Some tips and tricks about the documentation system
I had some trouble to use the new documentation system. I'm putting here some tips and tricks. This page was build by gathering informations from the mailing list and irc. This may not be the right way to do. Please expand and correct...
It has been said on the mailing list that this page is of general interest for the sage community and should not stay hidden inside combinat. I would be happy to move it elsewhere, if someone suggest me a proper place and from where to link it. If you move it, please don't forget to update the link at the bottom of the sage-combinat home page -- Florent.
Contents
1. How to write and compile Sage documentation
The format is called ReST for ReStructuredText and the doc builder is called Sphinx
1.1. For the impatient
- The two most important things to know are
``inline literal`` for sage raw code
`LaTeX interpreted text` for mathematics
Any line ending with :: means that the following indented things are a literal block (usually sage: commands)
1.2. The ReST Format
The link quickref gives a not so short description of the format
1.3. Step by step instruction for building the doc
- First issue a
sage -b
to make sure that the sage is up-to-date with your modifications. Then depending of the desired format you call
sage -docbuild reference <format>
For example, I use the html format so that I call
sage -b && sage -docbuild reference html
Then the compiled doc is found at
$SAGE_ROOT/devel/sage/doc/output/html/en/reference/index.html
You can use you browser to view it...
- You can get some help on the docbuild system by:
sage -docbuild -help
explains all the sage -docbuild options.
1.4. Setting hyperlink to modules, classes, methods, etc
The full explanation can be found at http://sphinx.pocoo.org/markup/inline.html
It is not possible to define chapters and labels and things in the autogenerated documentation ("because of the way it is produced" according to Mike Hansen), but as you will see there should be no needs. Indeed, it is possible to generate a link to the documentation for any module, class, method, function, etc. The syntax is
:role:`title <target>`
or
:role:`target`
where
role is the kind of thing you what to link to (ie mod for module, class for classes, meth for methods, func for functions, etc;
target is the python name of the object (class, module, method...) which carry the doc to be linked to;
title is the name the link appear in the browser.
If you don't provide any title then target will be used.
For example, to link the dyck_word module, you'd do something like :mod:`sage.combinat.dyck_word` or if you prefer :mod:`Dyck words<sage.combinat.dyck_word>`. Note that, in the first case, the full qualified python address is used which is usually too long. You can prefix it with a "~" to get only the final name. For example in the huge link
:meth:`~sage.combinat.non_decreasing_parking_function.NonDecreasingParkingFunction.to_dyck_word`
only ".to_dyck_word()" will appear. Note that the parentheses in the link are auto-generated.
Finally local name are handled. That is, for example, in the definition of a class (and any of its members or methods), you can link to any member or method of the same class by simply giving the name of it prepended by a dot ".". You dont need to give the full address of it. For example:
:meth:`.to_dyck_word`
set up a link of the .to_dyck_word() method of the current class if it exists. If not the doc builder search going up in the class/module hierarchy of python until it find a object under this name or reach the toplevel module without finding it. If it occur the title is typeset in boldface without any link produced and also without any error or warning. Note that without the prepended dot the object is searched starting from the toplevel to the innermost module/class.
- I don't know is it's possible and how to activate some report of the missing targets -- Florent
1.5. Adding a new file to the doc
If you write a new file say sage/combinat/family.py and you want your doc to be added to the system you have to add your file in the relevant index.rst file usually located in the tree:
$SAGE_ROOT/devel/sage-combinat/doc/en/reference
Going back to my example I have to add to the file
$SAGE_ROOT/devel/sage-combinat/doc/en/reference/combinat/index.rst
the following line
Combinatorics
=============
.. toctree::
:maxdepth: 2
../sage/combinat/combinat
[...]
../sage/combinat/dyck_word
+ ../sage/combinat/family
../sage/combinat/finite_class
[...]
1.6. How to find the unincluded docs ?
They are currently a lot of file that hasn't been referenced. They do not appear in the doc. You can generate the list of those files by
sage -docbuild reference print_unincluded_modules
2. Trouble shooting
2.1. Compilation fails with "Too many open files"
- On a machine I got the following error:
File "/home/combi/hivert/Sage/sage-3.4/local/lib/python2.5/subprocess.py", line 1003, in _execute_child errpipe_read, errpipe_write = os.pipe() OSError: [Errno 24] Too many open files The full traceback has been saved in /tmp/sphinx-err--kaK6F.log, if you want to report the issue to the author. Please also report this if it was a user error, so that a better error message can be provided next time. Send reports to [email protected]. Thanks! Build finished. The built documents can be found in /home/combi/hivert/Sage/sage/devel/sage/doc/output/html/en/reference
I don't understand why but I nevertheless managed to build the doc using jsmath
sage -docbuild --jsmath all html
2.2. If you have deleted some doc file
Suppose that you added your file to some index.rst and then you delete it (e.g. by unapplying some patch). This cause some trouble because the build system left some garbage. Here there after unapplying the patch the file enumerated_sets.py does not exists anymore:
OSError: [Errno 2] No such file or directory: '/usr/local/sage/sage-3.4/devel/sage-combinat/doc/en/reference/sage/categories/enumerated_sets.rst'
Right now I don't know a good fix. Here are the methods I use:
Delete all the copy of enumerated_sets.py and enumerated_sets.pyc at the various positions of $SAGE_ROOT/devel/sage/build
Delete the enumerated_sets.rst file
If this still not work you can simply
Nuke the whole $SAGE_ROOT/devel/sage/doc/output tree !
3. Do you want to know more ?
Why was it decided to switch ?
The new format of doc is called reStructuredText it is hosted on sourceforge at ReST.
4. Random tips and Tricks
4.1. How to use "sage -t" outside sage tree
It does work, on has to use .py files. First do a
export SAGE_PATH=<path_to_your_files>
then for each function, import your functions from the appropriate module/file, e.g.,
from my_module import my_func
Here is what worked for me (John Cremona). Suppose that I have a stand-alone .py file, say myfile.py, containing various functions with doctests.
- No need to set any environment variables
- Put the line
from sage.all import *
at the top of the file.
- cd to the directory the file is in and type
sage -t myfile.py
4.2. Emacs mode for editing ReST files
It seems to be included in every major Linux distributions.
For Ubuntu 8.10 things worked out of the box with python-docutils.rpm installed.
For SuSE 11.1, the file is in docutils.rpm but not in emacs search path so you have to link it from
/usr/share/doc/packages/docutils/tools/editors/emacs/rst.el
to whatever place in emacs load path. To load it you have also to load lazy-lock before because is not automatically loaded since it is marked as obsolete:
(require 'lazy-lock) (require 'rst)
You can find informations on http://docutils.sourceforge.net/docs/user/emacs.html
Have a nice doc !!!