From eed8f56c787a251a6cad0f4291ca8f4055e463cf Mon Sep 17 00:00:00 2001
From: Jack Mitchell <ml@embed.me.uk>
Date: Fri, 22 Jan 2021 10:16:08 +0000
Subject: [PATCH] hack around numpy get_include to force looking in target
sysroot
---
sklearn/__check_build/setup.py | 4 ++--
sklearn/cluster/setup.py | 12 ++++++------
sklearn/datasets/setup.py | 4 ++--
sklearn/decomposition/setup.py | 6 +++---
sklearn/ensemble/setup.py | 22 +++++++++++-----------
sklearn/feature_extraction/setup.py | 4 ++--
sklearn/linear_model/setup.py | 8 ++++----
sklearn/manifold/setup.py | 6 +++---
sklearn/metrics/cluster/setup.py | 4 ++--
sklearn/neighbors/setup.py | 15 +++++++--------
sklearn/preprocessing/setup.py | 4 ++--
sklearn/setup.py | 4 ++--
sklearn/svm/setup.py | 11 ++++++-----
sklearn/tree/setup.py | 10 +++++-----
sklearn/utils/setup.py | 16 ++++++++--------
15 files changed, 65 insertions(+), 65 deletions(-)
diff --git a/sklearn/__check_build/setup.py b/sklearn/__check_build/setup.py
index b8c30d9c8..e2bfc90ee 100644
--- a/sklearn/__check_build/setup.py
+++ b/sklearn/__check_build/setup.py
@@ -1,7 +1,7 @@
# Author: Virgile Fritsch <virgile.fritsch@inria.fr>
# License: BSD 3 clause
-import numpy
+import numpy, os
def configuration(parent_package='', top_path=None):
@@ -9,7 +9,7 @@ def configuration(parent_package='', top_path=None):
config = Configuration('__check_build', parent_package, top_path)
config.add_extension('_check_build',
sources=['_check_build.pyx'],
- include_dirs=[numpy.get_include()])
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]])
return config
diff --git a/sklearn/cluster/setup.py b/sklearn/cluster/setup.py
index 48ed25c5c..bd395e3aa 100644
--- a/sklearn/cluster/setup.py
+++ b/sklearn/cluster/setup.py
@@ -2,7 +2,7 @@
# License: BSD 3 clause
import os
-import numpy
+import numpy, os
def configuration(parent_package='', top_path=None):
@@ -16,28 +16,28 @@ def configuration(parent_package='', top_path=None):
config.add_extension('_dbscan_inner',
sources=['_dbscan_inner.pyx'],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
language="c++")
config.add_extension('_hierarchical_fast',
sources=['_hierarchical_fast.pyx'],
language="c++",
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries)
config.add_extension('_k_means_fast',
sources=['_k_means_fast.pyx'],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries)
config.add_extension('_k_means_lloyd',
sources=['_k_means_lloyd.pyx'],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries)
config.add_extension('_k_means_elkan',
sources=['_k_means_elkan.pyx'],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries)
config.add_subpackage('tests')
diff --git a/sklearn/datasets/setup.py b/sklearn/datasets/setup.py
index 1107505d4..de4ac3c87 100644
--- a/sklearn/datasets/setup.py
+++ b/sklearn/datasets/setup.py
@@ -1,5 +1,5 @@
-import numpy
+import numpy, os
import os
import platform
@@ -14,7 +14,7 @@ def configuration(parent_package='', top_path=None):
if platform.python_implementation() != 'PyPy':
config.add_extension('_svmlight_format_fast',
sources=['_svmlight_format_fast.pyx'],
- include_dirs=[numpy.get_include()])
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]])
config.add_subpackage('tests')
return config
diff --git a/sklearn/decomposition/setup.py b/sklearn/decomposition/setup.py
index f915d6d78..26799c0af 100644
--- a/sklearn/decomposition/setup.py
+++ b/sklearn/decomposition/setup.py
@@ -1,5 +1,5 @@
import os
-import numpy
+import numpy, os
from numpy.distutils.misc_util import Configuration
@@ -12,12 +12,12 @@ def configuration(parent_package="", top_path=None):
config.add_extension("_online_lda_fast",
sources=["_online_lda_fast.pyx"],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries)
config.add_extension('_cdnmf_fast',
sources=['_cdnmf_fast.pyx'],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries)
config.add_subpackage("tests")
diff --git a/sklearn/ensemble/setup.py b/sklearn/ensemble/setup.py
index 05d71cf31..c12382220 100644
--- a/sklearn/ensemble/setup.py
+++ b/sklearn/ensemble/setup.py
@@ -1,4 +1,4 @@
-import numpy
+import numpy, os
