Mailman 3 March 2009 - SciPy-Dev

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by oliphant＠ee.byu.edu 23 Mar '09

23 Mar '09

Here are your banks documents.

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ANNOUNCE: ETS 3.2.0 Released
by Dave Peterson 23 Mar '09

23 Mar '09

Hello, I'm pleased to announce that Enthought Tool Suite (ETS) version 3.2.0 has been tagged and released! Source distributions (.tar.gz) have been uploaded to PyPi, and Windows binaries will be follow shortly. A full install of ETS can be done using Setuptools via a command like: easy_install -U "ets[nonets] >= 3.2.0" NOTE 1: Users of an old ETS release will need to first uninstall prior to installing the new ETS. NOTE 2: If you get a 'SandboxViolation' error, simply re-run the command again -- it may take multiple invocations to get everything installed. (This error appears to be a long-standing incompatibility between numpy.distutils and setuptools.) Please see below for a list of what's new in this release. What Is ETS? =========== The Enthought Tool Suite (ETS) is a collection of components developed by Enthought and the open-source community, which we use every day to construct custom scientific applications. It includes a wide variety of components, including: * an extensible application framework * application building blocks * 2-D and 3-D graphics libraries * scientific and math libraries * developer tools The cornerstone on which these tools rest is the Traits package, which provides explicit type declarations in Python; its features include initialization, validation, delegation, notification, and visualization of typed attributes. More information on ETS is available from the development home page: http://code.enthought.com/projects/index.php Changelog ========= ETS 3.2.0 is a feature-added update to ETS 3.1.0, including numerous bug-fixes. Some of the notable changes include: Chaco ----- * Domain limits - Mappers now can declare the "limits" of their valid domain. PanTool and ZoomTool respect these limits. (pwang) * Adding "hide_grids" parameter to Plot.img_plot() and Plot.contour_plot() so users can override the default behavior of hiding grids. (pwang) * Refactored examples to declare a Demo object so they can be be run with the demo.py example launcher. (vibha) * Adding chaco.overlays package with some canned SVG overlays. (bhendrix) * DragZoom now can scale both X and Y axes independently corresponding to the mouse cursor motion along the X and Y axes (similar to the zoom behavior in Matplotlib). (pwang) * New Examples: * world map (bhendrix) * more financial plots (pwang) * scatter_toggle (pwang) * stacked_axis (pwang) * Fixing the chaco.scales TimeFormatter to use the built-in localtime() instead of the one in the safetime.py module due to Daylight Savings Time issues with timedelta. (r23231, pwang) * Improved behavior of ScatterPlot when it doesn't get the type of metadata it expects in its "selections" and "selection_masks" metadata keys (r23121, pwang) * Setting the .range2d attribute on GridMapper now properly sets the two DataRange1D instances of its sub-mappers. (r23119, pwang) * ScatterPlot.map_index() now respects the index_only flag (r23060, pwang) * Fixed occasional traceback/bug in LinePlot that occurred when data was completely outside the visible range (r23059, pwang) * Implementing is_in() on legends to account for padding and alignment (caused by tools that move the legend) (r23052, bhendrix) * Legend behaves properly when there are no plots to display (r23012, judah) * Fixed LogScale in the chaco.scales package to correctly handle the case when the length of the interval is less than a decade (r22907, warren.weckesser) * Fixed traceback when calling copy_traits() on a DataView (r22894, vibha) * Scatter plots generated by Plot.plot() now properly use the "auto" coloring feature of Plot. (r22727, pwang) * Reduced the size of screenshots in the user manual. (r22720, rkern) Mayavi ------ * 17, 18 March, 2009 (PR): * NEW: A simple example to show how one can use TVTK’s visual module with mlab. [23250] * BUG: The size trait was being overridden and was different from the parent causing a bug with resizing the viewer. [23243] * 15 March, 2009 (GV): * ENH: Add a volume factory to mlab that knows how to set color, vmin and vmax for the volume module [23221]. * 14 March, 2009 (PR): * API/TEST: Added a new testing entry point: ‘mayavi -t’ now runs tests in separate process, for isolation. Added enthought.mayavi.api.test to allow for simple testing from the interpreter [23195]...[23200], [23213], [23214], [23223]. * BUG: The volume module was directly importing the wx_gradient_editor leading to an import error when no wxPython is available. This has been tested and fixed. Thanks to Christoph Bohme for reporting this issue. [23191] * 14 March, 2009 (GV): * BUG: [mlab]: fix positioning for titles [23194], and opacity for titles and text [23193]. * ENH: Add the mlab_source attribute on all objects created by mlab, when possible [23201], [23209]. * ENH: Add a message to help the first-time user, using the new banner feature of the IPython shell view [23208]. * 13 March, 2009 (PR): * NEW/API: Adding a powerful TCP/UDP server for scripting mayavi via the network. This is available in enthought.mayavi.tools.server and is fully documented. It uses twisted and currently only works with wxPython. It is completely insecure though since it allows a remote user to do practically anything from mayavi. * 13 March, 2009 (GV) * API: rename mlab.orientationaxes to mlab.orientation_axes [23184] * 11 March, 2009 (GV) * API: Expose ‘traverse’ in mlab.pipeline [23181] * 10 March, 2009 (PR) * BUG: Fixed a subtle bug that affected the