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Update Numpy 1.16.4 patch
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‎graalpython/lib-graalpython/patches/numpy/sdist/numpy-1.16.4.patch‎

Lines changed: 158 additions & 78 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
diff --git a/numpy/__init__.py b/numpy/__init__.py
2-
index ba88c733f..e4db40429 100644
2+
index ba88c73..e4db404 100644
33
--- a/numpy/__init__.py
44
+++ b/numpy/__init__.py
55
@@ -206,7 +206,7 @@ else:
@@ -12,7 +12,7 @@ index ba88c733f..e4db40429 100644
1212
msg = ("The current Numpy installation ({!r}) fails to "
1313
"pass simple sanity checks. This can be caused for example "
1414
diff --git a/numpy/core/getlimits.py b/numpy/core/getlimits.py
15-
index 544b8b35f..799f669e6 100644
15+
index 544b8b3..799f669 100644
1616
--- a/numpy/core/getlimits.py
1717
+++ b/numpy/core/getlimits.py
1818
@@ -154,87 +154,6 @@ def _register_known_types():
@@ -103,10 +103,47 @@ index 544b8b35f..799f669e6 100644
103103

104104
def _get_machar(ftype):
105105
""" Get MachAr instance or MachAr-like instance
106+
diff --git a/numpy/core/include/numpy/npy_common.h b/numpy/core/include/numpy/npy_common.h
107+
index 64aaaac..4e80fce 100644
108+
--- a/numpy/core/include/numpy/npy_common.h
109+
+++ b/numpy/core/include/numpy/npy_common.h
110+
@@ -1080,4 +1080,10 @@ typedef npy_int64 npy_datetime;
111+
112+
/* End of typedefs for numarray style bit-width names */
113+
114+
+#if !GRAALVM_PYTHON && (PY_VERSION_HEX < 0x03090000)
115+
+#define Py_SET_REFCNT(ob, v) ((_PyObject_CAST(ob)->ob_refcnt = (v)))
116+
+#define Py_SET_TYPE(ob, v) ((_PyObject_CAST(ob)->ob_type) = (v))
117+
+#define Py_SET_SIZE(ob, v) ((_PyVarObject_CAST(ob)->ob_size = (Py_ssize_t) (v)))
118+
+#endif
119+
+
120+
#endif
121+
diff --git a/numpy/core/setup.py b/numpy/core/setup.py
122+
index aad0aae..de1afd0 100644
123+
--- a/numpy/core/setup.py
124+
+++ b/numpy/core/setup.py
125+
@@ -757,7 +757,7 @@ def configuration(parent_package='',top_path=None):
126+
join('src', 'common', 'numpyos.c'),
127+
]
128+
129+
- blas_info = get_info('blas_opt', 0)
130+
+ blas_info = None # get_info('blas_opt', 0)
131+
if blas_info and ('HAVE_CBLAS', None) in blas_info.get('define_macros', []):
132+
extra_info = blas_info
133+
# These files are also in MANIFEST.in so that they are always in
106134
diff --git a/numpy/core/setup_common.py b/numpy/core/setup_common.py
107-
index f837df112..d3ce70ddd 100644
135+
index f837df1..ef8bc9a 100644
108136
--- a/numpy/core/setup_common.py
109137
+++ b/numpy/core/setup_common.py
138+
@@ -110,7 +110,7 @@ MANDATORY_FUNCS = ["sin", "cos", "tan", "sinh", "cosh", "tanh", "fabs",
139+
OPTIONAL_STDFUNCS = ["expm1", "log1p", "acosh", "asinh", "atanh",
140+
"rint", "trunc", "exp2", "log2", "hypot", "atan2", "pow",
141+
"copysign", "nextafter", "ftello", "fseeko",
142+
