[IPython-User] SAGE notebook vs iPython notebook

Flavio Coelho fccoelho@gmail....
Sun Jan 8 06:38:23 CST 2012

Thanks for taking the time to write this historic perspective Fernando, I
always wanted to know the details of these parallel developments.

You should definitely turn this into a blog post, as is! I am already
forwarding this email to some colleagues which are not on this list but
will like to learn about this.



On Sun, Jan 8, 2012 at 02:26, Fernando Perez <fperez.net@gmail.com> wrote:

> Hi,
> On Thu, Jan 5, 2012 at 8:06 PM, Oleg Mikulchenklo <olmikul@gmail.com>
> wrote:
> > What is relation and comparison between iPython notebook  and SAGE
> notebook?
> > Can someone provide motivation and roadmap for iPython notebook as
> > alternative to SAGE notebook?
> Let me try to provide some perspective on this, since it's a valid
> question that is probably in the minds of others as well.  This is
> just *my* take on it, and other devs are welcome to pitch in as well
> with their view.  Apology in advance, this is quite long, but I'm
> trying to do justice to many years of development, multiple
> interactions between the two projects and the contributions of many
> people.  I apologize in advance to anyone I've forgotten (but please
> do correct me as I want to have a full record that's reasonably
> trustworthy).
> Let's go back to the beginning: when I started IPython in late 2001, I
> was a graduate student in physics and had used extensively first
> Maple, then Mathematica, both of which have notebook environments.  I
> also used Pascal (earlier) then C/C++, but those two (plus IDL for
> numerics) were the interactive environments that I knew well, and my
> experience with them shaped my view.  In particular, I was a heavy
> user of the Mathematica notebooks and liked them a lot.
> I started using Python in 2001 and liked it, but the interactive
> prompt felt like a crippled toy compared to the systems above or to a
> Unix shell.  When I found out about sys.displayhook, I realized that
> by putting in a callable object, I would be able to hold state and
> capture previous results for reuse.  I then wrote a python startup
> file to provide these features, giving me a 'mini-mathematica' in
> python by also loading Numeric and Gnuplot.  Thus was my
> 'ipython-0.0.1' born, 259 lines to be loaded as $PYTYHONSTARTUP.  In
> case you are curious, I'm attaching it here, it's kind of funny that I
> can 'release' IPython 0.0.1 as an email attachment...
> I also read an article
> (http://onjava.com/pub/a/python/2001/10/11/pythonnews.html) that
> mentioned two good interactive systems for Python, LazyPython and IPP.
>  I contacted their authors,  Nathan Gray and Janko Hauser, seeking to
> join forces to create IPython together.  They were both very gracious
> and let me use their code, but didn't have the time to participate in
> the effort.  As any self-respecting graduate student with a
> dissertation deadline looming would do, I threw myself full-time into
> building the first 'real' IPython by merging my code with both of
> theirs.  Eventually I did graduate, by the way.
> The point of this little trip down memory lane is to indicate that
> from day 1, Mathematica and its notebooks (and the Maple worksheets
> before) were in my mind as my 'ideal' environment for daily
> computational scientific work. In 2005 we had two Google SoC students
> and we took a stab at building, using WX, a notebook system.  Robert
> Kern then put some more work into the problem, but unfortunately that
> prototype never really became fully usable.
> In early 2006, William Stein organized what was probably the first
> Sage Days at UCSD and invited me; William and I had been in touch
> since 2005 as he was using IPython for the sage terminal interface.  I
> suggested Robert come as well, and he demoed the notebook prototype he
> had at that point.  It was very clear that the system wasn't
> production ready, and William was already starting to think about a
> notebook-like system for sage as well. Eventually he started working
> on a browser-based system, and by Sage Days 2 in October 2006, as
> shown by the coding sprint topics
> (http://wiki.sagemath.org/sd2-sprint), the sage notebook was already
> usable.
> Sage going at it separately was completely reasonable and justified:
> we were moving slowly and by that point even we weren't convinced the
> wx approach would go anywhere. William is a force of nature and was
> trying to get sage very usable very fast, so building something
> integrated for his needs was certainly the right choice.
> We continued working on ipython, and actually had another attempt at a
> notebook-type system in 2007. By that point Brian and Min had come on
