Generalized Permutohedra and type H4 4-uniform polytopes

[jipilab]

One sort of generalized permutahedra consists in putting the starting point, which is usually taken inside the fundamental chamber, on the boundary of the fundamental chamber.

See ​https://arxiv.org/abs/1904.11029 for a recent related paper.

This ticket implements the generalized permutahedra and on the way, adds the fifteen H4 4-uniform polytopes.

See ​https://en.wikipedia.org/wiki/H4_polytope for a list of them.

Many of them are quite large and can only be computed in reasonable time using the backend normaliz.

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​a546fba

Added names on top

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​91c43a6

Made the H4 types regular

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​57d9b7d	Started fixing regularity
​ef9faa9	Fixed the regular construction

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​8056264

Fixed typo in docstring

[embray]

As the Sage-8.8 release milestone is pending, we should delete the sage-8.8 milestone for tickets that are not actively being worked on or that still require significant work to move forward. If you feel that this ticket should be included in the next Sage release at the soonest please set its milestone to the next release milestone (sage-8.9).

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​cce2590	Merge branch 'develop' into h4_polytopes
​0c5b8d9	Fix py3 code and tests for Sage8.9beta3
​d66f7e2	pep8
​a6a5452	fixed some doctests

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​71fbfdf

Fixed a test

[chapoton]

apparemment, la doc ne compile pas, voir patchbot

[jipilab]

Replying to chapoton:

apparemment, la doc ne compile pas, voir patchbot

Hm, all right. I'm on it!

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​d4260a6

trivial doc fix

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​95d6bda

fix coding in library

[chapoton]

• missing the word 'polytope' here, I think:

  The runcitruncated 600-cell is a 4-dimensional 4-uniform in the `H_4`
  

and the same in all the examples.

• Here, you could remove the []

  sum([adjusted_col[j]**2 for j in range(n) if j != i])
  

apart from that, ready to go..

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​5971228

Added 'polytope' and fixed sum

[chapoton]

ok, good to go

[jipilab]

Merci!

[vbraun]

This dies on most 32-bit buildbots:

sage: perm_b3 = polytopes.generalized_permutahedron(['B',3]); perm_b3 ## line 2324 ##
A 3-dimensional polyhedron in (Number Field in a with defining polynomial x^2 - 2 with a = 1.414213562373095?)^3 defined as the convex hull of 48 vertices
sage: perm_b3_reg = polytopes.generalized_permutahedron(['B',3],regular=True); perm_b3_reg # long time - 12sec. ## line 2326 ##
------------------------------------------------------------------------
/home/buildbot/slave/sage_git/build/local/lib/python2.7/site-packages/cysignals/signals.so(+0x5f22)[0xf5fbdf22]
/home/buildbot/slave/sage_git/build/local/lib/python2.7/site-packages/cysignals/signals.so(+0x5fc6)[0xf5fbdfc6]
/home/buildbot/slave/sage_git/build/local/lib/python2.7/site-packages/cysignals/signals.so(+0x76e5)[0xf5fbf6e5]
linux-gate.so.1(__kernel_sigreturn+0x0)[0xf77b6ca0]
/home/buildbot/slave/sage_git/build/local/lib/libgmp.so.23(__gmpn_mul_basecase+0x83)[0xf6cabd4b]
------------------------------------------------------------------------
Attaching gdb to process id 20319.
Cannot find gdb installed
GDB is not installed.
Install gdb for enhanced tracebacks.
------------------------------------------------------------------------
**********************************************************************
----------------------------------------------------------------------
sage -t --long src/sage/geometry/polyhedron/library.py  # Timed out
----------------------------------------------------------------------

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​a1ad959

Made a doctest not tested due to time

[chapoton]

ok, let us try again

[vbraun]

**********************************************************************
File "src/sage/geometry/polyhedron/library.py", line 2324, in sage.geometry.polyhedron.library.Polytopes.generalized_permutahedron
Failed example:
    perm_b3 = polytopes.generalized_permutahedron(['B',3]); perm_b3
Expected:
    A 3-dimensional polyhedron in (Number Field in a with defining polynomial x^2 - 2 with a = 1.414213562373095?)^3 defined as the convex hull of 48 vertices
    A 3-dimensional polyhedron in AA^3 defined as the convex hull of 48 vertices
Got:
    A 3-dimensional polyhedron in (Number Field in a with defining polynomial x^2 - 2 with a = 1.414213562373095?)^3 defined as the convex hull of 48 vertices
**********************************************************************
1 item had failures:
   1 of  21 in sage.geometry.polyhedron.library.Polytopes.generalized_permutahedron
    [240 tests, 1 failure, 156.68 s]
----------------------------------------------------------------------
sage -t --long src/sage/geometry/polyhedron/library.py  # 1 doctest failed
----------------------------------------------------------------------

