IPython, Sage, Dependencies, Anaconda, and Package Integration?

Question

I've just started using IPython for interactive development and exploratory research, which I've found really exciting with all the cool features and possibilities. I am using the Anaconda package manager to manage dependencies, which includes IPython.

From what I've read, one goal of the IPython team is to eventually integrate Sage Math (CAS) into IPython, as a cell magic. Does anyone know if this is still under development? Or rather, if I wanted to use Sage now, is writing an extension the only way to do this [1]?

[1] https://github.com/ipython/ipython/wiki/Extensions-Index

Also, if I install additional packages for scientific development, not included in the Anaconda distribution, is that as easy as just pip or do I have to go through a Anaconda package build to handle dependencies and such? If I were only using IPython, I could understand just doing easy_install or pip as recommended in the docs, but I believe that overwrites existing dependencies within Anaconda. If I use pip, how does that affect Anaconda dependencies if I do not install in an Anaconda environment, which I take is the equivalent as virtualenv.py, and is this the way to also set up revision control (i.e. Mercurial)?

To clarify, I do not want to run IPython from within Sage, I want to run Sage, as a CAS, from within IPython. I'd rather go the Sage approach of integrating domain specific languages. Or in contrast, will IPython extensions replace Sage?

I'm a self taught programmer, not a professional software developer. As an engineer, I am used to Matlab, Mathematica, and commercial solutions, that allow me to abstract away the plumbing. I'm trying to wrap my mind around getting everything glued together, but it's like a mix of spaghetti soup and a dynamic link library, due to lack of knowledge. I'm probably using the wrong approach.

What I want is Anaconda/Enthought package management (IPython, pandas, etc..), custom rolled Sage through hooks/extensions or magics, extensions to packages not included in Anaconda (i.e. Matlab see [1] above), and revision control with Git and Mercurial. How would professional developers set this up on a Mac or Linux box?

Bidwell

Welcome to Stackoverflow. To use the site to best advantage, you're best off making individual questions specific and focussed. What you're asking here is a series of questions, some of them quite open-ended (which isn't what Stackoverflow is designed for). – Nonie

Answer 1

Answering the first question:

Sage is a huge collection of mathematical software, including IPython. There's no way we'd integrate all of that into IPython.

Possibly what you've heard is that we're going to integrate Sage-style 'interacts' into IPython. That's where you have a slider to control the value of some input variable, and the output updates as you move it around, based on a calculation written in Python. That is still on our roadmap to add to IPython.

Another possibility is that you're thinking of SymPy, a Python-based CAS. SymPy works well within IPython, especially if you call sympy.init_printing() to get the fancy representations of expressions.

Nonie

Also worth noting that SymPy comes with Anaconda, so you should be able to just do import sympy from within IPython and get going straightaway. – Livingston

Answer 2

I wrote an IPython extension to load Sage customizations into the IPython notebook---in fact, that's how many of the customizations to IPython are done for the normal Sage interface. It basically turns the IPython notebook into an interface to Sage (e.g., preparsing is done, etc.).

You do need to run it from Sage's copy of IPython, though. Just start the IPython notebook:

sage -ipython notebook

and then load the sage extension in a cell:

%load_ext sage.misc.sage_extension

Pretty soon we'll upgrade to IPython 1.0 (I've made the changes necessary, and it needs to be reviewed). If you want to run IPython 1.0 already, email the sage-support mailing list and I'll post instructions.

To answer your other question, Sage includes many packages that are not available in Anaconda. Sage depends on these packages heavily for many features. I suppose there is a possibility getting Sage and its dependencies distributed with something like Anaconda, but no one is working on that as far as I know. There is some work on packaging Sage up for different linux distributions and replacing the package manager for Sage.

Peay

You can also install any normal python package into Sage. Just do sage -sh -c "easy_install pandas" or whatever. Or do: sage -sh -c "easy_install pip" and then use pip: sage -sh -c "pip install pandas". Sage also also comes with mercurial and soon will come with git. – Peay

Answer 3

To clarify, I do not want to run Ipython from within Sage, I want to run Sage, as a CAS, from within Ipython. I'd rather go the Sage approach of integrating domain specific languages. Or in contrast, will Ipython extensions replace Sage?

If you want to run Sage within Ipython, the easiest thing to do is to use Sage's copy of Ipython:

$ sage -ipython
Python 2.7.5 (default, Aug  1 2013, 18:11:00) 
Type "copyright", "credits" or "license" for more information.

IPython 0.13.1 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]: from sage.all import *

In [2]: integrate(x^2,x)
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-2-006357f5d9c0> in <module>()
----> 1 integrate(x^2,x)

NameError: name 'x' is not defined

In [3]: var('x')
Out[3]: x

In [4]: integrate(x^2,x)
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-4-006357f5d9c0> in <module>()
----> 1 integrate(x^2,x)

/Users/.../sage-5.11.rc0/local/lib/python2.7/site-packages/sage/structure/element.so in sage.structure.element.Element.__xor__ (sage/structure/element.c:6754)()

RuntimeError: Use ** for exponentiation, not '^', which means xor
in Python, and has the wrong precedence.

In [5]: integrate(x**2,x)
Out[5]: 1/3*x^3

Note that there are some differences between this and Sage - for instance, there is no preparsing of the syntax. Presumably if you had Sage someplace your own installation of Ipython can find it, you could do this there too (though there is no easy_install and the Python versions might not match correctly!).

Engenia

Answer 4

Please observe that Sage, as it currently is and should be in the near future, is a huge package that runs in POSIX (Linux-like) OSes only. If you intend it to run in Windows you must use VirtualBox with Sage running under a VM.

If you want a simple CAS that is simple to install and runs everywhere that Python does, you should consider taking a look at Sympy. It doesn't interact with all the software that Sage does, but is simple to use, lightweight (no external libraries needed) and is already included in the base Anaconda distribution.

Besides, it can be easily used inside other Python programs, since it's just like any other module and doesn't make changes to the Python syntax.

Juvenal