Mailman 3 March 2014 - NumPy-Discussion

[ANN] OpenOpt Suite release 0.53: Stochastic programming addon now is BSD-licensed
by Dmitrey 15 Mar '14

15 Mar '14

hi all, I'm glad to inform you about new OpenOpt Suite release 0.53: Stochastic programming addon now is available for free Some minor changes -------------------------------------------------- Regards, D. http://openopt.org/Dmitrey

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ANN: HDF5 for Python 2.3.0 BETA
by Andrew Collette 14 Mar '14

14 Mar '14

Announcing HDF5 for Python (h5py) 2.3.0 BETA ============================================ The h5py team is happy to announce the availability of h5py 2.3.0 beta. This beta release will be available for approximately two weeks. What's h5py? ------------ The h5py package is a Pythonic interface to the HDF5 binary data format. It lets you store huge amounts of numerical data, and easily manipulate that data from NumPy. For example, you can slice into multi-terabyte datasets stored on disk, as if they were real NumPy arrays. Thousands of datasets can be stored in a single file, categorized and tagged however you want. Changes ------- This release introduces some important new features, including: * Support for arbitrary vlen data * Improved exception messages * Improved setuptools support * Multiple additions to the low-level API * Improved support for MPI features * Single-step build for HDF5 on Windows A complete description of changes is available online: http://docs.h5py.org/en/latest/whatsnew/2.3.html Where to get it --------------- Downloads, documentation, and more are available at the h5py website: http://www.h5py.org Acknowledgements ---------------- The h5py package relies on third-party testing and contributions. For the 2.3 release, thanks especially to: * Martin Teichmann * Florian Rathgerber * Pierre de Buyl * Thomas Caswell * Andy Salnikov * Darren Dale * Robert David Grant * Toon Verstraelen * Many others who contributed bug reports and testing

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python array
by Sudheer Joseph 14 Mar '14

14 Mar '14

Dear experts, I am encountering a strange behaviour of python data array as below. I have been trying to use the data from a netcdf file(attached herewith) to do certain calculation using below code. If I take absolute value of the same array and look for values <.5 I get a different value than the original array. But the fact is that this particular case do not have any negative values in the array( but there are other files where it can have negative values so the condition is put). I do not see any reason for getting different numbers for values <.5 in case of bt and expected it to be same as that of r2010. If any one has a guess on what is behind this behaviour please help. In [14]: from netCDF4 import Dataset as nc In [15]: nf=nc('r2010.nc') In [16]: r2010=nf.variables['R2010'][:] In [17]: bt=abs(r2010) In [18]: bt[bt<=.5].shape Out[18]: (2872,) In [19]: r2010[r2010<.5].shape Out[19]: (36738,) bt.min() Out[20]: 0.0027588337040836768 In [21]: bt.max() Out[21]: 3.5078965479057089 In [22]: r2010.max() Out[22]: 3.5078965479057089 In [23]: r2010.min() Out[23]: 0.0027588337040836768 *************************************************************** Sudheer Joseph Indian National Centre for Ocean Information Services Ministry of Earth Sciences, Govt. of India POST BOX NO: 21, IDA Jeedeemetla P.O. Via Pragathi Nagar,Kukatpally, Hyderabad; Pin:5000 55 Tel:+91-40-23886047(O),Fax:+91-40-23895011(O), Tel:+91-40-23044600(R),Tel:+91-40-9440832534(Mobile) E-mail:sjo.India@gmail.com;sudheer.joseph@yahoo.com Web- http://oppamthadathil.tripod.com ***************************************************************

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Removal of doc/numpybook
by Charles R Harris 13 Mar '14

13 Mar '14

Hi All, In a note on a PR, Ralf has suggested the removal of doc/numpybook. I believe most of the content is now part of the numpy documentation, and the book itself is outdated in some parts. Thoughts? Chuck

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GSoC application template available
by Ralf Gommers 13 Mar '14

13 Mar '14

Hi GSoC students, The PSF just made their application template for this year available: https://wiki.python.org/moin/SummerOfCode/ApplicationTemplate2014. There are a few things in there that are required (for one, submit a patch to numpy or scipy if you haven't done so yet), and some good recommendations. Cheers, Ralf

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Matrix multiplication infix operator PEP nearly ready to go
by Nathaniel Smith 13 Mar '14

