Mailman 3 May 2004 - SciPy-Dev

blas missing functions
by p.joyot＠estia.fr 25 May '04

25 May '04

Dear scipy developper, I try to use blas from scipy. I have found all the blas level 1 functions in fblas. But they are only a small number of level 2 and 3 functions in fblas or cblas For exemple i want the dger function. It is an installation problem ? Why these functions are not defined in generic_fblas{2,3}.pyf ? Is it a waste of time to add this funtion ? Thank you for your help Pierre JOYOT ESTIA LIPSI Technopole Izarbel 64210 BIDART Tél: 0559438445 Fax: 0559438401

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ANN: Job Openings at Enthought
by eric jones 17 May '04

17 May '04

Hello, This is a bit of a status report I guess for SciPy (www.scipy.org) and Enthought (www.enthought.com), but, really, it is a long winded job posting. Among other things, Enthought develops scientific software for clients. Python is central to to our strategy in this arena. We have long supported SciPy and believe strongly in Open Source Software. The purpose is to give people a feeling about what we do, the technical challenges we face, and the skills needed to meet them. SciPy ----- There has been a lot of work on SciPy lately by the Travis Oliphant, Travis Vaught, Pearu Peterson, Joe Cooper, and on the website by Jon-Eric Steinbomer and Janet Swisher. The site is now upgraded to Plone and we have a SciPy 0.3 package out. If you're interested in seeing the activity level at scipy.org, please visit. http://www.scipy.org/map?rmurl=http%3A//scipy.net/scipyusage/ It looks like we're averaging about a 100 downloads a day if you add up all source and binary distributions. When SciPy 0.1 was released a couple a years ago, I think we averaged about 10. Its extremely difficult to extrapolate a user base from such information, the obvious growth is good news. Other Stuff ----------- In addition to SciPy we have multiple projects going on right now that either already plug into or will be plugins to a Python-based scientific application framework called Envisage (sorta like an IDE for science apps) that we're working on. The idea is: (1) To lower the bar as far as work required to get a GUI put on the front end of a scientific algorithm. (2) Develop scientific plugins that can play well together so that, for instance, an electromagnetics simulator built by one person can be used in conjunction with an optimization plugin built by another person and results can be visualized with a 3D plugin. This is a hard, long path that requires much work and though. We have started the process and actually have built an app on a very early version of the Envisage framework. The app works great, but it's usage of the framework is a little mixed at this point. There were a lot of compromises we ended up making on the framework side in order to ship on time. Also, I am not sure whether "easy-to-program" and "flexible architecture for compatible plugins" are not mutually exclusive. I always have in my mind that I want a smart scientist to be able to build the GUI in a short amount of time after the algorithm (which is the "hard part") is finished. I still harbor this wish, but the lessons I've had over the last couple of years suggest that the GUI is actually the most expensive part of development for large apps. This is partially due to the fact that commercial apps are rarely built around "research" algorithms -- meaning that the algorithm code usually already exists in some form. Still, UIs take tons of time. Testing them is hard. Flexibility requires more complexity (factories, adapters, etc.) than seems necessary at first. Further, building *good* UI's is really hard. Scientist rarely have the patience or perspective for it -- and yet it is very often difficult to build a good UI for science apps without a scientist's understanding of the underlying problem. We have a number of tools along with SciPy that we're building that are pieces of this puzzle. 1. Traits -- They at the heart of everything we do. They provide some explicit typing, default GUI's, an observer event model for anything that uses them. They can also require some getting used to. 2. Kiva/Enable -- This is the generic drawing system for Python. 3. Chaco -- Interactive 2D Plotting 4. PyFace -- MVC layer on top of wxPython. Supports trees, menus, and a few other things right now. This will grow. 5. Envisage -- Plugin based GUI framework for scientific applications. Beyond the basic GUI that comes from Envisage, we already have a couple plugins for profiling code using hotshot and also searching for memory leaks. David Morrill wrote these and they are called gotcha and enroll. Martin Chilvers wrote a simple scintilla based plugin for editing scripts, and a PyCrust shell is available by default in the app (not a plugin at the moment). We would love to see a number of other plugins: a. Debugger. b. IPython-like PyCrust going. c. A more full featured script editing plugin. (there is a huge list of features here). d. Mayavi e. etc. These are all used actively in commercial products that we deliver. However, they are also in various stages of development and will continue to evolve and grow. Some are still pretty green. Portions of these are openly available now. All five of the listed tool sets will be open at some point this summer when they are cleaned up a bit. Jobs ---- All of this leads to the fact that we are hiring and looking for smart, pleasant, communicative people with integrity that are excited about building this sort of stuff. There is a lot of software architecture to be done that needs talented designers. There is UI design/development that needs scientists that care about UIs or UI developers/designers that are really quick at grasping scientific problems. We also need really strong scientists/scientific developers to do some of the backend coding for commercial products and also SciPy development. If you have a background in geophysics, electromagnetics (especially multi-pole methods) that is a big plus. For this, a PhD is helpful, but not required. Parallel computing skills wouldn't hurt. 3D visualization a la VTK/Python is a major need. So is knowledge about 2D rendering to help finish out Kiva and the Enable toolset. Strong Python skills, Python extension writing knowledge and strong C/C++ skills are a big benefit. Design/development with or of Java NetBeans or Eclipse-like architecture is great -- or any other solid GUI architecture. Dedication to writing clean/clear code meant for other humans to read is a requirement. We have 3 or 4 scientific/python positions to fill over the coming months, and we're looking for candidates that have the best mix of the above skills. You'll join our existing team of scientist/engineers, computer scientists, technical writers, and an HCI specialist. We like this mix and feel it is the best way to build this sort of software. If you are interested in working at Enthought, please send us your resume at jobs(a)enthought.com. If not, please send this posting to the smartest people you know that fit some part of the above description (Python experience not explicitly required). Salaries are competitive. Candidates must be willing to relocate to Austin, Tx. thanks, eric jones PS: There are additional positions listed at http://www.enthought.com/careers.htm for those interested in business application development (not necessarily with Python).

