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Byteflow Blog Engine ( 11 May 2008 )

Byteflow Blog Engine. This looks like the most full-featured of the Django blog engines by a pretty big margin, including OpenID client and server support. A product of the growing Russian Django community.

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IDE update ( 10 May 2008 )

Last night the Utah Python User Group held an editor/IDE smackdown. I'm not going to write an exhaustive summary, but here are some highlights:

ViM's OmniComplete is actually pretty decent. Calltip support in the GUI is also good. (GUI? ViM? Yeah, weird.)
Emacs completion, from Rope, is also good. Emacs's refusal to make any concession to GUIs though keeps things clunky. Not that it isn't great that Everything Works over plain ssh; that's fine, but going through classic Emacs buffers for docstrings or completion means everything takes more keystrokes than it should while being less useful than having that information Always On.
Rope also gives Emacs refactoring support that works surprisingly well.
PyDev still sees a big win from the Eclipse platform. Specifically, even though Subclipse and Subversive are a bit weak compared to the gold standard (that would be TortoiseSVN), they are much better than what you get with Komodo or Wing. Now that I am on OS X (no Tortoise) this is a bigger issue for me than it used to be.
PyDev Extensions has refactoring support now, too.
Komodo has limited support for completion inside django templates. Which is impressive, since the commands allowed in django templates aren't really Python, which is to say that you can't just use the same completion support that you use for normal Python code.
Mako template support with completion, anyone?
The latest versions of Komodo and Wing both integrate unittest support. Wing also supports doctest out of the box. Meaning, you click a button, your tests run, you get a pretty summary with click-to-go-to-the-source-of-the-error support. This might get me to finally upgrade to Wing 3. It's not that "python test.py" is so hard, so much as I do it so often that even a little more convenience adds up.

I was surprised how well ViM and Emacs do with Python now. ViM's modern inline interface for code completion and Emacs's refactoring support are particularly nice. The IDEs still win on the I part (Integration), in particular debugging and (for Eclipse at least) svn support.

Update: Ryan McGuire blogged about his Emacs presentation in more detail.

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ironpythoninaction.com: New Chapters and Sourcecode Available ( 09 May 2008 )

Three new chapters have been added to the Manning Early Access Program for IronPython in Action. There are now eleven out of fifteen chapters available. ... [130 words]

pygr gets some summer love ( 09 May 2008 )

(pygr is a neatbioinformatics framework in Python.)

After some commenters on my last post seemed happy to hear that pygrwas the focus of some summer work, I realized I had only discussed thepygr summer work in a post to the biology-in-python list.

Whoops.

So, here's the scoop: not only is pygr the focus of Rachel McCreary'sGoogle Summer of Code project,but Jenny Qian will be using pygr to build an ENSEMBL interface,also as part of the Google Summer of Code.

That's not all!

In addition to Rachel and Jenny (under the sterling mentorship ofChris Lee, Robert Kirkpatrick, Namshin Kim, and myself) I have two MSUstudents working with me over the summer, Alex Nolley and MarieBuckner. They'll both be working with pygr-related things, althoughlike Jenny their efforts may end up being more on ways to use pygrthan on pygr's code itself.

I also have a grad student or two that may drop in on pygr, if only touse it for something research-y.

So all in all, pygr will get a lot of love this summer. Hopefully we canpolish the code and documentation and tutorials to the point where thelearning curve is as minimal as it can get, and this fabulous package willbecome readily available to many others...

Why am I personally putting so much effort into pygr? Well, I've beenusing it more and more over the last few months, and (somewhat likescipy)it's transformed my work by turning annoyingly difficult dataorganization problems into trivial Python transformations. I canliterally throw together a custom genome browser in a matter of hours-- I've implemented two or three already, for different projects --and it has enabled several new research program. pygr seems to be oneof those rare packages (kind of like Python itself) that is not onlyfunctional and effective but presents a unified and coherentintellectual interface. pygr is the only good middleware layer I'veseen for sequence intertwingling in bioinformatics. It's not thatmature yet, but it has serious promise, and I'm hoping to get in onthe ground floor, so to speak :).

cheers,

--titus

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TarPipe Python API ( 09 May 2008 )

My Tarpipe Workflow

For those of you who don’t know TarPipe, it is a web application that makes it easier to create your workflows on the web. This workflow above just receives via the API a title and a photo and uploads it to Photobucket (which sucks, but a Flickr Connector, among others, is being released very soon) and the enters the image link in my flickr account. Right now Tarpipe hasn’t launched yet, but I have access to developer’s preview (which you may also ask) and I have played with it’s API.

So I picked my language of choice: Python and I made a library to access TarPipe API from Python. And it’s as easy as:

sudo easy_install tarpipe-pythonpython

And then

import tarpipet = tarpipe.TarPipe(token="your workflow token")t.upload(title="hello from python",body="testing TarPipe from Python",image="/Users/youruser/Images/test.png")

As simple as that. The project is hosted at Google Code (you can checkout from the svn if you want). And it’s licensed under LGPL, which will deserve a post later on.

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