[jipilab]

Replying to vbraun:

**********************************************************************
File "src/sage/geometry/polyhedron/library.py", line 2324, in sage.geometry.polyhedron.library.Polytopes.generalized_permutahedron
Failed example:
    perm_b3 = polytopes.generalized_permutahedron(['B',3]); perm_b3
Expected:
    A 3-dimensional polyhedron in (Number Field in a with defining polynomial x^2 - 2 with a = 1.414213562373095?)^3 defined as the convex hull of 48 vertices
    A 3-dimensional polyhedron in AA^3 defined as the convex hull of 48 vertices
Got:
    A 3-dimensional polyhedron in (Number Field in a with defining polynomial x^2 - 2 with a = 1.414213562373095?)^3 defined as the convex hull of 48 vertices
**********************************************************************
1 item had failures:
   1 of  21 in sage.geometry.polyhedron.library.Polytopes.generalized_permutahedron
    [240 tests, 1 failure, 156.68 s]
----------------------------------------------------------------------
sage -t --long src/sage/geometry/polyhedron/library.py  # 1 doctest failed
----------------------------------------------------------------------

I have trouble figuring out how this failure occurred.

The expected block is not as the attached branch would predict. Namely, the second line is absent. I merged the last version of develop into this ticket and made a test on my machine and I got:

jplabbe@blackbomb:~/sage/src/sage/geometry/polyhedron$ sage -t library.py 
Using --optional=4ti2,bliss,build,dochtml,e_antic,gfortran,latte_int,lidia,lrslib,memlimit,ninja_build,normaliz,pynormaliz,python2,sage,topcom
Doctesting 1 file.
sage -t library.py
    [305 tests, 77.99 s]
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 78.1 seconds
    cpu time: 78.0 seconds
    cumulative wall time: 78.0 seconds

I get 305 tests in total. Would it be possible to get more feedback on how this failing doctest occurred? (which optional packages were used?)

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​cc1a6ab

Merge branch 'develop' into h4_polytopes

[jipilab]

Let's have another run of bots to see if the problem still occurs. This failure is strange.

[chapoton]

patchbot reports another failure

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​b67e0c5

Added missing not tested tag

[jipilab]

Found it.

It was a missing tag from fixing comment 19. Should be good to go now...

[chapoton]

Adding tags on the results of doctests make no sense.

This does not fix the patchbot failure.

[jipilab]

Replying to chapoton:

Adding tags on the results of doctests make no sense.

This does not fix the patchbot failure.

That's what I thought at first too!

But then, that's the only way I can make sense of seeing

Expected:
    A 3-dimensional polyhedron in (Number Field in a with defining polynomial x^2 - 2 with a = 1.414213562373095?)^3 defined as the convex hull of 48 vertices
    A 3-dimensional polyhedron in AA^3 defined as the convex hull of 48 vertices

which are two distinct consecutive outputs of test, the second of which is not tested. I was thinking that it might preparse the string and remove the not tested things and thus the expected block would now consist of two lines.

Otherwise, I have no clue how come the expected block would consist of two lines, it is simply not as the source entails!?

Puzzled.

[jipilab]

Replying to chapoton:

Adding tags on the results of doctests make no sense.

This does not fix the patchbot failure.

From the patch bot shortog, the following information is a bit obscure:

Expected:
    There are 7 tests in sage/combinat/finite_state_machine.py that are not being run
    There are 3 unexpected tests being run in sage/doctest/parsing.py
    There are 1 unexpected tests being run in sage/doctest/reporting.py
    There are 3 tests in sage/rings/invariants/invariant_theory.py that are not being run
Got:
    There are 7 tests in sage/combinat/finite_state_machine.py that are not being run
    There are 3 unexpected tests being run in sage/doctest/parsing.py
    There are 1 unexpected tests being run in sage/doctest/reporting.py
    There are 1 unexpected tests being run in sage/geometry/polyhedron/library.py
    There are 3 tests in sage/rings/invariants/invariant_theory.py that are not being run
**********************************************************************

I guess it is the same test that causes a problem, but I have no output to inspect. Also, I am curious, what is an "unexpected test"? It's the first time I see such a thing.

[git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

[jipilab]

Replying to git:

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

I removed the unless tag on the doctest result...

[chapoton]

Apparemment, ce qui pose problème est le fait que l'annotation contienne "64-bits".

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​bd1fd21

fix details

[chapoton]

ok, let us try again

[jipilab]

Replying to chapoton:

Apparemment, ce qui pose problème est le fait que l'annotation contienne "64-bits".

Wow. I see. Good to know. It looks like it's passing the test now at least.