8000 ENH: implement nep 0015: merge multiarray and umath by mattip · Pull Request #10915 · numpy/numpy · GitHub
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ENH: implement nep 0015: merge multiarray and umath #10915

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Merged
merged 12 commits into from
Aug 31, 2018
Merged

ENH: implement nep 0015: merge multiarray and umath #10915

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31df302
MAINT: merge umath, multiarray into _multiarray, add python wrappers
mattip Apr 24, 2018
e8aea2e
MAINT: define _MULTIARRAYMODULE to use functions directly (not via Py…
mattip Apr 25, 2018
f88d576
MAINT: move declararions into umathmodule.h
mattip Jul 2, 2018
ad1f5b5
MAINT: fix more name replacements, __all__ imports
mattip Apr 25, 2018
92f01dd
MAINT: move scalar math intialization to before setup_scalartypes
mattip Apr 27, 2018
bd4500f
MAINT: move private -> common
mattip Jun 25, 2018
1bca48b
MAINT: move unchanging, non-api files to common
mattip Jun 25, 2018
c49f779
MAINT: create common_{src,dep}, move header includes to appropriate p…
mattip Jun 27, 2018
c9914e4
DOC: write release note
mattip Jul 17, 2018
9592ee2
MAINT: export newly added c-extension function
mattip Jul 18, 2018
8725087
DOC: add docstring to new python files
mattip Aug 1, 2018
03e0814
MAINT: remove code that codecov pointed out is superflous
mattip Aug 3, 2018
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4 changes: 2 additions & 2 deletions MANIFEST.in
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Expand Up @@ -14,8 +14,8 @@ recursive-include numpy/_build_utils *
recursive-include numpy/linalg/lapack_lite *.c *.h
include tox.ini
# Add sdist files whose use depends on local configuration.
include numpy/core/src/multiarray/cblasfuncs.c
include numpy/core/src/multiarray/python_xerbla.c
include numpy/core/src/common/cblasfuncs.c
include numpy/core/src/common/python_xerbla.c
# Adding scons build related files not found by distutils
recursive-include numpy/core/code_generators *.py *.txt
recursive-include numpy/core *.in *.h
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9 changes: 9 additions & 0 deletions doc/release/1.16.0-notes.rst
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Expand Up @@ -107,3 +107,12 @@ raise a ``DeprecationWarning`` if the array is not numerical (i.e.,
if ``np.positive(array)`` raises a ``TypeError``. For ``ndarray``
subclasses that override the default ``__array_ufunc__`` implementation,
the ``TypeError`` is passed on.
Umath and multiarray c-extension modules merged into a single module
--------------------------------------------------------------------

The two modules were merged, according to the first step in `NEP 15`_.
Previously `np.core.umath` and `np.core.multiarray` were the c-extension
modules, they are now python wrappers to the single `np.core/_multiarray_math`
c-extension module.

.. _`NEP 15` : http://www.numpy.org/neps/nep-0015-merge-multiarray-umath.html
4 changes: 2 additions & 2 deletions numpy/core/code_generators/generate_numpy_api.py
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Expand Up @@ -46,11 +46,11 @@
_import_array(void)
{
int st;
PyObject *numpy = PyImport_ImportModule("numpy.core.multiarray");
PyObject *numpy = PyImport_ImportModule("numpy.core._multiarray_umath");
PyObject *c_api = NULL;

if (numpy == NULL) {
PyErr_SetString(PyExc_ImportError, "numpy.core.multiarray failed to import");
PyErr_SetString(PyExc_ImportError, "numpy.core._multiarray_umath failed to import");
return -1;
}
c_api = PyObject_GetAttrString(numpy, "_ARRAY_API");
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5 changes: 3 additions & 2 deletions numpy/core/code_generators/generate_ufunc_api.py
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Expand Up @@ -36,11 +36,12 @@
static NPY_INLINE int
_import_umath(void)
{
PyObject *numpy = PyImport_ImportModule("numpy.core.umath");
PyObject *numpy = PyImport_ImportModule("numpy.core._multiarray_umath");
PyObject *c_api = NULL;

