Expected 96 from C header, got 88 from PyObject when importing "en_core_sci_sm" version 0.5.4

[mevol]

How to reproduce the behaviour

The issue occurs during import of "en_core_sci_sm" version 0.5.4. The error trace is below. The issue seems to be related to numpy. This error has occurred previously and seems to be recurring whenever the numpy version changes.

Traceback (most recent call last):
File "/Users/melaniev/Documents/code/PDBe_public_repos/IUCr-annotation-pipeline/.venv/bin/pipeline_predict", line 4, in
from pipeline.predicting.run_local_inference_for_ner import main
File "/Users/melaniev/Documents/code/PDBe_public_repos/IUCr-annotation-pipeline/.venv/lib/python3.11/site-packages/pipeline/predicting/run_local_inference_for_ner.py", line 12, in
from pipeline.predicting.inference_tools import (
File "/Users/melaniev/Documents/code/PDBe_public_repos/IUCr-annotation-pipeline/.venv/lib/python3.11/site-packages/pipeline/predicting/inference_tools.py", line 2, in
import en_core_sci_sm
File "/Users/melaniev/Documents/code/PDBe_public_repos/IUCr-annotation-pipeline/.venv/lib/python3.11/site-packages/en_core_sci_sm/init.py", line 2, in
from spacy.util import load_model_from_init_py, get_model_meta
File "/Users/melaniev/Documents/code/PDBe_public_repos/IUCr-annotation-pipeline/.venv/lib/python3.11/site-packages/spacy/init.py", line 6, in
from .errors import setup_default_warnings
File "/Users/melaniev/Documents/code/PDBe_public_repos/IUCr-annotation-pipeline/.venv/lib/python3.11/site-packages/spacy/errors.py", line 3, in
from .compat import Literal
File "/Users/melaniev/Documents/code/PDBe_public_repos/IUCr-annotation-pipeline/.venv/lib/python3.11/site-packages/spacy/compat.py", line 39, in
from thinc.api import Optimizer # noqa: F401
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/melaniev/Documents/code/PDBe_public_repos/IUCr-annotation-pipeline/.venv/lib/python3.11/site-packages/thinc/api.py", line 1, in
from .backends import (
File "/Users/melaniev/Documents/code/PDBe_public_repos/IUCr-annotation-pipeline/.venv/lib/python3.11/site-packages/thinc/backends/init.py", line 17, in
from .cupy_ops import CupyOps
File "/Users/melaniev/Documents/code/PDBe_public_repos/IUCr-annotation-pipeline/.venv/lib/python3.11/site-packages/thinc/backends/cupy_ops.py", line 16, in
from .numpy_ops import NumpyOps
File "thinc/backends/numpy_ops.pyx", line 1, in init thinc.backends.numpy_ops
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

Your Environment

• Operating System: Tahoe 26.5.2
• Python Version Used: 3.11.14
• spaCy Version Used: 3.7.5
• Environment Information: numpy==2.4.6; onnx==1.22.0; onnxruntime==1.27.0; optimum==2.2.0; transformers==5.14.1; torch==2.13.0; tokenizers==0.22.2; pandas==3.0.3; beautifulsoup4==4.15.0