upgrade Normaliz to 3.8.8, PyNormaliz to 2.12, add script package libnauty

[videlec]

Tarballs: see checksums.ini

These new releases include dynamic bitset classes that allow dynamic h-representation computations.

We also install nauty header and library in order that Normaliz compile with nauty support (for computing automorphism group).

Depends on #30262

Upstream: Fixed upstream, but not in a stable release.

CC: @mkoeppe @jplab @isuruf @w-bruns @tscrim @kliem @LaisRast @slel

Component: packages: standard

Keywords: package upgrade days101

Author: Vincent Delecroix, Jonathan Kliem, Matthias Koeppe

Branch: c55a701

Reviewer: Jonathan Kliem, Matthias Koeppe

Issue created by migration from https://trac.sagemath.org/ticket/27952

[videlec]

New commits:

fdb67b5

upgrade normaliz to 3.7.3

[videlec]

Commit: fdb67b5

[videlec]

Branch: u/vdelecroix/normaliz

[videlec]

Changed keywords from none to package upgrade

[sagetrac-git]

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

7b7168b

upgrade normaliz to 3.7.3 and PyNormaliz to 2.7

[sagetrac-git]

Changed commit from fdb67b5 to 7b7168b

[videlec]

Author: Vincent Delecroix

[videlec]

Dependencies: #27920

[videlec]

comment:9

Self tests do not pass on my computer

$ python3 setup.py test
/opt/sage/sage-py3-gcc/local/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'long_description_content_type'
  warnings.warn(msg)
running test
Doctest must_be_matrices-39.txt
  2 tests
Doctest test_rational_cones.txt
  34 tests
Doctest segfault-45.txt
  3 tests
Doctest autom.txt
Doctest failures

[videlec]

comment:10

And I confirm the segfault in a Python3 console

$ python3
Python 3.7.3 (default, May 26 2019, 12:00:16) 
[GCC 8.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from PyNormaliz import Cone, NmzCone, NmzResult
>>> V = [[-1, -1, 1], [-1, 0, 1], [-1, 1, 1], [0, -1, 1], [0, 0, 1], [0, 1, 1], [1, -1, 1], [1, 0, 1], [1, 1, 1]]
>>> cube2 = NmzCone(vertices=V)
>>> NmzResult(cube2,"Automorphisms") == [8, [[[], []], []], [[[0, 2, 1, 3], [1, 0, 3, 2]], [[0, 1, 2, 3]]], [[[1, 0, 3, 2], [0, 2, 1, 3]], [[0, 1, 2, 3]]]]
Erreur de segmentation (core dumped)

[sagetrac-git]

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

72af741

normaliz 3.7.3 upgrade / PyNormaliz 2.8 upgrade

[sagetrac-git]

Changed commit from 7b7168b to 72af741

[videlec]

comment:12

segfault probably due to e-antic version. I am about to release 0.1.3

[videlec]

comment:13

Most probably, the segfault is due to the fact that Normaliz was not built with nauty support

checking whether nauty headers and library are available... checking for densenauty in -lnauty... no

[mkoeppe]

comment:155

Replying to @kliem:

Replying to @mkoeppe:

Is this condition tested by a doctest?

Matrix(ZZ, nmz_vertices + nmz_rays).rank() == Matrix(ZZ, nmz_rays).rank() + 1

...
The question is simply: Is the far face a facet or not? If it is a facet, we need to add an inequality to the normaliz cone. The lines don't make a difference with regard to that question.

Thanks for the explanation and adding the new comments and tests.

This is a positive review for your contributions on this ticket.

---

New commits:

3f2d872	Merge tag '9.2.beta8' into t/27952/normaliz
84db571	build/pkgs/normaliz: Update to 3.8.8
e1fc147	Merge tag '9.2.beta10' into t/27952/normaliz

[mkoeppe]

Changed commit from f3e8fc2 to e1fc147

[mkoeppe]

comment:156

Replying to @kliem:

[normaliz-3.8.7] checking whether e-antic headers and library are available... configure: error: e-antic is not available but was requested

Tried it with "my" new patchbot. Doesn't work.

Please check again with the new release.

[mkoeppe]

Changed reviewer from Jonathan Kliem, Matthias Koeppe to Jonathan Kliem, Matthias Koeppe, github.com/mkoeppe/sage/runs/1045214008, github.com/mkoeppe/sage/actions/runs/230112232

[kliem]

comment:158

Replying to @mkoeppe:

Replying to @kliem:

[normaliz-3.8.7] checking whether e-antic headers and library are available... configure: error: e-antic is not available but was requested

Tried it with "my" new patchbot. Doesn't work.

Please check again with the new release.

Seems to work well. At least all tests in the geometry folder passed.

This is great, because this is an improvement (see above). Before this ticket, pynormaliz is not working at all.

[kliem]

comment:159

Replying to @mkoeppe:

Replying to @kliem:

Replying to @mkoeppe:

Is this condition tested by a doctest?