> board and we had built the Twisted-based parallel tools. Using this,
> Min got a notebook prototype working using an SQL/SQLAlchemy backend.
> Like Sage this used a browser for the client but retained the 'IPython
> experience', something the Sage notebook didn't provide.
> This is a key difference of our approach and the Sage nb, so it' worth
> clarifying what I mean: the Sage notebook took the route of using the
> filesystem for notebook operations, so you can't meaningfully use 'ls'
> in it or move around the filesystem yourself with 'cd', because sage
> will always execute your code in hidden directories with each cell
> actually being a separate subdirectory.  This is a perfectly valid
> approach and lets the notebook do many useful things, but it is also
> very different from the ipython model where we always keep the user
> very close to the filesystem and OS.  For us, it's really important
> that you can access local scripts, use %run, see arbitrary files
> conveniently, as in data analysis and numerical simulation we make
> extensive use of the filesystem.  So the sage model wasn't really a
> good fit for us.
> Furthermore, we wanted a notebook that would provide the entire
> 'IPython experience', meaning that magics, aliases, syntax extensions
> and all other special IPython features worked the same in the notebook
> and terminal.  The sage nb reimplemented some of these things in its
> own way: they reused the % syntax but it has a different meaning, they
> took some of the ipython introspection code and built their own x?/??
> system, etc. In some cases it's almost like ipython, in others the
> behavior is fairly different, which is fine for Sage but doesn't work
> for us.
> So we continued with our own efforts, even though by then the Sage
> notebook was fairly mature by this time.  For a number of reasons (I
> honestly don't recall all the details), Min's browser-based notebook
> prototype also never reached production quality.
> Eventually, in 2009 we were able to fund Brian to dig into the heart
> of the beast, and attack the fundamental problem that made ipython
> development so slow and hard: the fact that the main codebase was an
> outgrowth of that original merge from 2001 of my hack, IPP and
> LazyPython, by now having become an incomprehensible and terribly
> interconnected code with barely any test suite.  Brian was able to
> devote a summer full-time to dismantling these pieces and reassembling
> them so that they would continue to work as before (with only minimal
> regressions), but now in a vastly more approachable and cleanly
> modularized codebase.
> This is where early 2010 found us, and then zerendipity struck: while
> on a month-long teaching trip to Colombia I read an article about
> ZeroMQ (http://lwn.net/Articles/370307) and talked to Brian about it,
> as it seemed to provide the right abstractions for us with a simpler
> model than Twisted.  Brian then blew me away, by writing in just two
> days a new set of clean Cython-based bindings: we now had pyzmq!  It
> became clear that we had the right tools to build a two-process
> implementation of IPython that could give us the 'real ipython' but
> communicating with a different frontend, and this is precisely what we
> wanted for cleaner parallel computing, multiprocess clients and a
> notebook.  When I returned from Colombia I had a free weekend and
> drove down to his place, and in just two days we had a prototype of a
> python shell over zmq working, proving that we could indeed build
> everything we needed.
> Shortly thereafter, we had discussions with Enthought who offered to
> support Brian and I to work in collaboration with Evan Patterson, and
> build the Qt console using this architecture.  Our little prototype
> had been just a proof of concept, but this support allowed us to spend
> the time necessary to apply the same ideas to the real IPython. Brian
> and I would build a zeromq kernel with all the IPython functionality,
> while Evan built a Qt console that would drive it using our
> communications protocol.  This worked extremely well, and by late 2010
> we had a more or less complete Qt console working.
> In October 2010 James Gao (a Berkeley neuroscience graduate student)
> wrote up a quick prototype of a web notebook, demonstrating that the
> kernel design really worked well and could be easily used by a
> completely different client.  And then in the summer of 2011, Brian
> took James' prototype and built up a fully working system, this time
> using the Tornado web server (which ironically, we'd looked at in
> early 2010 as a candidate for our communications, but dismissed it as
> it wasn't really the tool for that job), JQuery, CodeMirror and
> MathJax.  That's the notebook that we then polished over the next few
