[yt-dev] Request comments/vote on use of notebooks in yt docs

[Brian O'Shea]

Hi folks,

I'm sorry for not responding to Nathan and Cameron's emails from a couple
of days ago in a timely fashion.

I believe that people who use yt to do data analysis in a production
setting are primarily using scripts, as Britton said.  This is certainly
true in my own research group, and I think generally true when people are
doing batch analysis of large datasets (and/or lots of datasets) on
supercomputers.  If the cookbook is truly meant to help users that are new
to yt, it makes sense to present the cookbook code in the manner that most
closely approximates how a new user will actually use it, so presenting the
code as scripts in the cookbook makes the most sense to me.  Also, the
current implementation of the cookbook is relatively compact, so it's easy
to scroll through and extract what one needs, which is useful for the OTHER
use of the cookbook, which is for more advanced users to quickly zip
through and remind themselves of how the heck a piece of functionality
works.  Using iPython notebooks would make the cookbook much longer, or
force us to break it up into a bunch of segments.  Either way, it would
also be harder to quickly parse through because the actual commands the
user cares about are embedded inside quite a bit of extraneous (for this
purpose) text.  I'm concerned that this mailing list's enthusiasm for the
new, shiny thing, while commendable in many ways, is driving us away from
the original purposes of the cookbook, at least as I understand them.

That said, I do think that iPython notebooks are very cool, and I intend to
use them as a teaching tool in a class I'm teaching next semester. It's
also pretty clear which way the wind is blowing on this mailing list, so
putting iPython notebooks into the cookbook in some way appears to be
inevitable.  So, why not flip it around and have the script be the
standard, compact way of viewing the data, but one can click on a link to
take the user to a notebook that they can look at, and which can be
downloaded?  That allows the cookbook to be relatively easy to parse, and
also lets people who want to see the notebooks do so.

--Brian (though possibly "Grampa Brian" is a more appropriate signoff,
given the tone of my email)


On Sat, Oct 26, 2013 at 12:09 PM, Britton Smith <brittonsmith at gmail.com>wrote:

