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[in limbo] Fix deprecation warnings from numpy 1.2 #4205

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jasongrout opened this issue Sep 27, 2008 · 13 comments
Closed

[in limbo] Fix deprecation warnings from numpy 1.2 #4205

jasongrout opened this issue Sep 27, 2008 · 13 comments
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@williamstein
Labels
c: linear algebra r: wontfix t: bug
Milestone
sage-4.0.2

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@jasongrout
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Apparently we use the numpy C API in the RDF/CDF vector classes, which causes deprecation warnings with numpy 1.2. This patch updates this code to use current functions in numpy 1.2.

Component: linear algebra

Issue created by migration from https://trac.sagemath.org/ticket/4205
@jasongrout jasongrout added this to the sage-4.0.2 milestone Sep 27, 2008
@jasongrout
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comment:1

This patch depends on the patches at #3498. Both patches touch the numpy.pxd file, so this needs to be applied after the patches at #3498.

@jasongrout
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comment:2

sage -t sage/modules/*.pyx passes with the patch applied.

@sagetrac-mabshoff
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sagetrac-mabshoff mannequin commented Sep 27, 2008

comment:3

With #3498 and numpy-deprecations.patch applied we get some segfaults:

sage -t -long devel/sage/sage/numerical/optimize.py # Segfault
sage -t -long devel/sage/sage/modules/real_double_vector.pyx # Segfault
sage -t -long devel/sage/sage/modules/complex_double_vector.pyx # Segfault

We need the following patch to quiet one deprecation warning:

--- a/sage/numerical/test.py    Fri Sep 26 18:15:26 2008 -0500
+++ b/sage/numerical/test.py    Sat Sep 27 01:03:08 2008 -0700
@@ -6,7 +6,7 @@
 sage: from scipy import optimize
 sage: from scipy import special
 sage: from scipy import integrate
-sage: from scipy import linsolve   
+sage: from scipy.sparse.linalg.dsolve import linsolve   
 sage: from scipy import interpolate
 sage: from scipy import sparse    
 sage: import arpack

Various other deprecation warnings which I was too lazy to fix :p

sage -t -long devel/sage/sage/plot/plot3d/list_plot3d.py    
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/list_plot3d.py", line 68:
    sage: list_plot3d(m, texture='yellow', interpolation_type='nn',frame_aspect_ratio=[1,1,1/3])
Expected nothing
Got:
    doctest:1431: DeprecationWarning: scipy.stats.corrcoef is deprecated; please update your code to use numpy.corrcoef.
    Please note that:
        - numpy.corrcoef rowvar argument defaults to true, not false
        - numpy.corrcoef bias argument defaults to false, not true
    <BLANKLINE>
    doctest:1395: DeprecationWarning: scipy.stats.cov is deprecated; please update your code to use numpy.cov.
    Please note that:
        - numpy.cov rowvar argument defaults to true, not false
        - numpy.cov bias argument defaults to false, not true
    <BLANKLINE>
    doctest:413: DeprecationWarning: scipy.stats.mean is deprecated; please update your code to use numpy.mean.
    Please note that:
        - numpy.mean axis argument defaults to None, not 0
        - numpy.mean has a ddof argument to replace bias in a more general manner.
          scipy.stats.mean(a, bias=True) can be replaced by numpy.mean(x,
    axis=0, ddof=1).
    <BLANKLINE>
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/list_plot3d.py", line 74:
    sage: list_plot3d(m, texture='yellow', interpolation_type='spline',frame_aspect_ratio=[1,1,1/3])
Expected nothing
Got:
    doctest:760: DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew.
    doctest:760: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr.
    doctest:837: DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew.
    doctest:837: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr.
    <BLANKLINE>
**********************************************************************

Some numerical noise:

sage -t -long devel/sage/sage/matrix/matrix_double_dense.pyx
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/matrix_double_dense.py", line 854:
    sage: U*U.transpose()
Expected:
    [              1.0 2.13506512817e-16]
    [2.13506512817e-16               1.0]
Got:
    [              1.0 2.66876364757e-16]
    [2.66876364757e-16               1.0]
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/matrix_double_dense.py", line 859:
    sage: V*V.transpose()
Expected:
    [               1.0  2.02230810223e-16 -2.11947972194e-16]
    [ 2.02230810223e-16                1.0  7.09339271349e-17]
    [-2.11947972194e-16  7.09339271349e-17                1.0]
Got:
    [               1.0  5.94955942151e-17 -1.77117977403e-16]
    [ 5.94955942151e-17                1.0 -8.87690528723e-17]
    [-1.77117977403e-16 -8.87690528723e-17                1.0]
**********************************************************************

