8000 Specify .pyx in setup.files for cython generated extensions · scikit-learn/scikit-learn@69c5ae1 · GitHub
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lestevelesteve
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Specify .pyx in setup.files for cython generated extensions
More natural this way. Tweak the extensions to generate from .c and .cpp files for a release.
1 parent 7c731a6 commit 69c5ae1

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17 files changed

+122
-233
lines changed

17 files changed

+122
-233
lines changed

‎sklearn/__check_build/setup.py

Lines changed: 2 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -3,16 +3,12 @@
33

44
import numpy
55

6-
from sklearn._build_utils import add_cython_extension
7-
86

97
def configuration(parent_package='', top_path=None):
108
from numpy.distutils.misc_util import Configuration
119
config = Configuration('__check_build', parent_package, top_path)
12-
add_cython_extension(top_path,
13-
config,
14-
'_check_build',
15-
sources=['_check_build.c'],
10+
config.add_extension('_check_build',
11+
sources=['_check_build.pyx'],
1612
include_dirs=[numpy.get_include()])
1713

1814
return config

‎sklearn/_build_utils/__init__.py

Lines changed: 26 additions & 30 deletions
Original file line numberDiff line numberDiff line change
@@ -37,40 +37,36 @@ def atlas_not_found(blas_info_):
3737
return cblas_libs, blas_info
3838

3939

40-
def get_cython_source(filename):
41-
is_c_filename = filename.endswith('.c')
42-
is_cpp_filename = filename.endswith('.cpp')
43-
44-
# files in src are .c and .cpp files that are not cython-generated
45-
if ('src' + os.sep) in filename and (is_c_filename or is_cpp_filename):
46-
return filename
47-
elif is_c_filename:
48-
filename = filename[:-1]
49-
elif is_cpp_filename:
50-
filename = filename[:-3]
40+
def tweak_extensions_to_build_from_c_and_cpp_files(extensions):
41+
"""Modify the extensions to build from the .c and .cpp files.
42+
43+
This is useful for releases, this way cython is not required to
44+
run python setup.py install.
45+
"""
46+
for extension in extensions:
47+
sources = []
48+
for sfile in extension.sources:
49+
path, ext = os.path.splitext(sfile)
50+
if ext in ('.pyx', '.py'):
51+
if extension.language == 'c++':
52+
ext = '.cpp'
53+
else:
54+
ext = '.c'
55+
sfile = path + ext
56+
sources.append(sfile)
57+
extension.sources = sources
58+
59+
60+
def tweak_extensions(top_path, config):
61+
"""Tweaks between release and development mode."""
62+
is_release = os.path.exists(os.path.join(top_path, 'PKG-INFO'))
63+
64+
if is_release:
65+
tweak_extensions_to_build_from_c_and_cpp_files(config.ext_modules)
5166
else:
52-
raise ValueError('Only .c and .cpp files are supported. '
53-
'Got {0!r} instead'.format(filename))
54-
return filename + 'pyx'
55-
56-
57-
def add_cython_extension(top_path, config, name, sources, **kwargs):
58-
is_dev_version = not os.path.exists(os.path.join(top_path, 'PKG-INFO'))
59-
60-
if is_dev_version:
61-
sources = [get_cython_source(filename) for filename in sources]
62-
63-
config.add_extension(name, sources, **kwargs)
64-
65-
66-
def maybe_cythonize_extensions(top_path, config):
67-
is_dev_version = not os.path.exists(os.path.join(top_path, 'PKG-INFO'))
68-
69-
if is_dev_version:
7067
try:
7168
from Cython.Build import cythonize
7269
except ImportError:
7370
raise ValueError('Please install cython in order '
7471
'to build a scikit-learn development version')
75-
7672
config.ext_modules = cythonize(config.ext_modules)

‎sklearn/cluster/setup.py

Lines changed: 16 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,6 @@
66
import numpy
77

88
from sklearn._build_utils import get_blas_info
9-
from sklearn._build_utils import add_cython_extension
109

1110

1211
def configuration(parent_package='', top_path=None):
@@ -20,39 +19,31 @@ def configuration(parent_package='', top_path=None):
2019
libraries.append('m')
2120

2221
config = Configuration('cluster', parent_package, top_path)
23-
add_cython_extension(top_path,
24-
config,
25-
'_dbscan_inner',
26-
sources=['_dbscan_inner.cpp'],
22+
config.add_extension('_dbscan_inner',
23+
sources=['_dbscan_inner.pyx'],
2724
include_dirs=[numpy.get_include()],
2825
language="c++")
2926

