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scipy/numpy-deprecation-warnings.patch

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Fix FTBFS with Py3.8
2019-06-10 12:34:49 +00:00
diff -ru scipy-1.2.1/scipy/odr/__odrpack.c scipy-1.2.1_patched/scipy/odr/__odrpack.c
--- scipy-1.2.1/scipy/odr/__odrpack.c 2019-01-28 04:57:51.000000000 +0100
+++ scipy-1.2.1_patched/scipy/odr/__odrpack.c 2019-06-06 16:11:32.947892754 +0200
@@ -9,6 +9,8 @@
*
*/
+#define PY_SSIZE_T_CLEAN
+#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#include "odrpack.h"
@@ -44,7 +46,7 @@
double *fjacb, double *fjacd, int *istop)
{
PyObject *arg01, *arglist;
- PyObject *result;
+ PyObject *result = NULL;
PyArrayObject *result_array = NULL;
PyArrayObject *pyXplusD;
void *beta_dst;
@@ -57,14 +59,14 @@
dim2[0] = *m;
dim2[1] = *n;
pyXplusD = (PyArrayObject *) PyArray_SimpleNew(2, dim2, NPY_DOUBLE);
- memcpy(pyXplusD->data, (void *)xplusd, (*m) * (*n) * sizeof(double));
+ memcpy(PyArray_DATA(pyXplusD), (void *)xplusd, (*m) * (*n) * sizeof(double));
}
else
{
npy_intp dim1[1];
dim1[0] = *n;
pyXplusD = (PyArrayObject *) PyArray_SimpleNew(1, dim1, NPY_DOUBLE);
- memcpy(pyXplusD->data, (void *)xplusd, (*n) * sizeof(double));
+ memcpy(PyArray_DATA(pyXplusD), (void *)xplusd, (*n) * sizeof(double));
}
PyTuple_SetItem(arg01, 0, odr_global.pyBeta);
@@ -84,7 +86,7 @@
Py_DECREF(arg01);
*istop = 0;
- beta_dst = ((PyArrayObject *) (odr_global.pyBeta))->data;
+ beta_dst = (PyArray_DATA((PyArrayObject *) odr_global.pyBeta));
if (beta != beta_dst) {
memcpy(beta_dst, (void *)beta, (*np) * sizeof(double));
}
@@ -121,7 +123,7 @@
"Result from function call is not a proper array of floats.");
}
- memcpy((void *)f, result_array->data, (*n) * (*nq) * sizeof(double));
+ memcpy((void *)f, PyArray_DATA(result_array), (*n) * (*nq) * sizeof(double));
Py_DECREF(result_array);
}
@@ -161,7 +163,7 @@
{
/* result_array should be rank-3 */
- if (result_array->nd != 3)
+ if (PyArray_NDIM(result_array) != 3)
{
Py_DECREF(result_array);
PYERR2(odr_error, "Beta Jacobian is not rank-3");
@@ -171,14 +173,14 @@
{
/* result_array should be rank-2 */
- if (result_array->nd != 2)
+ if (PyArray_NDIM(result_array) != 2)
{
Py_DECREF(result_array);
PYERR2(odr_error, "Beta Jacobian is not rank-2");
}
}
- memcpy((void *)fjacb, result_array->data,
+ memcpy((void *)fjacb, PyArray_DATA(result_array),
(*n) * (*nq) * (*np) * sizeof(double));
Py_DECREF(result_array);
@@ -220,7 +222,7 @@
{
/* result_array should be rank-3 */
- if (result_array->nd != 3)
+ if (PyArray_NDIM(result_array) != 3)
{
Py_DECREF(result_array);
PYERR2(odr_error, "xplusd Jacobian is not rank-3");
@@ -230,7 +232,7 @@
{
/* result_array should be rank-2 */
- if (result_array->nd != 2)
+ if (PyArray_NDIM(result_array) != 2)
{
Py_DECREF(result_array);