- "strtoll", "strtoull", "cbrt", "strtold_l", "fallocate",
143+
+ "strtoll", "strtoull", "cbrt", "fallocate",
144+
"backtrace", "madvise"]
145+
146+
110147
@@ -243,8 +243,8 @@ def check_long_double_representation(cmd):
111148
except ValueError:
112149
# try linking to support CC="gcc -flto" or icc -ipo
@@ -118,21 +155,8 @@ index f837df112..d3ce70ddd 100644
118155
src, obj = cmd._compile(body, None, None, 'c')
119156
cmd.temp_files.append("_configtest")
120157
cmd.compiler.link_executable([obj], "_configtest")
121-
diff --git a/numpy/core/setup.py b/numpy/core/setup.py
122-
index 8b2ded1f2..8a9295a27 100755
123-
--- a/numpy/core/setup.py
124-
+++ b/numpy/core/setup.py
125-
@@ -755,7 +755,7 @@ def configuration(parent_package='',top_path=None):
126-
join('src', 'common', 'numpyos.c'),
127-
]
128-
129-
- blas_info = get_info('blas_opt', 0)
130-
+ blas_info = None # get_info('blas_opt', 0)
131-
if blas_info and ('HAVE_CBLAS', None) in blas_info.get('define_macros', []):
132-
extra_info = blas_info
133-
# These files are also in MANIFEST.in so that they are always in
134158
diff --git a/numpy/core/src/multiarray/_multiarray_tests.c.src b/numpy/core/src/multiarray/_multiarray_tests.c.src
135-
index 9061c0518..bb1dcff0c 100644
159+
index 9061c05..bb1dcff 100644
136160
--- a/numpy/core/src/multiarray/_multiarray_tests.c.src
137161
+++ b/numpy/core/src/multiarray/_multiarray_tests.c.src
138162
@@ -1728,21 +1728,7 @@ get_fpu_mode(PyObject *NPY_UNUSED(self), PyObject *args)
@@ -158,7 +182,7 @@ index 9061c0518..bb1dcff0c 100644
158182

159183
/*
160184
diff --git a/numpy/core/src/multiarray/alloc.c b/numpy/core/src/multiarray/alloc.c
161-
index 6755095d7..e2fbae64f 100644
185+
index 6755095..e2fbae6 100644
162186
--- a/numpy/core/src/multiarray/alloc.c
163187
+++ b/numpy/core/src/multiarray/alloc.c
164188
@@ -73,14 +73,6 @@ _npy_alloc_cache(npy_uintp nelem, npy_uintp esz, npy_uint msz,
@@ -176,8 +200,34 @@ index 6755095d7..e2fbae64f 100644
176200
#endif
177201
}
178202
return p;
203+
diff --git a/numpy/core/src/multiarray/scalarapi.c b/numpy/core/src/multiarray/scalarapi.c
204+
index bc435d1..b1e1e2f 100644
205+
--- a/numpy/core/src/multiarray/scalarapi.c
206+
+++ b/numpy/core/src/multiarray/scalarapi.c
207+
@@ -789,7 +789,7 @@ PyArray_Scalar(void *data, PyArray_Descr *descr, PyObject *base)
208+
vobj->descr = descr;
209+
Py_INCREF(descr);
210+
vobj->obval = NULL;
211+
- Py_SIZE(vobj) = itemsize;
212+
+ Py_SET_SIZE(vobj, itemsize);
213+
vobj->flags = NPY_ARRAY_CARRAY | NPY_ARRAY_F_CONTIGUOUS | NPY_ARRAY_OWNDATA;
214+
swap = 0;
215+
if (PyDataType_HASFIELDS(descr)) {
216+
diff --git a/numpy/core/src/multiarray/scalartypes.c.src b/numpy/core/src/multiarray/scalartypes.c.src
217+
index 52de312..4a8a4c4 100644
218+
--- a/numpy/core/src/multiarray/scalartypes.c.src
219+
+++ b/numpy/core/src/multiarray/scalartypes.c.src
220+