Matrix(ZZ, nmz_vertices + nmz_rays).rank() == Matrix(ZZ, nmz_rays).rank() + 1

...
The question is simply: Is the far face a facet or not? If it is a facet, we need to add an inequality to the normaliz cone. The lines don't make a difference with regard to that question.

Thanks for the explanation and adding the new comments and tests.

This is a positive review for your contributions on this ticket.

Positive review on the other part.

[kliem]

Changed reviewer from Jonathan Kliem, Matthias Koeppe, github.com/mkoeppe/sage/runs/1045214008, github.com/mkoeppe/sage/actions/runs/230112232 to Jonathan Kliem, Matthias Koeppe

[vbraun]

comment:161

**********************************************************************
File "src/sage/geometry/polyhedron/backend_normaliz.py", line 871, in sage.geometry.polyhedron.backend_normaliz.Polyhedron_normaliz._test_far_facet_condition
Failed example:
    P = Polyhedron(vertices=[[1,0], [0,1]],
                   rays=[[1,1]], backend='normaliz')     # optional - pynormaliz
Exception raised:
    Traceback (most recent call last):
      File "/home/release/Sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 715, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/release/Sage/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1139, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.geometry.polyhedron.backend_normaliz.Polyhedron_normaliz._test_far_facet_condition[0]>", line 2, in <module>
        rays=[[Integer(1),Integer(1)]], backend='normaliz')     # optional - pynormaliz
      File "sage/misc/lazy_import.pyx", line 353, in sage.misc.lazy_import.LazyImport.__call__ (build/cythonized/sage/misc/lazy_import.c:3736)
        return self.get_object()(*args, **kwds)
      File "/home/release/Sage/local/lib/python3.7/site-packages/sage/geometry/polyhedron/constructor.py", line 662, in Polyhedron
        return parent(Vrep, Hrep, convert=convert, verbose=verbose)
      File "sage/structure/parent.pyx", line 902, in sage.structure.parent.Parent.__call__ (build/cythonized/sage/structure/parent.c:9364)
        return mor._call_with_args(x, args, kwds)
      File "sage/structure/coerce_maps.pyx", line 180, in sage.structure.coerce_maps.DefaultConvertMap_unique._call_with_args (build/cythonized/sage/structure/coerce_maps.c:5154)
        raise
      File "sage/structure/coerce_maps.pyx", line 175, in sage.structure.coerce_maps.DefaultConvertMap_unique._call_with_args (build/cythonized/sage/structure/coerce_maps.c:5042)
        return C._element_constructor(x, *args, **kwds)
      File "/home/release/Sage/local/lib/python3.7/site-packages/sage/geometry/polyhedron/parent.py", line 598, in _element_constructor_
        return self.element_class(self, Vrep, Hrep, **kwds)
      File "/home/release/Sage/local/lib/python3.7/site-packages/sage/geometry/polyhedron/backend_normaliz.py", line 238, in __init__
        Polyhedron_base.__init__(self, parent, Vrep, Hrep, **kwds)
      File "/home/release/Sage/local/lib/python3.7/site-packages/sage/geometry/polyhedron/base.py", line 249, in __init__
        self._init_from_Vrepresentation(vertices, rays, lines, **kwds)
      File "/home/release/Sage/local/lib/python3.7/site-packages/sage/geometry/polyhedron/backend_normaliz.py", line 565, in _init_from_Vrepresentation
        self._init_from_normaliz_data(data, normaliz_field=normaliz_field, verbose=verbose)
      File "/home/release/Sage/local/lib/python3.7/site-packages/sage/geometry/polyhedron/backend_normaliz.py", line 387, in _init_from_normaliz_data
        cone = self._cone_from_normaliz_data(data, verbose)
      File "/home/release/Sage/local/lib/python3.7/site-packages/sage/geometry/polyhedron/backend_normaliz.py", line 419, in _cone_from_normaliz_data
        PythonModule("PyNormaliz", spkg="pynormaliz").require()
      File "/home/release/Sage/local/lib/python3.7/site-packages/sage/features/__init__.py", line 191, in require
        raise FeatureNotPresentError(self, presence.reason, presence.resolution)
    sage.features.FeatureNotPresentError: PyNormaliz is not available.
    Failed to import `PyNormaliz`.
    To install PyNormaliz you can try to run 'sage -i pynormaliz'.
**********************************************************************

[sagetrac-git]

Changed commit from e1fc147 to ce2b8f9

[sagetrac-git]

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

ce2b8f9

src/sage/geometry/polyhedron/backend_normaliz.py: Put # optional - pynormaliz on the first line, not continuation line

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1 and set ticket back to needs_review. New commits:

c55a701

src/sage/geometry/polyhedron/backend_normaliz.py: Put # optional - pynormaliz on the first line, not continuation line (one more)

[sagetrac-git]

Changed commit from ce2b8f9 to c55a701

[vbraun]

Changed branch from u/mkoeppe/normaliz to c55a701

[dimpase]

Changed commit from c55a701 to none

[dimpase]

comment:167

a bug in libnauty spkg-configure

the 1st two args of AC_SEARCH_LIBS are swapped.