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gh-35063: Add notes about recent changes on KnotInfo <!-- ^^^^^ Please provide a concise, informative and self-explanatory title. Don't put issue numbers in there, do this in the PR body below. For example, instead of "Fixes #1234" use "Introduce new method to calculate 1+1" --> ### 📚 Description <!-- Describe your changes here in detail --> <!-- Why is this change required? What problem does it solve? --> <!-- If it resolves an open issue, please link to the issue here. For example "Closes #1337" --> This is a follow up of #33969, which used the Khovanov polynomial KnotInfo data in a new conversion method. Unfortunately, this data has since been removed from the website (but not from the database). This PR merely adds appropriate notes to the documentation of the KnotInfo interface module. Since the missing data may cause confusion, it would be great if the notes will be included in release 9.8. ### 📝 Checklist <!-- Put an `x` in all the boxes that apply. --> <!-- If your change requires a documentation PR, please link it appropriately --> <!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! --> - [x] I have made sure that the title is self-explanatory and the description concisely explains the PR. - [ ] I have linked an issue or discussion. - [ ] I have created tests covering the changes. - [x] I have updated the documentation accordingly. ### ⌛ Dependencies <!-- List all open pull requests that this PR logically depends on --> <!-- - #xyz: short description why this is a dependency - #abc: ... --> URL: #35063 Reported by: Sebastian Oehms Reviewer(s): Matthias Köppe, Sebastian Oehms
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src/sage/knots/knotinfo.py

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@@ -48,6 +48,12 @@
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the according documentation of :meth:`KnotInfoBase.homfly_polynomial`,
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:meth:`KnotInfoBase.jones_polynomial` and :meth:`KnotInfoBase.alexander_polynomial`.
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Furthermore, note that not all columns available in the database are visible on the web
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pages (see also the related note under :meth:`KnotInfoBase.khovanov_polynomial`).
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It is planned to remove non-visible columns from the database in the future (see
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the `Python Wrapper <https://github.com/soehms/database_knotinfo#readme>`__ for
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updated information).
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EXAMPLES::
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sage: from sage.knots.knotinfo import KnotInfo
@@ -1714,9 +1720,23 @@ def khovanov_polynomial(self, var1='q', var2='t', base_ring=ZZ, original=False):
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.. NOTE ::
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The Khovanov polynomial given in KnotInfo corresponds to the mirror
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image of the given knot for a `list of 140 exceptions
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<https://raw.githubusercontent.com/soehms/database_knotinfo/main/hints/list_of_mirrored_khovanov_polynonmial.txt>`__.
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The data used here were calculated with the program
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`KhoHo <https://github.com/AShumakovitch/KhoHo>`__. They are no longer
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visible on the website as of October 30, 2022. Instead, data
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computed with `KnotJob <https://www.maths.dur.ac.uk/users/dirk.schuetz/knotjob.html>`__
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are now displayed. The latter program is more accurate in terms of
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orientation and reflection as it is based on ``PD`` code.
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Even if they are not visible on the website, the data produced by
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``KhoHo`` are still available in the database. But maybe this will be
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discontinued (check out the `Python wrapper <https://github.com/soehms/database_knotinfo#readme>`__ for updated information).
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This interface will be adapted to the changes in an upcoming
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release.
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Since the results of ``KhoHo`` were computed using the ``DT`` notation,
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the Khovanov polynomial returned by this method belongs to the
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mirror image of the given knot for a `list of 140 exceptions
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<https://raw.githubusercontent.com/soehms/database_knotinfo/ main /hints/list_of_mirrored_khovanov_polynonmial.txt>`__.
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EXAMPLES::
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