@@ -3067,7 +3067,7 @@ void_arrtype_new(PyTypeObject *type, PyObject *args, PyObject *NPY_UNUSED(kwds))
221+
return PyErr_NoMemory();
222+
}
223+
((PyVoidScalarObject *)ret)->obval = destptr;
224+
- Py_SIZE((PyVoidScalarObject *)ret) = (int) memu;
225+
+ Py_SET_SIZE((PyVoidScalarObject *)ret, (int) memu);
226+
((PyVoidScalarObject *)ret)->descr =
227+
PyArray_DescrNewFromType(NPY_VOID);
228+
((PyVoidScalarObject *)ret)->descr->elsize = (int) memu;
179229
diff --git a/numpy/core/src/multiarray/typeinfo.c b/numpy/core/src/multiarray/typeinfo.c
180-
index 14c4f27cb..c5a72b123 100644
230+
index 14c4f27..c5a72b1 100644
181231
--- a/numpy/core/src/multiarray/typeinfo.c
182232
+++ b/numpy/core/src/multiarray/typeinfo.c
183233
@@ -105,8 +105,7 @@ PyArray_typeinforanged(
@@ -191,7 +241,7 @@ index 14c4f27cb..c5a72b123 100644
191241
static int
192242
PyStructSequence_InitType2(PyTypeObject *type, PyStructSequence_Desc *desc) {
193243
diff --git a/numpy/core/src/npymath/ieee754.c.src b/numpy/core/src/npymath/ieee754.c.src
194-
index d960838c8..56a8056aa 100644
244+
index d960838..56a8056 100644
195245
--- a/numpy/core/src/npymath/ieee754.c.src
196246
+++ b/numpy/core/src/npymath/ieee754.c.src
197247
@@ -558,12 +558,10 @@ npy_longdouble npy_nextafterl(npy_longdouble x, npy_longdouble y)
@@ -464,8 +514,21 @@ index d960838c8..56a8056aa 100644
464514
}
465515

466516
#endif
517+
diff --git a/numpy/core/src/umath/_rational_tests.c.src b/numpy/core/src/umath/_rational_tests.c.src
518+
index 9e74845..ce21ee4 100644
519+
--- a/numpy/core/src/umath/_rational_tests.c.src
520+
+++ b/numpy/core/src/umath/_rational_tests.c.src
521+
@@ -1193,7 +1193,7 @@ PyMODINIT_FUNC init_rational_tests(void) {
522+
npyrational_arrfuncs.fill = npyrational_fill;
523+
npyrational_arrfuncs.fillwithscalar = npyrational_fillwithscalar;
524+
/* Left undefined: scanfunc, fromstr, sort, argsort */
525+
- Py_TYPE(&npyrational_descr) = &PyArrayDescr_Type;
526+
+ Py_SET_TYPE(&npyrational_descr, &PyArrayDescr_Type);
527+
npy_rational = PyArray_RegisterDataType(&npyrational_descr);
528+
if (npy_rational<0) {
529+
goto fail;
467530
diff --git a/numpy/core/src/umath/extobj.c b/numpy/core/src/umath/extobj.c
468-
index aea1815e8..b83fab9e5 100644
531+
index aea1815..b83fab9 100644
469532
--- a/numpy/core/src/umath/extobj.c
470533
+++ b/numpy/core/src/umath/extobj.c
471534
@@ -282,7 +282,7 @@ _check_ufunc_fperr(int errmask, PyObject *extobj, const char *ufunc_name) {
@@ -478,7 +541,7 @@ index aea1815e8..b83fab9e5 100644
478541
return 0;
479542
}
480543
diff --git a/numpy/core/src/umath/loops.c.src b/numpy/core/src/umath/loops.c.src
481-
index 975a5e6b8..55f3a4605 100644
544+
index 975a5e6..55f3a46 100644
482545
--- a/numpy/core/src/umath/loops.c.src
483546
+++ b/numpy/core/src/umath/loops.c.src
484547
@@ -1872,7 +1872,7 @@ NPY_NO_EXPORT void
@@ -554,7 +617,7 @@ index 975a5e6b8..55f3a4605 100644
554617
/**end repeat1**/
