Webs and spiders - Githubissues

BruceWestbury commented 3 years ago

The terminology of webs and spiders is due to Kuperberg. Here we implement webs as planar graphs with boundary.

CC: @tscrim @mantepse

Component: combinatorics

Keywords: planar graph

Author: Bruce Westbury

Branch/Commit: public/ticket-31209 @ 5a49b8e

Issue created by migration from https://trac.sagemath.org/ticket/31209

BruceWestbury commented 3 years ago

Branch: u/Bruce/spider

mantepse commented 3 years ago

comment:2

Wonderful!

See also #25901 and #25173

New commits:

9332771 Moved spherical_spider.py to combinat directory

mantepse commented 3 years ago

Commit: 9332771

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

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

a870d6a Did some debugging

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

Changed commit from 9332771 to a870d6a

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

Changed commit from a870d6a to e5051e7

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

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

`5a61bc6`	`Added faces, is_separable methods`
`6d6ba0f`	Corrected `_repr_` for closed diagrams
`e5051e7`	`All existing doctests pass.`

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

Changed commit from e5051e7 to 1f99737

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

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

`3be0b4a`	`Added doctests`
`ce172c4`	`Added is_simple`
`b402a8f`	`Added method plot for drawing a diagram.`
`1f99737`	`Corrected doctest`

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

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

`8e1943b`	`Created _layout for plot and _latex_`
`d08f08b`	`Removed ClonableElement`
`9d0a09d`	`Changed to richcmp`

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

Changed commit from 1f99737 to 9d0a09d

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

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

`1274e5f`	`Debugged from_permutation`
`a5bd8c6`	`Improved coverage, fixed errors reported by patchbot`

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

Changed commit from 9d0a09d to a5bd8c6

fchapoton commented 3 years ago

comment:9

WTF

if not π in BaxterPermutations():

Please avoid unicode identifiers.

fchapoton commented 3 years ago

comment:10

Sorry for the "wtf", do not take it personally.

But please, please, do not do that. Let us keep the code identifiers ASCII.

Some comments on the question here:

https://stackoverflow.com/questions/2649544/unicode-identifiers-in-python

fchapoton commented 3 years ago

comment:11

by the way, Gretzler is Getzler

BruceWestbury commented 3 years ago

comment:12

Replying to @fchapoton:

by the way, Gretzler is Getzler

Thanks for spotting that mistake.

BruceWestbury commented 3 years ago

comment:13

Replying to @fchapoton:

Sorry for the "wtf", do not take it personally.

No problem with WTF

But please, please, do not do that. Let us keep the code identifiers ASCII.

I don't have strong views on this and will change this.

Some comments on the question here:

https://stackoverflow.com/questions/2649544/unicode-identifiers-in-python

I would still like to understand why this is bad practice. The discussion in the link is interesting and has some gotchas I didn't know about. Using unicode for function names as in the discussion would get a WTF from me. I also would not think of using a unicode identifier outside of a mathematical context.

I have simply used a greek letter as a local identifier following standard practice in mathematical literature. My understanding is that this is fine in a notebook.

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

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

1bb2424 Removed unicode identifier, started on improving drawing edges.

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

Changed commit from a5bd8c6 to 1bb2424

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

Changed commit from 1bb2424 to d88ac28

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

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

`6c199bc`	`Finished _stitch and implements polygon`
`2fc92a9`	`Fixed doctests to use polygon`
`d88ac28`	`All tests passed!`

fchapoton commented 3 years ago

comment:16

failing doctest, and pyflakes plugin not green

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

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

`bfdcea0`	`Merge branch 'develop' into spider`
`1cfa02a`	`Completed ccoverage and fixed pyflakes`

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

Changed commit from d88ac28 to 1cfa02a

BruceWestbury commented 3 years ago

comment:18

Replying to @fchapoton:

failing doctest, and pyflakes plugin not green

The pyflakes is now green.

All tests passed! when I ran them locally. The bot says four tests failed but they seem to be elsewhere.

fchapoton commented 3 years ago

comment:19

sorry, but I am not going to make a full review

arxiv links could use the arxiv role :arxiv:`....`

BruceWestbury commented 3 years ago

comment:20

Replying to @fchapoton:

sorry, but I am not going to make a full review

I am not expecting a positive review as it does not yet do the calculation I want it for. I paused here because i) I needed a break and ii) Travis said it was better to break up a large project to make life easier for the reviewer.