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RE: [SciPy-dev] scipy cow and proc.py
by Virgilio, Vincent 13 May '04

13 May '04

> -----Original Message----- > From: scipy-dev-bounces(a)scipy.net > [mailto:scipy-dev-bounces@scipy.net] On Behalf Of Pearu Peterson > Sent: Thursday, May 13, 2004 4:14 AM > To: SciPy Developers List > Subject: RE: [SciPy-dev] scipy cow and proc.py > > > > > On Wed, 12 May 2004, Virgilio, Vincent wrote: > > > Unfortunately scipy.cow still hangs during cow.start(), even with a > > machine list of local nodes/ports only. Hm, I had this working some > > earlier today . . . > > It turns out that proc.py is not portable even within linux systems. > For example, /proc/meminfo may have different headings when using > different kernels. As a result, mem_info, for one instance, > is failing > with Linux 2.6 kernel. So, proc.py needs some work.. > > Pearu > > _______________________________________________ > Scipy-dev mailing list > Scipy-dev(a)scipy.net > http://www.scipy.net/mailman/listinfo/scipy-dev > Well I'm not surprised. I don't know how to reliably track the /proc filesystem in Linux. Which, anyway, leaves Windows out in the cold. In fact, I don't know anything about how Python handles such portability issues. In Cygwin (Windows, of course), there is the glue layer in cygwin1.dll, which provides a canonical POSIX interface. Might there be something similar in the Python core release, which can be imitated and extended in the direction of proc.py? Eventually, I'll look closely at proc.py, as time permits (is that qualified enough?). It'll be my first exposure to such Pythonic things. Vince Virgilio ************************************ This email and any files transmitted with it are proprietary and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the sender. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of ITT Industries, Inc. The recipient should check this email and any attachments for the presence of viruses. ITT Industries accepts no liability for any damage caused by any virus transmitted by this email. ************************************

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RE: [SciPy-dev] scipy cow and proc.py
by Virgilio, Vincent 13 May '04