555618

556619
diff --git a/numpy/core/src/umath/reduction.c b/numpy/core/src/umath/reduction.c
557-
index 791d3693f..317ee714f 100644
620+
index 791d369..317ee71 100644
558621
--- a/numpy/core/src/umath/reduction.c
559622
+++ b/numpy/core/src/umath/reduction.c
560623
@@ -534,7 +534,7 @@ PyUFunc_ReduceWrapper(PyArrayObject *operand, PyArrayObject *out,
@@ -567,7 +630,7 @@ index 791d3693f..317ee714f 100644
567630
if (NpyIter_GetIterSize(iter) != 0) {
568631
NpyIter_IterNextFunc *iternext;
569632
diff --git a/numpy/core/src/umath/scalarmath.c.src b/numpy/core/src/umath/scalarmath.c.src
570-
index a7987acda..aae7c30e3 100644
633+
index a7987ac..aae7c30 100644
571634
--- a/numpy/core/src/umath/scalarmath.c.src
572635
+++ b/numpy/core/src/umath/scalarmath.c.src
573636
@@ -846,7 +846,7 @@ static PyObject *
@@ -634,7 +697,7 @@ index a7987acda..aae7c30e3 100644
634697
int bufsize, errmask;
635698
PyObject *errobj;
636699
diff --git a/numpy/core/src/umath/simd.inc.src b/numpy/core/src/umath/simd.inc.src
637-
index 4bb8569be..8b120d7ff 100644
700+
index 4bb8569..8b120d7 100644
638701
--- a/numpy/core/src/umath/simd.inc.src
639702
+++ b/numpy/core/src/umath/simd.inc.src
640703
@@ -1047,7 +1047,7 @@ sse2_@kind@_@TYPE@(@type@ * ip, @type@ * op, const npy_intp n)
@@ -665,7 +728,7 @@ index 4bb8569be..8b120d7ff 100644
665728
/**end repeat1**/
666729

667730
diff --git a/numpy/core/src/umath/ufunc_object.c b/numpy/core/src/umath/ufunc_object.c
668-
index d1b029c18..2bdff3d6c 100644
731+
index d1b029c..2bdff3d 100644
669732
--- a/numpy/core/src/umath/ufunc_object.c
670733
+++ b/numpy/core/src/umath/ufunc_object.c
671734
@@ -107,7 +107,7 @@ PyUFunc_getfperr(void)
@@ -722,11 +785,24 @@ index d1b029c18..2bdff3d6c 100644
722785

723786
retval = execute_legacy_ufunc_loop(ufunc, trivial_loop_ok,
724787
op, dtypes, order,
788+
diff --git a/numpy/distutils/ccompiler.py b/numpy/distutils/ccompiler.py
789+
index 14451fa..85e64cc 100644
790+
--- a/numpy/distutils/ccompiler.py
791+
+++ b/numpy/distutils/ccompiler.py
792+
@@ -682,7 +682,7 @@ def CCompiler_cxx_compiler(self):
793+
return self
794+
795+
cxx = copy(self)
796+
- cxx.compiler_so = [cxx.compiler_cxx[0]] + cxx.compiler_so[1:]
797+
+ cxx.compiler_so = cxx.compiler_cxx + cxx.compiler_so[1:]
798+
if sys.platform.startswith('aix') and 'ld_so_aix' in cxx.linker_so[0]:
799+
# AIX needs the ld_so_aix script included with Python
800+
cxx.linker_so = [cxx.linker_so[0], cxx.compiler_cxx[0]] \
725801
diff --git a/numpy/distutils/system_info.py b/numpy/distutils/system_info.py
726-
index 9e192329f63..85a0c932145 100644
802+
index 806f4f7..358112d 100644
727803
--- a/numpy/distutils/system_info.py
728804
+++ b/numpy/distutils/system_info.py
729-
@@ -2494,8 +2494,6 @@ def calc_info(self):
805+
@@ -1922,8 +1922,6 @@ class accelerate_info(system_info):
730806
'accelerate' in libraries):
731807
if intel:
732808