if (numpy == NULL) {
PyErr_SetString(PyExc_ImportError, "numpy.core.umath failed to import");
PyErr_SetString(PyExc_ImportError,
"numpy.core._multiarray_umath failed to import");
return -1;
}
c_api = PyObject_GetAttrString(numpy, "_UFUNC_API");
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2 changes: 2 additions & 0 deletions numpy/core/code_generators/generate_umath.py
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Expand Up @@ -1080,6 +1080,8 @@ def make_code(funcdict, filename):
Please make changes to the code generator program (%s)
**/
#include "cpuid.h"
#include "ufunc_object.h"
#include "ufunc_type_resolution.h"
%s

static int
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34 changes: 34 additions & 0 deletions numpy/core/multiarray.py
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@@ -0,0 +1,34 @@
"""
Create the numpy.core.multiarray namespace for backward compatibility. In v1.16
the multiarray and umath c-extension modules were merged into a single
_multiarray_umath extension module. So we replicate the old namespace
by importing from the extension module.
"""

from . import _multiarray_umath
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I think this file could do with either a docstring or a comment, explaining why it exists and is just a bunch of imports

from numpy.core._multiarray_umath import *
from numpy.core._multiarray_umath import (_fastCopyAndTranspose, _flagdict, _insert,
_reconstruct, _vec_string, _ARRAY_API, _monotonicity)

__all__ = ['_ARRAY_API', 'ALLOW_THREADS 10000 9;, 'BUFSIZE', 'CLIP', 'DATETIMEUNITS',
'ITEM_HASOBJECT', 'ITEM_IS_POINTER', 'LIST_PICKLE', 'MAXDIMS',
'MAY_SHARE_BOUNDS', 'MAY_SHARE_EXACT', 'NEEDS_INIT', 'NEEDS_PYAPI',
'RAISE', 'USE_GETITEM', 'USE_SETITEM', 'WRAP',
'_fastCopyAndTranspose', '_flagdict', '_insert', '_reconstruct',
'_vec_string', '_monotonicity',
'add_docstring', 'arange', 'array', 'bincount', 'broadcast', 'busday_count',
'busday_offset', 'busdaycalendar', 'can_cast', 'compare_chararrays',
'concatenate', 'copyto', 'correlate', 'correlate2', 'count_nonzero',
'c_einsum', 'datetime_as_string', 'datetime_data', 'digitize', 'dot',
'dragon4_positional', 'dragon4_scientific', 'dtype', 'empty', 'empty_like',
'error', 'flagsobj', 'flatiter', 'format_longfloat', 'frombuffer',
'fromfile', 'fromiter', 'fromstring', 'getbuffer', 'inner', 'int_asbuffer',
'interp', 'interp_complex', 'is_busday', 'lexsort', 'matmul',
'may_share_memory', 'min_scalar_type', 'ndarray', 'nditer', 'nested_iters',
'newbuffer', 'normalize_axis_index', 'packbits', 'promote_types',
'putmask', 'ravel_multi_index', 'result_type', 'scalar',
'set_datetimeparse_function', 'set_legacy_print_mode', 'set_numeric_ops',
'set_string_function', 'set_typeDict', 'shares_memory', 'test_interrupt',
'tracemalloc_domain', 'typeinfo', 'unpackbits', 'unravel_index', 'vdot',
'where', 'zeros']

