Skip to content

Navigation Menu

Sign in
Appearance settings

Search code, repositories, users, issues, pull requests...

Provide feedback

We read every piece of feedback, and take your input very seriously.

Saved searches

Use saved searches to filter your results more quickly
Appearance settings

Commit 9b801fc

Browse filesBrowse files
jeremiedbbjjerphan
authored and
Itay
committed
MAINT Consistent cython types from _typedefs (scikit-learn#25942)
Co-authored-by: Julien Jerphanion <git@jjerphan.xyz>
1 parent 5325d9c commit 9b801fc
Copy full SHA for 9b801fc

12 files changed

+898
-922
lines changed

‎setup.py

Copy file name to clipboardExpand all lines: setup.py
+3-4Lines changed: 3 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -265,7 +265,6 @@ def check_package_status(package, min_version):
265265
{
266266
"sources": ["_middle_term_computer.pyx.tp", "_middle_term_computer.pxd.tp"],
267267
"language": "c++",
268-
"include_np": True,
269268
"extra_compile_args": ["-std=c++11"],
270269
},
271270
{
@@ -397,9 +396,9 @@ def check_package_status(package, min_version):
397396
},
398397
{"sources": ["_random.pyx"], "include_np": True},
399398
{"sources": ["_logistic_sigmoid.pyx"], "include_np": True},
400-
{"sources": ["_typedefs.pyx"], "include_np": True},
401-
{"sources": ["_heap.pyx"], "include_np": True},
402-
{"sources": ["_sorting.pyx"], "include_np": True},
399+
{"sources": ["_typedefs.pyx"]},
400+
{"sources": ["_heap.pyx"]},
401+
{"sources": ["_sorting.pyx"]},
403402
{"sources": ["_vector_sentinel.pyx"], "language": "c++", "include_np": True},
404403
{"sources": ["_isfinite.pyx"]},
405404
],

‎sklearn/cluster/_hierarchical_fast.pyx

Copy file name to clipboardExpand all lines: sklearn/cluster/_hierarchical_fast.pyx
+3-3Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@ cimport cython
55

66
from ..metrics._dist_metrics cimport DistanceMetric
77
from ..utils._fast_dict cimport IntFloatDict
8-
from ..utils._typedefs cimport float64_t, intp_t, bool_t
8+
from ..utils._typedefs cimport float64_t, intp_t, uint8_t
99

1010
# C++
1111
from cython.operator cimport dereference as deref, preincrement as inc
@@ -119,7 +119,7 @@ def _get_parents(
119119
nodes,
120120
heads,
121121
const intp_t[:] parents,
122-
bool_t[::1] not_visited
122+
uint8_t[::1] not_visited
123123
):
124124
"""Returns the heads of the given nodes, as defined by parents.
125125
@@ -465,7 +465,7 @@ def mst_linkage_core(
465465
"""
466466
cdef:
467467
intp_t n_samples = raw_data.shape[0]
468-
bool_t[:] in_tree = np.zeros(n_samples, dtype=bool)
468+
uint8_t[:] in_tree = np.zeros(n_samples, dtype=bool)
469469
float64_t[:, ::1] result = np.zeros((n_samples - 1, 3))
470470

471471
intp_t current_node = 0

‎sklearn/metrics/_dist_metrics.pxd.tp

Copy file name to clipboardExpand all lines: sklearn/metrics/_dist_metrics.pxd.tp
+54-59Lines changed: 54 additions & 59 deletions
Original file line numberDiff line numberDiff line change
@@ -9,26 +9,21 @@ implementation_specific_values = [
99
# for the float64 case as to still be able to expose the original
1010
# float64 implementation under the same API, namely `DistanceMetric`.
1111
#
12-
# On the other hand, '32' bit is used for `name_suffix` for the float32
12+
# On the other hand, '32' is used for `name_suffix` for the float32
1313
# case to remove ambiguity and use `DistanceMetric32`, which is not
1414
# publicly exposed.
1515
#
1616
# The metric mapping is adapted accordingly to route to the correct
1717
# implementations.
1818
#
19-
# We also use 64bit types as defined in `sklearn.utils._typedefs`
20-
# to maintain backward compatibility at the symbol level for extra
21-
# safety.
22-
#
23-
('', 'DTYPE_t', 'DTYPE'),
24-
('32', 'cnp.float32_t', 'np.float32')
19+
('', 'float64_t', 'np.float64'),
20+
('32', 'float32_t', 'np.float32')
2521
]
2622