from numpy.distutils.misc_util import Configuration
@@ -7,7 +7,7 @@ def configuration(parent_package="", top_path=None):
config.add_extension("_gradient_boosting",
sources=["_gradient_boosting.pyx"],
- include_dirs=[numpy.get_include()])
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]])
config.add_subpackage("tests")
@@ -15,39 +15,39 @@ def configuration(parent_package="", top_path=None):
config.add_extension(
"_hist_gradient_boosting._gradient_boosting",
sources=["_hist_gradient_boosting/_gradient_boosting.pyx"],
- include_dirs=[numpy.get_include()])
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]])
config.add_extension("_hist_gradient_boosting.histogram",
sources=["_hist_gradient_boosting/histogram.pyx"],
- include_dirs=[numpy.get_include()])
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]])
config.add_extension("_hist_gradient_boosting.splitting",
sources=["_hist_gradient_boosting/splitting.pyx"],
- include_dirs=[numpy.get_include()])
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]])
config.add_extension("_hist_gradient_boosting._binning",
sources=["_hist_gradient_boosting/_binning.pyx"],
- include_dirs=[numpy.get_include()])
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]])
config.add_extension("_hist_gradient_boosting._predictor",
sources=["_hist_gradient_boosting/_predictor.pyx"],
- include_dirs=[numpy.get_include()])
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]])
config.add_extension("_hist_gradient_boosting._loss",
sources=["_hist_gradient_boosting/_loss.pyx"],
- include_dirs=[numpy.get_include()])
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]])
config.add_extension("_hist_gradient_boosting._bitset",
sources=["_hist_gradient_boosting/_bitset.pyx"],
- include_dirs=[numpy.get_include()])
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]])
config.add_extension("_hist_gradient_boosting.common",
sources=["_hist_gradient_boosting/common.pyx"],
- include_dirs=[numpy.get_include()])
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]])
config.add_extension("_hist_gradient_boosting.utils",
sources=["_hist_gradient_boosting/utils.pyx"],
- include_dirs=[numpy.get_include()])
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]])
config.add_subpackage("_hist_gradient_boosting.tests")
diff --git a/sklearn/feature_extraction/setup.py b/sklearn/feature_extraction/setup.py
index 8c3bbb100..a872c7603 100644
--- a/sklearn/feature_extraction/setup.py
+++ b/sklearn/feature_extraction/setup.py
@@ -3,7 +3,7 @@ import platform
def configuration(parent_package='', top_path=None):
- import numpy
+ import numpy, os
from numpy.distutils.misc_util import Configuration
config = Configuration('feature_extraction', parent_package, top_path)
@@ -14,7 +14,7 @@ def configuration(parent_package='', top_path=None):
if platform.python_implementation() != 'PyPy':
config.add_extension('_hashing_fast',
sources=['_hashing_fast.pyx'],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries)
config.add_subpackage("tests")
diff --git a/sklearn/linear_model/setup.py b/sklearn/linear_model/setup.py
index d0c9e8c04..962340210 100644
--- a/sklearn/linear_model/setup.py
+++ b/sklearn/linear_model/setup.py
@@ -1,5 +1,5 @@
import os
-import numpy
+import numpy, os
from sklearn._build_utils import gen_from_templates
@@ -15,12 +15,12 @@ def configuration(parent_package='', top_path=None):
config.add_extension('_cd_fast',
sources=['_cd_fast.pyx'],
- include_dirs=numpy.get_include(),
+ include_dirs=os.environ["NUMPY_INCLUDE_PATH"],
libraries=libraries)
config.add_extension('_sgd_fast',
sources=['_sgd_fast.pyx'],
- include_dirs=numpy.get_include(),
+ include_dirs=os.environ["NUMPY_INCLUDE_PATH"],
libraries=libraries)
# generate sag_fast from template
@@ -29,7 +29,7 @@ def configuration(parent_package='', top_path=None):
config.add_extension('_sag_fast',
sources=['_sag_fast.pyx'],
- include_dirs=numpy.get_include())
+ include_dirs=os.environ["NUMPY_INCLUDE_PATH"])
# add other directories
config.add_subpackage('tests')
diff --git a/sklearn/manifold/setup.py b/sklearn/manifold/setup.py
index 0db2d5d04..959a4996a 100644
