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ENH, DEP refactor updateifcopy #9451

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b2837ab
ENH: add API to resolve UPDATEONCOPY outside dealloc, test and use
mattip Jul 23, 2017
586d53e
ENH, DEC NPY_ARRAY_UPDATEIFCOPY -> NPY_ARRAY_UPATEIFCOPY_CLEAR_B4_EXIT
mattip Aug 19, 2017
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15 changes: 15 additions & 0 deletions doc/release/1.14.0-notes.rst
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Expand Up @@ -60,6 +60,21 @@ let us know.
C API changes
=============

Change internal UPDATEIFCOPY semantics
--------------------------------------
When ndarrays are created with the ``UPDATEIFCOPY`` flag, a temporary copy of
the data is created. The writeback to the original data occurrs at ndarray
deallocation. Refactor the writeback into a new PyArray_ResolveUpdateIfCopy
function and use it internally wherever such an array is created. The only
visible change in behavior is that if compiled with ``-DDEPRECATE_UPDATEIFCOPY``
or if run on PyPy, and writeback resolution has not occurred before calling
``array_dealloc``, NumPy will now raise a DeprecationWarning.

Additionally, deprecrate the NPY_ARRAY_UPDATEIFCOPY flag, replace it with
NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT. This was done to encourage downstream
consumers of the C-API to properly use the PyArray_ResolveUpdateIfCopy
function. Calling ndarray creation functions such as PyArray_FromArray where
flags uses NPY_ARRAY_UPDATEIFCOPY will raise a DeprecationWarning.

New Features
============
Expand Down
2 changes: 1 addition & 1 deletion numpy/core/code_generators/cversions.txt
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Expand Up @@ -36,5 +36,5 @@
0x0000000a = 9b8bce614655d3eb02acddcb508203cb

# Version 11 (NumPy 1.13) Added PyArray_MapIterArrayCopyIfOverlap
# Version 11 (NumPy 1.14) No Change
# Version 11 (NumPy 1.14) Added PyArray_ResolveUpdateIfCopy
0x0000000b = edb1ba83730c650fd9bc5772a919cda7
2 changes: 2 additions & 0 deletions numpy/core/code_generators/numpy_api.py
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Expand Up @@ -346,6 +346,8 @@
# End 1.10 API
'PyArray_MapIterArrayCopyIfOverlap': (301,),
# End 1.13 API
'PyArray_ResolveUpdateIfCopy': (302,),
# End 1.14 API
}

ufunc_types_api = {
Expand Down
4 changes: 2 additions & 2 deletions numpy/core/include/numpy/ndarrayobject.h
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Expand Up @@ -174,10 +174,10 @@ static NPY_INLINE void
PyArray_XDECREF_ERR(PyArrayObject *arr)
{
if (arr != NULL) {
if (PyArray_FLAGS(arr) & NPY_ARRAY_UPDATEIFCOPY) {
if (PyArray_FLAGS(arr) & NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT) {
PyArrayObject *base = (PyArrayObject *)PyArray_BASE(arr);
PyArray_ENABLEFLAGS(base, NPY_ARRAY_WRITEABLE);
PyArray_CLEARFLAGS(arr, NPY_ARRAY_UPDATEIFCOPY);
PyArray_CLEARFLAGS(arr, NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT);
}
Py_DECREF(arr);
}
Expand Down
7 changes: 4 additions & 3 deletions numpy/core/include/numpy/ndarraytypes.h
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Expand Up @@ -870,7 +870,8 @@ typedef int (PyArray_FinalizeFunc)(PyArrayObject *, PyObject *);
* This flag may be requested in constructor functions.
* This flag may be tested for in PyArray_FLAGS(arr).
*/
#define NPY_ARRAY_UPDATEIFCOPY 0x1000
#define NPY_ARRAY_UPDATEIFCOPY 0x1000 /* Deprecated in 1.14 */
#define NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT 0x2000

/*
* NOTE: there are also internal flags defined in multiarray/arrayobject.h,
Expand All @@ -894,11 +895,11 @@ typedef int (PyArray_FinalizeFunc)(PyArrayObject *, PyObject *);
#define NPY_ARRAY_IN_ARRAY (NPY_ARRAY_CARRAY_RO)
#define NPY_ARRAY_OUT_ARRAY (NPY_ARRAY_CARRAY)
#define NPY_ARRAY_INOUT_ARRAY (NPY_ARRAY_CARRAY | \
NPY_ARRAY_UPDATEIFCOPY)
NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT)
#define NPY_ARRAY_IN_FARRAY (NPY_ARRAY_FARRAY_RO)
#define NPY_ARRAY_OUT_FARRAY (NPY_ARRAY_FARRAY)
#define NPY_ARRAY_INOUT_FARRAY (NPY_ARRAY_FARRAY | \
NPY_ARRAY_UPDATEIFCOPY)
NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT)