Some more:

sage -t -long devel/sage/sage/finance/time_series.pyx       
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/time_series.py", line 531:
    sage: F = v.autoregressive_fit(100)
Expected nothing
Got:
    doctest:1: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr.
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/time_series.py", line 569:
    sage: F = v[:-1].autoregressive_fit(5); F
Expected:
    [1.0019, -0.0524, -0.0643, 0.1323, -0.0539]
Got:
    doctest:1: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr.
    [1.0019, -0.0524, -0.0643, 0.1323, -0.0539]
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/time_series.py", line 95:
    sage: w = v.numpy()
Expected nothing
Got:
    doctest:1: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr.
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/time_series.py", line 1487:
    sage: bm.hurst_exponent()
Expected:
    0.527450972...
Got:
    doctest:413: DeprecationWarning: scipy.stats.mean is deprecated; please update your code to use numpy.mean.
    Please note that:
        - numpy.mean axis argument defaults to None, not 0
        - numpy.mean has a ddof argument to replace bias in a more general manner.
          scipy.stats.mean(a, bias=True) can be replaced by numpy.mean(x,
    axis=0, ddof=1).
    0.52745097242535754
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/time_series.py", line 1494:
    sage: fbm = finance.fractional_brownian_motion_simulation(0.7,0.1,10^5,1)[0]
Expected nothing
Got:
    doctest:1: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr.
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/time_series.py", line 1844:
    sage: w = v.numpy(copy=False); w
Expected:
    array([ 1. , -3. ,  4.5, -2. ])
Got:
    doctest:1: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr.
    array([ 1. , -3. ,  4.5, -2. ])
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/time_series.py", line 2154:
    sage: w = v.fft(); w
Expected:
    [45.0000, -4.5000, 12.3636, -4.5000, 5.3629, -4.5000, 2.5981, -4.5000, 0.7935]
Got:
    doctest:1: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr.
    [45.0000, -4.5000, 12.3636, -4.5000, 5.3629, -4.5000, 2.5981, -4.5000, 0.7935]
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/time_series.py", line 2206:
    sage: v.ifft()
Expected:
    [5.1000, -5.6876, 1.4764, -1.0774, 0.4249, -0.1000, -0.2249, 0.6663, -1.2764, 1.6988]
Got:
    doctest:1: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr.
    [5.1000, -5.6876, 1.4764, -1.0774, 0.4249, -0.1000, -0.2249, 0.6663, -1.2764, 1.6988]
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/time_series.py", line 2299:
    sage: y = finance.multifractal_cascade_random_walk_simulation(3700,0.02,0.01,0.01,1000,100)
Expected nothing
Got:
    doctest:1: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr.
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/time_series.py", line 2356:
    sage: for v in y_out:
          s1.append(sum([(v[:-i].autoregressive_forecast(F)-v[-i])**Integer(2) for i in range(Integer(1),Integer(20))]))
          F2 = v[:-len(F)].autoregressive_fit(len(F))
          s2.append(sum([(v[:-i].autoregressive_forecast(F2)-v[-i])**Integer(2) for i in range(Integer(1),Integer(20))]))
Expected nothing
Got:
    doctest:3: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr.
**********************************************************************

and finally:

sage -t -long devel/sage/sage/finance/fractal.pyx    
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/fractal.py", line 66:
    sage: sim = finance.stationary_gaussian_simulation(s, N)[0]
Expected nothing
Got:
    doctest:1: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr.
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/fractal.py", line 155:
    sage: finance.fractional_gaussian_noise_simulation(0.8,1,10,2)
Expected:
    [[-0.1157, 0.7025, 0.4949, 0.3324, 0.7110, 0.7248, -0.4048, 0.3103, -0.3465, 0.2964],
     [-0.5981, -0.6932, 0.5947, -0.9995, -0.7726, -0.9070, -1.3538, -1.2221, -0.0290, 1.0077]]
Got:
    doctest:1: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr.
    [[-0.1157, 0.7025, 0.4949, 0.3324, 0.7110, 0.7248, -0.4048, 0.3103, -0.3465, 0.2964], 
    [-0.5981, -0.6932, 0.5947, -0.9995, -0.7726, -0.9070, -1.3538, -1.2221, -0.0290, 1.0077]]
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/fractal.py", line 201:
    sage: finance.fractional_brownian_motion_simulation(0.8,0.1,8,1)
Expected:
    [[-0.0754, 0.1874, 0.2735, 0.5059, 0.6824, 0.6267, 0.6465, 0.6289]]
Got:
    doctest:1: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr.
    [[-0.0754, 0.1874, 0.2735, 0.5059, 0.6824, 0.6267, 0.6465, 0.6289]]
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/fractal.py", line 237:
    sage: a = finance.multifractal_cascade_random_walk_simulation(3770,0.02,0.01,0.01,10,3)
Expected nothing
Got:
    doctest:1: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr.
**********************************************************************