13 May '04

Hi Pearu, I dropped proc.py into scipy/Lib, deleted scipy/MANIFEST, the reran python2.3 setup.py bdist_rpm --fix-python. The generated scipy rpm included proc.py, and installed it into the correct location. I was able to import scipy.proc and use various functions. It looks like a success. Unfortunately scipy.cow still hangs during cow.start(), even with a machine list of local nodes/ports only. Hm, I had this working some earlier today . . . Also, I'm having trouble with scipy in help; I type help(), then scipy, and get the below traceback. I'm using the latest CVS. Thanks, Vince Virgilio ------------------------------------------------------------------------ --- AttributeError Traceback (most recent call last) /nas/static/abi/gs/cal-hifi/metrics/abigs_output/<console> /var/tmp/python2.3-2.3.3-root/usr/lib/python2.3/site.py in __call__(self, *args, **kwds) 307 def __call__(self, *args, **kwds): 308 import pydoc --> 309 return pydoc.help(*args, **kwds) 310 311 __builtin__.help = _Helper() /usr/lib/python2.3/site-packages/scipy_base/ppimport.py in _scipy_pydoc_help_cal l(self, *args, **kwds) 379 def _scipy_pydoc_help_call(self,*args,**kwds): 380 _old_pydoc_help_call.__doc__ --> 381 return _old_pydoc_help_call(self, *map(_ppresolve_ignore_failure ,args), 382 **kwds) 383 _pydoc.help.__class__.__call__ = _new.instancemethod(_scipy_pydoc_he lp_call, /var/tmp/python2.3-2.3.3-root/usr/lib/python2.3/pydoc.py in __call__(self, reque st) 1548 else: 1549 self.intro() -> 1550 self.interact() 1551 self.output.write(''' 1552 You are now leaving help and returning to the Python interpreter. /var/tmp/python2.3-2.3.3-root/usr/lib/python2.3/pydoc.py in interact(self) 1567 request = strip(replace(request, '"', '', "'", '')) 1568 if lower(request) in ['q', 'quit']: break -> 1569 self.help(request) 1570 1571 def help(self, request): /var/tmp/python2.3-2.3.3-root/usr/lib/python2.3/pydoc.py in help(self, request) 1579 elif request in self.keywords: self.showtopic(request) 1580 elif request in self.topics: self.showtopic(request) -> 1581 elif request: doc(request, 'Help on %s:') 1582 elif isinstance(request, Helper): self() 1583 else: doc(request, 'Help on %s:') /var/tmp/python2.3-2.3.3-root/usr/lib/python2.3/pydoc.py in doc(thing, title, fo rceload) 1375 pager(title % desc + '\n\n' + text.document(object, name)) 1376 except (ImportError, ErrorDuringImport), value: -> 1377 print value 1378 1379 def writedoc(thing, forceload=0): /var/tmp/python2.3-2.3.3-root/usr/lib/python2.3/pydoc.py in resolve(thing, force load) 1356 """Given an object or a path to an object, get the object and its na me.""" 1357 if isinstance(thing, str): -> 1358 object = locate(thing, forceload) 1359 if not object: 1360 raise ImportError, 'no Python documentation found for %r' % thing /usr/lib/python2.3/site-packages/scipy_base/ppimport.py in _scipy_pydoc_locate(t hing, forceload) 404 _old_pydoc_locate.__doc__ 405 return _old_pydoc_locate(_ppresolve_ignore_failure(thing), --> 406 forceload=forceload) 407 _pydoc.locate = _scipy_pydoc_locate 408 /var/tmp/python2.3-2.3.3-root/usr/lib/python2.3/pydoc.py in locate(path, forcelo ad) 1332 def locate(path, forceload=0): 1333 """Locate an object by name or dotted path, importing as necessary." "" -> 1334 parts = [part for part in split(path, '.') if part] 1335 module, n = None, 0 1336 while n < len(parts): /var/tmp/python2.3-2.3.3-root/usr/lib/python2.3/string.py in split(s, sep, maxsp lit) 119 120 """ --> 121 return s.split(sep, maxsplit) 122 splitfields = split 123 /usr/lib/python2.3/site-packages/scipy_base/shape_base.py in split(ary, indices_ or_sections, axis) 404 except TypeError: 405 sections = indices_or_sections --> 406 N = ary.shape[axis] 407 if N % sections: 408 raise ValueError, 'array split does not result in an equal d ivision' AttributeError: 'str' object has no attribute > -----Original Message----- > From: scipy-dev-bounces(a)scipy.net > [mailto:scipy-dev-bounces@scipy.net] On Behalf Of Pearu Peterson > Sent: Wednesday, May 12, 2004 1:31 PM > To: SciPy Developers List > Subject: Re: [SciPy-dev] scipy cow and proc.py > > > > > On Wed, 12 May 2004, Virgilio, Vincent wrote: > > > > > Hello, > > > > I am trying to use the scipy cow module, and find partial > functionality > > in it. It fails in classes which require scipy.proc. > > > > I couldn't find proc.py in CVS under /scipy, but it is present in > > /scipy1. > > > > Is there a standard way to access the functionality in proc.py? Or > > should I checkout /scipy1 and copy proc.py over to /scipy? > > Yes, try copying proc.py to scipy/Lib directory, rereun scipy install > command, and let us know if it works. > > Thanks, > Pearu > > _______________________________________________ > Scipy-dev mailing list > Scipy-dev(a)scipy.net > http://www.scipy.net/mailman/listinfo/scipy-dev > ************************************ This email and any files transmitted with it are proprietary and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the sender. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of ITT Industries, Inc. The recipient should check this email and any attachments for the presence of viruses. ITT Industries accepts no liability for any damage caused by any virus transmitted by this email. ************************************