#define NPY_ARRAY_UPDATE_ALL (NPY_ARRAY_C_CONTIGUOUS | \
NPY_ARRAY_F_CONTIGUOUS | \
Expand Down
2 changes: 1 addition & 1 deletion numpy/core/include/numpy/npy_1_7_deprecated_api.h
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Expand Up @@ -46,7 +46,7 @@
#define NPY_ALIGNED NPY_ARRAY_ALIGNED
#define NPY_NOTSWAPPED NPY_ARRAY_NOTSWAPPED
#define NPY_WRITEABLE NPY_ARRAY_WRITEABLE
#define NPY_UPDATEIFCOPY NPY_ARRAY_UPDATEIFCOPY
#define NPY_UPDATEIFCOPY NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT
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This should be reverted -- if someone's using the deprecated NPY_UPDATEIFCOPY alias, then they should get NPY_ARRAY_UPDATEIFCOPY semantics.

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ok

#define NPY_BEHAVED NPY_ARRAY_BEHAVED
#define NPY_BEHAVED_NS NPY_ARRAY_BEHAVED_NS
#define NPY_CARRAY NPY_ARRAY_CARRAY
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94 changes: 71 additions & 23 deletions numpy/core/src/multiarray/arrayobject.c
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Expand Up @@ -112,7 +112,7 @@ PyArray_SetUpdateIfCopyBase(PyArrayObject *arr, PyArrayObject *base)
* references.
*/
((PyArrayObject_fields *)arr)->base = (PyObject *)base;
PyArray_ENABLEFLAGS(arr, NPY_ARRAY_UPDATEIFCOPY);
PyArray_ENABLEFLAGS(arr, NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT);
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Ugh, this is dubious. PyArray_SetUpdateIfCopyBase is public, so there might be third-party code that uses it and expects the GC to resolve the UPDATEIFCOPY. I guess we need to make PyArray_SetUpdateIfCopyBase keep using NPY_ARRAY_UPDATEIFCOPY and issue a deprecation warning, and add a new function PyArray_SetUpdateIfCopyBaseWithExplicitResolve or something like that.

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ok, will add a PyArray_CopyDataFromBase that will set the new flag, and use it instead across the code base

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Sorry, I don't understand the naming scheme here. IIRC (from my phone), PyArray_SetUpdateIfCopyBase sets the UPDATEIFCOPY flag and sets the ->base member, but it doesn't copy any data does it? I was suggesting having a version that's identical except that it sets the new flag instead of the old one and doesn't warn. What does PyArray_CopyDataFromBase do?

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correct, so maybe PyArray_SetUpToCopyData?

PyArray_CLEARFLAGS(base, NPY_ARRAY_WRITEABLE);

return 0;
Expand Down Expand Up @@ -372,10 +372,63 @@ PyArray_TypeNumFromName(char *str)
return NPY_NOTYPE;
}

/*NUMPY_API
*
* If UPDATEIFCOPY and self has data, reset the base WRITEABLE flag,
* copy the local data to base, release the local data, and set flags
* appropriately. Return 0 if not relevant, 1 if success, < 0 on failure
*/
NPY_NO_EXPORT int
PyArray_ResolveUpdateIfCopy(PyArrayObject * self)
{
PyArrayObject_fields *fa = (PyArrayObject_fields *)self;
if (fa && fa->base) {
if (fa->flags & NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT) {
/*
* UPDATEIFCOPY means that fa->base's data
* should be updated with the contents
* of self.
* fa->base->flags is not WRITEABLE to protect the relationship
* unlock it.
*/
int retval = 0;
PyArray_ENABLEFLAGS(((PyArrayObject *)fa->base),
NPY_ARRAY_WRITEABLE);
PyArray_CLEARFLAGS(self, NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT);
retval = PyArray_CopyAnyInto((PyArrayObject *)fa->base, self);
if (retval < 0) {
/* this should never happen, how did the two copies of data
* get out of sync?
*/
return retval;
}
if ((fa->flags & NPY_ARRAY_OWNDATA) && fa->data) {
/* Free internal references if an Object array */
if (PyDataType_FLAGCHK(fa->descr, NPY_ITEM_REFCOUNT)) {
Py_INCREF(self); /*hold on to self */
PyArray_XDECREF(self);
Py_DECREF(self);
}
npy_free_cache(fa->data, PyArray_NBYTES(self));
fa->data = NULL;
PyArray_CLEARFLAGS(self, NPY_ARRAY_OWNDATA);
}
return 1;
}
}
return 0;
}

