Unluckily, there are still several errors. Some are related to the upstream chgnet and scipy and cannot be fixed here.

@njzjz sorry for the lack of reply here! looks like this is almost finished. thanks for the effort! feel free to skip the failing chgnet tests for now. re scipy, we'll have to pin to <1.14 as the newest release dropped Python 3.9 support. but 1.13.0 already supports numpy v2

I really appreciate the pioneering work @njzjz! Meanwhile in case anyone missed this, ruff now has a dedicated rule NPY201 to handle API migration automatically :)

ruff check path/to/code/ --select NPY201

For cross reference, I've submitted the SciPy issue to scipy/scipy#21052

I do not know how to fix the rest of the errors and need help.

@njzjz feel free to skip the two failing chgnet tests. we'll migrate it to numpy v2 once pymatgen has. for test_delta_func, you can conditionally skip it like this:

@pytest.mark.skipif(sys.platform == "win32" and np.__version__ > "2.0.0", reason="Fails on Windows with numpy > 2.0.0, awaiting https://github.com/scipy/scipy/issues/21052 resolution")
def test_delta_func():
    x = np.array([0, 1, 2, 3, 4, 5])

not sure about TestWavecar.test_get_parchg. that might need a closer look. maybe @esoteric-ephemera has some ideas on what's going wrong?

Just did some investigation on the failure of TestWavecar.test_get_parchg, unfortunately I wasn't able to come to a definite conclusion, but still share my findings in case it's helpful.

I believe this failure has something to do with the float point precision (though I don't know exactly how), with the following script on Windows Python 3.12:

import numpy as np

from pymatgen.io.vasp import Poscar, Wavecar


TEST_DIR = "tests/files/io/vasp"
poscar = Poscar.from_file(f"{TEST_DIR}/inputs/POSCAR")
w = Wavecar(f"{TEST_DIR}/outputs/WAVECAR.H2.ncl")

w.coeffs.append([np.ones((2, 100))])
c = w.get_parchg(poscar, -1, 0, phase=False, spinor=None)

print(np.min(c.data["total"]))  # 0.0 in NumPy 1.x, 8.738907122657083e-33 in NumPy 2.x
assert not np.all(c.data["total"] > 0.0)  # AssertionError

Note the min value in c.data["total"] is very close to zero (the min positive value with float32 is around 10^-38).

From the "NumPy 2.0 migration guide", there seems to be two changes related to this:

1. The default Windows integer was int32 for NumPy 1.x, and is now int64 (confirmed on my Windows PC), for Linux/Mac it's always int64
2. The change in the scalar promotion rules

However, with these changes, I would expect the precision on Windows to be consistent with Linux on NumPy 2.x. Perhaps someone more familiar with the internal workings of Wavecar would know the reason :)

The failing tests for tests/io/abinit/test_abiobjects.py looks like another randomly failing test. I cannot recreate it on my Windows PC.

The failing tests for tests/io/abinit/test_abiobjects.py looks like another randomly failing test. I cannot recreate it on my Windows PC.

probably something to report to https://github.com/Unidata/netcdf4-python, even if just to say the error message is self-contradictory...

E OSError: Error loading charset-233f44715e5aacaf3a688c2faff5ddf7.dll; The operation completed successfully.

The failing tests for tests/io/abinit/test_abiobjects.py looks like another randomly failing test. I cannot recreate it on my Windows PC.

probably something to report to https://github.com/Unidata/netcdf4-python, even if just to say the error message is self-contradictory...

Agreed, just for my own record, it failed in another PR randomly https://github.com/materialsproject/pymatgen/actions/runs/10268736299/job/28412461926?pr=3892

E OSError: Error loading charset-233f44715e5aacaf3a688c2faff5ddf7.dll; The operation completed successfully.

This part of the code is generated by delvewheel here. I think I can report there.

According to the Windows documentation, this error message means no error. So it may be incorrect to throw an error (while it is also strange that LoadLibraryExW returns nothing but gives ERROR_SUCCESS).

ERROR_SUCCESS
0 (0x0)
The operation completed successfully.

See also https://stackoverflow.com/questions/7524142/what-does-windows-error-0-error-success-mean

E OSError: Error loading charset-233f44715e5aacaf3a688c2faff5ddf7.dll; The operation completed successfully.

Submitted to adang1345/delvewheel#51

@njzjz can you pin pyproject to the fixed delvewheel>=1.7.4

@njzjz can you pin pyproject to the fixed delvewheel>=1.7.4

This may not work, as delvewheel is a build-time dependency, not a runtime dependency.

This may not work, as delvewheel is a build-time dependency, not a runtime dependency.

ah, didn't realize that. so the place to pin that would be here

but looks like we're in the green anyway so would be good to remove the temp install command in test.yml

thanks again @njzjz! 👍

Just recorded another failure in https://github.com/materialsproject/pymatgen/actions/runs/10319015504/job/28566565139:

OSError: Error loading libxml2-14375db763c77d38e40bbe5c028add84.dll; The operation completed successfully.