30-
add_cython_extension(top_path,
31-
config,
32-
'_hierarchical',
33-
sources=['_hierarchical.cpp'],
27+
config.add_extension('_hierarchical',
28+
sources=['_hierarchical.pyx'],
3429
language="c++",
3530
include_dirs=[numpy.get_include()],
3631
libraries=libraries)
37-
add_cython_extension(top_path,
38-
config,
39-
'_k_means_elkan',
40-
sources=['_k_means_elkan.c'],
32+
config.add_extension('_k_means_elkan',
33+
sources=['_k_means_elkan.pyx'],
4134
include_dirs=[numpy.get_include()],
4235
libraries=libraries)
4336

44-
add_cython_extension(
45-
top_path,
46-
config,
47-
'_k_means',
48-
libraries=cblas_libs,
49-
sources=['_k_means.c'],
50-
include_dirs=[join('..', 'src', 'cblas'),
51-
numpy.get_include(),
52-
blas_info.pop('include_dirs', [])],
53-
extra_compile_args=blas_info.pop('extra_compile_args', []),
54-
**blas_info
55-
)
37+
config.add_extension('_k_means',
38+
libraries=cblas_libs,
39+
sources=['_k_means.pyx'],
40+
include_dirs=[join('..', 'src', 'cblas'),
41+
numpy.get_include(),
42+
blas_info.pop('include_dirs', [])],
43+
extra_compile_args=blas_info.pop(
44+
'extra_compile_args', []),
45+
**blas_info
46+
)
5647

5748
config.add_subpackage('tests')
5849

‎sklearn/datasets/setup.py

Lines changed: 2 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -2,8 +2,6 @@
22
import numpy
33
import os
44

5-
from sklearn._build_utils import add_cython_extension
6-
75

86
def configuration(parent_package='', top_path=None):
97
from numpy.distutils.misc_util import Configuration
@@ -12,10 +10,8 @@ def configuration(parent_package='', top_path=None):
1210
config.add_data_dir('descr')
1311
config.add_data_dir('images')
1412
config.add_data_dir(os.path.join('tests', 'data'))
15-
add_cython_extension(top_path,
16-
config,
17-
'_svmlight_format',
18-
sources=['_svmlight_format.c'],
13+
config.add_extension('_svmlight_format',
14+
sources=['_svmlight_format.pyx'],
1915
include_dirs=[numpy.get_include()])
2016
config.add_subpackage('tests')
2117
return config

‎sklearn/decomposition/setup.py

Lines changed: 4 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -2,8 +2,6 @@
22
import numpy
33
from numpy.distutils.misc_util import Configuration
44

5-
from sklearn._build_utils import add_cython_extension
6-
75

86
def configuration(parent_package="", top_path=None):
97
config = Configuration("decomposition", parent_package, top_path)
@@ -12,17 +10,13 @@ def configuration(parent_package="", top_path=None):
1210
if os.name == 'posix':
1311
libraries.append('m')
1412

15-
add_cython_extension(top_path,
16-
config,
17-
"_online_lda",
18-
sources=["_online_lda.c"],
13+
config.add_extension("_online_lda",
14+
sources=["_online_lda.pyx"],
1915
include_dirs=[numpy.get_include()],
2016
libraries=libraries)
2117

22-
add_cython_extension(top_path,
23-
config,
24-
'cdnmf_fast',
25-
sources=['cdnmf_fast.c'],
18+
config.add_extension('cdnmf_fast',
19+
sources=['cdnmf_fast.pyx'],
2620
include_dirs=[numpy.get_include()],
2721
libraries=libraries)
2822

‎sklearn/ensemble/setup.py

Lines changed: 2 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,15 +1,11 @@
11
import numpy
22
from numpy.distutils.misc_util import Configuration
33

4-
from sklearn._build_utils import add_cython_extension
5-
64

75
def configuration(parent_package="", top_path=None):
86
config = Configuration("ensemble", parent_package, top_path)
9-
add_cython_extension(top_path,
10-
config,
11-
"_gradient_boosting",
12-
sources=["_gradient_boosting.c"],
7+
config.add_extension("_gradient_boosting",
8+
sources=["_gradient_boosting.pyx"],
139
include_dirs=[numpy.get_include()])
1410

1511
config.add_subpackage("tests")

‎sklearn/feature_extraction/setup.py

Lines changed: 2 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,5 @@
11
import os
22

3-
from sklearn._build_utils import add_cython_extension
4-
53

64
def configuration(parent_package='', top_path=None):
75
import numpy
@@ -12,10 +10,8 @@ def configuration(parent_package='', top_path=None):
1210
if os.name == 'posix':
1311
libraries.append('m')
1412

15-
add_cython_extension(top_path,
16-
config,
17-
'_hashing',
18-
sources=['_hashing.c'],
13+
config.add_extension('_hashing',
14+
sources=['_hashing.pyx'],
1915
include_dirs=[numpy.get_include()],
2016
libraries=libraries)
2117
config.add_subpackage("tests")

