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

Sat Oct 26 13:41:40 PDT 2013

I'll see if I can put together a template of what I originally envisioned
for this, so that people don't think I'm doing away with the current
functionality of the cookbook.  But for now here is a description.

What I sought and seemingly failed to convey was for the cookbook to still
have the "scripts" displayed inline as they currently are.  But when I say
scripts, I mean sphinx'ified ipython notebooks, where instead of showing
the images at the end of the script as is currently done, it would show the
images that were generated in the script after the line in the text that
generated them along with comments included inline in the notebook.  So one
could still scroll down the webpage looking at demonstrations of a variety
of functions in yt the way they currently can.  The difference, however,
would be that one could download those notebooks (as well as just the
python scripts themselves) so that a user could execute these notebooks (or
python scripts) locally.  In my mind, we are not losing any functionality
from the old page at all, and we're merely moving it to a slightly
different format that provides additional benefits, while still retaining
the ability to display and download python scripts as one can currently do.
 In essence, this is what Brian is recommending at the end of his email.

Brian, I don't think your statement that "using notebooks would make the
cookbook much longer" is true.  You mean from including comments in the
scripts?  Maybe it will increase its length by 10% but not much, and I
think comments are ideal for helping out both new and experienced users
alike to interpret what these scripts do.  However, the cookbook *will* get
longer because we're going to add a bunch of additional scripts in the
coming few days, but that's good, and that's going to happen regardless of
the format switch.

Cameron

On Sat, Oct 26, 2013 at 1:16 PM, Butler,Michael J <butler85 at astro.ufl.edu>wrote:

> **
>
> I'm personally +1 on Brian's email on this subject
>
>
>
> On Sat, 26 Oct 2013 16:08:45 -0400, Brian O'Shea wrote:
>
>  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
>>>>>>
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-- 
Cameron Hummels
Postdoctoral Researcher
Steward Observatory
University of Arizona
http://chummels.org
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