PYERR2(odr_error, "xplusd Jacobian is not rank-2");
@@ -240,14 +242,14 @@
{
/* result_array should be rank-1 */
- if (result_array->nd != 1)
+ if (PyArray_NDIM(result_array) != 1)
{
Py_DECREF(result_array);
PYERR2(odr_error, "xplusd Jacobian is not rank-1");
}
}
- memcpy((void *)fjacd, result_array->data,
+ memcpy((void *)fjacd, PyArray_DATA(result_array),
(*n) * (*nq) * (*m) * sizeof(double));
Py_DECREF(result_array);
}
@@ -291,7 +293,7 @@
return NULL;
}
- lwkmn = work->dimensions[0];
+ lwkmn = PyArray_DIMS(work)[0];
F_FUNC(dwinf,DWINF)(&n, &m, &np, &nq, &ldwe, &ld2we, &isodr,
&delta, &eps, &xplus, &fn, &sd, &vcv, &rvar, &wss, &wssde,
@@ -352,15 +354,15 @@
wrk6--;
wrk7--;
- dim1[0] = beta->dimensions[0];
+ dim1[0] = PyArray_DIMS(beta)[0];
sd_beta = (PyArrayObject *) PyArray_SimpleNew(1, dim1, NPY_DOUBLE);
- dim2[0] = beta->dimensions[0];
- dim2[1] = beta->dimensions[0];
+ dim2[0] = PyArray_DIMS(beta)[0];
+ dim2[1] = PyArray_DIMS(beta)[0];
cov_beta = (PyArrayObject *) PyArray_SimpleNew(2, dim2, NPY_DOUBLE);
- memcpy(sd_beta->data, (void *)((double *)(work->data) + sd),
+ memcpy(PyArray_DATA(sd_beta), (void *)((double *)(PyArray_DATA(work)) + sd),
np * sizeof(double));
- memcpy(cov_beta->data, (void *)((double *)(work->data) + vcv),
+ memcpy(PyArray_DATA(cov_beta), (void *)((double *)(PyArray_DATA(work)) + vcv),
np * np * sizeof(double));
if (!full_output)
@@ -427,21 +429,21 @@
fnA = (PyArrayObject *) PyArray_SimpleNew(2, dim2, NPY_DOUBLE);
}
- memcpy(deltaA->data, (void *)((double *)(work->data) + delta),
+ memcpy(PyArray_DATA(deltaA), (void *)((double *)(PyArray_DATA(work)) + delta),
m * n * sizeof(double));
- memcpy(epsA->data, (void *)((double *)(work->data) + eps),
+ memcpy(PyArray_DATA(epsA), (void *)((double *)(PyArray_DATA(work)) + eps),
nq * n * sizeof(double));
- memcpy(xplusA->data, (void *)((double *)(work->data) + xplus),
+ memcpy(PyArray_DATA(xplusA), (void *)((double *)(PyArray_DATA(work)) + xplus),
m * n * sizeof(double));
- memcpy(fnA->data, (void *)((double *)(work->data) + fn),
+ memcpy(PyArray_DATA(fnA), (void *)((double *)(PyArray_DATA(work)) + fn),
nq * n * sizeof(double));
- res_var = *((double *)(work->data) + rvar);
- sum_square = *((double *)(work->data) + wss);
- sum_square_delta = *((double *)(work->data) + wssde);
- sum_square_eps = *((double *)(work->data) + wssep);
- inv_condnum = *((double *)(work->data) + rcond);
- rel_error = *((double *)(work->data) + eta);
+ res_var = *((double *)(PyArray_DATA(work)) + rvar);
+ sum_square = *((double *)(PyArray_DATA(work)) + wss);
+ sum_square_delta = *((double *)(PyArray_DATA(work)) + wssde);
+ sum_square_eps = *((double *)(PyArray_DATA(work)) + wssep);
+ inv_condnum = *((double *)(PyArray_DATA(work)) + rcond);
+ rel_error = *((double *)(PyArray_DATA(work)) + eta);
retobj =
Py_BuildValue