2723
}}
28-
cimport numpy as cnp
2924
from libc.math cimport sqrt, exp
3025

31-
from ..utils._typedefs cimport DTYPE_t, ITYPE_t, SPARSE_INDEX_TYPE_t
26+
from ..utils._typedefs cimport float64_t, float32_t, int32_t, intp_t
3227

3328
{{for name_suffix, INPUT_DTYPE_t, INPUT_DTYPE in implementation_specific_values}}
3429

@@ -37,37 +32,37 @@ from ..utils._typedefs cimport DTYPE_t, ITYPE_t, SPARSE_INDEX_TYPE_t
3732
#
3833
# We use these for the default (euclidean) case so that they can be
3934
# inlined. This leads to faster computation for the most common case
40-
cdef inline DTYPE_t euclidean_dist{{name_suffix}}(
35+
cdef inline float64_t euclidean_dist{{name_suffix}}(
4136
const {{INPUT_DTYPE_t}}* x1,
4237
const {{INPUT_DTYPE_t}}* x2,
43-
ITYPE_t size,
38+
intp_t size,
4439
) except -1 nogil:
45-
cdef DTYPE_t tmp, d=0
46-
cdef cnp.intp_t j
40+
cdef float64_t tmp, d=0
41+
cdef intp_t j
4742
for j in range(size):
48-
tmp = <DTYPE_t> (x1[j] - x2[j])
43+
tmp = <float64_t> (x1[j] - x2[j])
4944
d += tmp * tmp
5045
return sqrt(d)
5146

5247

53-
cdef inline DTYPE_t euclidean_rdist{{name_suffix}}(
48+
cdef inline float64_t euclidean_rdist{{name_suffix}}(
5449
const {{INPUT_DTYPE_t}}* x1,
5550
const {{INPUT_DTYPE_t}}* x2,
56-
ITYPE_t size,
51+
intp_t size,
5752
) except -1 nogil:
58-
cdef DTYPE_t tmp, d=0
59-
cdef cnp.intp_t j
53+
cdef float64_t tmp, d=0
54+
cdef intp_t j
6055
for j in range(size):
61-
tmp = <DTYPE_t>(x1[j] - x2[j])
56+
tmp = <float64_t>(x1[j] - x2[j])
6257
d += tmp * tmp
6358
return d
6459

6560

66-
cdef inline DTYPE_t euclidean_dist_to_rdist{{name_suffix}}(const {{INPUT_DTYPE_t}} dist) except -1 nogil:
61+
cdef inline float64_t euclidean_dist_to_rdist{{name_suffix}}(const {{INPUT_DTYPE_t}} dist) except -1 nogil:
6762
return dist * dist
6863

6964

70-
cdef inline DTYPE_t euclidean_rdist_to_dist{{name_suffix}}(const {{INPUT_DTYPE_t}} dist) except -1 nogil:
65+
cdef inline float64_t euclidean_rdist_to_dist{{name_suffix}}(const {{INPUT_DTYPE_t}} dist) except -1 nogil:
7166
return sqrt(dist)
7267

7368

@@ -78,89 +73,89 @@ cdef class DistanceMetric{{name_suffix}}:
7873
# we must define them here so that cython's limited polymorphism will work.
7974
# Because we don't expect to instantiate a lot of these objects, the
8075
# extra memory overhead of this setup should not be an issue.
81-
cdef DTYPE_t p
82-
cdef const DTYPE_t[::1] vec
83-
cdef const DTYPE_t[:, ::1] mat
84-
cdef ITYPE_t size
76+
cdef float64_t p
77+
cdef const float64_t[::1] vec
78+
cdef const float64_t[:, ::1] mat
79+
cdef intp_t size
8580
cdef object func
8681
cdef object kwargs
8782

88-
cdef DTYPE_t dist(
83+
cdef float64_t dist(
8984
self,
9085
const {{INPUT_DTYPE_t}}* x1,
9186
const {{INPUT_DTYPE_t}}* x2,
92-
ITYPE_t size,
87+
intp_t size,
9388
) except -1 nogil
9489

95-
cdef DTYPE_t rdist(
90+
cdef float64_t rdist(
9691
self,
9792
const {{INPUT_DTYPE_t}}* x1,
9893
const {{INPUT_DTYPE_t}}* x2,
99-
ITYPE_t size,
94+
intp_t size,
10095
) except -1 nogil
10196