/*********************** end C-API functions **********************/

/* array object functions */

#ifdef PYPY_VERSION
#ifndef DEPRECATE_UPDATEIFCOPY
#define DEPRECATE_UPDATEIFCOPY
#endif
#endif

static void
array_dealloc(PyArrayObject *self)
{
Expand All @@ -387,27 +440,24 @@ array_dealloc(PyArrayObject *self)
PyObject_ClearWeakRefs((PyObject *)self);
}
if (fa->base) {
/*
* UPDATEIFCOPY means that base points to an
* array that should be updated with the contents
* of this array upon destruction.
* fa->base->flags must have been WRITEABLE
* (checked previously) and it was locked here
* thus, unlock it.
*/
if (fa->flags & NPY_ARRAY_UPDATEIFCOPY) {
PyArray_ENABLEFLAGS(((PyArrayObject *)fa->base),
NPY_ARRAY_WRITEABLE);
Py_INCREF(self); /* hold on to self in next call */
if (PyArray_CopyAnyInto((PyArrayObject *)fa->base, self) < 0) {
PyErr_Print();
PyErr_Clear();
}
/*
* Don't need to DECREF -- because we are deleting
*self already...
int retval;
Py_INCREF(self); /* hold on to self in next call */
retval = PyArray_ResolveUpdateIfCopy(self);
if (retval < 0)
{
PyErr_Print();
PyErr_Clear();
}
#ifdef DEPRECATE_UPDATEIFCOPY
if (retval > 0) {
DEPRECATE("UPDATEIFCOPY resolution in array_dealloc is "
"incompatible with PyPy and will be removed in "
"the future");
/* dealloc must not raise an error, even if warning filters are set
*/
PyErr_Clear();
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I think this should use PyErr_WriteUnraisable() or similar – otherwise when someone sets a warning filter to deprecations into errors, then the effect will be to hide this warning entirely!

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good catch, will add a test as well

}
#endif
/*
* In any case base is pointing to something that we need
* to DECREF -- either a view or a buffer object
Expand Down Expand Up @@ -482,7 +532,7 @@ PyArray_DebugPrint(PyArrayObject *obj)
printf(" NPY_ALIGNED");
if (fobj->flags & NPY_ARRAY_WRITEABLE)
printf(" NPY_WRITEABLE");
if (fobj->flags & NPY_ARRAY_UPDATEIFCOPY)
if (fobj->flags & NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT)
printf(" NPY_UPDATEIFCOPY");
printf("\n");

Expand All @@ -507,8 +557,6 @@ PyArray_SetDatetimeParseFunction(PyObject *op)
{
}



/*NUMPY_API
*/
NPY_NO_EXPORT int
Expand Down
9 changes: 6 additions & 3 deletions numpy/core/src/multiarray/calculation.c
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Expand Up @@ -118,7 +118,7 @@ PyArray_ArgMax(PyArrayObject *op, int axis, PyArrayObject *out)
}
rp = (PyArrayObject *)PyArray_FromArray(out,
PyArray_DescrFromType(NPY_INTP),
NPY_ARRAY_CARRAY | NPY_ARRAY_UPDATEIFCOPY);
NPY_ARRAY_CARRAY | NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT);
if (rp == NULL) {
goto fail;
}
Expand All @@ -136,6 +136,7 @@ PyArray_ArgMax(PyArrayObject *op, int axis, PyArrayObject *out)
Py_DECREF(ap);
/* Trigger the UPDATEIFCOPY if necessary */
if (out != NULL && out != rp) {
PyArray_ResolveUpdateIfCopy(rp);
Py_DECREF(rp);
rp = out;
Py_INCREF(rp);
Expand Down Expand Up @@ -233,7 +234,7 @@ PyArray_ArgMin(PyArrayObject *op, int axis, PyArrayObject *out)
}
rp = (PyArrayObject *)PyArray_FromArray(out,
PyArray_DescrFromType(NPY_INTP),
NPY_ARRAY_CARRAY | NPY_ARRAY_UPDATEIFCOPY);
NPY_ARRAY_CARRAY | NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT);
if (rp == NULL) {
goto fail;
}
Expand All @@ -251,6 +252,7 @@ PyArray_ArgMin(PyArrayObject *op, int axis, PyArrayObject *out)
Py_DECREF(ap);
/* Trigger the UPDATEIFCOPY if necessary */
if (out != NULL && out != rp) {
PyArray_ResolveUpdateIfCopy(rp);
Py_DECREF(rp);
rp = out;
Py_INCREF(rp);
Expand Down Expand Up @@ -1117,7 +1119,7 @@ PyArray_Clip(PyArrayObject *self, PyObject *min, PyObject *max, PyArrayObject *o
oflags = NPY_ARRAY_FARRAY;
else
oflags = NPY_ARRAY_CARRAY;
oflags |= NPY_ARRAY_UPDATEIFCOPY | NPY_ARRAY_FORCECAST;
oflags |= NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT | NPY_ARRAY_FORCECAST;
Py_INCREF(indescr);
newout = (PyArrayObject*)PyArray_FromArray(out, indescr, oflags);
if (newout == NULL) {
Expand Down Expand Up @@ -1153,6 +1155,7 @@ PyArray_Clip(PyArrayObject *self, PyObject *min, PyObject *max, PyArrayObject *o
Py_XDECREF(maxa);
Py_DECREF(newin);
/* Copy back into out if out was not already a nice array. */
PyArray_ResolveUpdateIfCopy(newout);
Py_DECREF(newout);
return (PyObject *)out;