@@ -623,7 +625,7 @@
PYERR(PyExc_ValueError,
"y could not be made into a suitable array");
}
- n = y->dimensions[y->nd - 1]; /* pick the last dimension */
+ n = PyArray_DIMS(y)[PyArray_NDIM(y) - 1]; /* pick the last dimension */
if ((x =
(PyArrayObject *) PyArray_CopyFromObject(px, NPY_DOUBLE, 1,
2)) == NULL)
@@ -631,18 +633,18 @@
PYERR(PyExc_ValueError,
"x could not be made into a suitable array");
}
- if (n != x->dimensions[x->nd - 1])
+ if (n != PyArray_DIMS(x)[PyArray_NDIM(x) - 1])
{
PYERR(PyExc_ValueError,
"x and y don't have matching numbers of observations");
}
- if (y->nd == 1)
+ if (PyArray_NDIM(y) == 1)
{
nq = 1;
}
else
{
- nq = y->dimensions[0];
+ nq = PyArray_DIMS(y)[0];
}
ldx = ldy = n;
@@ -664,17 +666,17 @@
"x could not be made into a suitable array");
}
- n = x->dimensions[x->nd - 1];
+ n = PyArray_DIMS(x)[PyArray_NDIM(x) - 1];
ldx = n;
}
- if (x->nd == 1)
+ if (PyArray_NDIM(x) == 1)
{
m = 1;
}
else
{
- m = x->dimensions[0];
+ m = PyArray_DIMS(x)[0];
} /* x, y */
if ((beta =
@@ -684,14 +686,14 @@
PYERR(PyExc_ValueError,
"initbeta could not be made into a suitable array");
}
- np = beta->dimensions[0];
+ np = PyArray_DIMS(beta)[0];
if (pwe == NULL)
{
ldwe = ld2we = 1;
dim1[0] = n;
we = (PyArrayObject *) PyArray_SimpleNew(1, dim1, NPY_DOUBLE);
- ((double *)(we->data))[0] = -1.0;
+ ((double *)(PyArray_DATA(we)))[0] = -1.0;
}
else if (PyNumber_Check(pwe) && !PyArray_Check(pwe))
{
@@ -711,11 +713,11 @@
we = (PyArrayObject *) PyArray_SimpleNew(3, dim3, NPY_DOUBLE);
if (implicit)
{
- ((double *)(we->data))[0] = val;
+ ((double *)(PyArray_DATA(we)))[0] = val;
}
else
{
- ((double *)(we->data))[0] = -val;
+ ((double *)(PyArray_DATA(we)))[0] = -val;
}
ldwe = ld2we = 1;
}
@@ -730,29 +732,29 @@
PYERR(PyExc_ValueError, "could not convert we to a suitable array");
}
- if (we->nd == 1 && nq == 1)
+ if (PyArray_NDIM(we) == 1 && nq == 1)
{
ldwe = n;
ld2we = 1;
}
- else if (we->nd == 1 && we->dimensions[0] == nq)
+ else if (PyArray_NDIM(we) == 1 && PyArray_DIMS(we)[0] == nq)
{
/* we is a rank-1 array with diagonal weightings to be broadcast
* to all observations */
ldwe = 1;
ld2we = 1;
}
- else if (we->nd == 3 && we->dimensions[0] == nq
- && we->dimensions[1] == nq && we->dimensions[2] == 1)
+ else if (PyArray_NDIM(we) == 3 && PyArray_DIMS(we)[0] == nq
+ && PyArray_DIMS(we)[1] == nq && PyArray_DIMS(we)[2] == 1)
{
/* we is a rank-3 array with the covariant weightings
to be broadcast to all observations */
ldwe = 1;
ld2we = nq;
}
- else if (we->nd == 2 && we->dimensions[0] == nq
- && we->dimensions[1] == nq)
+ else if (PyArray_NDIM(we) == 2 && PyArray_DIMS(we)[0] == nq
+ && PyArray_DIMS(we)[1] == nq)
{
/* we is a rank-2 array with the full covariant weightings
to be broadcast to all observations */
@@ -760,16 +762,16 @@
ld2we = nq;
}
- else if (we->nd == 2 && we->dimensions[0] == nq