ImagePlaneWidget. This happened because the scalar_type of the output data from the VTKDataSource was not being set correctly. Getting the range of any input scalars also seems to silence warnings from VTK. This should hopefully fix issues with the use of the IPW with multiple scalars. I’ve added two tests for this, one is an integration test since those errors really show up only when the display is used. The other is a traditional unittest. [23166] * 08 March, 2009 (GV) * ENH: Raises an error when the user passes to mlab an array with infinite values [23150] * 07 March, 2009 (PR) * BUG: A subtle bug with a really gross error in the GridPlane component, I was using the extents when I should really have been looking at the dimensions. The extract grid filter was also not flushing the data changes downstream leading to errors that are also fixed now. These errors would manifest when you use an ExtractGrid to select a VOI or a sample rate and then used a grid plane down stream causing very wierd and incorrect rendering of the grid plane (thanks to conflation of extents and dimensions). This bug was seen at NAL for a while and also reported by Fred with a nice CME. The CME was then converted to a nice unittest by Suyog and then improved. Thanks to them all. [23146] * 28 February, 2009 (PR) * BUG: Fixed some issues reported by Ondrej Certik regarding the use Of mlab.options.offscreen, mlab.options.backend = ‘test’, removed cruft from earlier ‘null’ backend, fixed bug with incorrect imports, add_dataset set no longer adds one new null engine each time figure=False is passed, added test case for the options.backend test. [23088] * 23 February, 2009 (PR) * ENH: Updating show so that it supports a stop keyword argument that pops up a little UI that lets the user stop the mainloop temporarily and continue using Python [23049] * 21 February, 2009 (GV) * ENH: Add a richer view for the pipeline to the MayaviScene [23035] * ENH: Add safegards to capture wrong triangle array sizes in mlab.triangular_mesh_source. [23037] * 21 February, 2009 (PR) * ENH: Making the transform data filter recordable. [23033] * NEW: A simple animator class to make it relatively to create animations. [23036] [23039] * 20 February, 2009 (PR) * ENH: Added readers for various image file formats, poly data readers and unstructured grid readers. These include DICOM, GESigna, DEM, MetaImage (mha,mhd) MINC, AVSucd, GAMBIT, Exodus, STL, Points, Particle, PLY, PDB, SLC, OBJ, Facet and BYU files. Also added several tests for most of this functionality along with small data files. These are additions from PR’s project staff, Suyog Jain and Sreekanth Ravindran. [23013] * ENH: We now change the default so the ImagePlaneWidget does not control the LUT. Also made the IPW recordable. [23011] * 18 February, 2009 (GV) * ENH: Add a preference manager view for editing preferences outside envisage [22998] * 08 February, 2009 (GV) * ENH: Center the glyphs created by barchart on the data points, as mentioned by Rauli Ruohonen [22906] * 29 January, 2009 (GV) * ENH: Make it possible to avoid redraws with mlab by using mlab.gcf().scene.disable_render = True [22869] * 28 January, 2009 (PR and GV) * ENH: Make the mlab.pipeline.user_defined factory function usable to add arbitrary filters on the pipeline. [22867], [22865] * 11 January, 2009 (GV) * ENH: Make mlab.imshow use the ImageActor. Enhance the ImageActor to map scalars to colors when needed. [22816] Traits ------ * Fixed a bug whereby faulty error handling in the PyProtocols Pyrex speedup code keeps references to tracebacks that have been handled. In so doing, clean up the same code such that it can be used with a modern Pyrex release (a bare raise can no longer be used outside of an except: clause). * RangeEditor factory now supports a 'logslider' mode: Thanks to Matthew Turk for the patch * TabularEditor factory now supports editing of all columns: Thanks to Didrik Pinte for the patch * DateEditor factory in 'custom' style now supports multi-select feature. * DateEditor and TimeEditor now support the 'readonly' style. * Fixed a bug in the ArrayEditor factory that was causing multiple trait change events to get fired when the underlying array is changed externally to the editor: Thanks to Matthew Turk for he patch. * Fixed a circular import error in Color, Font and RGBColor traits * Fixed a bug in the factory for ArrayViewEditor so it now calls the toolkit backend-specific editor TraitsBackendWX --------------- * RangeEditor now supports a 'logslider' mode: Thanks to Matthew Turk for the patch * TabularEditor now supports editing of all columns: Thanks to Didrik Pinte for the patch * DateEditor in 'custom' style now supports multi-select feature. * DateEditor and TimeEditor now support the 'readonly' style. * Added a trait to the wx pyface workbench View to indicate if the view dock window should be closeable. * Fixed the DirectoryEditor to popup the correct file dialog (thanks to Luca Fasano and Phil Thompson) * Fixed a circular import error in Color, Font and RGBColor traits * Fixed a bug in the ColorEditor that was causing the revert action to not work correctly. * Fixed a bug that caused a traceback when trying to undock a pyface dock window * Fixed a bug in the 'livemodal' view that caused the UI to become unresponsive if the 'updated' event was fired on the contained view. * Fixed bugs in ListEditor (notebook style) that caused a loss of sync between the 'selected' trait and the activated dock window. TraitsBackendQt --------------- * RangeEditor now supports a 'logslider' mode: Thanks to Matthew Turk for the patch * Fixed the DirectoryEditor to popup the correct file dialog (thanks to Luca Fasano and Phil Thompson)