‎sklearn/linear_model/setup.py

Lines changed: 5 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,6 @@
44
import numpy
55

66
from sklearn._build_utils import get_blas_info
7-
from sklearn._build_utils import add_cython_extension
87

98

109
def configuration(parent_package='', top_path=None):
@@ -17,20 +16,16 @@ def configuration(parent_package='', top_path=None):
1716
if os.name == 'posix':
1817
cblas_libs.append('m')
1918

20-
add_cython_extension(top_path,
21-
config,
22-
'cd_fast', sources=['cd_fast.c'],
19+
config.add_extension('cd_fast', sources=['cd_fast.pyx'],
2320
libraries=cblas_libs,
2421
include_dirs=[join('..', 'src', 'cblas'),
2522
numpy.get_include(),
2623
blas_info.pop('include_dirs', [])],
2724
extra_compile_args=blas_info.pop('extra_compile_args',
2825
[]), **blas_info)
2926

30-
add_cython_extension(top_path,
31-
config,
32-
'sgd_fast',
33-
sources=['sgd_fast.c'],
27+
config.add_extension('sgd_fast',
28+
sources=['sgd_fast.pyx'],
3429
include_dirs=[join('..', 'src', 'cblas'),
3530
numpy.get_include(),
3631
blas_info.pop('include_dirs', [])],
@@ -39,10 +34,8 @@ def configuration(parent_package='', top_path=None):
3934
[]),
4035
**blas_info)
4136

42-
add_cython_extension(top_path,
43-
config,
44-
'sag_fast',
45-
sources=['sag_fast.c'],
37+
config.add_extension('sag_fast',
38+
sources=['sag_fast.pyx'],
4639
include_dirs=numpy.get_include())
4740

4841
# add other directories

‎sklearn/manifold/setup.py

Lines changed: 4 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -4,29 +4,24 @@
44
import numpy
55
from numpy.distutils.misc_util import Configuration
66
from sklearn._build_utils import get_blas_info
7-
from sklearn._build_utils import add_cython_extension
87

98

109
def configuration(parent_package="", top_path=None):
1110
config = Configuration("manifold", parent_package, top_path)
1211
libraries = []
1312
if os.name == 'posix':
1413
libraries.append('m')
15-
add_cython_extension(top_path,
16-
config,
17-
"_utils",
18-
sources=["_utils.c"],
14+
config.add_extension("_utils",
15+
sources=["_utils.pyx"],
1916
include_dirs=[numpy.get_include()],
2017
libraries=libraries,
2118
extra_compile_args=["-O3"])
2219
cblas_libs, blas_info = get_blas_info()
2320
eca = blas_info.pop('extra_compile_args', [])
2421
eca.append("-O4")
25-
add_cython_extension(top_path,
26-
config,
27-
"_barnes_hut_tsne",
22+
config.add_extension("_barnes_hut_tsne",
2823
libraries=cblas_libs,
29-
sources=["_barnes_hut_tsne.c"],
24+
sources=["_barnes_hut_tsne.pyx"],
3025
include_dirs=[join('..', 'src', 'cblas'),
3126
numpy.get_include(),
3227
blas_info.pop('include_dirs', [])],

‎sklearn/metrics/cluster/setup.py

Lines changed: 2 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -3,18 +3,14 @@
33
import numpy
44
from numpy.distutils.misc_util import Configuration
55

6-
from sklearn._build_utils import add_cython_extension
7-
86

97
def configuration(parent_package="", top_path=None):
108
config = Configuration("metrics/cluster", parent_package, top_path)
119
libraries = []
1210
if os.name == 'posix':
1311
libraries.append('m')
14-
add_cython_extension(top_path,
15-
config,
16-
"expected_mutual_info_fast",
17-
sources=["expected_mutual_info_fast.c"],
12+
config.add_extension("expected_mutual_info_fast",
13+
sources=["expected_mutual_info_fast.pyx"],
1814
include_dirs=[numpy.get_include()],
1915
libraries=libraries)
2016

‎sklearn/metrics/setup.py

Lines changed: 2 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,6 @@
55
from numpy.distutils.misc_util import Configuration
66

77
from sklearn._build_utils import get_blas_info
8-
from sklearn._build_utils import add_cython_extension
98

109

1110
def configuration(parent_package="", top_path=None):
@@ -15,10 +14,8 @@ def configuration(parent_package="", top_path=None):
1514
if os.name == 'posix':
1615
cblas_libs.append('m')
1716

18-
add_cython_extension(top_path,
19-
config,
20-
"pairwise_fast",
21-
sources=["pairwise_fast.c"],
17+
config.add_extension("pairwise_fast",
18+
sources=["pairwise_fast.pyx"],
2219
include_dirs=[os.path.join('..', 'src', 'cblas'),
2320
numpy.get_include(),
2421
blas_info.pop('include_dirs', [])],

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