- && we->dimensions[1] == n)
+ else if (PyArray_NDIM(we) == 2 && PyArray_DIMS(we)[0] == nq
+ && PyArray_DIMS(we)[1] == n)
{
/* we is a rank-2 array with the diagonal elements of the
covariant weightings for each observation */
ldwe = n;
ld2we = 1;
}
- else if (we->nd == 3 && we->dimensions[0] == nq
- && we->dimensions[1] == nq && we->dimensions[2] == n)
+ else if (PyArray_NDIM(we) == 3 && PyArray_DIMS(we)[0] == nq
+ && PyArray_DIMS(we)[1] == nq && PyArray_DIMS(we)[2] == n)
{
/* we is the full specification of the covariant weights
for each observation */
@@ -788,7 +790,7 @@
dim1[0] = m;
wd = (PyArrayObject *) PyArray_SimpleNew(1, dim1, NPY_DOUBLE);
- ((double *)(wd->data))[0] = -1.0;
+ ((double *)(PyArray_DATA(wd)))[0] = -1.0;
}
else if (PyNumber_Check(pwd) && !PyArray_Check(pwd))
{
@@ -806,7 +808,7 @@
dim3[1] = 1;
dim3[2] = m;
wd = (PyArrayObject *) PyArray_SimpleNew(3, dim3, NPY_DOUBLE);
- ((double *)(wd->data))[0] = -val;
+ ((double *)(PyArray_DATA(wd)))[0] = -val;
ldwd = ld2wd = 1;
}
else if (PySequence_Check(pwd))
@@ -820,12 +822,12 @@
PYERR(PyExc_ValueError, "could not convert wd to a suitable array");
}
- if (wd->nd == 1 && m == 1)
+ if (PyArray_NDIM(wd) == 1 && m == 1)
{
ldwd = n;
ld2wd = 1;
}
- else if (wd->nd == 1 && wd->dimensions[0] == m)
+ else if (PyArray_NDIM(wd) == 1 && PyArray_DIMS(wd)[0] == m)
{
/* wd is a rank-1 array with diagonal weightings to be broadcast
* to all observations */
@@ -833,16 +835,16 @@
ld2wd = 1;
}
- else if (wd->nd == 3 && wd->dimensions[0] == m
- && wd->dimensions[1] == m && wd->dimensions[2] == 1)
+ else if (PyArray_NDIM(wd) == 3 && PyArray_DIMS(wd)[0] == m
+ && PyArray_DIMS(wd)[1] == m && PyArray_DIMS(wd)[2] == 1)
{
/* wd is a rank-3 array with the covariant wdightings
to be broadcast to all observations */
ldwd = 1;
ld2wd = m;
}
- else if (wd->nd == 2 && wd->dimensions[0] == m
- && wd->dimensions[1] == m)
+ else if (PyArray_NDIM(wd) == 2 && PyArray_DIMS(wd)[0] == m
+ && PyArray_DIMS(wd)[1] == m)
{
/* wd is a rank-2 array with the full covariant weightings
to be broadcast to all observations */
@@ -850,16 +852,16 @@
ld2wd = m;
}
- else if (wd->nd == 2 && wd->dimensions[0] == m
- && wd->dimensions[1] == n)
+ else if (PyArray_NDIM(wd) == 2 && PyArray_DIMS(wd)[0] == m
+ && PyArray_DIMS(wd)[1] == n)
{
/* wd is a rank-2 array with the diagonal elements of the
covariant weightings for each observation */
ldwd = n;
ld2wd = 1;
}
- else if (wd->nd == 3 && wd->dimensions[0] == m
- && wd->dimensions[1] == m && wd->dimensions[2] == n)
+ else if (PyArray_NDIM(wd) == 3 && PyArray_DIMS(wd)[0] == m
+ && PyArray_DIMS(wd)[1] == m && PyArray_DIMS(wd)[2] == n)
{
/* wd is the full specification of the covariant weights
for each observation */
@@ -878,7 +880,7 @@
{
dim1[0] = np;
ifixb = (PyArrayObject *) PyArray_SimpleNew(1, dim1, NPY_INT);
