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Improve SnapPy integration with Sage knots and links#40105

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soehms:integration_snappy_knots
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Improve SnapPy integration with Sage knots and links#40105
soehms wants to merge 34 commits intosagemath:developfrom
soehms:integration_snappy_knots

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@soehms soehms commented May 14, 2025 •
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Currently, the usage of SnapPy in connection with Sage's knots and links is not really supported, although it can be installed as an optional package. The aim of this PR is to start with an improvement of the integration. In detail the following is done:

  1. add SnapPy as a feature
  2. add direct access to the SnapPy instance of a link by a new method snappy_link
  3. add an alternative implementation to some Sage methods, for example for jones_polynomial
  4. add functionality currently missing in Sage but available in SnapPy, for example verify_hyperbolicity, simplify, deconnect_sum
  5. add new functionality with the help of SnapPy functionality, for example symmetry_type

📝 Checklist

  • The title is concise and informative.
  • 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 and checked the documentation preview.

⌛ Dependencies

@soehms soehms added this to the sage-10.7 milestone May 14, 2025
@tscrim tscrim self-requested a review May 19, 2025 04:11
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soehms commented May 23, 2025

I ran a modified CI-Linux-incremental workflow (the modification just allowed me to set the optional packages to test manually). In these runs all test (exept for an unrelated test in src/sage/rings/complex_double.pyx in tow cases) passed (even for Fedora 41 which failed by a system problem: The hosted runner lost communication with the server). Here some examples:

