Monday, June 4, 2012

My Eclipse/PyDev/git workflow for Sage

I want to briefly describe how I code for Sage so that others can comment on how to improve the workflow or maybe learn something from it.

For Python (and actually for all programming languages, meanwhile), I've always been using Eclipse as an IDE. With PyDev you get pretty nice Python syntax highlighting, code outlines, and features such as code completion, although I have never used that a lot. PyDev has even added Cython support for .pyx files recently—yeah!

I have added the complete Sage tree (which is located in /Applications/sage/ on my Mac) as an Eclipse project. As recommended and described earlier, I created a new branch ("sandbox") using sage -clone lattices; consequently, I'm working on the files in sage/devel/sage-lattices.

Test-driven development makes much sense in general, and especially when working on Sage:
  • Due to the fact that you have to rebuild Sage every time you change something, working completely "interactive" isn't possible.
  • You don't want to type the code to "bootstrap" your tests (e.g. creating lattices) every single time you change something.
  • Eventually, lots of examples are demanded in the documentation anyway.
This is why I usually add some examples that I want to be working in Python docstrings, then code something, and then run the tests. Running the tests is done by
./sage -bt devel/sage-lattices/sage/lattices/
which will rebuild the changed components of Sage (compiling Cython code if necessary) and then run the tests defined in Usually it says "All tests passed!" in the end; otherwise it gives an overview of the test cases (examples) that failed.

To see how the documentation that is generated from docstrings looks like, I sometimes rebuild it. For some strange reasons, the documentation generator (Sphinx) does not always recognize that I changed something in the source files. To avoid having to rebuild the complete reference manual (which takes quite a while) every time, I created a small documentation part that only includes the lattices chapter. This is easily done by adding a folder to doc/en and creating files, index.rst, and lattices.rst therein. The latter basically contains

.. automodule:: sage.lattices.lattice
Then, the relevant documentation can be rebuilt using
sage --docbuild lattices html -S -a,-E
(-S passes arguments on to Sphinx, -a,-E erase and recreate everything.)

On a side note: When building the HTML documentation on my Mac, I got a bunch of warnings saying "Incompatible library version: libfontconfig.1.dylib requires version 13.0.0 or later, but libfreetype.6.dylib provides version 10.0.0". It seems that the system-wide version of dvipng that I installed through Fink referenced a library "libfreetype" that was loaded through Sage, but with an insufficiently recent version. I simply resolved this by replacing the libfreetype* files in sage/local/lib with the Fink files from /sw/lib. Now the HTML documentation displays beautiful PNG graphics for LaTeX formulas.

I tried to use the integrated Eclipse/PyDev Python debugger with Sage, but ran into some problems. First, you have to launch Eclipse through the Sage shell, i.e. using
sage -sh
But then, after selecting sage-python as interpreter, when I tried to run the doctests in debug mode, I still got some weird ImportErrors. I could reproduce them using sage-python alone (leaving Eclipse out) and reported the issue on sage-trac.

Despite test-driven development, sometimes I still want to play around with things in Sage interactively.  To reload my lattice module after having done
from sage.lattices import lattice
at one point, I still have to rebuild everything (using the mentioned sage -bt ... command which tests things as well), and then reload it using
lattice = reload(lattice)
Then I can go on creating lattices, e.g. by
L = lattice.Lattice([[1, 0], [0, 1]])
and experiment with them.

When I am done working on something, I do a git commit to my sage repository using
git commit -am "my commit message"
Using the Eclipse git interface is terribly slow when working on the entire Sage tree (even though only a few files are checked in), so I'm using the terminal for this. Usually I also push commits to the github repository using
git push

Usually I have at least three terminal windows open: one entirely for running the doctests, one for handling git, and one for "experiments" in Sage. To finally include a picture on this blog as well, here's how this might look like:

Please let me know if you have any suggestions.

Finally, some useful documentation links:


  1. Hey this is great! This is definitely helpful

    I've been working with sage + pydev on a little project for myself.

    This will definitely help me work on documentation!

    Thanks. Good look with the Lattice Coding!

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  3. It is really a great work and the way in which u r sharing the knowledge is excellent.
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