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Initial tests for optimize.fsolve()
by Yosef Meller 22 Mar '09

22 Mar '09

Added a test problem and two initial tests that just check that nothing croaks: a run without a jacobian and a run with a jacobian. Now, I kind of lost track of the whole workflow discussion, so please tell me what process to follow to get this in. Also, is the huge docstring in TestFSolve.pressure_network() an overkill? Yours, Yosef.

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Has IPython been useful to you? Please let me know...
by Fernando Perez 22 Mar '09

22 Mar '09

Hi all, [ apologies for the semi-spam, I'll keep this brief and expect all replies off-list ] IPython is a project that many of you on this list are likely to use in your daily work, either directly or indirectly (if you've embedded it or used it as a component of some other system). I would simply like to ask you, if IPython has been significantly useful for a project you use, lead, develop, etc., to let me know. For legal/professional reasons, I need to gather information about who has found IPython to be of value. I started IPython as a toy 'afternoon hack' in late 2001, and today it continues to grow, as the nicely summarized Ohloh stats show: https://www.ohloh.net/p/ipython (obviously, this is now the result of the work of many, not just myself, as is true of any healthy open source project as it grows). But I have never systematically tracked its impact, and now I need to do so. So, if you have used IPython and it has made a significant contribution to your project, work, research, company, whatever, I'd be very grateful if you let me know. A short paragraph on what this benefit has been is all I ask. Once I gather any information I get, I would contact directly some of the responders to ask for your authorization before quoting you. I should stress that any information you give me will only go in a documentation packet in support of my legal/residency process here in the USA (think of it as an oversized, obnoxiously detailed CV that goes beyond just publications and regular academic information). To keep traffic off this list, please send your replies directly to me, either at this address or my regular work one: Fernando.Perez(a)berkeley.edu In advance, many thanks to anyone willing to reply. I've never asked for anything in return for working on IPython and the ecosystem of scientific Python tools, but this is actually very important, so any information you can provide me will be very useful. Best regards, Fernando Perez.