I am now ready to continue with this project.

tscrim commented 3 years ago

comment:21

Some quick comments:

IMO all of the Python3 type annotation adds clutter. I would recommend using it more sparingly.
Why are you providing a __str__? I don't see why this is necessary.
while(flag): -> while flag:
parent should be the first argument to any Element class. This is something we want across all of Sage. You then shouldn't need to implement an _element_constructor_.
Use .. TODO::.
Put UniqueRepresentation first in the MRO.
I don't see the reason why you need the baxter parameter in from_permutation.
Start your doc on the line after the """. This is the convention we use in Sage.
You have some inconsistent indentation.
set(c.keys()) -> set(c)
Your doctests in normalize are incorrectly formatted.
Add the file to the documentation.
Check the formatting of the module-level documentation.
You should not import everything from the module. There is a major conflict with Vector, and only SphericalWeb should be imported as that is the only thing directly used by the user.

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

Changed commit from 1cfa02a to abdbf06

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

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

`26a74dd`	`Preliminary corrections`
`abdbf06`	Removed `_element_constructor_` so SphericalSpider is no longer callable.

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

Changed commit from abdbf06 to 8d8de0a

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

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

8d8de0a Added file to module_list.rst and edited entry in combinat/all.py

BruceWestbury commented 3 years ago

comment:24

Thank you Travis. I think your comments have been more or less dealt with.

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

Changed commit from 8d8de0a to 31122ad

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

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

`5364d6f`	`Started work on Boundary and Boundaries classes`
`e59e87d`	`Added Parent class Boundaries and Element class Boundary`
`f1ce071`	`Removed Vector, Boundary, Boundaries`
`eaf7a86`	`Removed Boundary and started work on doctests`
`64b81ae`	`Worked on doctests`
`319c26b`	`More work on doctests`
`1bc8803`	`Added preprocessing to SphericalSpider`
`c989010`	`Changed Strand from NamedTuple to namedtuple`
`31122ad`	`All tests passed!`

BruceWestbury commented 3 years ago

comment:26

I have now implemented SphericalSpider as a Parent parametrised by the boundary values.

There are two issues that seem to me to be "work arounds". One is that I have both Strand and halfedge. I can almost do away with halfedge and work with "is" and "equal by value". My best guess at the problem I encountered is that dictionaries don't work with "is". I have not tried overwriting hash. The other is that I have included four methods of SphericalSpider as static methods (namely, vertex, loop, empty, polygon). This seems clumsy.

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

Changed commit from 31122ad to cb66fa7

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

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

`ebbc703`	`Removed halfedge and Strand from all.py`
`7a0b180`	`Added the static method from_Guass_code`
`61d9c5b`	`Minor changes`
`cb66fa7`	`Implemented linear extension of rotate`

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

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

`c7881d8`	`Started implementing WebAlgebra`
`0c4db0d`	`Added replace_linear (without tests)`
`a0b91e1`	`Added more methods for skein relations (without tests)`
`da81cd7`	`Added methods one_basis, product_on_basis, U to WebAlgebra`
`4d4c111`	`Added homomorphism from braid group to Temperley-Lieb algebra`
`5a2ef54`	`Added from_diagram`
`bf64788`	`Debugged from_diagram`

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

Changed commit from cb66fa7 to bf64788

BruceWestbury commented 3 years ago

comment:29

I have been making progress with adding functionality. In particular, you can almost calculate the Jones polynomial. However it seems to me that the code is getting unwieldy and I could do with some advice on making this more organised and adding more structure. For example, the next stage is to work with quotients given by skein relations.

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

Changed commit from bf64788 to eed5b86

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

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

`7739575`	`Added FreeLinearSpider`
`41a2bdb`	`Worked on doctests`
`c3ab274`	`Started adding skein relations for rank two Lie algebras`
`031c5e6`	`A2 relations completed`
`eed5b86`	`B2 and G2 skein relations added`

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

Changed commit from eed5b86 to 5934f86

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

Branch pushed to git repo; I updated commit sha1. Last 10 new commits:

`3c5353a`	`Improved doctests and check for crossings`
`f666282`	`Corrected search to check embedding preserves data on halfedges`
`cedb49e`	`Added doctest for apply_linear`
`a2c8056`	`Added doctest for apply_rule`
`77515f1`	`Corrected canonical()`
`28f415b`	`Got doctest for simplify to work`
`34e0bf6`	`Improved doctets`
`2d82e0c`	`Revise normalize`
`f019cf9`	`Simplified and corrected normalise`
`5934f86`	`Simplfy passes doctest`

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

Changed commit from 5934f86 to f09f0c2

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

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

`5c6dedf`	`Thrashing around`
`a79a13d`	`Removed the class FreeSphericalSpider`
`1f1d4d5`	`Finished from_gauss_code`
`dc31cb0`	`Made cp and b immutable`
`b312940`	`Made e immutable`
`089f14f`	`Finished making cp and e immutable`
`f09f0c2`	`More doctests (simplify)`

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

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

f3d2b4a Passes pycodestyle

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 3 years ago

Changed commit from f09f0c2 to f3d2b4a

sagemath / sage

Webs and spiders #31209