Invalid type error compiling cluster.pyx with Cython

[cloudbroken]

Thank you for making this interesting tool.
I tried installing it with Cython, but was getting type errors compiling cluster.pyx.
Let me disclaim that I am a python novice, and may therefore be making some kind of obvious mistake.

Error compiling Cython file:
------------------------------------------------------------
...

            delta_LL[i, j] = delta
            delta_LL[j, i] = delta

    # array of cluster label
    cdef np.ndarray[np.int_t, ndim = 1] clusters = np.arange(clst.N_boxes)
                       ^
------------------------------------------------------------

cellstates/cluster.pyx:365:23: Invalid type.

Error compiling Cython file:
------------------------------------------------------------
...
    cells are optimally placed.
    """

    cdef:
        int cell, c_best, move_count = 0
        np.ndarray[np.int_t, ndim = 1] cell_iter
                      ^
------------------------------------------------------------

cellstates/cluster.pyx:430:22: Invalid type.

Error compiling Cython file:
------------------------------------------------------------
...
            if np.any(mask):
                l = l[mask]
                d = d[mask, :]

        self.LAMBDA = <np.ndarray[np.float_t, ndim = 1]> l
        self.data = <np.ndarray[np.int_t, ndim = 2]?> d
                                   ^
------------------------------------------------------------

cellstates/cluster.pyx:539:35: Invalid type.

The compilation problem was resolved by explicitly declaring the array type as np.int64_t as follows:

Line 365: cdef np.ndarray[np.int64_t, ndim=1] clusters = np.arange(clst.N_boxes, dtype=np.int64)
Line 430: np.ndarray[np.int64_t, ndim = 1] cell_iter
LIne 539: self.data = <np.ndarray[np.int64_t, ndim = 2]?> d

Environment

_libgcc_mutex             0.1                        main
_openmp_mutex             5.1                       1_gnu
bzip2                     1.0.8                h5eee18b_6
ca-certificates           2024.7.2             h06a4308_0
cellstates                0.1                      pypi_0    pypi
contourpy                 1.3.0                    pypi_0    pypi
cycler                    0.12.1                   pypi_0    pypi
cython                    3.0.11                   pypi_0    pypi
expat                     2.6.3                h6a678d5_0
fonttools                 4.53.1                   pypi_0    pypi
kiwisolver                1.4.7                    pypi_0    pypi
ld_impl_linux-64          2.38                 h1181459_1
libffi                    3.4.4                h6a678d5_1
libgcc-ng                 11.2.0               h1234567_1
libgomp                   11.2.0               h1234567_1
libstdcxx-ng              11.2.0               h1234567_1
libuuid                   1.41.5               h5eee18b_0
matplotlib                3.9.2                    pypi_0    pypi
ncurses                   6.4                  h6a678d5_0
numpy                     2.1.1                    pypi_0    pypi
openssl                   3.0.15               h5eee18b_0
packaging                 24.1                     pypi_0    pypi
pandas                    2.2.2                    pypi_0    pypi
pillow                    10.4.0                   pypi_0    pypi
pip                       24.2                     pypi_0    pypi
pyparsing                 3.1.4                    pypi_0    pypi
python                    3.12.4               h5148396_1
python-dateutil           2.9.0.post0              pypi_0    pypi
pytz                      2024.1                   pypi_0    pypi
readline                  8.2                  h5eee18b_0
scipy                     1.14.1                   pypi_0    pypi
setuptools                72.1.0                   pypi_0    pypi
six                       1.16.0                   pypi_0    pypi
sqlite                    3.45.3               h5eee18b_0
tk                        8.6.14               h39e8969_0
tzdata                    2024.1                   pypi_0    pypi
wheel                     0.43.0                   pypi_0    pypi
xz                        5.4.6                h5eee18b_1
zlib                      1.2.13               h5eee18b_1```

[Biomiha]

This also worked for me. Much appreciated, thanks!