

Hey @Notenlish and @anzhi0708, sorry, but I was out for part of last week, and I'm still catching up with stuff from this week. I'll get around to looking at this tomorrow or early next week. Just wanted to let you know that it's still in my queue!

[connernilsen]

@Notenlish and @anzhi0708, sorry you're experiencing this issue. I'll try to help you get this working, and see if there are any bugs we need to fix in the process.

Can you both answer these questions for me?

1. Just to double check, your venv is located at /home/noten/Documents/GitHub/hukuksuzlugun-bedeli/.venv, right?
2. What do you see when you ls .venv/lib/python3.12/site-packages?
3. Do you have the virtual environment activated when you're running Pyrefly?
4. Which version of Pyrefly are you running (pyrefly --version)?

Also @anzhi0708, are you running Pyrefly on cmd, powershell, linux subsystem, or something else?

[Notenlish]

1. yes
2. output:

noten@noten:~/Documents/GitHub/hukuksuzlugun-bedeli$ ls .venv/lib/python3.12/site-packages
aerich                              colorama-0.4.6.dist-info         MarkupSafe-3.0.2.dist-info             rich_toolkit
aerich-0.9.0.dist-info              cv2                              mdurl                                  rich_toolkit-0.14.6.dist-info
aiofiles                            dateutil                         mdurl-0.1.2.dist-info                  ruff
aiofiles-24.1.0.dist-info           dictdiffer                       multidict                              ruff-0.11.9.dist-info
aiohappyeyeballs                    dictdiffer-0.9.0.dist-info       multidict-6.4.4.dist-info              shellingham
aiohappyeyeballs-2.6.1.dist-info    dns                              multipart                              shellingham-1.5.4.dist-info
aiohttp                             dnspython-2.7.0.dist-info        numpy                                  six-1.17.0.dist-info
aiohttp-3.11.18.dist-info           dotenv                           numpy-2.2.5.dist-info                  six.py
aioredis                            dotenv-0.9.9.dist-info           numpy.libs                             sniffio
aioredis-2.0.1.dist-info            email_validator                  opencv_python-4.11.0.86.dist-info      sniffio-1.3.1.dist-info
aiosignal                           email_validator-2.2.0.dist-info  opencv_python.libs                     soupsieve
aiosignal-1.3.2.dist-info           evds                             pandas                                 soupsieve-2.7.dist-info
aiosqlite                           evds-0.3.2.dist-info             pandas-2.2.3.dist-info                 sqlalchemy
aiosqlite-0.21.0.dist-info          fastapi                          passlib                                sqlalchemy-2.0.40.dist-info
alembic                             fastapi-0.115.12.dist-info       passlib-1.7.4.dist-info                starlette
alembic-1.15.2.dist-info            fastapi_admin                    pendulum                               starlette-0.46.2.dist-info
annotated_types                     fastapi_admin-1.0.4.dist-info    pendulum-3.1.0.dist-info               tomlkit
annotated_types-0.7.0.dist-info     fastapi_cli                      pip                                    tomlkit-0.13.2.dist-info
anyio                               fastapi_cli-0.0.7.dist-info      pip-24.0.dist-info                     tortoise
anyio-4.9.0.dist-info               frozenlist                       propcache                              tortoise_orm-0.25.0.dist-info
apscheduler                         frozenlist-1.6.0.dist-info       propcache-0.3.1.dist-info              typer
APScheduler-3.11.0.dist-info        greenlet                         psycopg2                               typer-0.15.4.dist-info
asyncclick                          greenlet-3.2.1.dist-info         psycopg2_binary-2.9.10.dist-info       typing_extensions-4.13.2.dist-info
asyncclick-8.1.8.0.dist-info        h11                              psycopg2_binary.libs                   typing_extensions.py
asyncpg                             h11-0.16.0.dist-info             __pycache__                            typing_inspection
asyncpg-0.30.0.dist-info            httpcore                         pydantic                               typing_inspection-0.4.0.dist-info
async_timeout                       httpcore-1.0.9.dist-info         pydantic-2.11.4.dist-info              tzdata
async_timeout-5.0.1.dist-info       httptools                        pydantic_core                          tzdata-2025.2.dist-info
attr                                httptools-0.6.4.dist-info        pydantic_core-2.33.2.dist-info         tzlocal
attrs                               httpx                            pygments                               tzlocal-5.3.1.dist-info
attrs-25.3.0.dist-info              httpx-0.28.1.dist-info           pygments-2.19.1.dist-info              urllib3
babel                               idna                             pypika_tortoise                        urllib3-2.4.0.dist-info
babel-2.17.0.dist-info              idna-3.10.dist-info              pypika_tortoise-0.5.0.dist-info        uvicorn
bcrypt                              imutils                          python_dateutil-2.9.0.post0.dist-info  uvicorn-0.34.2.dist-info
bcrypt-4.3.0.dist-info              imutils-0.5.4.dist-info          python_dotenv-1.1.0.dist-info          uvloop
beautifulsoup4-4.13.4.dist-info     iso8601                          python_multipart                       uvloop-0.21.0.dist-info
bs4                                 iso8601-2.1.0.dist-info          python_multipart-0.0.20.dist-info      watchfiles
certifi                             jinja2                           pytz                                   watchfiles-1.0.5.dist-info
certifi-2025.4.26.dist-info         jinja2-3.1.6.dist-info           pytz-2025.2.dist-info                  websockets
CHANGELOG.md                        LICENSE                          PyYAML-6.0.2.dist-info                 websockets-15.0.1.dist-info
charset_normalizer                  mako                             README.md                              _yaml
charset_normalizer-3.4.2.dist-info  mako-1.3.10.dist-info            requests                               yaml
click                               markdown_it                      requests-2.32.3.dist-info              yarl
click-8.1.8.dist-info               markdown_it_py-3.0.0.dist-info   rich                                   yarl-1.20.0.dist-info
colorama                            markupsafe                       rich-14.0.0.dist-info

