Split graph_generators into several files

[nathanncohen]

This tickets addresses the fact that Jeroen is not happy with the length of graph_generators.py :-P

It splits the file into new ones, added in the graph/generators/ folder, according to the classifiation of the methods that appears in the module's documentation.

APPLY:

• attachment: trac_13862.patch
• attachment: trac_13862-cleaning_and_moving.patch
• attachment: trac_13862-doc.patch
• attachment: trac_13862-code_reformatting.patch
• attachment: trac_13862-moves_3_constructors.patch

CC: @dcoudert

Component: graph theory

Author: Nathann Cohen

Reviewer: David Coudert

Merged: sage-5.6.beta2

Issue created by migration from https://trac.sagemath.org/ticket/13862

[nathanncohen]

Author: Nathann Cohen

[nathanncohen]

comment:2

This patch creates the following files and moves into them the methods from GraphGenerator that are associated to it in the list at the top of the graph_generators module documentation.

• basic.py
• degree_sequence.py
• families.py
• platonic_solids.py
• random.py
• smallgraphs.py
• world_map.py

This patch passes all tests, but is not clean yet and lacks documentations. Others will follow.

Nathann

[nathanncohen]

comment:3

Attachment: trac_13862.patch.gz

What this additional (attachment: trac_13862-cleaning_and_moving.patch) patch does :

• Moves _circle_embedding and _line_embedding to graph_plot.py. These methods are now imported at the beginning of generators/* modules that need need.
• Removes LCFGraph from the list of basc graphs (this methods creates a family of graphs). It was already in the list of "families" graphs.
• Moves the Harary Graph to the "families" file. Same thing here : there are many Harary graphs.
• Moves DorogovtsevGoltsevMendesGraph to families.py. Not worth creating an independent "pseudofractal" module at the moment.
• Moves IntervalGraph to families. This one was not liste among the "families", which is why it was still in graph_generators.py after the first patch.
• Adds the Nauru Graph to the list of small graphs.

Some work on the doc is still needed.

Nathann

[nathanncohen]

Attachment: trac_13862-cleaning_and_moving.patch.gz

[nathanncohen]

comment:4

Apply trac_13862.patch, trac_13862-cleaning_and_moving.patch

[nathanncohen]

comment:6

What this new patch (attachment: trac_13862-doc.patch) does :

• Moves the "Usage" part of the graph_generators module's doc to graph_plot, as it explains how graphs are displayed.
• HEAVY rewrite of the fuctions lists at the top of graph_generators. Now the methods are listed in 3xN tables, so that they are easier to browse. This required to define an (ugly) helper function in graph_generators.py. But the lists at the top of that file are now easier to read (both in html and in sage.graphs.graph_generators?) and easier to update (just add a string in a list).
• NauruGraph isadded to the list of small graphs

This patch's almost ready.

Nathann

[nathanncohen]

Attachment: trac_13862-doc.patch.gz

[nathanncohen]

comment:7

What this patch does (attachment: trac_13862-code_reformatting.patch):

• Removes all occurrences to self, as the former methods are now functions and belong to no class.
• Adds a line of doc to all new files, saying that their documentation actually appears in graph_generators

Lots of code formatting :-P

(only one patch left)

Nathann

[nathanncohen]

comment:8

Attachment: trac_13862-code_reformatting.patch.gz

What this patch does (attachment: trac_13862-moves_3_constructors.patch):

• Moves CompleteGraph, CompleteBipartiteGraph and CompleteMultipartiteGraph from families.py to basic.py
• Adds CompleteMultipartiteGraph to the lists, as it did not appears before O_o

And nooooow, this ticket is ready to be reviewed !!! :-P

Nathann

[dcoudert]

comment:9

Hello,

the long tests fail on families.py

**********************************************************************
File "/path-to-sage/sage-5.6.beta0/devel/sage-myclone/sage/graphs/generators/families.py", line 1815:
    sage: G = graphs.RingedTree(5)
Exception raised:
    Traceback (most recent call last):
      File "/path-to-sage/sage-5.6.beta0/local/bin/ncadoctest.py", line 1231, in run_one_test
        self.run_one_example(test, example, filename, compileflags)
      File "/path-to-sage/sage-5.6.beta0/local/bin/sagedoctest.py", line 38, in run_one_example
        OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags)
      File "/path-to-sage/sage-5.6.beta0/local/bin/ncadoctest.py", line 1172, in run_one_example
        compileflags, 1) in test.globs
      File "<doctest __main__.example_25[2]>", line 1, in <module>
        G = graphs.RingedTree(Integer(5))###line 1815:
    sage: G = graphs.RingedTree(5)
      File "/path-to-sage/sage-5.6.beta0/local/lib/python/site-packages/sage/graphs/generators/families.py", line 1845, in RingedTree
        from sage.graphs.graph_plot import GraphGenerators
    ImportError: cannot import name GraphGenerators

I have run tests only on the graph directory. I don't know if this patch could impact other modules.

Also, you should add possible dependencies with other patches e.g., #13809.

[nathanncohen]

Attachment: trac_13862-unapply_13809.patch.gz

[nathanncohen]

Attachment: trac_13862-reapply_13809.patch.gz

Attachment: trac_13862-moves_3_constructors.patch.gz

[nathanncohen]

comment:10

God... I ran tests on these files a crazy amount of times but I forgot long tests :-P

Updated ! I cheated a bit by first removing #13809 then adding it again, but this set of patch is.... HEAVY to work with :-P

Nathann

Apply trac_13862-unapply_13809.patch, trac_13862.patch, trac_13862-cleaning_and_moving.patch, trac_13862-doc.patch, trac_13862-code_reformatting.patch, trac_13862-moves_3_constructors.patch, trac_13862-reapply_13809.patch

[dcoudert]

comment:11

Install OK, doctest OK including long tests, and docbuild OK.
For me the patch is good to go!

I have added the dependency to the patch description.

This is definitely a huge patch, but it has to be done. Good job.

[dcoudert]

Dependencies: #13809

[nathanncohen]

comment:12

Wow. Glad to see that :-D

Thaaaaaaaaaaaaankss !!!

Nathann

[jdemeyer]

Changed dependencies from #13809 to none

[jdemeyer]

Reviewer: David Coudert

[nathanncohen]

comment:15

Apply trac_13862.patch, trac_13862-cleaning_and_moving.patch, trac_13862-doc.patch, trac_13862-code_reformatting.patch, trac_13862-moves_3_constructors.patch

[jdemeyer]

Merged: sage-5.6.beta2