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update to numpy 2.0 #262

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update to numpy 2.0 #262

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2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ authors = [
description = "Synteny and rearrangement identifier between whole-genome assemblies"
readme = "README.md"
# Limit python version as pysam is not available for higher python versions
requires-python = ">=3.8, <=3.10"
requires-python = ">=3.8"
keywords = ["Structural Variation", "SV", "Pangenomics", "Bioinformatics"]
license = {text = "MIT"}
dependencies = [
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10 changes: 5 additions & 5 deletions syri/pyxFiles/function.pxd
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Expand Up @@ -15,15 +15,15 @@ cimport numpy as np
cimport cython
np.random.seed(1)

cpdef inline getOverlapWithSynBlocks(np.ndarray[np.int_t, ndim=1] start, np.ndarray[np.int_t, ndim=1] end, np.ndarray chrom, np.ndarray[np.int_t, ndim=1] in_start, np.ndarray[np.int_t, ndim=1] in_end, np.ndarray in_chrom, np.int_t threshold, np.int_t count, np.int_t tUC, np.float_t tUP):
cpdef inline getOverlapWithSynBlocks(np.ndarray[np.int64_t, ndim=1] start, np.ndarray[np.int64_t, ndim=1] end, np.ndarray chrom, np.ndarray[np.int64_t, ndim=1] in_start, np.ndarray[np.int64_t, ndim=1] in_end, np.ndarray in_chrom, np.int64_t threshold, np.int64_t count, np.int64_t tUC, np.float_t tUP):

assert(len(start) == len(end) == len(chrom) ==count)
assert(len(in_start) == len(in_end) == len(in_chrom))

cdef Py_ssize_t i, j, n = len(in_start)
cdef np.int_t blockuni, s, e
cdef np.int64_t blockuni, s, e
cdef np.ndarray[np.npy_bool, ndim = 1, cast=True] uni = np.zeros(count, dtype="bool")
cdef np.ndarray[np.int_t, ndim=1] blocks
cdef np.ndarray[np.int64_t, ndim=1] blocks

for i in range(count):
blocks = np.zeros(n, dtype="int")
Expand Down Expand Up @@ -63,10 +63,10 @@ cpdef inline getmeblocks(long[:] astart, long[:] aend, long[:] bstart, long[:] b
# Function take the coordinates and cluster information of all translocated blocks and identifies mutually exclusive
# blocks (candidates with which a given candidate cannot co-exist) by comparing the coordinates of each block to the coordinates of the member blocks in its cluster
logger = logging.getLogger("getmeblocks")
cdef np.ndarray[np.int_t, ndim=1] members, temp
cdef np.ndarray[np.int64_t, ndim=1] members, temp
cdef np.ndarray[np.npy_bool, ndim=1, cast=True] meb, meb_a, meb_b, rem = np.zeros(len(astart), dtype="bool")
cdef int overlap
cdef np.int_t i, j, index
cdef np.int64_t i, j, index
meblock = {} ## for blocks which are overlapping with inplace blocks
melist = {} ## for blocks which are not overlapping with inplace blocks

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