3. Not really sure why, but when I start zed it uses an unrelated virtual environment. If I do source .venv/bin/activate then I can use the correct venv but I'm not sure if this applies to the process running pyrefly.
   Even If I run pyrefly manually from the terminal with the correct venv it still cannot figure out dependencies correctly and thinks that they're not installed.
4. 0.16.2

[anzhi0708]

@Notenlish and @anzhi0708, sorry you're experiencing this issue. I'll try to help you get this working, and see if there are any bugs we need to fix in the process.

Can you both answer these questions for me?

1. Just to double check, your venv is located at /home/noten/Documents/GitHub/hukuksuzlugun-bedeli/.venv, right?
2. What do you see when you ls .venv/lib/python3.12/site-packages?
3. Do you have the virtual environment activated when you're running Pyrefly?
4. Which version of Pyrefly are you running (pyrefly --version)?

Also @anzhi0708, are you running Pyrefly on cmd, powershell, linux subsystem, or something else?

Hey @connernilsen good evening!

All the dependencies for my project installed by uv are located in the .venv/lib/python3.13/site-packages directory, and I'm not in an activated virtual environment. That's because all my command-line operations within the project are executed via uv, such as uv run python -m myproject.mymodule, uv run main.py, uv run python, etc.

Additionally, I use pyrefly across all platforms, including Ubuntu, Windows 11, and Termux (Android).

Currently, the issue seems to be that
unless I explicitly run pyrefly init . and manually declare tool.pyrefly.python_interpreter = "./.venv/bin/python" (on Linux) or ./.venv/Scripts/python.exe (on Windows) in pyproject.toml, pyrefly will fall back to using the system's default global Python interpreter and its dependencies.

[anzhi0708]

unless I explicitly run pyrefly init . and manually declare tool.pyrefly.python_interpreter = "./.venv/bin/python" (on Linux) or ./.venv/Scripts/python.exe (on Windows) in pyproject.toml, pyrefly will fall back to using the system's default global Python interpreter and its dependencies.

By the way, the editor I use is helix. From my perspective, once I understand how to select the Python interpreter for pyrefly, it seems to come down to a matter of choice — that is, whether pyrefly should default to using the system-wide interpreter, or automatically detect at startup whether it's inside a likely virtual environment directory and default to using the interpreter provided by that environment.

