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merged 7 commits into from
Jun 1, 2025

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soehms
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@soehms soehms commented May 22, 2025

In #33965 and #33969, I introduced two methods named khovanov_polynomial, one for the Link class and the other for KnotInfo. Unfortunately, I misused the ring argument in both. IIRC, the analogy to the other polynomial link invariants led me to use the base_ring argument to specify the base ring of the polynomial. However, this was not a good idea, since the Khovanov polynomial, as a Poincaré polynomial of homology, always has integer coefficients. On the other hand, a ring argument is needed to specify the underlying homology.

This will be corrected in this PR. In particular, I will deprecate the existing base_ring argument and introduce a new ring argument, which corresponds to the ring argument of the khovanov_homology method of the Link class. I take the occasion to remove the deprecation warning for the argument KhoHo released in March 2024.

Furthermore, I introduce a new argument torsion to display the torsion parts of the integral homology according to the KnotInfo convention.

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tscrim commented May 22, 2025

Let me know when this is ready and I will review it.

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soehms commented May 23, 2025

Let me know when this is ready and I will review it.

Many thanks, Travis! There are still a lot of failing CI runs, but as far as I see they are all unrelated, for example in test-long a-f it is due to a missing shared library for Singular:

#31 4376.4   [sagemath_doc_html-none]   [spkg-install]   File "/sage/src/sage/schemes/curves/projective_curve.py", line 144, in <module>
#31 4376.4   [sagemath_doc_html-none]   [spkg-install]     from sage.libs.singular.function import singular_function, lib as singular_lib, get_printlevel, set_printlevel
#31 4376.4   [sagemath_doc_html-none]   [spkg-install]   File "sage/libs/singular/function.pyx", line 98, in init sage.libs.singular.function
#31 4376.4   [sagemath_doc_html-none]   [spkg-install] ImportError: libSingular-4.4.0.so: cannot open shared object file: No such file or directory
#31 4376.4   [sagemath_doc_html-none]   [spkg-install] Error: 'sage --docbuild --all-documents' failed
#31 4376.4   [sagemath_doc_html-none]   [spkg-install] make[5]: *** [Makefile:41: doc-inventory-reference] Error 1
#31 4376.4   [sagemath_doc_html-none]   [spkg-install] make[5]: Target 'doc-html' not remade because of errors.

So I set it ready for review!

@soehms soehms marked this pull request as ready for review May 23, 2025 07:56
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tscrim commented May 23, 2025

Such CI failures are happening across many PRs right now. Anyways, I will try to take a look at it next week.

soehms and others added 5 commits May 26, 2025 08:03
Co-authored-by: Travis Scrimshaw <clfrngrown@aol.com>
Co-authored-by: Travis Scrimshaw <clfrngrown@aol.com>
Co-authored-by: Travis Scrimshaw <clfrngrown@aol.com>
Co-authored-by: Travis Scrimshaw <clfrngrown@aol.com>
Co-authored-by: Travis Scrimshaw <clfrngrown@aol.com>
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Thank you. LGTM now.

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soehms commented May 26, 2025

Thank you. LGTM now.

Thank you!

vbraun pushed a commit to vbraun/sage that referenced this pull request May 28, 2025
sagemathgh-40149: Revision of the Khovanov polynomial
    
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description below. -->
<!-- ^ For example, instead of "Fixes sagemath#12345" use "Introduce new method
to calculate 1 + 2". -->
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example, "Fixes sagemath#12345". -->

In sagemath#33965 and sagemath#33969, I introduced two methods named
`khovanov_polynomial`, one for the `Link` class and the other for
`KnotInfo`. Unfortunately, I misused the ring argument in both. IIRC,
the analogy to the other polynomial link invariants led me to use the
`base_ring` argument to specify the base ring of the polynomial.
However, this was not a good idea, since the Khovanov polynomial, as a
Poincaré polynomial of homology, always has integer coefficients. On the
other hand, a ring argument is needed to specify the underlying
homology.

This will be corrected in this PR. In particular, I will deprecate the
existing `base_ring` argument and introduce a new `ring` argument, which
corresponds to the `ring` argument of the `khovanov_homology` method of
the `Link` class. I take the occasion to remove the deprecation warning
for the argument `KhoHo` released in March 2024.

Furthermore, I introduce a new argument `torsion` to display the torsion
parts of the integral homology according to the [KnotInfo convention](ht
tps://knotinfo.math.indiana.edu/descriptions/khovanov_odd_integral_polyn
omial.html).


### 📝 Checklist

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- [x] The description explains in detail what this PR is about.
- [x] I have linked a relevant issue or discussion.
- [x] I have created tests covering the changes.
- [ ] I have updated the documentation and checked the documentation
preview.

### ⌛ Dependencies

<!-- List all open PRs that this PR logically depends on. For example,
-->
<!-- - sagemath#12345: short description why this is a dependency -->
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URL: sagemath#40149
Reported by: Sebastian Oehms
Reviewer(s): Travis Scrimshaw
@vbraun vbraun merged commit 173c0e5 into sagemath:develop Jun 1, 2025
14 of 22 checks passed
@soehms soehms deleted the khovanov_ring_arg_revision branch June 1, 2025 22:19
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3 participants