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Will scipy 0.8 depend on numpy 1.3.0 ?
by David Cournapeau 22 Mar '09

22 Mar '09

Hi, Everything in the title: will scipy 0.8 depend on numpy 1.3 or do we still want to maintain compatibility with the 1.2 serie ? cheers, David

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Tests for optimize.fsolve
by Yosef Meller 21 Mar '09

21 Mar '09

I'm looking in optimize/test_optimize/ and see no test for optimize.fsolve(). Is it because there isn't any or because I'm looking at the wrong place or something else? Thanks.

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special.multigammaln missing in docs
by josef.pktd＠gmail.com 21 Mar '09

21 Mar '09

While searching in trac, I found that in changeset 3181 multigammaln was added to scipy.special. It is missing in the docs for special, special.rst. I don't want to add it myself, because I don't know in which category it belongs. Josef

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Checking matrix dtype in umfpack.py
by Pietro Berkes 20 Mar '09

20 Mar '09

Dear all, on a Mac OS X 10.5, with the latest scipy SVN version I get a few errors from the sparse package when running scipy.test() . They all look more or less like this: ====================================================================== ERROR: Prefactorize (with UMFPACK) matrix for solving with multiple rhs ---------------------------------------------------------------------- Traceback (most recent call last): File "numpy/testing/decorators.py", line 82, in skipper File "/Users/berkes/local/python_libs/lib/python2.5/site-packages/scipy/sparse/linalg/dsolve/umfpack/tests/test_umfpack.py", line 90, in test_factorized_umfpack solve = linsolve.factorized( a ) File "/Users/berkes/local/python_libs//lib/python2.5/site-packages/scipy/sparse/linalg/dsolve/linsolve.py", line 160, in factorized umf.numeric( A ) File "umfpack/umfpack.py", line 395, in numeric File "umfpack/umfpack.py", line 356, in symbolic File "umfpack/umfpack.py", line 341, in _getIndx ValueError: matrix must have float64 values This is due to a non-robust type checking in umfpack.py in the function _getIndx. I suggest to replace this code if self.isReal: if mtx.data.dtype != nm.dtype('<f8'): raise ValueError, 'matrix must have float64 values' else: if mtx.data.dtype != nm.dtype('<c16'): raise ValueError, 'matrix must have complex128 values' with the more robust if self.isReal: if mtx.data.dtype.type != nm.float64: raise ValueError, 'matrix must have float64 values' else: if mtx.data.dtype.type != nm.complex128: raise ValueError, 'matrix must have complex128 values' At least, this solved the problem for me... Cheers, Pietro

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GSoC Project Ideas Questions
by Skipper Seabold 20 Mar '09

20 Mar '09

Hello all, I am a PhD student in economics, and I am very interested in getting involved with the GSoC 2009 and most specifically SciPy/Numpy. I was wondering if there was an application template available yet, so I could get started. Also wondering if there were priorities in place for the project ideas. I'm trying to decide where I might be most useful. Any advice would be appreciated. Along this line, does anyone have the source of Jonathan Taylor's statistical models? Links I have seen are broken. (Sorry for the cross post from SoC2009-General.) Best, Skipper Seabold

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double exponential integrator
by Thouis (Ray) Jones 20 Mar '09

20 Mar '09

I'm soliciting feedback on an implementation of integration using the double exponential transform. I've tentatively placed it in scipy.integrate as de_integrate. It's available at this url and branch: http://broad.mit.edu/~thouis/scipy.git DEintegrator (assuming I've set up my git repository correctly, which is quite possibly not the case.) See http://www.johndcook.com/double_exponential_integration.html for an explanation of the double exponential transform. It's main use is integrating functions that have a singularity at one or both ends of the integration limits, though it works reasonably well for arbitrary functions, though my implementation could be made more robust in many ways. I've also included code for generating the constants necessary for integrations with infinite limits (0 to infinity as well as -inf to +inf). Thouis Jones

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