102-
cdef DTYPE_t dist_csr(
97+
cdef float64_t dist_csr(
10398
self,
10499
const {{INPUT_DTYPE_t}}* x1_data,
105-
const SPARSE_INDEX_TYPE_t[:] x1_indices,
100+
const int32_t[:] x1_indices,
106101
const {{INPUT_DTYPE_t}}* x2_data,
107-
const SPARSE_INDEX_TYPE_t[:] x2_indices,
108-
const SPARSE_INDEX_TYPE_t x1_start,
109-
const SPARSE_INDEX_TYPE_t x1_end,
110-
const SPARSE_INDEX_TYPE_t x2_start,
111-
const SPARSE_INDEX_TYPE_t x2_end,
112-
const ITYPE_t size,
102+
const int32_t[:] x2_indices,
103+
const int32_t x1_start,
104+
const int32_t x1_end,
105+
const int32_t x2_start,
106+
const int32_t x2_end,
107+
const intp_t size,
113108
) except -1 nogil
114109

115-
cdef DTYPE_t rdist_csr(
110+
cdef float64_t rdist_csr(
116111
self,
117112
const {{INPUT_DTYPE_t}}* x1_data,
118-
const SPARSE_INDEX_TYPE_t[:] x1_indices,
113+
const int32_t[:] x1_indices,
119114
const {{INPUT_DTYPE_t}}* x2_data,
120-
const SPARSE_INDEX_TYPE_t[:] x2_indices,
121-
const SPARSE_INDEX_TYPE_t x1_start,
122-
const SPARSE_INDEX_TYPE_t x1_end,
123-
const SPARSE_INDEX_TYPE_t x2_start,
124-
const SPARSE_INDEX_TYPE_t x2_end,
125-
const ITYPE_t size,
115+
const int32_t[:] x2_indices,
116+
const int32_t x1_start,
117+
const int32_t x1_end,
118+
const int32_t x2_start,
119+
const int32_t x2_end,
120+
const intp_t size,
126121
) except -1 nogil
127122

128123
cdef int pdist(
129124
self,
130125
const {{INPUT_DTYPE_t}}[:, ::1] X,
131-
DTYPE_t[:, ::1] D,
126+
float64_t[:, ::1] D,
132127
) except -1
133128

134129
cdef int cdist(
135130
self,
136131
const {{INPUT_DTYPE_t}}[:, ::1] X,
137132
const {{INPUT_DTYPE_t}}[:, ::1] Y,
138-
DTYPE_t[:, ::1] D,
133+
float64_t[:, ::1] D,
139134
) except -1
140135

141136
cdef int pdist_csr(
142137
self,
143138
const {{INPUT_DTYPE_t}}* x1_data,
144-
const SPARSE_INDEX_TYPE_t[:] x1_indices,
145-
const SPARSE_INDEX_TYPE_t[:] x1_indptr,
146-
const ITYPE_t size,
147-
DTYPE_t[:, ::1] D,
139+
const int32_t[:] x1_indices,
140+
const int32_t[:] x1_indptr,
141+
const intp_t size,
142+
float64_t[:, ::1] D,
148143
) except -1 nogil
149144

150145
cdef int cdist_csr(
151146
self,
152147
const {{INPUT_DTYPE_t}}* x1_data,
153-
const SPARSE_INDEX_TYPE_t[:] x1_indices,
154-
const SPARSE_INDEX_TYPE_t[:] x1_indptr,
148+
const int32_t[:] x1_indices,
149+
const int32_t[:] x1_indptr,
155150
const {{INPUT_DTYPE_t}}* x2_data,
156-
const SPARSE_INDEX_TYPE_t[:] x2_indices,
157-
const SPARSE_INDEX_TYPE_t[:] x2_indptr,
158-
const ITYPE_t size,
159-
DTYPE_t[:, ::1] D,
151+
const int32_t[:] x2_indices,
152+
const int32_t[:] x2_indptr,
153+
const intp_t size,
154+
float64_t[:, ::1] D,
160155
) except -1 nogil
161156

162-
cdef DTYPE_t _rdist_to_dist(self, {{INPUT_DTYPE_t}} rdist) except -1 nogil
157+
cdef float64_t _rdist_to_dist(self, {{INPUT_DTYPE_t}} rdist) except -1 nogil
163158

164-
cdef DTYPE_t _dist_to_rdist(self, {{INPUT_DTYPE_t}} dist) except -1 nogil
159+
cdef float64_t _dist_to_rdist(self, {{INPUT_DTYPE_t}} dist) except -1 nogil
165160

166161
{{endfor}}

0 commit comments

Comments
0 (0)
Morty Proxy This is a proxified and sanitized view of the page, visit original site.