Pauli Virtanen | 15 Dec 20:47 2014
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ANN: Scipy 0.15.0 release candidate 1


Dear all,

Scipy 0.15.0 release candidate 1 is now available. If no surprises
turn up, the final release is planned within two weeks.

Source tarballs, full release notes etc. are available at
https://sourceforge.net/projects/scipy/files/scipy/0.15.0rc1/

Best regards,
Pauli Virtanen
Pauli Virtanen | 14 Dec 23:29 2014
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ANN: Scipy 0.14.1 release candidate 1


Dear all,

We have finished preparing the Scipy 0.14.1 release candidate 1.
If no regressions turn up, the final release is planned within the
following weeks.

The 0.14.1 release will be a bugfix-only release, addressing the
following issues:

gh-3630 NetCDF reading results in a segfault
gh-3631 SuperLU object not working as expected for complex matrices
gh-3733 Segfault from map_coordinates
gh-3780 Segfault when using CSR/CSC matrix and uint32/uint64
gh-3781 Fix omitted types in sparsetools typemaps
gh-3802 0.14.0 API breakage: _gen generators are missing from
scipy.stats.distributions API
gh-3805 ndimge test failures with numpy 1.10
gh-3812 == sometimes wrong on csr_matrix
gh-3853 Many scipy.sparse test errors/failures with numpy 1.9.0b2
gh-4084 Fix exception declarations for Cython 0.21.1 compatibility
gh-4093 Avoid a memory error in splev(x, tck, der=k)
gh-4104 Workaround SGEMV segfault in Accelerate (maintenance 0.14.x)
gh-4143 Fix ndimage functions for large data
gh-4149 Bug in expm for integer arrays
gh-4154 Ensure that the 'size' argument of PIL's 'resize' method is
a tuple
gh-4163 ZeroDivisionError in scipy.sparse.linalg.lsqr
gh-4164 Remove use of deprecated numpy API in lib/lapack/ f2py wrapper
gh-4180 pil resize support tuple fix
(Continue reading)

Ralf Gommers | 13 Dec 21:01 2014
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deprecating stats.pdf_fromgamma

Hi all,

Today I ran into stats.pdf_fromgamma again. That function, which does Gram-Chandler expansion to construct a distribution from 4 moments, is completely undocumented and untested. Statsmodels seems to be a better place to put this kind of functionality in, and it already contains the closely related Edgeworth expansion. See https://github.com/scipy/scipy/issues/699 for more details.

Therefore the proposal is to deprecate pdf_fromgamma for 0.16.0. Any objections?

Ralf

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Ralf Gommers | 13 Dec 13:05 2014
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when to drop numpy 1.5.x/1.6.x support?

Hi all,

During the last week there were 3 PRs that failed because they used features not available in numpy 1.5.x or 1.6.x:
  https://github.com/scipy/scipy/pull/4238 (copy kw to astype method)
  https://github.com/scipy/scipy/pull/4256 (out kw to ufuncs)
  https://github.com/scipy/scipy/pull/4260 (use of np.random.choice)

All those issues were/are fixable, but it looks like the balance of gain from keeping support for those numpy versions to development effort of supporting them is slowly shifting the wrong way. So questions:

1. Is anyone still relying on numpy 1.5.x or 1.6.x support for the next scipy releases?
2. Is it time to drop support for those versions, or if not then when?

Cheers,
Ralf

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Parke Loyd | 13 Dec 02:12 2014
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contribute wald-wolfowitz runs test to scipy.stats

Hi,

I wrote a bit of code that computes the test statistic and p-value for the wald-wolfowitz runs test. Seems like it would fit nicely alongside the other statistical tests in the stats module (ansari, bartlett, ...). The code is currently available here -- the function named runstest. 

The code works for my purposes, but I expect there is still much to be done before it will be ready for a pull request. Per the guide on contributing to SciPy, I figured I would get the conversation started to find out whether the community thought it a worthwhile contribution before making the effort to get it ready for a PR.