> There seems to be enough utility in having both the notebooks and at least
> some way of downloading pure python scripts.  On the one hand, the
> notebooks are illustrative for both yt usage and for learning ipython
> notebooks themselves.  As a teaching tool, they seem great.  On the other,
> I think the primary usage of yt for analysis is through scripting and we
> should try to preserve that notion and make these available as seeds for
> new users looking to build their own scripts.  I think that presenting the
> recipes with the notebook, but with a button to download as a script
> nearby, would be an option that satisfies everyone.
>
> Britton
>
>
> On Thu, Oct 24, 2013 at 9:54 PM, Chris Malone <chris.m.malone at gmail.com>wrote:
>
>> I'm +1 on this, with the possibility of providing also just the .py files
>> from nbconvert for those that won't/can't use notebooks.
>>
>> Chris
>>
>>
>> On Thu, Oct 24, 2013 at 12:28 PM, Sam Skillman <samskillman at gmail.com>wrote:
>>
>>> Hi all,
>>>
>>> I think if we don't take this opportunity to use notebooks during this
>>> major update to the documentation, we'll be kicking ourselves in about a
>>> year for missing it.  I'd like to voice my support for the following layout:
>>>
>>> 1) Write the cookbook examples in a notebook, annotating it with
>>> comments and reasoning in markdown cells. Use some amount of conventions
>>> for data loading so that with minimal work users could change the path to
>>> the data and run themselves.
>>> 2) Display the notebooks in the docs
>>> 3) Allow for download of both a stripped down (no images included)
>>> .ipynb and nbconverted script.
>>>
>>> The neat thing is that now you have all these .ipynb files in the doc
>>> repo. It would be stupid simple to then show people how to go to that
>>> folder, launch yt notebook, you can then interactively execute the examples
>>> after pointing to the data locations.  This would be really really nice in
>>> my opinion.
>>>
>>> Cheers,
>>> Sam
>>>
>>>
>>>
>>> On Wed, Oct 23, 2013 at 10:02 PM, Elizabeth Tasker <
>>> tasker at astro1.sci.hokudai.ac.jp> wrote:
>>>
>>>> Hi everyone,
>>>>
>>>> I agree with Brian. I've only recently discovered python notebooks and
>>>> I love them for my own analysis and when I'm looking at data together with
>>>> my students and we're exploring data sets, but I feel they are unnecessary
>>>> cumbersome for code examples.
>>>>
>>>> Most of the cookbook snippets have only one simple product (image, plot
>>>> etc), so you don't gain a great deal by showing the results from each line
>>>> in the notebook.
>>>>
>>>> Additionally, however great notebooks are, they're not as handy for
>>>> tasks that you need to perform repeatedly or for writing full length
>>>> analysis scripts. In my opinion, using yt as a front end to more detailed
>>>> analysis is one of its major strengths. If you take away the cookbook
>>>> scripts, we lack examples of yt in python programs.
>>>>
>>>> The notebooks are also not quite as easy to use as a downloaded code
>>>> snippet.
>>>>
>>>> Elizabeth
>>>>
>>>>
>>>>
>>>> On Oct 23, 2013, at 7:23 PM, Brian O'Shea <bwoshea at gmail.com> wrote:
>>>>
>>>> Hi Cameron,
>>>>
>>>> For what it's worth, as a user of yt I find the current cookbook format
>>>> to be incredibly useful.  I don't think notebooks would add to the utility
>>>> - it's easy enough for me to download the script and load it into a
>>>> notebook on my own machine if that's what I want to do.  It definitely
>>>> seems that the challenges (and possible downsides) substantially outweigh
>>>> the benefits, at least for me and my usage patterns.
>>>>
>>>> --Brian
>>>>
>>>>
>>>>
>>>> On Tue, Oct 22, 2013 at 4:13 PM, Cameron Hummels <chummels at gmail.com>wrote:
>>>>
>>>>> Hey everyone,
>>>>>
>>>>> The documentation sprint is next Monday and Tuesday for those of you
>>>>> who want to participate.  I'll send out another email regarding that in the
>>>>> next day or so.
>>>>>
>>>>> In preparation for that, though, I wanted to request input from the
>>>>> developer community on something related to the docs.
>>>>>
>>>>> Right now, the cookbook page contains a lot of recipes for doing
>>>>> various things, and I think it is hugely beneficial to the community to
>>>>> maintain this (I personally use this page a lot too!).  However, with the
>>>>> advent of ipython notebooks over the last year, we are faced with a
>>>>> question: should we move toward incorporating more notebooks into our
>>>>> documentation, and specifically, do you we want to transfer the existing
>>>>> cookbook to a series of notebooks for each task?
>>>>>
>>>>> Benefits:
>>>>> --Portability: users can download an entire notebook for both viewing
>>>>> how it should work as well as being able to execute it locally on their own
>>>>> datasets
>>>>> --Illustrative: Interim steps in a cookbook can produce output that
>>>>> can show up inside the notebook, instead of being a single script which
>>>>> generates an image/output at the end (as is the case in the current
>>>>> paradigm)
>>>>> --Narrative: notebooks provide more space for narrating each step,
>>>>> instead of confining any narrative to comments in the recipe itself
>>>>>
>>>>> Disadvantages:
>>>>> --Work: it is going to take a decent amount of work to move all of the
>>>>> recipes over from the existing cookbook to individual notebooks
>>>>> --Bulking of repo: In the current paradigm, images associated with
>>>>> each recipe are generated dynamically on the server by executing each
>>>>> script, thereby minimizing the number of files that need to be tracked by
>>>>> mercurial.  By moving to a notebook with images that are embedded in each
>>>>> notebook, we'd potentially increase the footprint of the repository
>>>>> substantially, especially if there were frequent updates of individual
>>>>> recipes.
>>>>>
>>>>> I also like the yt bootcamp notebooks that Matt put together a year
>>>>> ago.  I think they are great for getting new users up to speed on how to
>>>>> use various aspects of the code.  Perhaps this notebook could make its way
>>>>> into the beginning of the cookbook for a more streamlined approach to the
>>>>> documentation?
>>>>>
>>>>> So now is your chance to vote:
>>>>>
>>>>> Move cookbook to ipython notebooks? +/- 0-1?
>>>>>
>>>>> Move yt bootcamp to cookbook? +/- 0-1?
>>>>>
>>>>> Comments?  Suggestions?
>>>>>
>>>>> Cameron
>>>>>
>>>>> --
>>>>> Cameron Hummels
>>>>> Postdoctoral Researcher
>>>>> Steward Observatory
>>>>> University of Arizona
>>>>> http://chummels.org
>>>>>
>>>>> _______________________________________________
>>>>> yt-dev mailing list
>>>>> yt-dev at lists.spacepope.org
>>>>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
>>>>>
>>>>>
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