[connernilsen]

This is strange, it seems like you both have things set up correctly and that we should be finding everything.

Can you both run pyrefly check --verbose and attach the first few lines of that output (before the errors start)? There should be a line that looks like DEBUG: Config is ..., which is what I'm looking for.

Once you have that, can you find site_package_path_source, and if it's something that looks like Interpreter(<interpreter>), run <interpreter> -c "import sys; print(sys.path)", and also attach that to your response?

[anzhi0708]

Project Structure

Details

PS C:\Users\anzhi\dev\py\cbm_correct.py> ls


    Directory: C:\Users\anzhi\dev\py\cbm_correct.py


Mode                 LastWriteTime         Length Name
----                 -------------         ------ ----
d-----        2025-05-28   4:30 PM                .venv
d-----        2025-05-28   5:53 PM                build
-a----        2025-05-28   4:29 PM            109 .gitignore
-a----        2025-05-28   4:29 PM              5 .python-version
------        2025-05-28   4:32 PM           8861 main.py
------        2025-06-05   9:58 AM            396 pyproject.toml
-a----        2025-05-28   4:29 PM              0 README.md
-a----        2025-05-28   4:50 PM          27648 uv.lock


PS C:\Users\anzhi\dev\py\cbm_correct.py> hx .\main.py

---

"python_interpreter: None"
At this point, I have commented out the [tool.pyrefly] block in pyproject.toml, so when I edit main.py in my text editor, the pyrefly LSP reports that it cannot find the dependencies. Judging from the output python_interpreter: None, it seems that pyrefly failed to detect my virtual environment.