- *(int *)(ifixb->data) = -1; /* set first element negative */
+ *(int *)(PyArray_DATA(ifixb)) = -1; /* set first element negative */
}
else
{
@@ -892,7 +894,7 @@
"could not convert ifixb to a suitable array");
}
- if (ifixb->dimensions[0] != np)
+ if (PyArray_DIMS(ifixb)[0] != np)
{
PYERR(PyExc_ValueError,
"could not convert ifixb to a suitable array");
@@ -904,7 +906,7 @@
dim2[0] = m;
dim2[1] = 1;
ifixx = (PyArrayObject *) PyArray_SimpleNew(2, dim2, NPY_INT);
- *(int *)(ifixx->data) = -1; /* set first element negative */
+ *(int *)(PyArray_DATA(ifixx)) = -1; /* set first element negative */
ldifx = 1;
}
else
@@ -919,16 +921,16 @@
"could not convert ifixx to a suitable array");
}
- if (ifixx->nd == 1 && ifixx->dimensions[0] == m)
+ if (PyArray_NDIM(ifixx) == 1 && PyArray_DIMS(ifixx)[0] == m)
{
ldifx = 1;
}
- else if (ifixx->nd == 1 && ifixx->dimensions[0] == n && m == 1)
+ else if (PyArray_NDIM(ifixx) == 1 && PyArray_DIMS(ifixx)[0] == n && m == 1)
{
ldifx = n;
}
- else if (ifixx->nd == 2 && ifixx->dimensions[0] == m
- && ifixx->dimensions[1] == n)
+ else if (PyArray_NDIM(ifixx) == 2 && PyArray_DIMS(ifixx)[0] == m
+ && PyArray_DIMS(ifixx)[1] == n)
{
ldifx = n;
}
@@ -957,14 +959,14 @@
{
dim1[0] = np;
stpb = (PyArrayObject *) PyArray_SimpleNew(1, dim1, NPY_DOUBLE);
- *(double *)(stpb->data) = 0.0;
+ *(double *)(PyArray_DATA(stpb)) = 0.0;
}
else /* pstpb is a sequence */
{
if ((stpb =
(PyArrayObject *) PyArray_CopyFromObject(pstpb, NPY_DOUBLE, 1,
1)) == NULL
- || stpb->dimensions[0] != np)
+ || PyArray_DIMS(stpb)[0] != np)
{
PYERR(PyExc_ValueError,
"could not convert stpb to a suitable array");
@@ -976,7 +978,7 @@
dim2[0] = 1;
dim2[1] = m;
stpd = (PyArrayObject *) PyArray_SimpleNew(2, dim2, NPY_DOUBLE);
- *(double *)(stpd->data) = 0.0;
+ *(double *)(PyArray_DATA(stpd)) = 0.0;
ldstpd = 1;
}
else
@@ -989,16 +991,16 @@
"could not convert stpb to a suitable array");
}
- if (stpd->nd == 1 && stpd->dimensions[0] == m)
+ if (PyArray_NDIM(stpd) == 1 && PyArray_DIMS(stpd)[0] == m)
{
ldstpd = 1;
}
- else if (stpd->nd == 1 && stpd->dimensions[0] == n && m == 1)
+ else if (PyArray_NDIM(stpd) == 1 && PyArray_DIMS(stpd)[0] == n && m == 1)
{
ldstpd = n;
}
- else if (stpd->nd == 2 && stpd->dimensions[0] == n &&
- stpd->dimensions[1] == m)
+ else if (PyArray_NDIM(stpd) == 2 && PyArray_DIMS(stpd)[0] == n &&
+ PyArray_DIMS(stpd)[1] == m)
{
ldstpd = n;
}
@@ -1008,14 +1010,14 @@
{
dim1[0] = np;
sclb = (PyArrayObject *) PyArray_SimpleNew(1, dim1, NPY_DOUBLE);
- *(double *)(sclb->data) = 0.0;
+ *(double *)(PyArray_DATA(sclb)) = 0.0;
}
else /* psclb is a sequence */
{
if ((sclb =
(PyArrayObject *) PyArray_CopyFromObject(psclb, NPY_DOUBLE, 1,
1)) == NULL
- || sclb->dimensions[0] != np)
+ || PyArray_DIMS(sclb)[0] != np)
{
PYERR(PyExc_ValueError,