5 changes: 1 addition & 4 deletions numpy/core/numeric.py
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Expand Up @@ -2919,10 +2919,7 @@ def _setdef():

def extend_all(module):
existing = set(__all__)
try:
mall = getattr(module, '__all__')
except AttributeError:
mall = [k for k in module.__dict__.keys() if not k.startswith('_')]
mall = getattr(module, '__all__')
for a in mall:
if a not in existing:
__all__.append(a)
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138 changes: 69 additions & 69 deletions numpy/core/setup.py
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Expand Up @@ -514,9 +514,9 @@ def generate_config_h(ext, build_dir):

def generate_numpyconfig_h(ext, build_dir):
"""Depends on config.h: generate_config_h has to be called before !"""
# put private include directory in build_dir on search path
# put common include directory in build_dir on search path
# allows using code generation in headers headers
config.add_include_dirs(join(build_dir, "src", "private"))
config.add_include_dirs(join(build_dir, "src", "common"))
config.add_include_dirs(join(build_dir, "src", "npymath"))

target = join(build_dir, header_dir, '_numpyconfig.h')
Expand Down Expand Up @@ -603,7 +603,7 @@ def generate_api(ext, build_dir):
generate_numpy_api = generate_api_func('generate_numpy_api')
generate_ufunc_api = generate_api_func('generate_ufunc_api')

config.add_include_dirs(join(local_dir, "src", "private"))
config.add_include_dirs(join(local_dir, "src", "common"))
config.add_include_dirs(join(local_dir, "src"))
config.add_include_dirs(join(local_dir))

Expand Down Expand Up @@ -700,26 +700,65 @@ def get_mathlib_info(*args):
npysort_sources = [join('src', 'npysort', 'quicksort.c.src'),
join('src', 'npysort', 'mergesort.c.src'),
join('src', 'npysort', 'heapsort.c.src'),
join('src', 'private', 'npy_partition.h.src'),
join('src', 'common', 'npy_partition.h.src'),
join('src', 'npysort', 'selection.c.src'),
join('src', 'private', 'npy_binsearch.h.src'),
join('src', 'common', 'npy_binsearch.h.src'),
join('src', 'npysort', 'binsearch.c.src'),
]
config.add_library('npysort',
sources=npysort_sources,
include_dirs=[])

#######################################################################
# multiarray module #
# _multiarray_umath module - common part #
#######################################################################

common_deps = [
join('src', 'common', 'array_assign.h'),
join('src', 'common', 'binop_override.h'),
join('src', 'common', 'cblasfuncs.h'),
join('src', 'common', 'lowlevel_strided_loops.h'),
join('src', 'common', 'mem_overlap.h'),
join('src', 'common', 'npy_config.h'),
join('src', 'common', 'npy_extint128.h'),
join('src', 'common', 'npy_longdouble.h'),
join('src', 'common', 'templ_common.h.src'),
join('src', 'common', 'ucsnarrow.h'),
join('src', 'common', 'ufunc_override.h'),
join('src', 'common', 'umathmodule.h'),
]

common_src = [
join('src', 'common', 'array_assign.c'),
join('src', 'common', 'mem_overlap.c'),
join('src', 'common', 'npy_longdouble.c'),
join('src', 'common', 'templ_common.h.src'),
join('src', 'common', 'ucsnarrow.c'),
join('src', 'common', 'ufunc_override.c'),
]

blas_info = get_info('blas_opt', 0)
if blas_info and ('HAVE_CBLAS', None) in blas_info.get('define_macros', []):
extra_info = blas_info
# These files are also in MANIFEST.in so that they are always in
# the source distribution independently of HAVE_CBLAS.
common_src.extend([join('src', 'common', 'cblasfuncs.c'),
join('src', 'common', 'python_xerbla.c'),
])
if uses_accelerate_framework(blas_info):
common_src.extend(get_sgemv_fix())
else:
extra_info = {}

