ISGCI in Sage (a Graph Classes database http://www.graphclasses.org/ )

[ncohen]

This ticket creates a file

sage/graphs/isgci.py

That is a first implementation of an interface between Sage and the Graph Classes database ISGCI ![1]. With this interface, the XML content of the database can be read using dictionaries and lists (much easier to work with), and some operations are implemented like the comparison (relatively to inclusion) of graph classes.

There will be more work needed on this new feature, for instance the implementation of an easy way to query the database.

Along with the patch, two .sobj files should be added to the directory $SAGE_ROOT/data/graphs/. These files are an .sobj version of the database that I created on my own computer.

When this patch will be merged into Sage, it is likely that users that do not update their version of Sage will progressively then be working with an outdated version of the database, as the version will be the one used the day they downloaded their copy of Sage. To avoid that, this patch implements a function sage.graphs.isgci.update_db() that downloads a new version of the database from ISGCI's website and updates the current .sobj files.

Hence, instead of using my two files attached to this ticket, one can also call this method which will create them automatically.

I tried to make the documentation clear enough about all that is currently possible with ISGCI.

One of the discussions on sage-devel related to this database: ​http://groups.google.com/forum/#!searchin/sage-devel/This$20is$20the$20copy$20of$20several$20mails$20concerning$20ISGCI$20and$20what$20we$20could$20do$20with/sage-devel/N05a9w_UrIA/XGlVD7NT7p4J

Nathann

![1] ​http://www.graphclasses.org/

---

Apply :

• trac_11880.patch​
• trac_11880-graph_classes-review-nt.patch​

Add to SAGE_ROOT/data/graphs/:

• isgci_classes.sobj​
• isgci_inclusions.sobj​

[nthiery]

Hi Nathann!

I have just been trough the patch, and am overall happy with it! I noticed a couple typos, which I'll fix in a little patch.

Just one thing. Instead of:

    global classes, class_digraph 
    _load_ISGCI_if_not_loaded() 

what about using some idiom like:

    classes = igsci.classes()
    class_diagraph = igsci.class_digraph()

where classes would be a cached method (or cached function depending on whether igsci is a module or an object) whose first step would be to load the database; similarly class_digraph would be a cached method calling igsci.classes(), and then building the digraph, and so on.

Two other little suggestions:

• class_digraph -> inclusion_digraph?
• classs -> cls (it seems to be the standard shorthand to workaround the reserved keyword)

[ncohen]

where classes would be a cached method (or cached function depending on whether igsci is a module or an object) whose first step would be to load the database; similarly class_digraph would be a cached method calling igsci.classes(), and then building the digraph, and so on.

Ahahaah ! Of course, let us do it "the sage-combinat way". It would be nice to have isgci inherit from UniqueRepresentant?, and add some decorations inside of it :-)

I am waiting for your typo patch and I will change that if you did not do it already :-)

I also need to see how cachedmethod is written, just to breathe easier :-)

Two other little suggestions:

• class_digraph -> inclusion_digraph?
• classs -> cls (it seems to be the standard shorthand to workaround the reserved keyword)

+1 !

Nathann

[nthiery]

Replying to ncohen:

I am waiting for your typo patch and I will change that if you did not do it already :-)

Please go ahead if you feel like it; I won't have my reviewer's patch before tonight.

I also need to see how cachedmethod is written, just to breathe easier :-)

It's super optimized and in Cython since #11115, thanks to Simon.

Nicolas

[nthiery]

Hi Nathann!

I hope this won't conflict too much, since I did quite a few documentation changes after all. Feel free to take or drop all my suggestions in the attached reviewer's patch. I left also a couple TODO's; again mostly suggestions.

Cheers,

Nicolas

[nthiery]

I forgot: the patch is also on the Sage-Combinat queue if you want.

[hivert]

Replying to nthiery:

I forgot: the patch is also on the Sage-Combinat queue if you want.

Just for the record: There are problems with the added TODO in the doc:

/home/data/Sage-Install/sage-5.0.beta2/local/lib/python2.7/site-packages/sage/graphs/isgci.py:docstring of sage.graphs.isgci:109: ERROR: Error parsing content block for the "list-table" directive: two-level bullet list expected, but row 2 does not contain a second-level bullet list.

.. list-table::
   :widths: 20 30
   :header-rows: 1

   * - Class
     - Related methods

   * - BinaryTrees

     TODO: use .. seealso:: in all entries of this list?

     - :meth:`BalancedTree <sage.graphs.graph_generators.GraphGenerators.BalancedTree>`,
       :meth:`is_tree <sage.graphs.generic_graph.GenericGraph.is_tree>`
[...]

[nthiery]

Just for the record: There are problems with the added TODO in the doc:

Fixed.

[ncohen]

Helloooooo Nicolas !

Well, I updated the GraphClasses? class so that it now has classes() and inclusion_digraph() methods, and finally noticed that all the other functions (_load_ISGCI_[...]) or update_ISGCI) and all that stuff would be much better as methods of GraphClasses? as it is now unique. Now, moving functions around would make the patch impossible to read, as it would "remove all lines" and "add the same lines later in the file, with an increased indentation". Hence I will upload many patches to this ticket :

• the first one will contain the modifications I mentionned
• The second will *ONLY* move the methods in the file
• The third one will modify them so that they will work (because they will demand a self argument for instances, and other things).

I hope the review will not be too hard :-)

Nathann