--- a/sklearn/manifold/setup.py
+++ b/sklearn/manifold/setup.py
@@ -1,6 +1,6 @@
import os
-import numpy
+import numpy, os
def configuration(parent_package="", top_path=None):
@@ -14,13 +14,13 @@ def configuration(parent_package="", top_path=None):
config.add_extension("_utils",
sources=["_utils.pyx"],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries,
extra_compile_args=["-O3"])
config.add_extension("_barnes_hut_tsne",
sources=["_barnes_hut_tsne.pyx"],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries,
extra_compile_args=['-O3'])
diff --git a/sklearn/metrics/cluster/setup.py b/sklearn/metrics/cluster/setup.py
index c39e414d9..98640b5f3 100644
--- a/sklearn/metrics/cluster/setup.py
+++ b/sklearn/metrics/cluster/setup.py
@@ -1,6 +1,6 @@
import os
-import numpy
+import numpy, os
from numpy.distutils.misc_util import Configuration
@@ -11,7 +11,7 @@ def configuration(parent_package="", top_path=None):
libraries.append('m')
config.add_extension("_expected_mutual_info_fast",
sources=["_expected_mutual_info_fast.pyx"],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries)
config.add_subpackage("tests")
diff --git a/sklearn/neighbors/setup.py b/sklearn/neighbors/setup.py
index 926404467..aeedcb940 100644
--- a/sklearn/neighbors/setup.py
+++ b/sklearn/neighbors/setup.py
@@ -2,7 +2,7 @@ import os
def configuration(parent_package='', top_path=None):
- import numpy
+ import numpy, os
from numpy.distutils.misc_util import Configuration
config = Configuration('neighbors', parent_package, top_path)
@@ -12,28 +12,27 @@ def configuration(parent_package='', top_path=None):
config.add_extension('_ball_tree',
sources=['_ball_tree.pyx'],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries)
config.add_extension('_kd_tree',
sources=['_kd_tree.pyx'],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries)
config.add_extension('_dist_metrics',
sources=['_dist_metrics.pyx'],
- include_dirs=[numpy.get_include(),
- os.path.join(numpy.get_include(),
- 'numpy')],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"],
+ os.path.join(os.environ["NUMPY_INCLUDE_PATH"], 'numpy')],
libraries=libraries)
config.add_extension('_typedefs',
sources=['_typedefs.pyx'],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries)
config.add_extension("_quad_tree",
sources=["_quad_tree.pyx"],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries)
config.add_subpackage('tests')
diff --git a/sklearn/preprocessing/setup.py b/sklearn/preprocessing/setup.py
index 29dae9b8f..7c059d90f 100644
--- a/sklearn/preprocessing/setup.py
+++ b/sklearn/preprocessing/setup.py
@@ -2,7 +2,7 @@ import os
def configuration(parent_package='', top_path=None):
- import numpy
+ import numpy, os
from numpy.distutils.misc_util import Configuration
config = Configuration('preprocessing', parent_package, top_path)
@@ -12,7 +12,7 @@ def configuration(parent_package='', top_path=None):
config.add_extension('_csr_polynomial_expansion',
sources=['_csr_polynomial_expansion.pyx'],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries)
config.add_subpackage('tests')
diff --git a/sklearn/setup.py b/sklearn/setup.py
index e5d7e6e26..a814bca87 100644
--- a/sklearn/setup.py
+++ b/sklearn/setup.py
@@ -6,7 +6,7 @@ from sklearn._build_utils import cythonize_extensions
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
- import numpy
+ import numpy, os
libraries = []
if os.name == 'posix':
@@ -69,7 +69,7 @@ def configuration(parent_package='', top_path=None):
# add cython extension module for isotonic regression
config.add_extension('_isotonic',
sources=['_isotonic.pyx'],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries,
)
diff --git a/sklearn/svm/setup.py b/sklearn/svm/setup.py
index dffcff8eb..d01614780 100644
--- a/sklearn/svm/setup.py
+++ b/sklearn/svm/setup.py
@@ -1,6 +1,6 @@
import os
from os.path import join
-import numpy
+import numpy, os
def configuration(parent_package='', top_path=None):
@@ -13,7 +13,7 @@ def configuration(parent_package='', top_path=None):
# newrand wrappers
config.add_extension('_newrand',
sources=['_newrand.pyx'],
- include_dirs=[numpy.get_include(),
