Features for palp, polytopes_db, polytopes_db_4d

[mkoeppe]

palp is a standard package, but with modularization that does not mean that everyone has it. In particular, sagemath-polyhedra (#32432) will not ship it.

We add a feature test along the lines of the palp spkg-configure.m4 script and mark many doctests in sage.geometry as # optional - palp.

To help construct doctest examples without having to rely on palp, we endow several classes with _sage_input_ methods.

As a cosmetic change, nef-partitions now use a unicode symbol.

-            Nef-partition {0, 1, 3} U {2, 4, 5}
+            Nef-partition {0, 1, 3} ⊔ {2, 4, 5}

We also add feature tests for polytopes_db, polytopes_db_4d.

CC: @kliem @novoselt @seblabbe @dimpase

Component: refactoring

Author: Matthias Koeppe

Branch/Commit: d97479d

Reviewer: Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/32893

[mkoeppe]

Branch: u/mkoeppe/feature_for_palp

[mkoeppe]

Author: Matthias Koeppe

[mkoeppe]

Commit: 6be27b7

[mkoeppe]

New commits:

aee4ad2	src/sage/features/palp.py: New
73b5b50	src/sage/geometry/polyhedron/palp_database.py: Add # sage.doctest: optional - palp
55a228d	src/sage/geometry/lattice_polytope.py: Mark doctests # optional - palp
6be27b7	src/sage/geometry: Mark doctests # optional - palp

[novoselt]

comment:5

I find such markings ridiculous... If a module is useless without PALP, it would make much more sense to me to mark the module once as optional and not on every single line of examples.

My random guess is that modules for toric varieties will mostly stop working as well and again it would make much more sense to mark those modules as dependent on PALP and not each line.

[mkoeppe]

comment:6

Thanks for the feedback. I wouldn't go so far as to call the module useless. The explicit interaction of the polytope with a lattice in this class is valuable design and code that is not tied to the choice of PALP as a backend.

There is a lot of duplication / proliferation of incompatible variants among sage.geometry.lattice_polytope, sage.geometry.polyhedron.ppl_lattice_polytope, sage.geometry.polyhedron that is calling for refactoring. To mark which lines of lattice_polytope actually depend on palp (about 1/3 of the sage: lines in this file) was a first step to inform possible such refactoring steps.

Many of the # optional markings in tests for NefPartition could be avoided by constructing the example explicitly instead of using

        sage: o = lattice_polytope.cross_polytope(3)
        sage: np = o.nef_partitions()[0]; np                                    # optional - palp

repeatedly. Would this be agreeable?

[novoselt]

comment:7

Since I am not doing any work anymore, it is up to the people who do to agree on ;-)

[sagetrac-git]

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

74fdacf

LatticePolytopeClass, NefPartition, PointCollection, ToricLattice_ambient: Add `_sage_input_` methods

[sagetrac-git]

Changed commit from 6be27b7 to 74fdacf

[sagetrac-git]

Changed commit from 74fdacf to 9d726ce

[sagetrac-git]

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

9d726ce

LatticePolytopeClass, NefPartition, PointCollection, ToricLattice_ambient: Add `_sage_input_` methods

[sagetrac-git]

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

1c78501

src/sage/geometry/lattice_polytope.py: In NefPartition doctests, construct examples without using palp

[sagetrac-git]

Changed commit from 9d726ce to 1c78501

[mkoeppe]

comment:11

Replying to @mkoeppe:

To mark which lines of lattice_polytope actually depend on palp (about 1/3 of the sage: lines in this file)

down to less than 1/4 of the lines now

[sagetrac-git]

Changed commit from 1c78501 to 1025d65

[sagetrac-git]

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

1025d65

src/sage/geometry/lattice_polytope.py, src/sage/schemes/toric/fano_variety.py: Use unicode disjoint union symbol

[sagetrac-git]

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

55e812c

src/sage/geometry/lattice_polytope.py: Fix typo

[sagetrac-git]

Changed commit from 1025d65 to 55e812c

[sagetrac-git]

Changed commit from 55e812c to d97479d

[sagetrac-git]

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

d97479d

src/sage/features/databases.py (DatabaseReflexivePolytopes): New

[mkoeppe]

comment:19

Doctest failures are unrelated, needs review

[dimpase]

Reviewer: Dima Pasechnik

[dimpase]

comment:20

lgtm

[mkoeppe]

comment:21

Thank you!

[mkoeppe]

comment:22

Follow-up: #33467

[vbraun]

Changed branch from u/mkoeppe/feature_for_palp to d97479d