@sagetrac-mabshoff
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sagetrac-mabshoff mannequin commented Sep 27, 2008

comment:4

One more fix not yet in the patch:

[02:20am] mabshoff: mk
[02:21am] jason-:         cdef ndarray _n = numpy.array(list(self),dtype=numpy.dtype('float64'))
[02:21am] jason-: #        temp = PyArray_SimpleNew(1, dims, NPY_DOUBLE)
[02:21am] jason-: #        _n = temp
[02:21am] jason-: #        for i from 0<=i<_V.v.size:
[02:21am] jason-: #            _n[i] = float(_V.v.data[i])
[02:21am] jason-: comment from that line down to the end of the function
[02:21am] jason-: and replace it with the above numpy.array line.
[02:21am] jason-: oh, and add import numpy above that.
<SNIP>
[02:24am] mabshoff: sage: sage: v = vector(RDF,4,range(4))
[02:24am] mabshoff: sage: v.numpy()
[02:24am] mabshoff: array([ 0.,  1.,  2.,  3.])
[02:24am] mabshoff: sage: v
[02:24am] mabshoff: (0.0, 1.0, 2.0, 3.0)
[02:24am] mabshoff: so that works now
[02:24am] jason-: can I just replace it?
[02:24am] jason-: it's going to be really slow, but it works
[02:25am] mabshoff: well, I guess for now we can live with that.
[02:25am] jason-: well, I don't know how much slower
[02:25am] jason-: can you do a timeit test?
[02:25am] mabshoff: sure, in a minute

@sagetrac-mabshoff
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sagetrac-mabshoff mannequin commented Sep 27, 2008

comment:5

Attachment: numpy-deprecations.patch.gz

Ok, the latest patch has the following issues left:

sage -t -long devel/sage/sage/plot/plot3d/list_plot3d.py    
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/list_plot3d.py", line 68:
    sage: list_plot3d(m, texture='yellow', interpolation_type='nn',frame_aspect_ratio=[1,1,1/3])
Expected nothing
Got:
    doctest:1431: DeprecationWarning: scipy.stats.corrcoef is deprecated; please update your code to use numpy.corrcoef.
    Please note that:
        - numpy.corrcoef rowvar argument defaults to true, not false
        - numpy.corrcoef bias argument defaults to false, not true
    <BLANKLINE>
    doctest:1395: DeprecationWarning: scipy.stats.cov is deprecated; please update your code to use numpy.cov.
    Please note that:
        - numpy.cov rowvar argument defaults to true, not false
        - numpy.cov bias argument defaults to false, not true
    <BLANKLINE>
    doctest:413: DeprecationWarning: scipy.stats.mean is deprecated; please update your code to use numpy.mean.
    Please note that:
        - numpy.mean axis argument defaults to None, not 0
        - numpy.mean has a ddof argument to replace bias in a more general manner.
          scipy.stats.mean(a, bias=True) can be replaced by numpy.mean(x,
    axis=0, ddof=1).
    <BLANKLINE>
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/list_plot3d.py", line 74:
    sage: list_plot3d(m, texture='yellow', interpolation_type='spline',frame_aspect_ratio=[1,1,1/3])
Expected nothing
Got:
    doctest:760: DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew.
    doctest:760: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr.
    doctest:837: DeprecationWarning: PyArray_FromDims: use PyArray_SimpleNew.
    doctest:837: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr.
    <BLANKLINE>
**********************************************************************

and after fixing the same issue as in the other places, i.e

        cdef ndarray n = numpy.array(list(self),dtype=numpy.dtype('float64'))
        #cdef ndarray n = PyArray_SimpleNewFromData(1, dims, NPY_DOUBLE, self._values)
        if copy:
            return n.copy()
        else:
            return n