Ubuntu focal

2025-05-23T13:09:24.5087361Z ### make ptest-nodoc: Running ./sage -t --logfile=logs/test.log -p --optional=sage,optional,!sagemath_doc_html,!sagemath_doc_pdf --all
2025-05-23T13:09:24.5088139Z Running doctests with ID 2025-05-23-12-22-31-5e18a0b2.
2025-05-23T13:09:24.5088937Z Running with SAGE_LOCAL='/sage/local' and SAGE_VENV='/sage/local/var/lib/sage/venv-python3.12.5'
2025-05-23T13:09:24.5089775Z Using --optional=!sagemath_doc_html,!sagemath_doc_pdf,database_knotinfo,debian,pip,sage,sage_spkg
2025-05-23T13:09:24.5096549Z Features to be detected: 4ti2,SAGE_SRC,benzene,bliss,buckygen,conway_polynomials,coxeter3,csdp,cvxopt,cvxopt,database_cremona_ellcurve,database_cremona_mini_ellcurve,database_cubic_hecke,database_ellcurves,database_graphs,database_jones_numfield,database_knotinfo,dot2tex,dvipng,ecm,fpylll,fricas,gap_package_atlasrep,gap_package_design,gap_package_grape,gap_package_guava,gap_package_hap,gap_package_polenta,gap_package_polycyclic,gap_package_qpa,gap_package_quagroup,gfan,giac,glucose,graphviz,imagemagick,info,ipython,jmol,jupymake,jupyter_sphinx,kenzo,kissat,latte_int,lrcalc_python,lrslib,mathics,matroid_database,mcqd,meataxe,meson_editable,mpmath,msolve,nauty,networkx,numpy,palp,pandoc,pdf2svg,pdftocairo,pexpect,phitigra,pillow,plantri,polytopes_db,polytopes_db_4d,pplpy,primecountpy,ptyprocess,pycosat,pycryptosat,pynormaliz,pyparsing,python_igraph,requests,rpy2,rubiks,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.groups,sage.libs.braiding,sage.libs.ecl,sage.libs.flint,sage.libs.gap,sage.libs.giac,sage.libs.homfly,sage.libs.linbox,sage.libs.m4ri,sage.libs.ntl,sage.libs.pari,sage.libs.singular,sage.misc.cython,sage.modular,sage.modules,sage.numerical.mip,sage.plot,sage.rings.complex_double,sage.rings.finite_rings,sage.rings.function_field,sage.rings.number_field,sage.rings.padics,sage.rings.polynomial.pbori,sage.rings.real_double,sage.rings.real_mpfr,sage.sat,sage.schemes,sage.symbolic,sage_numerical_backends_coin,scipy,singular,sirocco,sloane_database,snappy,sphinx,symengine_py,sympy,tdlib,threejs,topcom
2025-05-23T13:09:24.5102784Z Doctesting entire Sage library.
2025-05-23T13:09:24.5103285Z Doctesting all documentation sources.
2025-05-23T13:09:24.5104197Z Sorting sources by runtime so that slower doctests are run first....
2025-05-23T13:09:24.5104737Z Doctesting 4705 files using 5 threads.
2025-05-23T13:09:24.5105940Z sage -t --warn-long 5.0 --random-seed=277545619004009458150098052305695272649 src/sage/databases/cubic_hecke_db.py
2025-05-23T13:09:24.5106568Z     [178 tests, 2.61s wall]
2025-05-23T13:09:24.5107320Z sage -t --warn-long 5.0 --random-seed=277545619004009458150098052305695272649 src/sage/knots/free_knotinfo_monoid.py
2025-05-23T13:09:24.5107890Z     [67 tests, 2.84s wall]
2025-05-23T13:09:24.5108612Z sage -t --warn-long 5.0 --random-seed=277545619004009458150098052305695272649 src/sage/knots/knot.py
2025-05-23T13:09:24.5109122Z     [104 tests, 2.97s wall]
2025-05-23T13:09:24.5109836Z sage -t --warn-long 5.0 --random-seed=277545619004009458150098052305695272649 src/sage/knots/knotinfo.py
2025-05-23T13:09:24.5110355Z     [379 tests, 6.61s wall]
2025-05-23T13:09:24.5111084Z sage -t --warn-long 5.0 --random-seed=277545619004009458150098052305695272649 src/sage/features/__init__.py
2025-05-23T13:09:24.5111843Z     [142 tests, 4.21s wall]
...
2025-05-23T13:09:24.5126149Z sage -t --warn-long 5.0 --random-seed=277545619004009458150098052305695272649 src/sage/features/snappy.py
2025-05-23T13:09:24.5126675Z     [4 tests, 0.01s wall]
...
2025-05-23T13:09:24.5250491Z sage -t --warn-long 5.0 --random-seed=277545619004009458150098052305695272649 src/sage/knots/link.py
2025-05-23T13:09:24.5251157Z     [682 tests, 22.83s wall]
...
2025-05-23T13:03:20.0894230Z     [18 tests, 3.68s wall]
2025-05-23T13:03:20.0895255Z ----------------------------------------------------------------------
2025-05-23T13:03:20.0899285Z sage -t --warn-long 5.0 --random-seed=277545619004009458150098052305695272649 src/sage/rings/complex_double.pyx  # 1 doctest failed
2025-05-23T13:03:20.0900139Z ----------------------------------------------------------------------
2025-05-23T13:03:20.0900571Z Total time for all tests: 2446.3 seconds
2025-05-23T13:03:20.0900910Z     cpu time: 8413.2 seconds
2025-05-23T13:03:20.0901259Z     cumulative wall time: 10308.3 seconds
2025-05-23T13:03:20.0907404Z Features detected for doctesting: bliss,conway_polynomials,coxeter3,cvxopt,database_cremona_mini_ellcurve,database_ellcurves,database_graphs,fpylll,gap_package_polycyclic,gfan,info,jupyter_sphinx,lrcalc_python,mcqd,meataxe,mpmath,nauty,networkx,numpy,palp,pexpect,pillow,polytopes_db,pplpy,primecountpy,ptyprocess,pyparsing,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.groups,sage.libs.braiding,sage.libs.ecl,sage.libs.flint,sage.libs.gap,sage.libs.homfly,sage.libs.linbox,sage.libs.m4ri,sage.libs.ntl,sage.libs.pari,sage.libs.singular,sage.misc.cython,sage.modular,sage.modules,sage.numerical.mip,sage.plot,sage.rings.complex_double,sage.rings.finite_rings,sage.rings.function_field,sage.rings.number_field,sage.rings.padics,sage.rings.polynomial.pbori,sage.rings.real_double,sage.rings.real_mpfr,sage.schemes,sage.symbolic,scipy,singular,sirocco,snappy,sphinx,sympy,tdlib,threejs
2025-05-23T13:03:20.9505121Z make[2]: warning: -j9 forced in submake: resetting jobserver mode.