Details

``` PS C:\Users\anzhi\dev\py\cbm_correct.py> pyrefly check --verbose INFO Found `C:\Users\anzhi\dev\py\cbm_correct.py\pyproject.toml` marking project root, checking root directory with default configuration DEBUG Config is: {project_includes: [C:\Users\anzhi\dev\py\cbm_correct.py\**\*], project_excludes: [C:\Users\anzhi\dev\py\cbm_correct.py\**\.[!\.]*, C:\Users\anzhi\dev\py\cbm_correct.py\**\*venv\**\*], search_path: [C:\Users\anzhi\dev\py\cbm_correct.py\], python_interpreter: None, python_environment: {python_platform: win32, python_version: 3.13.3, site_package_path: [C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.13_3.13.1008.0_x64__qbz5n2kfra8p0\DLLs, C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.13_3.13.1008.0_x64__qbz5n2kfra8p0\Lib, C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.13_3.13.1008.0_x64__qbz5n2kfra8p0, C:\Users\anzhi\dev\py\cbm_correct.py\.venv, C:\Users\anzhi\dev\py\cbm_correct.py\.venv\Lib\site-packages], site_package_path_source: Interpreter("C:\\Users\\anzhi\\dev\\py\\cbm_correct.py\\.venv\\Scripts\\python.exe")}, replace_imports_with_any: []} DEBUG Checking 3 files (listing took 3.00s) DEBUG Running with 4 threads [00:00:00] ░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░ 0/0 DEBUG Running epoch 1 ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:14:12-17: No matching overload found for function `round`, reporting errors for closest overload: `(number: _SupportsRound1[@_], ndigits: None = ...) -> @_` [no-matching-overload] ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:14:25-26: Argument `Literal[3]` is not assignable to parameter `ndigits` with type `None` in function `round` [bad-argument-type] ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:40:27-85: Object of class `NAType` has no attribute `fillna` [missing-attribute] ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:40:27-85: Object of class `NaTType` has no attribute `fillna` [missing-attribute] ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:40:27-85: Object of class `Number` has no attribute `fillna` [missing-attribute] ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:40:27-85: Object of class `Timedelta` has no attribute `fillna` [missing-attribute] ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:40:27-85: Object of class `Timestamp` has no attribute `fillna` [missing-attribute] ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:40:27-85: Object of class `float` has no attribute `fillna` [missing-attribute] ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:40:27-85: Object of class `ndarray` has no attribute `fillna` [missing-attribute] ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:40:27-85: Object of class `number` has no attribute `fillna` [missing-attribute] ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:60:16-24: `<` is not supported between `SupportsAbs[Unknown]` and `Literal[0]` Argument `SupportsAbs[Unknown]` is not assignable to parameter with type `int` in function `int.__gt__` [bad-argument-type] ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:62:34-69: No matching overload found for function `pandas.core.frame.DataFrame.sort_values`, reporting errors for closest overload: `(by: Hashable | Sequence[Hashable], *, axis: Literal['columns', 'index', 'rows'] | int, ascending: Unknown, inplace: Literal[False], kind: Literal['heapsort', 'mergesort', 'quicksort', 'stable'], na_position: Literal['first', 'last'], ignore_index: bool, key: ((Series) -> ExtensionArray | Index | Series | ndarray[Unknown, Unknown]) | None) -> DataFrame` [no-matching-overload] ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:62:34-69: Missing argument `by` in function `pandas.core.frame.DataFrame.sort_values` [missing-argument] ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:65:34-69: No matching overload found for function `pandas.core.frame.DataFrame.sort_values`, reporting errors for closest overload: `(by: Hashable | Sequence[Hashable], *, axis: Literal['columns', 'index', 'rows'] | int, ascending: Unknown, inplace: Literal[False], kind: Literal['heapsort', 'mergesort', 'quicksort', 'stable'], na_position: Literal['first', 'last'], ignore_index: bool, key: ((Series) -> ExtensionArray | Index | Series | ndarray[Unknown, Unknown]) | None) -> DataFrame` [no-matching-overload] ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:65:34-69: Missing argument `by` in function `pandas.core.frame.DataFrame.sort_values` [missing-argument] ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:72:20-28: `<` is not supported between `SupportsAbs[Unknown]` and `Literal[0]` Argument `SupportsAbs[Unknown]` is not assignable to parameter with type `int` in function `int.__gt__` [bad-argument-type] INFO 16 errors shown, 0 errors ignored, 3 modules, 855 transitive dependencies, 342,422 lines, took 7.22s (checking 4.21s; listing 3.00s), peak memory physical 241.4 MiB ```

---

After that, I explicitly specified the interpreter path in pyproject.toml. python_interpreter: Some("C:\Users\anzhi\dev\py\cbm_correct.py\./.venv/Scripts/python.exe")

Details

PS C:\Users\anzhi\dev\py\cbm_correct.py> hx .\pyproject.toml
PS C:\Users\anzhi\dev\py\cbm_correct.py> pyrefly check --verbose
 INFO Checking project configured at `C:\Users\anzhi\dev\py\cbm_correct.py\pyproject.toml`