we get

sage -t -long devel/sage/sage/finance/time_series.pyx       
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/time_series.py", line 1477:
    sage: bm.hurst_exponent()
Expected:
    0.527450972...
Got:
    doctest:413: DeprecationWarning: scipy.stats.mean is deprecated; please update your code to use numpy.mean.
    Please note that:
        - numpy.mean axis argument defaults to None, not 0
        - numpy.mean has a ddof argument to replace bias in a more general manner.
          scipy.stats.mean(a, bias=True) can be replaced by numpy.mean(x,
    axis=0, ddof=1).
    0.52745097242535754
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/time_series.py", line 1485:
    sage: fbm.hurst_exponent()
Expected:
    0.706511951...
Got:
    0.52044004048795489
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/time_series.py", line 1489:
    sage: fbm = finance.fractional_brownian_motion_simulation(0.2,0.1,10^5,1)[0]
Exception raised:
    Traceback (most recent call last):
      File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/local/lib/python2.5/doctest.py", line 1228, in __run
        compileflags, 1) in test.globs
      File "<doctest __main__.example_46[8]>", line 1, in <module>
        fbm = finance.fractional_brownian_motion_simulation(RealNumber('0.2'),RealNumber('0.1'),Integer(10)**Integer(5),Integer(1))[Integer(0)]###line 1489:
    sage: fbm = finance.fractional_brownian_motion_simulation(0.2,0.1,10^5,1)[0]
      File "fractal.pyx", line 210, in sage.finance.fractal.fractional_brownian_motion_simulation (sage/finance/fractal.c:1145)
      File "fractal.pyx", line 183, in sage.finance.fractal.fractional_gaussian_noise_simulation (sage/finance/fractal.c:1059)
      File "fractal.pyx", line 118, in sage.finance.fractal.stationary_gaussian_simulation (sage/finance/fractal.c:642)
    NotImplementedError: Stationary Gaussian simulation only implemented when Fourier transform is nonnegative
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/time_series.py", line 1490:
    sage: fbm.hurst_exponent()
Expected:
    0.278997441...
Got:
    0.52044004048795489

and some numerical noise, but this might be related to the stats function:

sage -t -long devel/sage/sage/finance/fractal.pyx           
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/fractal.py", line 69:
    sage: [sim.autocovariance(i) for i in [0..4]]
Expected:
    [0.98665816086255..., 0.69201577095377..., 0.56234006792017..., 0.48647965409871..., 0.43667043322102...]
Got:
    [353.87586761938252, 4.1452524114948925, 2.6438582436312341, -5.3373197046012857, 1.2666878806249871]
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/fractal.py", line 155:
    sage: finance.fractional_gaussian_noise_simulation(0.8,1,10,2)
Expected:
    [[-0.1157, 0.7025, 0.4949, 0.3324, 0.7110, 0.7248, -0.4048, 0.3103, -0.3465, 0.2964],
     [-0.5981, -0.6932, 0.5947, -0.9995, -0.7726, -0.9070, -1.3538, -1.2221, -0.0290, 1.0077]]
Got:
    [[3.0262, -0.9109, 0.8122, -1.0340, -1.6515, -1.6213, -0.9947, 1.2976, -0.8180, -0.2633], 
     [-1.5913, -0.6777, 2.7479, 1.5428, -0.0232, -1.4984, -0.9457, -1.0283, 0.6810, 0.1817]]
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/fractal.py", line 161:
    sage: finance.fractional_gaussian_noise_simulation(0.8,1,10,1)[0].sums()
Expected:
    [-0.1157, 0.5868, 1.0818, 1.4142, 2.1252, 2.8500, 2.4452, 2.7555, 2.4090, 2.7054]
Got:
    [3.0262, 2.1154, 2.9275, 1.8935, 0.2420, -1.3793, -2.3740, -1.0764, -1.8944, -2.1577]
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/fractal.py", line 201:
    sage: finance.fractional_brownian_motion_simulation(0.8,0.1,8,1)
Expected:
    [[-0.0754, 0.1874, 0.2735, 0.5059, 0.6824, 0.6267, 0.6465, 0.6289]]
Got:
    [[0.8560, 0.5983, 0.8280, 0.5356, 0.0685, -0.3901, -0.6715, -0.3045]]
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/fractal.py", line 204:
    sage: finance.fractional_brownian_motion_simulation(0.8,0.01,8,1)
Expected:
    [[-0.0239, 0.0593, 0.0865, 0.1600, 0.2158, 0.1982, 0.2044, 0.1989]]
Got:
    [[0.2707, 0.1892, 0.2618, 0.1694, 0.0216, -0.1234, -0.2123, -0.0963]]
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/fractal.py", line 206:
    sage: finance.fractional_brownian_motion_simulation(0.8,0.01,8,2)
Expected:
    [[-0.0167, 0.0342, 0.0261, 0.0856, 0.1735, 0.2541, 0.1409, 0.1692],
     [0.0244, -0.0153, 0.0125, -0.0363, 0.0764, 0.1009, 0.1598, 0.2133]]
Got:
    [[0.0866, 0.1219, 0.0045, 0.0102, -0.0459, -0.0883, 0.0837, 0.1999], 
     [0.3499, 0.3886, 0.5201, 0.4895, 0.6820, 0.7656, 0.8753, 0.8654]]
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/fractal.py", line 238:
    sage: a
Expected:
    [[-0.0096, 0.0025, 0.0066, 0.0016, 0.0078, 0.0051, 0.0047, -0.0013, 0.0003, -0.0043],
     [0.0003, 0.0035, 0.0257, 0.0358, 0.0377, 0.0563, 0.0661, 0.0746, 0.0749, 0.0689],
     [-0.0120, -0.0116, 0.0043, 0.0078, 0.0115, 0.0018, 0.0085, 0.0005, 0.0012, 0.0060]]
Got:
    [[-0.0600, -0.0520, -0.0482, -0.0526, -0.0463, -0.0477, -0.0482, -0.0557, -0.0543, -0.0614], 
     [0.0072, 0.0114, 0.0220, 0.0274, 0.0295, 0.0422, 0.0495, 0.0550, 0.0553, 0.0459], 
     [-0.1452, -0.1446, -0.1266, -0.1228, -0.1167, -0.1271, -0.1169, -0.1227, -0.1220, -0.1199]]
**********************************************************************
File "/scratch/mabshoff/release-cycle/sage-3.1.3.alpha2/tmp/fractal.py", line 244:
    sage: a[0].exp()
Expected:
    [0.9905, 1.0025, 1.0067, 1.0016, 1.0078, 1.0051, 1.0047, 0.9987, 1.0003, 0.9957]
Got:
    [0.9418, 0.9493, 0.9529, 0.9488, 0.9548, 0.9534, 0.9529, 0.9459, 0.9472, 0.9404]
**********************************************************************

