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Fix compilation warnings #691

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Fix compilation warnings #691

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215c920
fix deprecated numpy api and nogil warnings during cythonize
Oct 13, 2025
c588b01
fix warning during packaging
Oct 13, 2025
94e0c83
fix check_array warning
Oct 14, 2025
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7 changes: 4 additions & 3 deletions hdbscan/_hdbscan_boruvka.pyx
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
# distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
# cython: boundscheck=False
# cython: nonecheck=False
# cython: wraparound=False
Expand Down Expand Up @@ -89,7 +90,7 @@ cdef inline np.double_t balltree_min_dist_dual(
np.double_t radius2,
np.intp_t node1,
np.intp_t node2,
np.double_t[:, ::1] centroid_dist) nogil except -1:
np.double_t[:, ::1] centroid_dist) except -1 nogil:

cdef np.double_t dist_pt = centroid_dist[node1, node2]
return max(0, (dist_pt - radius1 - radius2))
Expand Down Expand Up @@ -139,7 +140,7 @@ cdef inline np.double_t kdtree_min_rdist_dual(
np.intp_t node1,
np.intp_t node2,
np.double_t[:, :, ::1] node_bounds,
np.intp_t num_features) nogil except -1:
np.intp_t num_features) except -1 nogil:

cdef np.double_t d, d1, d2, rdist = 0.0
cdef np.double_t zero = 0.0
Expand Down Expand Up @@ -603,7 +604,7 @@ cdef class KDTreeBoruvkaAlgorithm (object):
return self.components.shape[0]

cdef int dual_tree_traversal(self, np.intp_t node1,
np.intp_t node2) nogil except -1:
np.intp_t node2) except -1 nogil:
"""Perform a dual tree traversal, pruning wherever possible, to find
the nearest neighbor not in the same component for each component.
This is akin to a standard dual tree NN search, but we also prune
Expand Down
1 change: 1 addition & 0 deletions hdbscan/_hdbscan_linkage.pyx
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
# distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
# cython: boundscheck=False
# cython: nonecheck=False
# Minimum spanning tree single linkage implementation for hdbscan
Expand Down
1 change: 1 addition & 0 deletions hdbscan/_hdbscan_reachability.pyx
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
# distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
# cython: boundscheck=False
# cython: nonecheck=False
# cython: initializedcheck=False
Expand Down
1 change: 1 addition & 0 deletions hdbscan/_hdbscan_tree.pyx
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
# distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
# cython: boundscheck=False
# cython: nonecheck=False
# cython: initializedcheck=False
Expand Down
3 changes: 2 additions & 1 deletion hdbscan/_prediction_utils.pyx
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
#cython: boundscheck=False, nonecheck=False, initializedcheck=False
# distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
# cython: boundscheck=False, nonecheck=False, initializedcheck=False
# Utility routines in cython for prediction in hdbscan
# Authors: Leland McInnes
# License: 3-clause BSD
Expand Down
19 changes: 10 additions & 9 deletions hdbscan/dist_metrics.pxd
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Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
#!python
#cython: boundscheck=False
#cython: wraparound=False
#cython: cdivision=True
# distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
# cython: boundscheck=False
# cython: wraparound=False
# cython: cdivision=True

import cython
cimport cython
Expand Down Expand Up @@ -33,7 +34,7 @@ DTYPE = np.double
# We use these for the default (euclidean) case so that they can be
# inlined. This leads to faster computation for the most common case
cdef inline DTYPE_t euclidean_dist(DTYPE_t* x1, DTYPE_t* x2,
ITYPE_t size) nogil except -1:
ITYPE_t size) except -1 nogil:
cdef DTYPE_t tmp, d=0
cdef np.intp_t j
for j in range(size):
Expand All @@ -43,7 +44,7 @@ cdef inline DTYPE_t euclidean_dist(DTYPE_t* x1, DTYPE_t* x2,


cdef inline DTYPE_t euclidean_rdist(DTYPE_t* x1, DTYPE_t* x2,
ITYPE_t size) nogil except -1:
ITYPE_t size) except -1 nogil:
cdef DTYPE_t tmp, d=0
cdef np.intp_t j
for j in range(size):
Expand All @@ -52,7 +53,7 @@ cdef inline DTYPE_t euclidean_rdist(DTYPE_t* x1, DTYPE_t* x2,
return d


cdef inline DTYPE_t euclidean_dist_to_rdist(DTYPE_t dist) nogil except -1:
cdef inline DTYPE_t euclidean_dist_to_rdist(DTYPE_t dist) except -1 nogil:
return dist * dist


Expand All @@ -79,10 +80,10 @@ cdef class DistanceMetric:
cdef object kwargs

cdef DTYPE_t dist(self, DTYPE_t* x1, DTYPE_t* x2,
ITYPE_t size) nogil except -1
ITYPE_t size) except -1 nogil

cdef DTYPE_t rdist(self, DTYPE_t* x1, DTYPE_t* x2,
ITYPE_t size) nogil except -1
ITYPE_t size) except -1 nogil

cdef int pdist(self, DTYPE_t[:, ::1] X, DTYPE_t[:, ::1] D) except -1

Expand All @@ -91,4 +92,4 @@ cdef class DistanceMetric:

cdef DTYPE_t _rdist_to_dist(self, DTYPE_t rdist) except -1

cdef DTYPE_t _dist_to_rdist(self, DTYPE_t dist) nogil except -1
cdef DTYPE_t _dist_to_rdist(self, DTYPE_t dist) except -1 nogil
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