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RE: [SciPy-dev] scipy cow and proc.py
by Virgilio, Vincent 13 May '04

13 May '04

Hi Pearu, I vote to put proc.py next to cpuinfo.py, for some mild consistency. Thanks for the fix in CVS; I'll try it soon. Vince > -----Original Message----- > From: scipy-dev-bounces(a)scipy.net > [mailto:scipy-dev-bounces@scipy.net] On Behalf Of Pearu Peterson > Sent: Wednesday, May 12, 2004 4:04 PM > To: SciPy Developers List > Subject: RE: [SciPy-dev] scipy cow and proc.py > > > > > On Wed, 12 May 2004, Virgilio, Vincent wrote: > > > I dropped proc.py into scipy/Lib, deleted scipy/MANIFEST, the reran > > python2.3 setup.py bdist_rpm --fix-python. > > > > The generated scipy rpm included proc.py, and installed it into the > > correct location. I was able to import scipy.proc and use various > > functions. > > > > It looks like a success. > > Ok, then we should add proc.py to scipy, though it is > currently Linux-only > module. Maybe the proper place for it would be in scipy_base or > scipy_distutils (the latter has cpuinfo.py). > > > Unfortunately scipy.cow still hangs during cow.start(), even with a > > machine list of local nodes/ports only. Hm, I had this working some > > earlier today . . . > > > > Also, I'm having trouble with scipy in help; I type help(), > then scipy, > > and get the below traceback. I'm using the latest CVS. > > Fixed in CVS. > > Thanks, > Pearu > > _______________________________________________ > Scipy-dev mailing list > Scipy-dev(a)scipy.net > http://www.scipy.net/mailman/listinfo/scipy-dev > ************************************ This email and any files transmitted with it are proprietary and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the sender. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of ITT Industries, Inc. The recipient should check this email and any attachments for the presence of viruses. ITT Industries accepts no liability for any damage caused by any virus transmitted by this email. ************************************

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scipy cow and proc.py
by Virgilio, Vincent 12 May '04

12 May '04

Hello, I am trying to use the scipy cow module, and find partial functionality in it. It fails in classes which require scipy.proc. I couldn't find proc.py in CVS under /scipy, but it is present in /scipy1. Is there a standard way to access the functionality in proc.py? Or should I checkout /scipy1 and copy proc.py over to /scipy? Thanks for you help, Vince Virgilio ************************************ This email and any files transmitted with it are proprietary and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the sender. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of ITT Industries, Inc. The recipient should check this email and any attachments for the presence of viruses. ITT Industries accepts no liability for any damage caused by any virus transmitted by this email. ************************************

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RE: [SciPy-dev] scipy cow and proc.py
by Virgilio, Vincent 12 May '04

12 May '04

Thanks Pearu, I will do that ASAP. Vince > -----Original Message----- > From: scipy-dev-bounces(a)scipy.net > [mailto:scipy-dev-bounces@scipy.net] On Behalf Of Pearu Peterson > Sent: Wednesday, May 12, 2004 1:31 PM > To: SciPy Developers List > Subject: Re: [SciPy-dev] scipy cow and proc.py > > > > > On Wed, 12 May 2004, Virgilio, Vincent wrote: > > > > > Hello, > > > > I am trying to use the scipy cow module, and find partial > functionality > > in it. It fails in classes which require scipy.proc. > > > > I couldn't find proc.py in CVS under /scipy, but it is present in > > /scipy1. > > > > Is there a standard way to access the functionality in proc.py? Or > > should I checkout /scipy1 and copy proc.py over to /scipy? > > Yes, try copying proc.py to scipy/Lib directory, rereun scipy install > command, and let us know if it works. > > Thanks, > Pearu > > _______________________________________________ > Scipy-dev mailing list > Scipy-dev(a)scipy.net > http://www.scipy.net/mailman/listinfo/scipy-dev > ************************************ This email and any files transmitted with it are proprietary and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the sender. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of ITT Industries, Inc. The recipient should check this email and any attachments for the presence of viruses. ITT Industries accepts no liability for any damage caused by any virus transmitted by this email. ************************************