args.extend(['-msse3'])
@@ -735,7 +811,7 @@ index 9e192329f63..85a0c932145 100644
735811
args.extend([
736812
'-I/System/Library/Frameworks/vecLib.framework/Headers'])
737813
link_args.extend(['-Wl,-framework', '-Wl,Accelerate'])
738-
@@ -2504,8 +2502,6 @@ def calc_info(self):
814+
@@ -1932,8 +1930,6 @@ class accelerate_info(system_info):
739815
'veclib' in libraries):
740816
if intel:
741817
args.extend(['-msse3'])
@@ -744,21 +820,34 @@ index 9e192329f63..85a0c932145 100644
744820
args.extend([
745821
'-I/System/Library/Frameworks/vecLib.framework/Headers'])
746822
link_args.extend(['-Wl,-framework', '-Wl,vecLib'])
747-
diff --git a/numpy/distutils/ccompiler.py b/numpy/distutils/ccompiler.py
748-
index 14451fa66..85e64cc6e 100644
749-
--- a/numpy/distutils/ccompiler.py
750-
+++ b/numpy/distutils/ccompiler.py
751-
@@ -682,7 +682,7 @@ def CCompiler_cxx_compiler(self):
752-
return self
753-
754-
cxx = copy(self)
755-
- cxx.compiler_so = [cxx.compiler_cxx[0]] + cxx.compiler_so[1:]
756-
+ cxx.compiler_so = cxx.compiler_cxx + cxx.compiler_so[1:]
757-
if sys.platform.startswith('aix') and 'ld_so_aix' in cxx.linker_so[0]:
758-
# AIX needs the ld_so_aix script included with Python
759-
cxx.linker_so = [cxx.linker_so[0], cxx.compiler_cxx[0]] \
823+
diff --git a/numpy/f2py/rules.py b/numpy/f2py/rules.py
824+
index 23d36b2..264cc2c 100644
825+
--- a/numpy/f2py/rules.py
826+
+++ b/numpy/f2py/rules.py
827+
@@ -208,7 +208,7 @@ PyMODINIT_FUNC init#modulename#(void) {
828+
#else
829+
\tm = #modulename#_module = Py_InitModule(\"#modulename#\", f2py_module_methods);
830+
#endif
831+
-\tPy_TYPE(&PyFortran_Type) = &PyType_Type;
832+
+\tPy_SET_TYPE(&PyFortran_Type, &PyType_Type);
833+
\timport_array();
834+
\tif (PyErr_Occurred())
835+
\t\t{PyErr_SetString(PyExc_ImportError, \"can't initialize module #modulename# (failed to import numpy)\"); return RETVAL;}
836+
diff --git a/numpy/f2py/tests/src/array_from_pyobj/wrapmodule.c b/numpy/f2py/tests/src/array_from_pyobj/wrapmodule.c
837+
index 7f46303..f5bb77a 100644
838+
--- a/numpy/f2py/tests/src/array_from_pyobj/wrapmodule.c
839+
+++ b/numpy/f2py/tests/src/array_from_pyobj/wrapmodule.c
840+
@@ -143,7 +143,7 @@ PyMODINIT_FUNC inittest_array_from_pyobj_ext(void) {
841+
#else
842+
m = wrap_module = Py_InitModule("test_array_from_pyobj_ext", f2py_module_methods);
843+
#endif
844+
- Py_TYPE(&PyFortran_Type) = &PyType_Type;
845+
+ Py_SET_TYPE(&PyFortran_Type, &PyType_Type);
846+
import_array();
847+
if (PyErr_Occurred())
848+
Py_FatalError("can't initialize module wrap (failed to import numpy)");
760849
diff --git a/numpy/linalg/setup.py b/numpy/linalg/setup.py
761-
index 66c07c9e1..847116fdc 100644
850+
index 66c07c9..847116f 100644
762851
--- a/numpy/linalg/setup.py
763852
+++ b/numpy/linalg/setup.py
764853
@@ -29,6 +29,7 @@ def configuration(parent_package='', top_path=None):