DEBUG Config is: {project_includes: [C:\Users\anzhi\dev\py\cbm_correct.py\**\*], project_excludes: [C:\Users\anzhi\dev\py\cbm_correct.py\**\.[!\.]*, C:\Users\anzhi\dev\py\cbm_correct.py\**\*venv\**\*], search_path: [C:\Users\anzhi\dev\py\cbm_correct.py], python_interpreter: Some("C:\\Users\\anzhi\\dev\\py\\cbm_correct.py\\./.venv/Scripts/python.exe"), python_environment: {python_platform: win32, python_version: 3.13.3, site_package_path: [C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.13_3.13.1008.0_x64__qbz5n2kfra8p0\DLLs, C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.13_3.13.1008.0_x64__qbz5n2kfra8p0\Lib, C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.13_3.13.1008.0_x64__qbz5n2kfra8p0, C:\Users\anzhi\dev\py\cbm_correct.py\.venv, C:\Users\anzhi\dev\py\cbm_correct.py\.venv\Lib\site-packages], site_package_path_source: Interpreter("C:\\Users\\anzhi\\dev\\py\\cbm_correct.py\\./.venv/Scripts/python.exe")}, replace_imports_with_any: []}
DEBUG Checking 3 files (listing took 2.82s)
DEBUG Running with 4 threads
[00:00:00] ░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░       0/0      DEBUG Running epoch 1
ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:14:12-17: No matching overload found for function `round`, reporting errors for closest overload: `(number: _SupportsRound1[@_], ndigits: None = ...) -> @_` [no-matching-overload]
ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:14:25-26: Argument `Literal[3]` is not assignable to parameter `ndigits` with type `None` in function `round` [bad-argument-type]
ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:40:27-85: Object of class `NAType` has no attribute `fillna` [missing-attribute]
ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:40:27-85: Object of class `NaTType` has no attribute `fillna` [missing-attribute]
ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:40:27-85: Object of class `Number` has no attribute `fillna` [missing-attribute]
ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:40:27-85: Object of class `Timedelta` has no attribute `fillna` [missing-attribute]
ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:40:27-85: Object of class `Timestamp` has no attribute `fillna` [missing-attribute]
ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:40:27-85: Object of class `float` has no attribute `fillna` [missing-attribute]
ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:40:27-85: Object of class `ndarray` has no attribute `fillna` [missing-attribute]
ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:40:27-85: Object of class `number` has no attribute `fillna` [missing-attribute]
ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:60:16-24: `<` is not supported between `SupportsAbs[Unknown]` and `Literal[0]`
  Argument `SupportsAbs[Unknown]` is not assignable to parameter with type `int` in function `int.__gt__` [bad-argument-type]
ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:62:34-69: No matching overload found for function `pandas.core.frame.DataFrame.sort_values`, reporting errors for closest overload: `(by: Hashable | Sequence[Hashable], *, axis: Literal['columns', 'index', 'rows'] | int, ascending: Unknown, inplace: Literal[False], kind: Literal['heapsort', 'mergesort', 'quicksort', 'stable'], na_position: Literal['first', 'last'], ignore_index: bool, key: ((Series) -> ExtensionArray | Index | Series | ndarray[Unknown, Unknown]) | None) -> DataFrame` [no-matching-overload]
ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:62:34-69: Missing argument `by` in function `pandas.core.frame.DataFrame.sort_values` [missing-argument]
ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:65:34-69: No matching overload found for function `pandas.core.frame.DataFrame.sort_values`, reporting errors for closest overload: `(by: Hashable | Sequence[Hashable], *, axis: Literal['columns', 'index', 'rows'] | int, ascending: Unknown, inplace: Literal[False], kind: Literal['heapsort', 'mergesort', 'quicksort', 'stable'], na_position: Literal['first', 'last'], ignore_index: bool, key: ((Series) -> ExtensionArray | Index | Series | ndarray[Unknown, Unknown]) | None) -> DataFrame` [no-matching-overload]
ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:65:34-69: Missing argument `by` in function `pandas.core.frame.DataFrame.sort_values` [missing-argument]
ERROR C:\Users\anzhi\dev\py\cbm_correct.py\main.py:72:20-28: `<` is not supported between `SupportsAbs[Unknown]` and `Literal[0]`
  Argument `SupportsAbs[Unknown]` is not assignable to parameter with type `int` in function `int.__gt__` [bad-argument-type]
 INFO 16 errors shown, 0 errors ignored, 3 modules, 855 transitive dependencies, 342,422 lines, took 6.87s (checking 4.05s; listing 2.82s), peak memory physical 252.5 MiB
PS C:\Users\anzhi\dev\py\cbm_correct.py>

[connernilsen]

Wait @anzhi0708, is it working for you when manually supplying python_interpreter or not? I'm seeing "site_package_path": [..., C:\Users\anzhi\dev\py\cbm_correct.py\.venv\Lib\site-packages], which seems right.

I also don't see any import errors in the output you linked, and it seems like the full output provided by Pyrefly. Are you seeing import errors, or is there another issue going on that you're seeing?

[anzhi0708]

Hey @connernilsen

(1) After I manually specified the exact python_interpreter, everything started working fine.
(2) I use the pyrefly LSP 99% of the time—within my text editor. While editing code, the LSP reports import errors. I don’t understand why pyrefly check doesn’t report the same import errors when it fails to locate the interpreter.