#######################################################################
# _multiarray_umath module - multiarray part #
#######################################################################

multiarray_deps = [
join('src', 'multiarray', 'arrayobject.h'),
join('src', 'multiarray', 'arraytypes.h'),
join('src', 'multiarray', 'array_assign.h'),
join('src', 'multiarray', 'buffer.h'),
join('src', 'multiarray', 'calculation.h'),
join('src', 'multiarray', 'cblasfuncs.h'),
join('src', 'multiarray', 'common.h'),
join('src', 'multiarray', 'convert_datatype.h'),
join('src', 'multiarray', 'convert.h'),
Expand All @@ -742,17 +781,8 @@ def get_mathlib_info(*args):
join('src', 'multiarray', 'shape.h'),
join('src', 'multiarray', 'strfuncs.h'),
join('src', 'multiarray', 'typeinfo.h'),
join('src', 'multiarray', 'ucsnarrow.h'),
join('src', 'multiarray', 'usertypes.h'),
join('src', 'multiarray', 'vdot.h'),
join('src', 'private', 'npy_config.h'),
join('src', 'private', 'templ_common.h.src'),
join('src', 'private', 'lowlevel_strided_loops.h'),
join('src', 'private', 'mem_overlap.h'),
join('src', 'private', 'npy_longdouble.h'),
join('src', 'private', 'ufunc_override.h'),
join('src', 'private', 'binop_override.h'),
join('src', 'private', 'npy_extint128.h'),
join('include', 'numpy', 'arrayobject.h'),
join('include', 'numpy', '_neighborhood_iterator_imp.h'),
join('include', 'numpy', 'npy_endian.h'),
Expand All @@ -778,7 +808,6 @@ def get_mathlib_info(*args):
join('src', 'multiarray', 'alloc.c'),
join('src', 'multiarray', 'arrayobject.c'),
join('src', 'multiarray', 'arraytypes.c.src'),
join('src', 'multiarray', 'array_assign.c'),
join('src', 'multiarray', 'array_assign_scalar.c'),
join('src', 'multiarray', 'array_assign_array.c'),
join('src', 'multiarray', 'buffer.c'),
Expand Down Expand Up @@ -821,40 +850,11 @@ def get_mathlib_info(*args):
join('src', 'multiarray', 'temp_elide.c'),
join('src', 'multiarray', 'typeinfo.c'),
join('src', 'multiarray', 'usertypes.c'),
join('src', 'multiarray', 'ucsnarrow.c'),
join('src', 'multiarray', 'vdot.c'),
join('src', 'private', 'templ_common.h.src'),
join('src', 'private', 'mem_overlap.c'),
join('src', 'private', 'npy_longdouble.c'),
join('src', 'private', 'ufunc_override.c'),
]

blas_info = get_info('blas_opt', 0)
if blas_info and ('HAVE_CBLAS', None) in blas_info.get('define_macros', []):
extra_info = blas_info
# These files are also in MANIFEST.in so that they are always in
# the source distribution independently of HAVE_CBLAS.
multiarray_src.extend([join('src', 'multiarray', 'cblasfuncs.c'),
join('src', 'multiarray', 'python_xerbla.c'),
])
if uses_accelerate_framework(blas_info):
multiarray_src.extend(get_sgemv_fix())
else:
extra_info = {}

config.add_extension('multiarray',
sources=multiarray_src +
[generate_config_h,
generate_numpyconfig_h,
generate_numpy_api,
join(codegen_dir, 'generate_numpy_api.py'),
join('*.py')],
depends=deps + multiarray_deps,
libraries=['npymath', 'npysort'],
extra_info=extra_info)

#######################################################################
# umath module #
# _multiarray_umath module - umath part #
#######################################################################

def generate_umath_c(ext, build_dir):
Expand Down Expand Up @@ -883,34 +883,34 @@ def generate_umath_c(ext, build_dir):
join('src', 'umath', 'scalarmath.c.src'),
join('src', 'umath', 'ufunc_type_resolution.c'),
join('src', 'umath', 'override.c'),
join('src', 'private', 'mem_overlap.c'),
join('src', 'private', 'npy_longdouble.c'),
join('src', 'private', 'ufunc_override.c')]
]