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bdist_rpm failure with latest scipy (and f2py) from CVS
by Vincent N. Virgilio 11 May '04

11 May '04

Hello, This is my first time trying to build scipy from CVS. My platform is RedHat 8.0. I followed the build instructions on the scipy website. During my attempt to package f2py, "python2.3 setup.py bdist_rpm" failed at the end, complaining that some installed files were not packaged. Fine. So I issued "python setup.py install" instead; success. Then I tried to package scipy. I issued "python2.3 setup.py bdist_rpm", and got a similar failure as in f2py. It seems that atlas_version.so gets built in "site-packages" and not "site-packages/...linalg". RPM complains "installed but not packaged". No amount of fiddling with setup_linalg.py or setup_atlas_version.py could change this. I am in over my head. Have others seen this error? Is there a fix? Thanks, Vince Virgilio

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ANN: SciPy 2004 Conference - Python for Scientific Computing
by Travis N. Vaught 06 May '04

06 May '04

Greetings, The 1st annual *SciPy Conference* will be held this year at Caltech, September 2-3, 2004. As some of you may know, we've experienced great participation in two SciPy "Workshops" (with ~70 attendees in both 2002 and 2003) and this year we're graduating to a "conference." With the prestige of a conference comes the responsibility of a keynote address. This year, Jim Hugunin has answered the call and will be speaking to kickoff the meeting on Thursday September 2nd. Jim is the creator of Numeric Python, Jython, and co-designer of AspectJ. Jim is currently working on IronPython--a fast implementation of Python for .NET and Mono. Registration is now open. More information can be found here: http://www.scipy.org/wikis/scipy04 You may register early online for $100.00. Registration includes breakfast and lunch Thursday & Friday and a very nice dinner Thursday night. After July 16, registration will cost $150.00. Call for Presenters: If you are interested in presenting at the conference, you may submit an abstract in Plain Text, PDF or MS Word formats to abstracts(a)scipy.org -- the deadline for abstract submission is July 1, 2004. Papers and/or presentation slides are acceptable and are due by August 20, 2004. We're also planning three days of informal "Coding Sprints" prior to the conference -- August 30 to September 1, 2004. Conference registration is not required to participate in the sprints. Please email the list, however, if you plan to attend. Topics for these sprints will be determined via the mailing lists as well, so please submit any suggestions for topics to the scipy-user list: list signup: http://www.scipy.org/mailinglists/ list address: scipy-user(a)scipy.org Please forward this announcement to anyone/list that might be interested. I look forward to seeing you at the conference. Best Regards, Travis N. Vaught

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non-integer sequence index
by Travis N. Vaught 03 May '04

03 May '04

Did we add some scipy_distutils functionality that requires (doesn't prohibit) float sequence indexes? Builds for 2.1 and 2.2 are broken... building extension "scipy.sparse.sparsetools" sources Traceback (most recent call last): File "setup.py", line 112, in ? setup_package(ignore_packages) File "setup.py", line 99, in setup_package url = "http://www.scipy.org", File "scipy_core\scipy_distutils\core.py", line 72, in setup return old_setup(**new_attr) File "c:\Python22\lib\distutils\core.py", line 138, in setup dist.run_commands() File "c:\Python22\lib\distutils\dist.py", line 902, in run_commands self.run_command(cmd) File "c:\Python22\lib\distutils\dist.py", line 922, in run_command cmd_obj.run() File "c:\Python22\lib\distutils\command\build.py", line 107, in run self.run_command(cmd_name) File "c:\Python22\lib\distutils\cmd.py", line 330, in run_command self.distribution.run_command(command) File "c:\Python22\lib\distutils\dist.py", line 922, in run_command cmd_obj.run() File "scipy_core\scipy_distutils\command\build_src.py", line 82, in run self.build_sources() File "scipy_core\scipy_distutils\command\build_src.py", line 89, in build_sour ces self.build_extension_sources(ext) File "scipy_core\scipy_distutils\command\build_src.py", line 125, in build_ext ension_sources sources = self.template_sources(sources, ext) File "scipy_core\scipy_distutils\command\build_src.py", line 193, in template_ sources outstr = process_str(fid.read()) File "scipy_core\scipy_distutils\from_template.py", line 169, in process_str expanded = expand_sub(newstr[obj],get_line_header(newstr,sub[0])) TypeError: sequence index must be integer

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