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Why Python rocks for research

stat.washington.edu

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Re: Why Python rocks for research

#61

Post by hogu »

ogrisel wrote: post #31
hogu wrote: post #19

Earlier quoted context omitted.

I wasn't aware of pep8 when I started, most science people arrive at python from a different path. What I mean is, for a long time I knew much more about numpy than about python itself. there are some things in pep8 that are bad for science, the spaces around operations, and also the 80 chars to a line... scientific expressions are often long and complicated, yes you can do it while adhering to pep8, but its kind of…

The 80 chars limit has a justification: expressions that don't fit on 80 chars (or two lines using parens) are not readable anyway. In such a case temporary variables with meaningful names would both help respect the 80 chars constraint and make the expression easier to understand by the reader. Furthermore having 80 chars is great to have vertically split editors with the code on one panel and the tests or the docum…

I'm not saying there aren't reasons to have short lines.

But in science, we have longer and more complex expressions in general.

Our priorities are different.

Re: Why Python rocks for research

#62

Post by [deleted] »

hogu wrote: post #60
rdouble wrote: post #46

I've wasted most of my professional life tweaking various unix software to make it work. However, the typical scientific python setup proved to be too frustrating to install on OSX. The recommended solution is to just buy the Enthought distro. If I'm paying for software anyway, why is Enthought better than Matlab?

disclaimer I work for enthought I did my whole phd in matlab. EPD is much cheaper and is free for academics even if it weren't free, I would use it anyways. but it really isn't why is EPD better than matlab, it's why python is better than matlab. matlab is a domain specific application with a domain specific language. It doesn't work well with things outside of its domain. python is a general purpose language (And as…

[deleted]

Re: Why Python rocks for research

#63

Post by rdouble »

hogu wrote: post #60
rdouble wrote: post #46

I've wasted most of my professional life tweaking various unix software to make it work. However, the typical scientific python setup proved to be too frustrating to install on OSX. The recommended solution is to just buy the Enthought distro. If I'm paying for software anyway, why is Enthought better than Matlab?

disclaimer I work for enthought I did my whole phd in matlab. EPD is much cheaper and is free for academics even if it weren't free, I would use it anyways. but it really isn't why is EPD better than matlab, it's why python is better than matlab. matlab is a domain specific application with a domain specific language. It doesn't work well with things outside of its domain. python is a general purpose language (And as…

Thank you, that is the kind of response I was looking for. I will take a look at Enthought.

Re: Why Python rocks for research

#64

Post by timwiseman »

samd wrote: post #22
hogu wrote: post #10

Earlier quoted context omitted.

I've been a Matlab user for 10 yrs, recently switched to python because of the increased flexibility. never going back to Matlab ever again. Python math and science libs can be a little rough around the edges, but the flexibility more than makes up for it for me.

I'm a Matlab user myself, but I try to use Ruby whenever possible if for nothing else but to just get away from all the god damned matrices. I didn't realize Python had similar capabilities, I look forward to trying it out. But does Python have "Index exceeds matrix dimensions." errors? I just can't imagine life without seeing a few of those every day. That said, the workspace is really handy, is there some equivalen…

As infinite8s points out, EPD from enthought is really quite nice.

Personally, I rather like Python XY ( http://www.pythonxy.com/ )though. It is totally free, open source, and for small little scripts I am a huge fan of the Spyder IDE. It lacks some of the features of bulkier IDEs so I also use Eclipse from time to time. But Spyder is light and much faster than Eclipse with every feature I would want when working on small projects that can be contained in just one or two files.

Re: Why Python rocks for research

#65

Post by lliiffee »

rdouble wrote: post #46

I've wasted most of my professional life tweaking various unix software to make it work. However, the typical scientific python setup proved to be too frustrating to install on OSX. The recommended solution is to just buy the Enthought distro. If I'm paying for software anyway, why is Enthought better than Matlab?

Another option is to just install Sage. It "just works" to install. Though it is less about numerical computation than symbolic computation. (Though both are targets, there isn't really equal focus, in my opinion.)

Re: Why Python rocks for research

#66

Post by hogu »

rdouble wrote: post #63
hogu wrote: post #60

Earlier quoted context omitted.

disclaimer I work for enthought I did my whole phd in matlab. EPD is much cheaper and is free for academics even if it weren't free, I would use it anyways. but it really isn't why is EPD better than matlab, it's why python is better than matlab. matlab is a domain specific application with a domain specific language. It doesn't work well with things outside of its domain. python is a general purpose language (And as…

Thank you, that is the kind of response I was looking for. I will take a look at Enthought.

you WILL get frustrated by some things - some of the matrix concatenation operations are less convenient, some of the libraries are less polished, it's been worth it for me. msg me if you need help.

use IPython, not just python shell for interactivity.

also checkout 3d datavisualization with mayavi, that stuff is really awesome.

Re: Why Python rocks for research

#68

Post by osdf »

wgrover wrote: post #55
rdouble wrote: post #46

I've wasted most of my professional life tweaking various unix software to make it work. However, the typical scientific python setup proved to be too frustrating to install on OSX. The recommended solution is to just buy the Enthought distro. If I'm paying for software anyway, why is Enthought better than Matlab?

I've never had any problems putting a research-grade python setup on OSX - just use the .dmg installer files files available for python (2.6.X for compatibility), numpy, scipy, and matplotlib. But I agree that the Enthought Python Distro is also a good alternative (if a little bloated for my needs), and it's also free for academics.

For a basic setup on OS X, I found scipy superpack to be an excellent choice: http://stronginference.com/scipy-superpack/

Re: Why Python rocks for research

#69

Post by osdf »

bad_user wrote: post #15
RodgerTheGreat wrote: post #3

This article makes some fairly convincing arguments that Python is a more flexible tool than Matlab or Perl, but I can't help but come away with the sense that the author hasn't tried many other languages. There are an awful lot of languages that provide iterators, a powerful set of data structures, extensive libraries and facilities for structuring and maintaining large codebases. .Net languages (maybe F# would be g…

SciPy, NumPy, Matplotlib, Cython, Sphinx, PIL. The article should've also mentioned NLTK. IMHO, languages matter less than the available libraries, and in my experience only Java matches the depth of the Python ecosystem. That Python is a nice language to work with, that's just a bonus.

Also, (basic) GPU operations with cudamat (or even finer, gnumpy) at your fingertips.

Re: Why Python rocks for research

#70

Post by gkelly »

osdf wrote: post #68
wgrover wrote: post #55

Earlier quoted context omitted.

I've never had any problems putting a research-grade python setup on OSX - just use the .dmg installer files files available for python (2.6.X for compatibility), numpy, scipy, and matplotlib. But I agree that the Enthought Python Distro is also a good alternative (if a little bloated for my needs), and it's also free for academics.

For a basic setup on OS X, I found scipy superpack to be an excellent choice: http://stronginference.com/scipy-superpack/

I've found macports provides a ton of python libraries, like numpy, scipy, and matplotlib, all easily installed from the command line.
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