umath_deps = [
generate_umath_py,
join('include', 'numpy', 'npy_math.h'),
join('include', 'numpy', 'halffloat.h'),
join('src', 'multiarray', 'common.h'),
join('src', 'private', 'templ_common.h.src'),
join('src', 'common', 'templ_common.h.src'),
join('src', 'umath', 'simd.inc.src'),
join('src', 'umath', 'override.h'),
join(codegen_dir, 'generate_ufunc_api.py'),
join('src', 'private', 'lowlevel_strided_loops.h'),
join('src', 'private', 'mem_overlap.h'),
join('src', 'private', 'npy_longdouble.h'),
join('src', 'private', 'ufunc_override.h'),
join('src', 'private', 'binop_override.h')] + npymath_sources

config.add_extension('umath',
sources=umath_src +
]

config.add_extension('_multiarray_umath',
sources=multiarray_src + umath_src +
npymath_sources + common_src +
[generate_config_h,
generate_numpyconfig_h,
generate_umath_c,
generate_ufunc_api],
depends=deps + umath_deps,
libraries=['npymath'],
)
generate_numpyconfig_h,
generate_numpy_api,
join(codegen_dir, 'generate_numpy_api.py'),
join('*.py'),
generate_umath_c,
generate_ufunc_api,
],
depends=deps + multiarray_deps + umath_deps +
common_deps,
libraries=['npymath', 'npysort'],
extra_info=extra_info)

#######################################################################
# umath_tests module #
Expand Down Expand Up @@ -939,9 +939,9 @@ def generate_umath_c(ext, build_dir):

config.add_extension('_multiarray_tests',
sources=[join('src', 'multiarray', '_multiarray_tests.c.src'),
join('src', 'private', 'mem_overlap.c')],
depends=[join('src', 'private', 'mem_overlap.h'),
join('src', 'private', 'npy_extint128.h')],
join('src', 'common', 'mem_overlap.c')],
depends=[join('src', 'common', 'mem_overlap.h'),
join('src', 'common', 'npy_extint128.h')],
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I'm able to reproduce the gcov issue locally on linux & moving this extension addition block up above _multiarray_umath module prevents mem_overlap.c from being excluded from the C coverage report.

The diff is below and build / unit tests still seem fine locally for me:

diff --git a/numpy/core/setup.py b/numpy/core/setup.py
index b306aa4..1588a26 100644
--- a/numpy/core/setup.py
+++ b/numpy/core/setup.py
@@ -710,6 +710,17 @@ def configuration(parent_package='',top_path=None):
                        include_dirs=[])

     #######################################################################
+    #                     multiarray_tests module                         #
+    #######################################################################
+
+    config.add_extension('_multiarray_tests',
+                    sources=[join('src', 'multiarray', '_multiarray_tests.c.src'),
+                             join('src', 'common', 'mem_overlap.c')],
+                    depends=[join('src', 'common', 'mem_overlap.h'),
+                             join('src', 'common', 'npy_extint128.h')],
+                    libraries=['npymath'])
+
+    #######################################################################
     #             _multiarray_umath module - common part                  #
     #######################################################################

@@ -933,16 +944,6 @@ def configuration(parent_package='',top_path=None):
     config.add_extension('_struct_ufunc_tests',
                     sources=[join('src', 'umath', '_struct_ufunc_tests.c.src')])

-    #######################################################################
-    #                     multiarray_tests module                         #
-    #######################################################################
-
-    config.add_extension('_multiarray_tests',
-                    sources=[join('src', 'multiarray', '_multiarray_tests.c.src'),
-                             join('src', 'common', 'mem_overlap.c')],
-                    depends=[join('src', 'common', 'mem_overlap.h'),
-                             join('src', 'common', 'npy_extint128.h')],
-                    libraries=['npymath'])

I could open a PR to do this on master, but since @mattip has been working on this code for a while I'll let him judge if this might be suitable & avoids merged conflicts if we change here, etc.

libraries=['npymath'])

