bugfix: np.int deprecated

[StephDC]

np.int has been deprecated since numpy 1.20. ¹

For future proofing the code, this PR replaced np.int with np.int64.

With this modification, the program now at least imports in python 3.13 with the following dependencies, though I haven't test it on real data to check if the result remains the same.

Package            Version
------------------ -----------
biopython          1.85
certifi            2025.1.31
charset-normalizer 3.4.1
feather-format     0.4.1
idna               3.10
joblib             1.4.2
more-itertools     10.6.0
numpy              2.2.4
pandas             2.2.3
pip                24.3.1
pyarrow            19.0.1
pycurl             7.45.6
pysam              0.23.0
python-dateutil    2.9.0.post0
pytz               2025.2
requests           2.32.3
scikit-learn       1.6.1
scipy              1.15.2
six                1.17.0
threadpoolctl      3.6.0
tzdata             2025.2
urllib3            2.3.0
wget               3.2

Footnotes

1. https://numpy.org/devdocs/release/1.20.0-notes.html#using-the-aliases-of-builtin-types-like-np-int-is-deprecated ↩