add interface to nauty's genktreeg

[dcoudert]

Nauty has a generator of k-trees. We add an interface to this generator.
This is a complement of #36587.

📝 Checklist

• The title is concise, informative, and self-explanatory.
• The description explains in detail what this PR is about.
• I have linked a relevant issue or discussion.
• I have created tests covering the changes.
• I have updated the documentation accordingly.

⌛ Dependencies

[dcoudert]

Notice that genktreeg is currently not accessible from the homebrew install of nauty, it is missing in the formula https://github.com/Homebrew/homebrew-core/blob/32c869d54088962356f34b8fe2cb64f4e8740fe9/Formula/n/nauty.rb . I don't know how to report that.

So currently we must install nauty from source to access genktreeg.

[dcoudert]

Notice that genktreeg is currently not accessible from the homebrew install of nauty, it is missing in the formula https://github.com/Homebrew/homebrew-core/blob/32c869d54088962356f34b8fe2cb64f4e8740fe9/Formula/n/nauty.rb . I don't know how to report that.

So currently we must install nauty from source to access genktreeg.

Apparently also not the case for the pip installable version (see doctests errors).

[mkoeppe]

You can change build/pkgs/nauty/spkg-configure.m4 to add a test for this generator

[mkoeppe]

Right now we only test for features of nauty 2.8.0; this new generator was added in 2.8.8.

[dcoudert]

Thank you Matthias. Let me know if I should take the opportunity to add other generators, even if we don't have interfaces yet.

[mkoeppe]

Let me know if I should take the opportunity to add other generators, even if we don't have interfaces yet.

I think it's good enough to just test for this one - as a representative of the newest features in 2.8.8. It may be a good idea to update the comment in the spkg-configure.m4 file though

[dcoudert]

I have updated the comment.

[mkoeppe]

Let me know if I should take the opportunity to add other generators

Now I realize that you may have meant ... to add them in the installation script? +1 on that.

[mkoeppe]

Also so that the updated installation script takes effect on users' machines:

diff --git a/build/pkgs/nauty/package-version.txt b/build/pkgs/nauty/package-version.txt
index 80803faf1b9..b8635c72de3 100644
--- a/build/pkgs/nauty/package-version.txt
+++ b/build/pkgs/nauty/package-version.txt
@@ -1 +1 @@
-2.8.8
+2.8.8.p0

[mkoeppe]

Would it make sense to add # needs nauty to the doctests?

This would help with the Conda CI (which fails because it does not have a suitable nauty package; related to the discussion in #35593 (comment))

[dcoudert]

We may add # needs nauty, but I don't know how to detect all the doctests that will need this addition.

Also,; we currently have

src/sage/features/nauty.py:        sage: NautyExecutable('converseg').is_present()         # optional - nauty
src/sage/features/nauty.py:        sage: Nauty().is_present()                              # optional - nauty

[dcoudert]

I added some tags. Let's see if it is enough for the Conda CI

[tobiasdiez]

I added some tags. Let's see if it is enough for the Conda CI

Looks like this particular program is not included in the conda distribution. Perhaps the fix is as easy as changing https://github.com/conda-forge/nauty-feedstock/blob/f0bb97fb7503af89d94250541f2519cbc154008e/recipe/build.sh#L28 accordingly.

[dcoudert]

Several programs of nauty are missing in the conda and homebrew distributions (may be in other distributions as well): countneg, genktreeg, ransubg

PROGRAMS="
- addedgeg addptg amtog ancestorg assembleg biplabg catg complg converseg copyg countg cubhamg deledgeg
- delptg dimacs2g directg dreadnaut dretodot dretog edgetransg genbg genbgL geng gengL genposetg genquarticg genrang
- genspecialg gentourng gentreeg hamheuristic labelg linegraphg listg multig nbrhoodg
- newedgeg pickg planarg productg ranlabg shortg showg subdivideg twohamg underlyingg vcolg
- watercluster2 NRswitchg"
+ addedgeg addptg amtog ancestorg assembleg biplabg catg complg converseg copyg
+ countg countneg cubhamg deledgeg delptg dimacs2g directg dreadnaut dretodot
+ dretog edgetransg genbg genbgL geng gengL genposetg genquarticg genrang
+ genspecialg gentourng gentreeg genktreeg hamheuristic labelg linegraphg listg
+ multig nbrhoodg newedgeg pickg planarg productg ranlabg ransubg shortg showg
+ subdivideg twohamg underlyingg vcolg watercluster2 NRswitchg"

What's the right way to ask for modifications ?

[tobiasdiez]

Just make the edits (say in the web editor of github) and open a PR. Alternatively, I'm sure @isuruf or @saraedum are happy to help.

[dcoudert]

This now conda-forge/nauty-feedstock#24

[mkoeppe]

Also,; we currently have

src/sage/features/nauty.py:        sage: NautyExecutable('converseg').is_present()         # optional - nauty
src/sage/features/nauty.py:        sage: Nauty().is_present()                              # optional - nauty

These should be needs, not optional -- because nauty is a standard package.

./sage -fixdoctests --overwrite --no-test src/sage/features/nauty.py src/sage/graphs/graph_generators.py will fix this automatically for you

[mkoeppe]

The runtime feature test still thinks that the nauty feature is available, which is why the conda test is still failing. You'll need this:

diff --git a/src/sage/features/nauty.py b/src/sage/features/nauty.py
index 0bbe796e003..4a07264f927 100644
--- a/src/sage/features/nauty.py
+++ b/src/sage/features/nauty.py
@@ -62,7 +62,7 @@ class Nauty(JoinFeature):
         """
         JoinFeature.__init__(self, "nauty",
                              [NautyExecutable(name)
-                              for name in ('directg', 'gentourng', 'geng', 'genbg', 'gentreeg', 'converseg')])
+                              for name in ('directg', 'gentourng', 'geng', 'genbg', 'gentreeg', 'genktreeg')])
 
 
 def all_features():

[dcoudert]

Indeed. Fully updating nauty is more involved than what I though.

[github-actions]

Documentation preview for this PR (built with commit 5ad350c; changes) is ready! 🎉

[mkoeppe]

Looking good; ready for review?

[dcoudert]

Yes, I think it's ready for review.

[mkoeppe]

LGTM