#######################################################################
Expand Down
0 numpy/core/src/multiarray/array_assign.c → numpy/core/src/common/array_assign.c
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0 numpy/core/src/multiarray/array_assign.h → numpy/core/src/common/array_assign.h
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0 numpy/core/src/private/binop_override.h → numpy/core/src/common/binop_override.h
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0 numpy/core/src/multiarray/cblasfuncs.c → numpy/core/src/common/cblasfuncs.c
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0 numpy/core/src/multiarray/cblasfuncs.h → numpy/core/src/common/cblasfuncs.h
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0 numpy/core/src/private/get_attr_string.h → numpy/core/src/common/get_attr_string.h
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0 ...core/src/private/lowlevel_strided_loops.h → .../core/src/common/lowlevel_strided_loops.h
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0 numpy/core/src/private/mem_overlap.c → numpy/core/src/common/mem_overlap.c
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0 numpy/core/src/private/mem_overlap.h → numpy/core/src/common/mem_overlap.h
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0 numpy/core/src/private/npy_binsearch.h.src → numpy/core/src/common/npy_binsearch.h.src
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0 numpy/core/src/private/npy_cblas.h → numpy/core/src/common/npy_cblas.h
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0 numpy/core/src/private/npy_config.h → numpy/core/src/common/npy_config.h
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0 numpy/core/src/private/npy_extint128.h → numpy/core/src/common/npy_extint128.h
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0 numpy/core/src/private/npy_fpmath.h → numpy/core/src/common/npy_fpmath.h
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0 numpy/core/src/private/npy_import.h → numpy/core/src/common/npy_import.h
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0 numpy/core/src/private/npy_longdouble.c → numpy/core/src/common/npy_longdouble.c
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0 numpy/core/src/private/npy_longdouble.h → numpy/core/src/common/npy_longdouble.h
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0 numpy/core/src/private/npy_partition.h.src → numpy/core/src/common/npy_partition.h.src
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0 numpy/core/src/private/npy_pycompat.h → numpy/core/src/common/npy_pycompat.h
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0 numpy/core/src/private/npy_sort.h → numpy/core/src/common/npy_sort.h
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0 numpy/core/src/multiarray/python_xerbla.c → numpy/core/src/common/python_xerbla.c
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0 numpy/core/src/private/templ_common.h.src → numpy/core/src/common/templ_common.h.src
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0 numpy/core/src/multiarray/ucsnarrow.c → numpy/core/src/common/ucsnarrow.c
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0 numpy/core/src/multiarray/ucsnarrow.h → numpy/core/src/common/ucsnarrow.h
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0 numpy/core/src/private/ufunc_override.c → numpy/core/src/common/ufunc_override.c
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0 numpy/core/src/private/ufunc_override.h → numpy/core/src/common/ufunc_override.h
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8 changes: 8 additions & 0 deletions numpy/core/src/common/umathmodule.h
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Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
#include "__umath_generated.c"
#include "__ufunc_api.c"

PyObject * add_newdoc_ufunc(PyObject *NPY_UNUSED(dummy), PyObject *args);
PyObject * ufunc_frompyfunc(PyObject *NPY_UNUSED(dummy), PyObject *args, PyObject *NPY_UNUSED(kwds));
int initumath(PyObject *m);


2 changes: 1 addition & 1 deletion numpy/core/src/multiarray/descriptor.c
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Expand Up @@ -2401,7 +2401,7 @@ arraydescr_reduce(PyArray_Descr *self, PyObject *NPY_UNUSED(args))
if (ret == NULL) {
return NULL;
}
mod = PyImport_ImportModule("numpy.core.multiarray");
mod = PyImport_ImportModule("numpy.core._multiarray_umath");
if (mod == NULL) {
Py_DECREF(ret);
return NULL;
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2 changes: 1 addition & 1 deletion numpy/core/src/multiarray/methods.c
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Original file line number Diff line number Diff line change
Expand Up @@ -1566,7 +1566,7 @@ array_reduce(PyArrayObject *self, PyObject *NPY_UNUSED(args))
if (ret == NULL) {
return NULL;
}
mod = PyImport_ImportModule("numpy.core.multiarray");
mod = PyImport_ImportModule("numpy.core._multiarray_umath");
if (mod == NULL) {
Py_DECREF(ret);
return NULL;
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