> months to finally release in 0.12.
> As this long story shows, while it's taken us a very long time to get
> here, what we have now makes a lot of sense for us, even considering
> the existence of the Sage notebook and how good it is for many use
> cases.
> Our notebook is just one particular aspect of a much larger and richer
> architecture built around the concept of a Python interpreter
> abstracted over a JSON-based, explicitly defined communications
> protocol (
> http://ipython.org/ipython-doc/rel-0.12/development/messaging.html).
>  Even considering http clients, the notebook is still just one
> possible client: you can easily build an interface that only evaluates
> a single cell with a tiny bit of javascript like the Sage single cell
> server, for example.
> Furthermore, since Min also reimplemented the parallel machinery
> completely with pyzmq, now we have one truly common codebase for all
> of IPython. We still need to finish up a bit of integration between
> the interactive kernels and the parallel ones, but we plan to finish
> that soon.
> We deliberately wrote the notebook to be a lightweight, single-user
> program meant to keep its files next to the rest of your scripts and
> other files.  The sage notebook draws many parallels with the google
> docs model, requiring a login and showing all of your notebooks
> together, kept in a location separate from the rest of your files.  In
> contrast, we want the notebook to just start like any other program
> and for the ipynb files to be part of your normal workflow, ready to
> be version-controlled just like any other script or file and easy to
> manage on their own.
> There are other deliberate differences of interface and workflow:
> - We keep our In/Out prompts explicit because we have an entire system
> of caching variables that uses those numbers, and because those
> numbers give the user a visual clue of the execution order of cells,
> which may differ from the document's order.
> - We deliberately chose a structured JSON format for our documents.
> It's clear enough for human reading while allowing easy and powerful
> machine manipulation without having to write our own parsing.  So
> writing utilities like a rst or latex converters (as we recently
> showed) is very easy.
> - Our move to zmq allowed us (thanks to Thomas' tireless work) to ship
> the notebook working both on python2 and python3 out of the box.  The
> sage notebook only works on python2, and given their use of Twisted it
> will be probably some time before they can port to python3.
> - Because our notebook works in the normal filesystem, and lets you
> create .py files right next to the .ipynb just by passing --script at
> startup, you can reuse your notebooks like normal scripts, import from
> them, etc.  I'm not sure how to import a sage notebook from a normal
> python file, or if it's even possible.
> - We have a long list of plans for the document format: multi-sheet
> capabilities, latex-style preamble, per-cell metadata, structural
> cells to allow outline-level navigation and manipulation such as in
> LyX, ... For that, we need to control the document format ourselves so
> we can evolve it according to our needs and ideas.
> As you see, there are indeed a number of key differences between our
> notebook and the sage one, but there are very good technical reasons
> for this (in addition to the licensing point already mentioned).  The
> notebook integrates with our architecture and leverages it; you can
> for example use the interactive debugger via a console or qtconsole
> against a notebook kernel, something not possible with the sage
> notebook.
> I'd like to close by emphasizing that we have had multiple, productive
> collaborations with William and other Sage devs in the past, and I
> expect that to continue to be the case.  On certain points that
> collaboration has already led to convergence; e.g. the new Sage single
> cell server uses the IPython messaging protocol, after we worked
> closely with Jason Grout during a Sage Days event in March 2011 thanks
> to William's invitation.  In the future we may find other areas where
> we can reuse tools or approaches.  It is clear to us that the Sage
> notebook is a fantastic system, it just wasn't the right fit for
> IPython; I hope this very long post illustrates why.
> Whew, that was a lot!  I probably should turn this into a blog post at
> some point... Don't hesitate to ask questions on this, I promise much
> shorter replies in the future :)
> Cheers,
> f
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Flávio Codeço Coelho
+55(21) 3799-5567
Escola de Matemática Aplicada
Fundação Getúlio Vargas
Rio de Janeiro - RJ
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