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Why Python rocks for research

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Re: Why Python rocks for research

#11

Post by cageface »

apl wrote: post #8

In the end, it's all about the ecosystem. Perl wins for bioinformatics because there are boatloads of scientists already using it, with all the neat libraries and resources that brings. Equally, Python wins for, say, prototyping in robotics because of libraries, support and so on. There's nothing intrinsically science-apt about Python/Perl, but Ruby and friends can't compete when it comes to the programming environme…

As a language I prefer Ruby but the Python ecosystem for this kind of thing is definitely a huge advantage. You can actually do quite a bit with Ruby + GSL but it's still not really competitive.

Re: Why Python rocks for research

#12

Post by ogrisel »

And the corollary: Why do researchers never respect the PEP8 when they write python code?

Yes I am a bit overreacting since the blog post is very well written and I actually agree 100% with the content. But please people: respect the PEP8 [1]. It makes your readers feel at home while reading your code. It is very important if you want to get new contributors to your project. See [2] for instance.

[1] http://www.python.org/dev/peps/pep-0008/ [2] http://www.dataists.com/2010/10/whats-the-use-of-sharing-cod...

Re: Why Python rocks for research

#13

Post by Dn_Ab »

vog wrote: post #5
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…

> There are an awful lot of languages that provide ... Still, how many of them have a fast interactive interpreter ("command line") with a decent usability? How many of those provide good libraries for numerical as well as symbolic math? With an API that is easy to write, to understand and to extend? Python may not be the only language with those qualities, but there aren't many languages (and ecosystems around them)…

There are Ocaml, F# and Clojure with some combination of great tools, speed (clojure addressed this recently I think but i only have visual experience with clojure), light syntax, books and documentation, repl,excellent platform, wide libarary choice and or decent interop with C. Also F# is doing some really cool stuff to do with datasets awareness in the language.

Haskell seems a perfect fit for mathematical use and while I haven't used it in a couple years, I would hesitate to suggest it due to a lack of mature library options, difficulty of FFI and perhaps a steep initial curve.

Scala is a good language for an entire application but provides too much scaffolding for scientific applications.

R is fairly widely used but is also itself very quirky.

Re: Why Python rocks for research

#14

Post by apl »

cageface wrote: post #11
apl wrote: post #8

In the end, it's all about the ecosystem. Perl wins for bioinformatics because there are boatloads of scientists already using it, with all the neat libraries and resources that brings. Equally, Python wins for, say, prototyping in robotics because of libraries, support and so on. There's nothing intrinsically science-apt about Python/Perl, but Ruby and friends can't compete when it comes to the programming environme…

As a language I prefer Ruby but the Python ecosystem for this kind of thing is definitely a huge advantage. You can actually do quite a bit with Ruby + GSL but it's still not really competitive.

Yep, same with me. I do prefer Ruby, but it's just not feasible at the moment. Languages that get behind in a certain area enter a terribly vicious circle: There's no scientific community backing Ruby, so why would I develop something that'd make Ruby more competitive?

Re: Why Python rocks for research

#15

Post by bad_user »

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.

Re: Why Python rocks for research

#16

Post by djacobs »

apl wrote: post #14
cageface wrote: post #11

Earlier quoted context omitted.

As a language I prefer Ruby but the Python ecosystem for this kind of thing is definitely a huge advantage. You can actually do quite a bit with Ruby + GSL but it's still not really competitive.

Yep, same with me. I do prefer Ruby, but it's just not feasible at the moment. Languages that get behind in a certain area enter a terribly vicious circle: There's no scientific community backing Ruby, so why would I develop something that'd make Ruby more competitive?

I'm in the same boat and it seems like several others as well. I'm fine moving to Python for the moment, but I wonder how the Ruby community will ever know if there's enough of a demand for scientific tools to merit their development?

Re: Why Python rocks for research

#17

Post by kenjackson »

wwortiz wrote: post #7
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…

Do they all have equivalent libraries to python's scipy and matplotlib? I think that is why the author could move to python as these provide a pretty large subset of what matlab has and makes the transition less problematic. Java probably does and .NET may have something like this but I don't know of them or their amount of documentation.

.NET has various things in this space, but I think a lot are commercial products. .NET is not used as much in academia, so most things are targeted at professionals. With that said, you can probably get free/cheap licenses for many/most of commercial products.

But I think Python probably has the most active community as its been used as glue for a long time in this space.

Re: Why Python rocks for research

#18

Post by bad_user »

mechanical_fish wrote: post #6
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…

I only scanned the article very briefly, but my impression is that the important comparison is vs. Matlab. The other players aren't really in the author's game. It's a question of the use case and the community and the library support. In theory, .Net could displace Matlab or Python as the canonical platform for scientific researchers. And in theory Python could displace PHP as the canonical platform for classic CRUD…

When I use certain tools, I just want them to be popular enough and couldn't care less about the "canonical" way of doing things.

Re: Why Python rocks for research

#19

Post by hogu »

ogrisel wrote: post #12

And the corollary: Why do researchers never respect the PEP8 when they write python code? Yes I am a bit overreacting since the blog post is very well written and I actually agree 100% with the content. But please people: respect the PEP8 [1]. It makes your readers feel at home while reading your code. It is very important if you want to get new contributors to your project. See [2] for instance. [1] http://www.pytho…

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 a PITA

Re: Why Python rocks for research

#20

Post by Avshalom »

ogrisel wrote: post #12

And the corollary: Why do researchers never respect the PEP8 when they write python code? Yes I am a bit overreacting since the blog post is very well written and I actually agree 100% with the content. But please people: respect the PEP8 [1]. It makes your readers feel at home while reading your code. It is very important if you want to get new contributors to your project. See [2] for instance. [1] http://www.pytho…

Because researchers have never heard of pep8, and in general don't give a shit about domain specific politics unless it's their domain.
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