Best,
Parke
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Ryan Nelson | 11 Dec 19:29 2014
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Cookbook update

Hello Scipy-devs:

The link below on building a Qt app with a Matplotlib widget is very dated.

After several research/trial/error cycles, I reproduced the Qt4 plot window that you using the relevant pyplot commands. I suppose I could update the Cookbook page above, but I need editing rights. Is this still possible, or are we trying to point users to a new location?

Ryan

P.S. Here's the relevant code, in case it matters.

File = run.py
-------------------------------------------------------------------------
from test import Ui_MainWindow

from matplotlib.figure import Figure
from matplotlib.backends.backend_qt4agg import (
    FigureCanvasQTAgg as FigureCanvas,
    NavigationToolbar2QT as NavigationToolbar)

from PyQt4 import QtGui

class Main(QtGui.QMainWindow, Ui_MainWindow):
    def __init__(self, ):
        super(Main, self).__init__()
        self.setupUi(self)

        self.populatefigure()
        self.addtoolbar()
        self.plotdata()

    def populatefigure(self,):
        self.fig = Figure()
        self.canvas = FigureCanvas(self.fig)
        self.canvas.setParent(self.MplFigure)

        self.mplvbox = QtGui.QVBoxLayout()
        self.mplvbox.addWidget(self.canvas)
        self.MplFigure.setLayout(self.mplvbox)

    def addtoolbar(self,):
        self.toolbar = NavigationToolbar(self.canvas, self, 
                coordinates=True)
        self.addToolBar(self.toolbar)

    def addtoolbar2(self,):
        self.toolbar = NavigationToolbar(self.canvas, self.MplFigure, 
                coordinates=True)
        self.mplvbox.addWidget(self.toolbar)

    def plotdata(self,):
        self.axes = self.fig.add_subplot(111)
        self.axes.plot([1,3,2])
        self.canvas.draw()

if __name__ == "__main__":
    '''
    Run IPython as follows:
    $ ipython --gui='qt'
    [In 1]: %run run.py
    If running this file directly from the command line, remove the comments
    below and do the following:
    $ python run.py
    '''

    #import sys
    #app = QtGui.QApplication([])
    main = Main()
    main.show()
    #sys.exit(app.exec_())
-------------------------------------------------

File = test.py (created with Designer and pyuic4)
-------------------------------------------------------------------
# -*- coding: utf-8 -*-

# Form implementation generated from reading ui file 'test.ui'
#
# Created: Thu Dec 11 12:32:15 2014
#      by: PyQt4 UI code generator 4.11.3
#
# WARNING! All changes made in this file will be lost!

from PyQt4 import QtCore, QtGui

try:
    _fromUtf8 = QtCore.QString.fromUtf8
except AttributeError:
    def _fromUtf8(s):
        return s

try:
    _encoding = QtGui.QApplication.UnicodeUTF8
    def _translate(context, text, disambig):
        return QtGui.QApplication.translate(context, text, disambig, _encoding)
except AttributeError:
    def _translate(context, text, disambig):
        return QtGui.QApplication.translate(context, text, disambig)

class Ui_MainWindow(object):
    def setupUi(self, MainWindow):
        MainWindow.setObjectName(_fromUtf8("MainWindow"))
        MainWindow.resize(800, 600)
        self.centralwidget = QtGui.QWidget(MainWindow)
        self.centralwidget.setObjectName(_fromUtf8("centralwidget"))
        self.gridLayout = QtGui.QGridLayout(self.centralwidget)
        self.gridLayout.setObjectName(_fromUtf8("gridLayout"))
        self.MplFigure = QtGui.QWidget(self.centralwidget)
        self.MplFigure.setObjectName(_fromUtf8("MplFigure"))
        self.gridLayout.addWidget(self.MplFigure, 0, 0, 1, 1)
        MainWindow.setCentralWidget(self.centralwidget)

        self.retranslateUi(MainWindow)
        QtCore.QMetaObject.connectSlotsByName(MainWindow)

    def retranslateUi(self, MainWindow):
        MainWindow.setWindowTitle(_translate("MainWindow", "MainWindow", None))
-------------------------------------------------
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Deacon Sweeney | 11 Dec 18:09 2014