@robertwb
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robertwb commented Nov 4, 2008

comment:6

Hmm... what's up with

-sage: from scipy import linsolve   
+sage: from scipy.sparse.linalg.dsolve import linsolve

in sage/numerical/test.py? Does scipy.linsolve not work anymore?

Also, those doctest failures look like more than trivial noise, but I have no experience in the area so someone else should comment.

@williamstein
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comment:7
23:36 < mabshoff> #4205 isn't useful yet.
23:36 < wstein-4205> #4205 is scrwed up!
23:36 < wstein-4205> The thing says "needs review"
23:36 < wstein-4205> but it clearly "needs work".
23:37 < mabshoff> That one is more or less in limbo until we do the Scipy 0.7 update.
23:37 < mabshoff> Yep
23:37 < wstein-4205> And the patch itself just deletes *all* the C API code that Josh Kantor spent a *huge* amount
23:37 -!- craigcitro is now known as cc-4612
23:37 < wstein-4205> of time writing, and replaces it with a bunch of slow python numpy code.
23:37 < mabshoff> ok
23:37 < wstein-4205> Huh?
23:37 < wstein-4205> Or maybe I don't get it.
23:37 < mabshoff> Ask jason|log 
23:37 < wstein-4205> I'm changing it to "needs work".

@jasongrout
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comment:8

Sorry; as is obvious from the discussion and iterative approach, this ticket is indeed "needs work"; I thought that was how it was marked. I think in the initial iteration, we thought we had something good, so it started out as "needs review" and then we forgot to change it to "needs work" when we started playing whack-a-mole.

@jasongrout
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comment:9

And mabshoff is right, it's on hold until scipy 0.7 is release soon.

@jasongrout
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comment:10

In fact, this ticket may not be needed anymore if the patch from #4206 is applied.

@jasongrout jasongrout changed the title Fix deprecation warnings from numpy 1.2 [possibly not needed] Fix deprecation warnings from numpy 1.2 Nov 27, 2008
@sagetrac-mabshoff
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sagetrac-mabshoff mannequin commented Nov 28, 2008

comment:11

Some bits of this patch fix scipy import issues since things have moved around. Other than that I agree with Jason that we likely will end up canning the rest of this patch.

Cheers,

Michael

@sagetrac-mabshoff sagetrac-mabshoff mannequin changed the title [possibly not needed] Fix deprecation warnings from numpy 1.2 [in limbo] Fix deprecation warnings from numpy 1.2 Nov 28, 2008
@jasongrout
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comment:12

This ticket can probably be closed once #6140 and #3391 are closed.

@craigcitro
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comment:13

Closing this as wontfix, because it's superseded by #6140.

@sagetrac-mabshoff sagetrac-mabshoff mannequin mentioned this issue Sep 27, 2008
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