Fedora 41:

sage -t --warn-long 5.0 --random-seed=93077958085837172847315309431099481326 src/sage_setup/util.py
    [6 tests, 0.01s wall]
sage -t --warn-long 5.0 --random-seed=93077958085837172847315309431099481326 src/sage_docbuild/utils.py
    [12 tests, 3.15s wall]
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 2002.9 seconds
    cpu time: 6621.8 seconds
    cumulative wall time: 8048.2 seconds
Features detected for doctesting: bliss,conway_polynomials,coxeter3,cvxopt,database_cremona_mini_ellcurve,database_ellcurves,database_graphs,fpylll,gap_package_atlasrep,gap_package_design,gap_package_grape,gap_package_hap,gap_package_polenta,gap_package_polycyclic,gfan,graphviz,imagemagick,info,jupyter_sphinx,lrcalc_python,mcqd,meataxe,mpmath,nauty,networkx,numpy,palp,pexpect,pillow,plantri,polytopes_db,pplpy,primecountpy,ptyprocess,pyparsing,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.groups,sage.libs.braiding,sage.libs.ecl,sage.libs.flint,sage.libs.gap,sage.libs.homfly,sage.libs.linbox,sage.libs.m4ri,sage.libs.ntl,sage.libs.pari,sage.libs.singular,sage.misc.cython,sage.modular,sage.modules,sage.numerical.mip,sage.plot,sage.rings.complex_double,sage.rings.finite_rings,sage.rings.function_field,sage.rings.number_field,sage.rings.padics,sage.rings.polynomial.pbori,sage.rings.real_double,sage.rings.real_mpfr,sage.schemes,sage.symbolic,scipy,singular,sirocco,snappy,sphinx,sympy,tdlib,threejs,topcom

Note that snappy is listed under Features detected for doctesting!

@soehms soehms marked this pull request as ready for review May 23, 2025 14:50
@soehms soehms marked this pull request as draft May 26, 2025 06:29
@soehms soehms force-pushed the integration_snappy_knots branch from e9104e9 to ab9b718 Compare May 26, 2025 08:36
@soehms soehms marked this pull request as ready for review May 26, 2025 08:38
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github-actions bot commented Jun 2, 2025 •
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Documentation preview for this PR (built with commit dc1134d; changes) is ready! 🎉
This preview will update shortly after each push to this PR.

@soehms soehms marked this pull request as draft July 4, 2025 08:42
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soehms commented Jul 4, 2025

I convert this back to a draft in order to let the integration use the Sage interface framework in a similar way as I do for Regina in #40370.

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cxzhong commented Nov 26, 2025

Do you also work on this PR or this is ready for review? Thank you.

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soehms commented Nov 28, 2025

Do you also work on this PR or this is ready for review? Thank you.

Yes, according to my comment from July (#40105 (comment)), I'm still working on it. Unfortunately, due to a lack of time, it's taking longer than expected!

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arodau commented Jan 6, 2026

Hello @soehms,
I just found out that this project exists. I have been working independently on modifications of the Link library in Sage that might in part interfere with your PRs.
My own goal is to implement the oriented DT code as a valid input for links, with associated conversion methods to other input codes (Gauss, PD, etc) and several other methods related to the fundamental group, mostly.
The oriented DT code is already supported in SnapPy, so this could also be used as a way to "port" a Link instance back and forth between Sage and SnapPy.
I think I can merge my modifications with your latest PR in this draft but I want to know if you're OK with this since DT code implementation isn't strictly part of this draft's goals and you might be already working on further changes.

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soehms commented Jan 7, 2026

Hello @soehms, I just found out that this project exists. I have been working independently on modifications of the Link library in Sage that might in part interfere with your PRs. My own goal is to implement the oriented DT code as a valid input for links, with associated conversion methods to other input codes (Gauss, PD, etc) and several other methods related to the fundamental group, mostly. The oriented DT code is already supported in SnapPy, so this could also be used as a way to "port" a Link instance back and forth between Sage and SnapPy. I think I can merge my modifications with your latest PR in this draft but I want to know if you're OK with this since DT code implementation isn't strictly part of this draft's goals and you might be already working on further changes.

The pull request is currently marked as draft because I believe SnapPy should be accessible through the Sage Interface framework, similar to how I implemented access to Regina in issue #40370. I've already started working on this (by refactoring src/sage/interfaces/regina.py), but unfortunately, the project is stalled due to lack of time.

My suggestion: Create your pull request relative to the develop branch. If you find parts of my branch useful, simply add that code to yours. I'll then review it. As soon as I can work on the interface project again, I'll adjust the SnapPy access accordingly.

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