Opened 4 years ago
Closed 4 years ago
#22496 closed enhancement (fixed)
Improve and fix documentation of Combinatorial or Discrete Geometry
Reported by:  jipilab  Owned by:  

Priority:  major  Milestone:  sage7.6 
Component:  geometry  Keywords:  doc, polyhedron, geometry, days84 
Cc:  moritz, mkoeppe, vdelecroix, tmonteil, chapoton  Merged in:  
Authors:  JeanPhilippe Labbé  Reviewers:  Vincent Klein 
Report Upstream:  N/A  Work issues:  
Branch:  f931571 (Commits)  Commit:  f931571b273b1957634be1d4b98908df6dd88197 
Dependencies:  Stopgaps: 
Description (last modified by )
The reference manual for the currently called combinatorial geometry needs some logical reorganization.
http://doc.sagemath.org/html/en/reference/geometry/index.html
This ticket fixes the following:
 add the normaliz backend to the references and add a note on how to install it.
 fixes an indentation that caused the documentation not to build in the normaliz backend
 the section on combinatorial geometry is renamed by adding also Discrete
 the section on hyperbolic geometry gets moved in the table of content to Geometry and Topology and not inside Combinatorial and Discrete Geometry (which made no sense).
 the combinatorial and discrete geometry table of content is restructured logically.
 fixes a small bug in the documentation of the base class of polyhedron (missing backtick)
 added some links to other modules in the constructor of polyhedra to different classes and backends.
Change History (25)
comment:1 Changed 4 years ago by
 Branch set to u/jipilab/improve_doc_poly
comment:2 Changed 4 years ago by
 Commit set to e6beae2ab804628a3004063203c43fe867864649
comment:3 Changed 4 years ago by
 Type changed from PLEASE CHANGE to enhancement
comment:4 Changed 4 years ago by
 Cc chapoton added
comment:5 Changed 4 years ago by
Salut !
missing empty line here
+.. NOTE:: + This backend requires `PyNormaliz <https://pypi.python.org/pypi/PyNormaliz/1.5>`_.
and in several other places....
comment:6 Changed 4 years ago by
 Commit changed from e6beae2ab804628a3004063203c43fe867864649 to 38a89ebcb63d09a8b2e00e801d9360d138c42baf
Branch pushed to git repo; I updated commit sha1. New commits:
38a89eb  Added missing linespacing

comment:7 Changed 4 years ago by
 Commit changed from 38a89ebcb63d09a8b2e00e801d9360d138c42baf to 71b1f420886b5f615604810e83da7e11ffec575a
Branch pushed to git repo; I updated commit sha1. New commits:
71b1f42  Several small corrections

comment:8 Changed 4 years ago by
 Description modified (diff)
 Status changed from new to needs_review
comment:9 Changed 4 years ago by
 Commit changed from 71b1f420886b5f615604810e83da7e11ffec575a to 1a1e7b15735e4b69de2c91e18420b57fa66fba0d
Branch pushed to git repo; I updated commit sha1. New commits:
1a1e7b1  Corrected the indentation of an input block

comment:10 followup: ↓ 11 Changed 4 years ago by
I would not give cones and fan "Toric Varieties" title, there are classes for these which are based on fans and cones. Also lattice_polytope
logically fits with them better.
comment:11 in reply to: ↑ 10 Changed 4 years ago by
I would not give cones and fan "Toric Varieties" title, there are classes for these which are based on fans and cones.
I agree. I was sorting through the files and for the first version I put the 7 files whose documentation started with
This module was designed as a part of framework for toric varieties
together in a section called Toric Varieties.
Perhaps naming the section. Lattices, Cones, Fans, and related objects ? What do you think? Do you have any suggestions?
Also
lattice_polytope
logically fits with them better.
Okay. Are there other modules that would logically go with them as well?
comment:12 followup: ↓ 13 Changed 4 years ago by
"Toric Geometry" may be appropriate, just no "varieties" themselves, I think.
Everything under "Lattice polyhedra" may be clamped with it  while there are presumably other reasons to consider them, almost everything here was done with toric geometry and mirror symmetry applications in mind.
comment:13 in reply to: ↑ 12 Changed 4 years ago by
Replying to novoselt:
"Toric Geometry" may be appropriate, just no "varieties" themselves, I think.
Sounds good.
Everything under "Lattice polyhedra" may be clamped with it  while there are presumably other reasons to consider them, almost everything here was done with toric geometry and mirror symmetry applications in mind.
I could put it in the polyhedral computations section after the lattice polytopes, that would be good? One argument to keep "Toric geometry" in its own section is somehow to reflect a little bit the structure in the geometry component (although I admit it does not necessarily have to follow it...) since polyhedron is a module on its own and the toric geometry framework is located directly in geometry and not in polyhedron...
I'm fine with both.
comment:14 Changed 4 years ago by
 Commit changed from 1a1e7b15735e4b69de2c91e18420b57fa66fba0d to 51a05cf09ad151dd77eb37a9e088ea9b73efd60d
Branch pushed to git repo; I updated commit sha1. New commits:
51a05cf  Renamed subsection and moved it

