Changing the knot theory PD-code convention

[soehms]

📚 Description

According to a discussion following this comment of last February in #17030 this PR implements the transition of the PD-code convention from clockwise to anti-clockwise.

📝 Checklist

• The title is concise, informative, and self-explanatory.
• The description explains in detail what this PR is about.
• I have linked a relevant issue or discussion.
• I have created tests covering the changes.
• I have updated the documentation accordingly.

⌛ Dependencies

[github-actions]

Documentation preview for this PR is ready! 🎉
Built with commit: ff44af3

[tscrim]

@miguelmarco I am assuming from the positive review you also meant to approve this.

Also LGTM.

[NathanDunfield]

What version of Sage is this likely to appear in? We're about to do a release of SnapPy and want correctly convert from Sage's Link to SnapPy's depending on the Sage version.

[tscrim]

@NathanDunfield It almost certainly should get into 10.1, but I couldn't say which beta version (although there is a reasonable possibility it is the next one).

[soehms]

@miguelmarco I am assuming from the positive review you also meant to approve this.

Also LGTM.

Many thanks to you both!

[soehms]

@NathanDunfield It almost certainly should get into 10.1, but I couldn't say which beta version (although there is a reasonable possibility it is the next one).

I was hoping to do it for version 10.0, but unfortunately too much was preventing me from achieving that goal.

[NathanDunfield]

@soehms @tscrim: Thanks for the clarification. I have future-proofed SnapPy for this change in 3-manifolds/Spherogram@d0ce3de3253

[soehms]

@soehms @tscrim: Thanks for the clarification. I have future-proofed SnapPy for this change in 3-manifolds/Spherogram@d0ce3de3253

Great! Do you already know when it will be released? I think we should upgrade the SPKG afterwards to the new version, as well.

[NathanDunfield]

@soehms @tscrim: Thanks for the clarification. I have future-proofed SnapPy for this change in 3-manifolds/Spherogram@d0ce3de3253
Great! Do you already know when it will be released? I think we should upgrade the SPKG afterwards to the new version, as well.

SnapPy 3.1 with Spherogram 2.2 which supports this PD change in Sage was released yesterday on PyPI and Github.

[soehms]

@soehms @tscrim: Thanks for the clarification. I have future-proofed SnapPy for this change in 3-manifolds/Spherogram@d0ce3de3253
Great! Do you already know when it will be released? I think we should upgrade the SPKG afterwards to the new version, as well.

SnapPy 3.1 with Spherogram 2.2 which supports this PD change in Sage was released yesterday on PyPI and Github.

In fact, this was a last minute opportunity. Thanks very much!

[NathanDunfield]

SnapPy 3.1 with Spherogram 2.2 which supports this PD change in Sage was released yesterday on PyPI and Github.

In fact, this was a last minute opportunity. Thanks very much!

You're very welcome.

[vbraun]

Merge conflict

[vbraun]

Sorry, ticket number off by one ;)

[soehms]

@soehms @tscrim: Thanks for the clarification. I have future-proofed SnapPy for this change in 3-manifolds/Spherogram@d0ce3de3253
Great! Do you already know when it will be released? I think we should upgrade the SPKG afterwards to the new version, as well.

SnapPy 3.1 with Spherogram 2.2 which supports this PD change in Sage was released yesterday on PyPI and Github.

@NathanDunfield, it seems that this commit did not find its way into the Spherogram 2.2 release:

┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 10.1.beta3, Release Date: 2023-06-11              │
│ Using Python 3.8.10. Type "help()" for help.                       │
└────────────────────────────────────────────────────────────────────┘
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Warning: this is a prerelease version, and it may be unstable.     ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛

sage: import spherogram
sage: spherogram.version()
'2.2'
sage: L = spherogram.Link('K10n11')
sage: L.PD_code()
[(2, 0, 3, 19),
 (0, 6, 1, 5),
...
 (18, 14, 19, 13)]
sage: L.sage_link().pd_code()
[[3, 20, 4, 1],
 [1, 6, 2, 7],
...
 [19, 14, 20, 15]]
sage:
sage: spherogram.Link.sage_link??
Signature: spherogram.Link.sage_link(self)
Docstring:
   Convert to a SageMath Knot or Link:

      sage: L = Link('K10n11')   # Spherogram link
      sage: K = L.sage_link(); K
      Knot represented by 10 crossings
...
        if SageKnot is None:
            raise ValueError('Your SageMath does not seem to have a native link type')
        sage_type = SageKnot if len(self.link_components) == 1 else SageLink
        # Sage's PD_code lists strands *clockwise* not our *anticlockwise*.
        code = [[x[0], x[3], x[2], x[1]] for x in self.PD_code(min_strand_index=1)]
        return sage_type(code)
File:      ~/devel/sage/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/spherogram/links/invariants.py
Type:      function

[NathanDunfield]

Sorry, it seems I only fixed one of the directions (sage -> spherogram) and not the other (spherogram -> sage). I believe I have fixed sage_link here. Could you please test it out before I release it as 2.2.1?

[soehms]

Sorry, it seems I only fixed one of the directions (sage -> spherogram) and not the other (spherogram -> sage).

No problem! Indeed, your new code was not contained in the former commit.

I believe I have fixed sage_link here. Could you please test it out before I release it as 2.2.1?

It works! Many Thanks!

[NathanDunfield]

@soehms As a final check, could you do the following with Sage 10.1.beta3:

sage -python -m spherogram.test

You should see:

[...]
All doctests:
   0 failures out of 458 tests.
[...]
OK

Thanks.

[soehms]

@soehms As a final check, could you do the following with Sage 10.1.beta3:

All tests passed, too!

[NathanDunfield]

Thanks, I've released Spherogram 2.2.1 on PyPI.

[soehms]

Thanks, I've released Spherogram 2.2.1 on PyPI.

Thanks! Now, some optional doctests concerning SnapPy needs work on Sage side. I will open a corresponding follow up PR soon.

[soehms]

I will open a corresponding follow up PR soon.

This is #35755, now.