Mailman 3 December 2014 - SciPy-Dev

Asking for a code review: pole placement
by Robert Lucente - Pipeline Dec. 19, 2014

Dec. 19, 2014

Date: Mon, 15 Dec 2014 11:53:32 +0100 From: Irvin Probst <irvin.probst(a)ensta-bretagne.fr> Subject: [SciPy-Dev] Asking for a code review: pole placement Message-ID: <548EBDAC.9000107(a)ensta-bretagne.fr> >Licensing issues Perhaps eff.org might be able to help w/ some of the licensing stuff?

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ANN: Scipy 0.15.0 release candidate 1
by Pauli Virtanen Dec. 17, 2014

Dec. 17, 2014

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iEYEARECAAYFAlSPOukACgkQ6BQxb7O0pWB93QCeKdH90WDdAPELEyJjnboeG1Qj vtYAoLLGi6OzCErtI5DDLVwA/S5xre2R =ReL8 -----END PGP SIGNATURE-----

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deprecating stats.pdf_fromgamma
by Ralf Gommers Dec. 17, 2014

Dec. 17, 2014

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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when to drop numpy 1.5.x/1.6.x support?
by Ralf Gommers Dec. 17, 2014

Dec. 17, 2014

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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contribute wald-wolfowitz runs test to scipy.stats
by Parke Loyd Dec. 16, 2014

Dec. 16, 2014

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 <https://github.com/parkus/mypy/blob/master/statsutils.py> -- 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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Documentation page on API
by Yuxiang Wang Dec. 14, 2014

Dec. 14, 2014

(Sorry about sending this to the wrong list, scipy-user instead of scipy-dev, before; apologize to those who saw this twice) Hi all, I was reading through the link (http://docs.scipy.org/doc/scipy/reference/api.html#guidelines-for-importing…) and it mentioned that the first form is preferred over the second one under most circumstances: # first form from scipy import stats stats.lomax(...) # second form from scipy.stats import distributions distributions.lomax(...) I honestly think the second form is far more frequently used in the examples given in the document, for example: http://docs.scipy.org/doc/scipy/reference/tutorial/special.html http://docs.scipy.org/doc/scipy/reference/tutorial/integrate.html http://docs.scipy.org/doc/scipy/reference/tutorial/optimize.html http://docs.scipy.org/doc/scipy/reference/tutorial/interpolate.html http://docs.scipy.org/doc/scipy/reference/tutorial/fftpack.html Would you think it'd be better to update this link? -Shawn

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Several packages failing on sparse/csgraph/_validation.py
by Deacon Sweeney Dec. 14, 2014

Dec. 14, 2014

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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Cookbook update
by Ryan Nelson Dec. 11, 2014

Dec. 11, 2014

Hello Scipy-devs: The link below on building a Qt app with a Matplotlib widget is very dated. http://wiki.scipy.org/Cookbook/Matplotlib/Qt_with_IPython_and_Designer 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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Problem with scipy.integrate.nquad reported on stackoverflow
by Warren Weckesser Dec. 8, 2014

Dec. 8, 2014

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

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Pole placement
by Irvin Probst Dec. 6, 2014

Dec. 6, 2014

Hi, Is there any reason why scipy has no pole placement method (ppol in Scilab or place in Matlab)? I.e for a given linear system xdot=A*X+B*U, and a given set of poles P, find K such as eigenvalues(A-BK)=P ? Or did I miss it in the doc ? I'm aware of python-control (http://www.cds.caltech.edu/~murray/wiki/Control_Systems_Library_for_Python) but 99.9% of the time I use it it is ONLY for pole placement as scipy already provides enough tools for simple linear systems simulations, furthermore python-control's place() function only task is to call the relevant function in the Scilot library (which I also need to install BTW+ bindings from scylot). So, I've started to port in "pure" numpy/python matlab's place() function which is based on Kautsky et Al's algorithm, would it be of any intest for you ? It is not rocket science, and it is not finished yet, but I thought it could be useful for other people. Let me know what you think and sorry for the disturbance if it is not relevant for you. Regards -- Irvin

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