"could not convert sclb to a suitable array");
@@ -1027,7 +1029,7 @@
dim2[0] = 1;
dim2[1] = n;
scld = (PyArrayObject *) PyArray_SimpleNew(2, dim2, NPY_DOUBLE);
- *(double *)(scld->data) = 0.0;
+ *(double *)(PyArray_DATA(scld)) = 0.0;
ldscld = 1;
}
else
@@ -1040,16 +1042,16 @@
"could not convert stpb to a suitable array");
}
- if (scld->nd == 1 && scld->dimensions[0] == m)
+ if (PyArray_NDIM(scld) == 1 && PyArray_DIMS(scld)[0] == m)
{
ldscld = 1;
}
- else if (scld->nd == 1 && scld->dimensions[0] == n && m == 1)
+ else if (PyArray_NDIM(scld) == 1 && PyArray_DIMS(scld)[0] == n && m == 1)
{
ldscld = n;
}
- else if (scld->nd == 2 && scld->dimensions[0] == n &&
- scld->dimensions[1] == m)
+ else if (PyArray_NDIM(scld) == 2 && PyArray_DIMS(scld)[0] == n &&
+ PyArray_DIMS(scld)[1] == m)
{
ldscld = n;
}
@@ -1110,9 +1112,9 @@
PYERR(PyExc_ValueError,
"could not convert work to a suitable array");
}
- if (work->dimensions[0] < lwork)
+ if (PyArray_DIMS(work)[0] < lwork)
{
- printf("%d %d\n", work->dimensions[0], lwork);
+ printf("%ld %d\n", PyArray_DIMS(work)[0], lwork);
PYERR(PyExc_ValueError, "work is too small");
}
}
@@ -1133,7 +1135,7 @@
"could not convert iwork to a suitable array");
}
- if (iwork->dimensions[0] < liwork)
+ if (PyArray_DIMS(iwork)[0] < liwork)
{
PYERR(PyExc_ValueError, "iwork is too small");
}
@@ -1170,19 +1172,18 @@
Py_INCREF(beta);
odr_global.extra_args = extra_args;
Py_XINCREF(extra_args);
-
- /* now call DODRC */
- F_FUNC(dodrc,DODRC)(fcn_callback, &n, &m, &np, &nq, (double *)(beta->data),
- (double *)(y->data), &ldy, (double *)(x->data), &ldx,
- (double *)(we->data), &ldwe, &ld2we,
- (double *)(wd->data), &ldwd, &ld2wd,
- (int *)(ifixb->data), (int *)(ifixx->data), &ldifx,
- &job, &ndigit, &taufac, &sstol, &partol, &maxit,
- &iprint, &lunerr, &lunrpt,
- (double *)(stpb->data), (double *)(stpd->data), &ldstpd,
- (double *)(sclb->data), (double *)(scld->data), &ldscld,
- (double *)(work->data), &lwork, (int *)(iwork->data), &liwork,
- &info);
+ /* now call DODRC */
+ F_FUNC(dodrc,DODRC)(fcn_callback, &n, &m, &np, &nq, (double *)(PyArray_DATA(beta)),
+ (double *)(PyArray_DATA(y)), &ldy, (double *)(PyArray_DATA(x)), &ldx,
+ (double *)(PyArray_DATA(we)), &ldwe, &ld2we,
+ (double *)(PyArray_DATA(wd)), &ldwd, &ld2wd,
+ (int *)(PyArray_DATA(ifixb)), (int *)(PyArray_DATA(ifixx)), &ldifx,
+ &job, &ndigit, &taufac, &sstol, &partol, &maxit,
+ &iprint, &lunerr, &lunrpt,
+ (double *)(PyArray_DATA(stpb)), (double *)(PyArray_DATA(stpd)), &ldstpd,
+ (double *)(PyArray_DATA(sclb)), (double *)(PyArray_DATA(scld)), &ldscld,
+ (double *)(PyArray_DATA(work)), &lwork, (int *)(PyArray_DATA(iwork)), &liwork,
+ &info);
result = gen_output(n, m, np, nq, ldwe, ld2we,
beta, work, iwork, isodr, info, full_output);
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