Several packages failing on sparse/csgraph/_validation.py

Hello,

I'm having an unusual bug on a fresh installation of scipy on SUSE, with Python 2.7.8. There are several packages (stats, sparse, optimize, interpolate, etc) that all fail to import due to sparse/csgraph/_validation.py. Here is the error message from sparse:

>>> import scipy.sparse
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/itmi/Python-2.7.8_a/lib/python2.7/site-packages/scipy/sparse/__init__.py", line 206, in <module>
    from scipy.sparse.csgraph import _validation
  File "/itmi/Python-2.7.8_a/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py", line 122, in <module>
    from scipy.sparse.csgraph import _validation
  File "/itmi/Python-2.7.8_a/lib/python2.7/site-packages/scipy/sparse/csgraph/_validation.py", line 4, in <module>
    from scipy.sparse import csr_matrix, isspmatrix, isspmatrix_csc, isspmatrix_csr
ImportError: cannot import name csr_matrix

We have a bit of an unusual installation arrangement here, where I have to use the "module load" command to switch Python versions.

I can't find anything searching around, so I figured I'd reach out to the experts here while digging in further myself. Any insights would be very appreciated!

Thanks,

Deacon


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Eric Moore | 9 Dec 15:22 2014

Adding routines for updating QR decompositions

Hi,

I've just submitted PR #4249 adding qr_update, qr_insert and qr_delete for performing rank-k updates, adding rows or columns and removing rows or colums. 

https://github.com/scipy/scipy/pull/4249

Comments welcome.

Eric.
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Warren Weckesser | 5 Dec 13:15 2014
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Problem with scipy.integrate.nquad reported on stackoverflow

Could someone with a Windows installation of scipy 0.14.0 run the code
at http://stackoverflow.com/questions/27270044/big-integration-error-with-integrate-ndquad?

It works for me on Mac OS X.   In the comments to the question,
Jonathan March reported that the problem occurs with both 32 and 64
bit Windows 7.  Does the code work for anyone using Windows?  ("Work"
means the values reported for 'Intf1corr' and 'Intf2' are the same.)

Warren
Pierre Haessig | 2 Dec 12:52 2014

iirdesign fails with ftype='bessel'

Hi,

The scipy.signal.iirdesign function accepts different filter types like 
'butter' or 'ellip' (cf. 
http://docs.scipy.org/doc/scipy-0.14.0/reference/generated/scipy.signal.iirdesign.html).

However, it fails with the ftype 'bessel':
ValueError: bessel does not have order selection. Use iirfilter function.

This error is triggered at this line of code:
https://github.com/scipy/scipy/blob/master/scipy/signal/filter_design.py#L645

So in practice, the iirdesign function cannot accept the 'bessel' type. 
Shouldn't we remove it from the docstring ?
Or is this a pedagogical error, put here on purpose ?

best,
Pierre
Evgeni Burovski | 26 Nov 23:11 2014
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Blomberg open source event London 29-30 Nov

Hi,

In case somebody is interested and have not heard about it --- Blooomberg is organizing a two-day open source event for scientific python in London this weekend, Nov 28-29.

The event is RSVP:  

http://go.bloomberg.com/promo/invite/bloomberg-open-source-day-scientific-python/


Here are related annoucements/discussions in pydata and numpy lists: 
If you are not around, consider joining remotely --- I do not speak for the organizers, but we can always self-organize on github or ML.


See you on Saturday --- in person or online,

Evgeni
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Gmane