Expand Down
1 change: 1 addition & 0 deletions numpy/core/src/multiarray/cblasfuncs.c
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Expand Up @@ -770,6 +770,7 @@ cblas_matrixproduct(int typenum, PyArrayObject *ap1, PyArrayObject *ap2,
Py_DECREF(ap2);

/* Trigger possible copyback into `result` */
PyArray_ResolveUpdateIfCopy(out_buf);
Py_DECREF(out_buf);

return PyArray_Return(result);
Expand Down
3 changes: 2 additions & 1 deletion numpy/core/src/multiarray/compiled_base.c
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Expand Up @@ -327,7 +327,7 @@ arr_insert(PyObject *NPY_UNUSED(self), PyObject *args, PyObject *kwdict)
}

array = (PyArrayObject *)PyArray_FromArray((PyArrayObject *)array0, NULL,
NPY_ARRAY_CARRAY | NPY_ARRAY_UPDATEIFCOPY);
NPY_ARRAY_CARRAY | NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT);
if (array == NULL) {
goto fail;
}
Expand Down Expand Up @@ -402,6 +402,7 @@ arr_insert(PyObject *NPY_UNUSED(self), PyObject *args, PyObject *kwdict)

Py_XDECREF(values);
Py_XDECREF(mask);
PyArray_ResolveUpdateIfCopy(array);
Py_DECREF(array);
Py_RETURN_NONE;

Expand Down
28 changes: 21 additions & 7 deletions numpy/core/src/multiarray/ctors.c
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Expand Up @@ -1009,7 +1009,7 @@ PyArray_NewFromDescr_int(PyTypeObject *subtype, PyArray_Descr *descr, int nd,
}
}
else {
fa->flags = (flags & ~NPY_ARRAY_UPDATEIFCOPY);
fa->flags = (flags & ~NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT);
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This should clear both versions of the flag, I think?

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ok

}
fa->descr = descr;
fa->base = (PyObject *)NULL;
Expand Down Expand Up @@ -1703,7 +1703,8 @@ PyArray_FromAny(PyObject *op, PyArray_Descr *newtype, int min_depth,

/* If we got dimensions and dtype instead of an array */
if (arr == NULL) {
if (flags & NPY_ARRAY_UPDATEIFCOPY) {
if ((flags & NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT) ||
(flags & NPY_ARRAY_UPDATEIFCOPY)) {
Py_XDECREF(newtype);
PyErr_SetString(PyExc_TypeError,
"UPDATEIFCOPY used for non-array input.");
Expand Down Expand Up @@ -1811,6 +1812,7 @@ PyArray_FromAny(PyObject *op, PyArray_Descr *newtype, int min_depth,
* NPY_ARRAY_NOTSWAPPED,
* NPY_ARRAY_ENSURECOPY,
* NPY_ARRAY_UPDATEIFCOPY,
* NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT,
* NPY_ARRAY_FORCECAST,
* NPY_ARRAY_ENSUREARRAY,
* NPY_ARRAY_ELEMENTSTRIDES
Expand All @@ -1835,10 +1837,13 @@ PyArray_FromAny(PyObject *op, PyArray_Descr *newtype, int min_depth,
* Fortran arrays are always behaved (aligned,
* notswapped, and writeable) and not (C) CONTIGUOUS (if > 1d).
*
* NPY_ARRAY_UPDATEIFCOPY flag sets this flag in the returned array if a copy
* is made and the base argument points to the (possibly) misbehaved array.
* When the new array is deallocated, the original array held in base
* is updated with the contents of the new array.
* NPY_ARRAY_UPDATEIFCOPY is deprecated in favor of
* NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT in 1.14

* NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT flag sets this flag in the returned
* array if a copy is made and the base argument points to the (possibly)
* misbehaved array. Before returning to python, PyArray_ResolveUpdateIfCopy
* must be called to update the contents of the orignal array from the copy.
*
* NPY_ARRAY_FORCECAST will cause a cast to occur regardless of whether or not
* it is safe.
Expand Down Expand Up @@ -2005,7 +2010,16 @@ PyArray_FromArray(PyArrayObject *arr, PyArray_Descr *newtype, int flags)
return NULL;
}

if (flags & NPY_ARRAY_UPDATEIFCOPY) {
if ((flags & NPY_ARRAY_UPDATEIFCOPY) ||
(flags & NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT)) {
if (flags & NPY_ARRAY_UPDATEIFCOPY) {
if (DEPRECATE("Use NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT and"
" be sure to call PyArray_ResolveUpdateIfCopy") < 0) {
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Shouldn't this have an #ifdef around it?

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What kind of #ifdef?
We do not wish to issue a DeprecationWarning in the current version of NumPy?

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Ultimately yeah it should be deprecated, but I thought your plan was to initially introduce this with all the warnings hidden behind a DEPRECATE_UPDATEIFCOPY ifdef.

/* 2017-07-24, 1.14 */
Py_DECREF(ret);
return NULL;
}
}
Py_INCREF(arr);
if (PyArray_SetUpdateIfCopyBase(ret, arr) < 0) {
Py_DECREF(ret);
Expand Down
4 changes: 2 additions & 2 deletions numpy/core/src/multiarray/flagsobject.c
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Expand Up @@ -208,7 +208,7 @@ arrayflags_dealloc(PyArrayFlagsObject *self)

_define_get(NPY_ARRAY_C_CONTIGUOUS, contiguous)
_define_get(NPY_ARRAY_F_CONTIGUOUS, fortran)
_define_get(NPY_ARRAY_UPDATEIFCOPY, updateifcopy)
_define_get(NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT, updateifcopy)
_define_get(NPY_ARRAY_OWNDATA, owndata)
_define_get(NPY_ARRAY_ALIGNED, aligned)
_define_get(NPY_ARRAY_WRITEABLE, writeable)
Expand Down Expand Up @@ -595,7 +595,7 @@ arrayflags_print(PyArrayFlagsObject *self)
"OWNDATA", _torf_(fl, NPY_ARRAY_OWNDATA),
"WRITEABLE", _torf_(fl, NPY_ARRAY_WRITEABLE),
"ALIGNED", _torf_(fl, NPY_ARRAY_ALIGNED),
"UPDATEIFCOPY", _torf_(fl, NPY_ARRAY_UPDATEIFCOPY));
"UPDATEIFCOPY", _torf_(fl, NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT));
}


Expand Down
6 changes: 3 additions & 3 deletions numpy/core/src/multiarray/getset.c
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Expand Up @@ -365,10 +365,10 @@ array_data_set(PyArrayObject *self, PyObject *op)
PyDataMem_FREE(PyArray_DATA(self));
}
if (PyArray_BASE(self)) {
if (PyArray_FLAGS(self) & NPY_ARRAY_UPDATEIFCOPY) {
if (PyArray_FLAGS(self) & NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT) {
PyArray_ENABLEFLAGS((PyArrayObject *)PyArray_BASE(self),
NPY_ARRAY_WRITEABLE);
PyArray_CLEARFLAGS(self, NPY_ARRAY_UPDATEIFCOPY);
PyArray_CLEARFLAGS(self, NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT);
}
Py_DECREF(PyArray_BASE(self));
((PyArrayObject_fields *)self)->base = NULL;
Expand Down Expand Up @@ -604,7 +604,7 @@ array_struct_get(PyArrayObject *self)
inter->itemsize = PyArray_DESCR(self)->elsize;
inter->flags = PyArray_FLAGS(self);
/* reset unused flags */
inter->flags &= ~(NPY_ARRAY_UPDATEIFCOPY | NPY_ARRAY_OWNDATA);
inter->flags &= ~(NPY_ARRAY_UPDATEIFCOPY_CLEAR_B4_EXIT | NPY_ARRAY_OWNDATA);
if (PyArray_ISNOTSWAPPED(self)) inter->flags |= NPY_ARRAY_NOTSWAPPED;
/*
* Copy shape and strides over since these can be reset
Expand Down
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