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"],
join('src', 'newrand')],
depends=[join('src', 'newrand', 'newrand.h')],
language='c++',
@@ -34,6 +34,7 @@ def configuration(parent_package='', top_path=None):
extra_link_args=['-lstdc++'],
# Use C++11 to use the random number generator fix
extra_compiler_args=['-std=c++11'],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
)
libsvm_sources = ['_libsvm.pyx']
@@ -45,7 +46,7 @@ def configuration(parent_package='', top_path=None):
config.add_extension('_libsvm',
sources=libsvm_sources,
- include_dirs=[numpy.get_include(),
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"],
join('src', 'libsvm'),
join('src', 'newrand')],
libraries=['libsvm-skl'],
@@ -82,7 +83,7 @@ def configuration(parent_package='', top_path=None):
include_dirs=[join('.', 'src', 'liblinear'),
join('.', 'src', 'newrand'),
join('..', 'utils'),
- numpy.get_include()],
+ os.environ["NUMPY_INCLUDE_PATH"]],
depends=liblinear_depends,
# extra_compile_args=['-O0 -fno-inline'],
)
@@ -93,7 +94,7 @@ def configuration(parent_package='', top_path=None):
libsvm_sparse_sources = ['_libsvm_sparse.pyx']
config.add_extension('_libsvm_sparse', libraries=['libsvm-skl'],
sources=libsvm_sparse_sources,
- include_dirs=[numpy.get_include(),
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"],
join("src", "libsvm"),
join("src", "newrand")],
depends=[join("src", "libsvm", "svm.h"),
diff --git a/sklearn/tree/setup.py b/sklearn/tree/setup.py
index 079ae9d86..0308a5cf9 100644
--- a/sklearn/tree/setup.py
+++ b/sklearn/tree/setup.py
@@ -1,6 +1,6 @@
import os
-import numpy
+import numpy, os
from numpy.distutils.misc_util import Configuration
@@ -11,22 +11,22 @@ def configuration(parent_package="", top_path=None):
libraries.append('m')
config.add_extension("_tree",
sources=["_tree.pyx"],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries,
extra_compile_args=["-O3"])
config.add_extension("_splitter",
sources=["_splitter.pyx"],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries,
extra_compile_args=["-O3"])
config.add_extension("_criterion",
sources=["_criterion.pyx"],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries,
extra_compile_args=["-O3"])
config.add_extension("_utils",
sources=["_utils.pyx"],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries,
extra_compile_args=["-O3"])
diff --git a/sklearn/utils/setup.py b/sklearn/utils/setup.py
index 098adeecc..d24e1b1c8 100644
--- a/sklearn/utils/setup.py
+++ b/sklearn/utils/setup.py
@@ -5,7 +5,7 @@ from sklearn._build_utils import gen_from_templates
def configuration(parent_package='', top_path=None):
- import numpy
+ import numpy, os
from numpy.distutils.misc_util import Configuration
config = Configuration('utils', parent_package, top_path)
@@ -24,7 +24,7 @@ def configuration(parent_package='', top_path=None):
config.add_extension('arrayfuncs',
sources=['arrayfuncs.pyx'],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries)
config.add_extension('murmurhash',
@@ -34,12 +34,12 @@ def configuration(parent_package='', top_path=None):
config.add_extension('graph_shortest_path',
sources=['graph_shortest_path.pyx'],
- include_dirs=[numpy.get_include()])
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]])
config.add_extension('_fast_dict',
sources=['_fast_dict.pyx'],
language="c++",
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries)
config.add_extension('_openmp_helpers',
@@ -53,21 +53,21 @@ def configuration(parent_package='', top_path=None):
config.add_extension('_seq_dataset',
sources=['_seq_dataset.pyx'],
- include_dirs=[numpy.get_include()])
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]])
config.add_extension('_weight_vector',
sources=['_weight_vector.pyx'],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries)
config.add_extension("_random",
sources=["_random.pyx"],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries)
config.add_extension("_logistic_sigmoid",
sources=["_logistic_sigmoid.pyx"],
- include_dirs=[numpy.get_include()],
+ include_dirs=[os.environ["NUMPY_INCLUDE_PATH"]],
libraries=libraries)
config.add_subpackage('tests')