13 Mar '14

Hi all, The proposal to add an infix operator to Python for matrix multiplication is nearly ready for its debut on python-ideas; so if you want to look it over first, just want to check out where it's gone, then now's a good time: https://github.com/numpy/numpy/pull/4351 The basic idea here is to try to make the strongest argument we can for the simplest extension that we actually want, and then whether it gets accepted or rejected at least we'll know that's final. Absolutely all comments and feedback welcome. Cheers, -n -- Nathaniel J. Smith Postdoctoral researcher - Informatics - University of Edinburgh http://vorpus.org

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ANN: Biggus 0.5
by R Hattersley 12 Mar '14

12 Mar '14

I'm pleased to announce the release of Biggus version 0.5.0. Biggus is a pure Python library for handling virtual n-dimensional arrays of arbitrary size, and providing lazy/deferred evaluation of arithmetic and statistical operations. Biggus works with your n-dimensional array data in whatever form it currently resides - no data conversion is necessary. The documentation can be found at: http://biggus.readthedocs.org/ And it can be installed with pip via: pip install biggus The main feature of this release is a new multi-threaded evaluation engine which provides the ability to compute statistics efficiently across any axis. Future plans include: - Expand the range of arithmetic and statistical operators. - Extend the evaluation API to allow multiple simultaneous file-based outputs. - An API to simplify the creation of user-defined operators. - Multiply-concurrent execution of CPU intensive operators. - Low-level evaluation optimisation, e.g numexpr/numba. Constructive feedback is very welcome! - Raise an issue on GitHub, https://github.com/SciTools/biggus - Post on the discussion group: https://groups.google.com/forum/#!forum/scitools-biggus

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1.8.1rc1 on sourceforge.
by Charles R Harris 11 Mar '14

11 Mar '14

Hi All, Julian Taylor has put windows binaries and sources for the 1.8.1 release candidate up on sourceforge<http://sourceforge.net/projects/numpy/files/NumPy/1.8.1rc1/>. If things go well, it will taken to a full release in a week or so. Chuck

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2014 John Hunter Fellowship - Call for Applications
by Ralf Gommers 11 Mar '14

11 Mar '14

Hi all, I'm excited to announce, on behalf of the Numfocus board, that applications for the 2014 John Hunter Technology Fellowship are now being accepted. This is the first fellowship Numfocus is able to offer, which we see as a significant milestone. The John Hunter Technology Fellowship aims to bridge the gap between academia and real-world, open-source scientific computing projects by providing a capstone experience for individuals coming from a scientific, engineering or mathematics background. The program consists of a 6 month project-based training program for postdoctoral scientists or senior graduate students. Fellows work on scientific computing open source projects under the guidance of mentors who are leading scientists and software engineers. The aim of the Fellowship is to enable Fellows to develop the skills needed to contribute to cutting-edge open source software projects while at the same time advancing or supporting the research program they and their mentor are involved in. While proposals in any area of science and engineering are welcome, the following areas are encouraged in particular: - Accessible and reproducible computing - Enabling technology for open access publishing - Infrastructural technology supporting open-source scientific software stacks - Core open-source projects promoted by NumFOCUS Eligible applicants are postdoctoral scientists or senior PhD students, or have equivalent experience in physics, mathematics, engineering, statistics, or a related science. The program is open to applicants from any nationality and can be performed at any university or institute world-wide (US export laws permitting). All applications are due May 15, 2014 by 11:59 p.m. Central Standard Time. For more details on the program see: http://numfocus.org/john_hunter_fellowship_2014.html (this call) http://numfocus.org/fellowships.html (program) And for some background see this blog post: http://numfocus.org/announcing-the-numfocus-technology-fellowship-program.h… We're looking forward to receiving your applications! Ralf

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c api deprecations with NPY_NO_DEPRECATED_API
by Paul Brossier 11 Mar '14

11 Mar '14

hi all, I'm trying to understand how to use the deprecation mechanism. 1. When not defining NPY_NO_DEPRECATED_API, I get warnings (as expected): #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" 2. When defining NPY_NO_DEPRECATED_API, as mentioned in the above warning and in the documentation, I get this error: #error Should never include npy_deprecated_api directly. 3. If instead I include <numpy/npy_no_deprecated_api.h>, I get no warning at all, and the extension builds as expected. Now, why does the second error occur, whereas I do not include npy_deprecated_api.h, and most important, what is the correct way to use the deprecation mechanism? There seems to be a few issues related to this on github, most of them closed, but reading them did not help me understanding. The extension i'm trying to improve is aubio and can be found at http://aubio.org. A copy of the relevant code is at: https://github.com/piem/aubio/blob/develop/python/ext/aubio-types.h thanks, piem

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