Failed to import scipy with pyo3

[LangArthur]

Hi!

While I was working with pyo3 to execute python scripts in a rust project, I found an error when importing scipy which I cannot solve.

Environment

• Os: Windows 11
• Python v3.14.3
• pyo3 v0.28.3

I am working inside a virtual environment with venv.
I manually activate the venv with .venv\Scripts\activate

Problem

I reduce my code to this minimal example:

    Python::attach(|py| {
        let _mod = PyModule::import(py, "scipy").unwrap();
    });

which give the following error:

`Result::unwrap()` on an `Err` value: PyErr { type: <class 'ImportError'>, value: ImportError('The `scipy` install you are using seems to be broken, (extension modules cannot be imported), please try reinstalling.'), traceback: Some("Traceback (most recent call last):\n  File \"C:\\path\\to\\my\\program\\.venv\\Lib\\site-packages\\scipy\\__init__.py\", line 100, in <module>\n    raise ImportError(msg) from e\n") }
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

As recommanded in the error message, I tried a resintallation, without any success

I tried to import scipy directly from a python shell in my virtual environment, no error (I checked that python.exe was the one from .venv\Scripts)

I still suspect a bad configuration from my side, but I cannot found it.

Here a copy of my build.rs which set the wanted env variables (keep in mind this script is temporary and will be reworked). Btw, should I used build.rs or another way to set env variable?

fn main() {
    let origin = "C:\\path\\to\\my\\project";
    let custom_path = format!("{}\\{}", origin, ".venv\\Lib\\site-packages");
    let python_path = std::env::var("PYTHONPATH").unwrap_or_default();
    let new_python_path = format!("{}{};", python_path, custom_path);

    let custom_home = format!("{}\\{}", origin, ".venv\\Scripts");
    let python_home = std::env::var("PYTHONHOME").unwrap_or_default();
    let new_python_home = format!("{}{};", python_home, custom_home);

    println!("cargo:rustc-env=PYTHONPATH={}", new_python_path);
    println!("cargo:rustc-env=PYTHONHOME={}", new_python_home);
}

Thanks for the help!

[LangArthur]

A bit of sleep on it and the solution became clear: problem was because of env variable order.

my build.rs generated something like this

PYTHONPATH="C:\\<...>\\AppData\\Local\\Python\\pythoncore-3.14-64\\Lib";"C:\\path\\to\\my\\project\\.venv\\Lib\\site-packages"

while the correct one should be:

PYTHONPATH="C:\\path\\to\\my\\project\\.venv\\Lib\\site-packages";"C:\\<...>\\AppData\\Local\\Python\\pythoncore-3.14-64\\Lib"

(and same for PYTHONHOME obviously)

I think the problem did not show up with the other libraries (like numpy) because they were also installed globally.