comment:15 Changed 4 years ago by
 Dependencies set to #22469
comment:16 followup: ↓ 17 Changed 4 years ago by
 Dependencies #22469 deleted
A very related question (for another ticket, but it is good to have your opinion while you are at it) would be to move the isolated python files within src/sage/geometry/
into some appropriate directory, like riemannian_manifolds
for riemannian manifolds, polyhedron
for polyhedra, etc.
The files to classify are:
 cone.py
 fan_isomorphism.py
 fan_morphism.py
 fan.py
 hasse_diagram.py
 integral_points.pyx
 lattice_polytope.py
 linear_expression.py
 newton_polygon.py
 point_collection.pyx
 pseudolines.py
 ribbon_graph.py
 toric_lattice_element.pyx
 toric_lattice.py
 toric_plotter.py
comment:17 in reply to: ↑ 16 ; followup: ↓ 18 Changed 4 years ago by
Would make sense to have src/sage/geometry/toric
similar to src/sage/schemes/toric
with files
 cone.py
 fan_isomorphism.py
 fan_morphism.py
 fan.py
 lattice_polytope.py
 point_collection.pyx
 toric_lattice_element.pyx
 toric_lattice.py
 toric_plotter.py
comment:18 in reply to: ↑ 17 Changed 4 years ago by
Replying to novoselt:
Would make sense to have
src/sage/geometry/toric
similar tosrc/sage/schemes/toric
with files
 cone.py
 fan_isomorphism.py
 fan_morphism.py
 fan.py
 lattice_polytope.py
 point_collection.pyx
 toric_lattice_element.pyx
 toric_lattice.py
 toric_plotter.py
OK great, having such a src/sage/geometry/toric
would be a good step toward cleaning up src/sage/geometry
!
comment:19 Changed 4 years ago by
 Commit changed from 51a05cf09ad151dd77eb37a9e088ea9b73efd60d to 27f9f4dbd3073639df9addc26ec0f8dddf10b67f
Branch pushed to git repo; I updated commit sha1. New commits:
27f9f4d  Rebased on 7.6.beta6

comment:20 Changed 4 years ago by
 Dependencies set to #13517
Okay. I would say that it is ready to be reviewed again.
comment:21 Changed 4 years ago by
 Dependencies #13517 deleted
comment:22 Changed 4 years ago by
 Commit changed from 27f9f4dbd3073639df9addc26ec0f8dddf10b67f to f931571b273b1957634be1d4b98908df6dd88197
Branch pushed to git repo; I updated commit sha1. New commits:
f931571  Corrected indentation in doc

comment:23 Changed 4 years ago by
 Reviewers set to Vincent Klein
comment:24 Changed 4 years ago by
 Status changed from needs_review to positive_review
doctest passed on :
 src/sage/geometry/polyhedron/backend_normaliz.py
 src/sage/geometry/polyhedron/base.py
 src/sage/geometry/polyhedron/constructor.py
build of the doc passed and page discrete_geometry/index.html looks conform.
comment:25 Changed 4 years ago by
 Branch changed from u/jipilab/improve_doc_poly to f931571b273b1957634be1d4b98908df6dd88197
 Resolution set to fixed
 Status changed from positive_review to closed
Branch pushed to git repo; I updated commit sha1. New commits:
Corrected a title