@@ -770,7 +859,7 @@ index 66c07c9e1..847116fdc 100644
770859
print("### Warning: Using unoptimized lapack ###")
771860
return all_sources
772861
diff --git a/numpy/linalg/umath_linalg.c.src b/numpy/linalg/umath_linalg.c.src
773-
index 9fc68a7aa..6c04f96c1 100644
862+
index 9fc68a7..6c04f96 100644
774863
--- a/numpy/linalg/umath_linalg.c.src
775864
+++ b/numpy/linalg/umath_linalg.c.src
776865
@@ -386,7 +386,7 @@ static NPY_INLINE int
@@ -791,37 +880,28 @@ index 9fc68a7aa..6c04f96c1 100644
791880
}
792881
}
793882

794-
diff --git a/setup.py b/setup.py
795-
index 8b2ded1f2..8a9295a27 100755
796-
--- a/setup.py
797-
+++ b/setup.py
798-
@@ -364,6 +364,8 @@ def setup_package():
799-
metadata = dict(
800-
name = 'numpy',
801-
maintainer = "NumPy Developers",
802-
+ zip_safe = False, # Truffle: make sure we're not zipped
803-
+ include_package_data = True,
804-
maintainer_email = "numpy-discussion@python.org",
805-
description = DOCLINES[0],
806-
long_description = "\n".join(DOCLINES[2:]),
807-
@@ -376,7 +378,6 @@ def setup_package():
808-
test_suite='nose.collector',
809-
cmdclass={"sdist": sdist_checked},
810-
python_requires='>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*',
811-
- zip_safe=False,
812-
entry_points={
813-
'console_scripts': f2py_cmds
814-
},
815-
diff --git a/numpy/core/setup_common.py b/numpy/core/setup_common.py
816-
index d3ce70d..ef8bc9a 100644
817-
--- a/numpy/core/setup_common.py
818-
+++ b/numpy/core/setup_common.py
819-
@@ -110,7 +110,7 @@ MANDATORY_FUNCS = ["sin", "cos", "tan", "sinh", "cosh", "tanh", "fabs",
820-
OPTIONAL_STDFUNCS = ["expm1", "log1p", "acosh", "asinh", "atanh",
821-
"rint", "trunc", "exp2", "log2", "hypot", "atan2", "pow",
822-
"copysign", "nextafter", "ftello", "fseeko",
823-
- "strtoll", "strtoull", "cbrt", "strtold_l", "fallocate",
824-
+ "strtoll", "strtoull", "cbrt", "fallocate",
825-
"backtrace", "madvise"]
826-
827-
883+
diff --git a/numpy/random/mtrand/mtrand.c b/numpy/random/mtrand/mtrand.c
884+
index f9351e1..18c18e5 100644
885+
--- a/numpy/random/mtrand/mtrand.c
886+
+++ b/numpy/random/mtrand/mtrand.c
887+
@@ -1332,7 +1332,7 @@ static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
888+
if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) {
889+
Py_INCREF(x);
890+
PyList_SET_ITEM(list, len, x);
891+
- Py_SIZE(list) = len+1;
892+
+ Py_SET_SIZE(list, len+1);
893+
return 0;
894+
}
895+
return PyList_Append(list, x);
896+
@@ -37807,9 +37807,9 @@ static void __pyx_tp_dealloc_6mtrand_RandomState(PyObject *o) {
897+
{
898+
PyObject *etype, *eval, *etb;
899+
PyErr_Fetch(&etype, &eval, &etb);
900+
- ++Py_REFCNT(o);
901+
+ Py_SET_REFCNT(o, Py_REFCNT(o)+1);
902+
__pyx_pw_6mtrand_11RandomState_3__dealloc__(o);
903+
- --Py_REFCNT(o);
904+
+ Py_SET_REFCNT(o, Py_REFCNT(o)-1);
905+
PyErr_Restore(etype, eval, etb);
906+
}
907+
Py_CLEAR(p->lock);

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