snappy 3.0.3__cp38-cp38-macosx_11_0_arm64.whl → 3.2__cp38-cp38-macosx_11_0_arm64.whl

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  1. snappy/CyOpenGL.cpython-38-darwin.so +0 -0
  2. snappy/SnapPy.cpython-38-darwin.so +0 -0
  3. snappy/SnapPyHP.cpython-38-darwin.so +0 -0
  4. snappy/__init__.py +373 -426
  5. snappy/app.py +240 -75
  6. snappy/app_menus.py +93 -78
  7. snappy/browser.py +87 -63
  8. snappy/cache.py +5 -8
  9. snappy/canonical.py +249 -0
  10. snappy/{verify/cusp_shapes.py → cusps/__init__.py} +11 -19
  11. snappy/cusps/cusp_area_matrix.py +101 -0
  12. snappy/{verify/cusp_areas.py → cusps/cusp_areas_from_matrix.py} +39 -54
  13. snappy/cusps/maximal_cusp_area_matrix.py +136 -0
  14. snappy/cusps/test.py +21 -0
  15. snappy/cusps/trig_cusp_area_matrix.py +63 -0
  16. snappy/database.py +40 -31
  17. snappy/db_utilities.py +13 -14
  18. snappy/decorated_isosig.py +377 -133
  19. snappy/dev/extended_ptolemy/complexVolumesClosed.py +42 -9
  20. snappy/dev/extended_ptolemy/extended.py +32 -25
  21. snappy/dev/extended_ptolemy/giac_rur.py +23 -8
  22. snappy/dev/extended_ptolemy/phc_wrapper.py +10 -10
  23. snappy/dev/vericlosed/computeApproxHyperbolicStructureOrb.py +2 -1
  24. snappy/dev/vericlosed/gimbalLoopFinder.py +5 -5
  25. snappy/dev/vericlosed/hyperbolicStructure.py +3 -3
  26. snappy/dev/vericlosed/oneVertexTruncatedComplex.py +2 -2
  27. snappy/dev/vericlosed/truncatedComplex.py +3 -2
  28. snappy/dev/vericlosed/verifyHyperbolicStructureEngine.py +4 -3
  29. snappy/doc/_images/geodesics.jpg +0 -0
  30. snappy/doc/_images/m004_paper_plane_on_systole.jpg +0 -0
  31. snappy/doc/_images/m125_paper_plane.jpg +0 -0
  32. snappy/doc/_images/o9_00000_systole_paper_plane.jpg +0 -0
  33. snappy/doc/_images/o9_00000_systole_paper_plane_closer.jpg +0 -0
  34. snappy/doc/_sources/additional_classes.rst.txt +1 -0
  35. snappy/doc/_sources/credits.rst.txt +6 -1
  36. snappy/doc/_sources/development.rst.txt +69 -50
  37. snappy/doc/_sources/index.rst.txt +101 -66
  38. snappy/doc/_sources/installing.rst.txt +148 -165
  39. snappy/doc/_sources/news.rst.txt +136 -32
  40. snappy/doc/_sources/ptolemy.rst.txt +1 -1
  41. snappy/doc/_sources/ptolemy_examples1.rst.txt +9 -8
  42. snappy/doc/_sources/ptolemy_examples2.rst.txt +3 -3
  43. snappy/doc/_sources/ptolemy_examples3.rst.txt +14 -14
  44. snappy/doc/_sources/ptolemy_prelim.rst.txt +1 -1
  45. snappy/doc/_sources/snap.rst.txt +2 -2
  46. snappy/doc/_sources/snappy.rst.txt +1 -1
  47. snappy/doc/_sources/triangulation.rst.txt +3 -2
  48. snappy/doc/_sources/verify.rst.txt +89 -29
  49. snappy/doc/_sources/verify_internals.rst.txt +5 -16
  50. snappy/doc/_static/SnapPy-horizontal-128.png +0 -0
  51. snappy/doc/_static/SnapPy.ico +0 -0
  52. snappy/doc/_static/_sphinx_javascript_frameworks_compat.js +123 -0
  53. snappy/doc/_static/basic.css +47 -27
  54. snappy/doc/_static/css/badge_only.css +1 -0
  55. snappy/doc/_static/css/fonts/Roboto-Slab-Bold.woff +0 -0
  56. snappy/doc/_static/css/fonts/Roboto-Slab-Bold.woff2 +0 -0
  57. snappy/doc/_static/css/fonts/Roboto-Slab-Regular.woff +0 -0
  58. snappy/doc/_static/css/fonts/Roboto-Slab-Regular.woff2 +0 -0
  59. snappy/doc/_static/css/fonts/fontawesome-webfont.eot +0 -0
  60. snappy/doc/_static/css/fonts/fontawesome-webfont.svg +2671 -0
  61. snappy/doc/_static/css/fonts/fontawesome-webfont.ttf +0 -0
  62. snappy/doc/_static/css/fonts/fontawesome-webfont.woff +0 -0
  63. snappy/doc/_static/css/fonts/fontawesome-webfont.woff2 +0 -0
  64. snappy/doc/_static/css/fonts/lato-bold-italic.woff +0 -0
  65. snappy/doc/_static/css/fonts/lato-bold-italic.woff2 +0 -0
  66. snappy/doc/_static/css/fonts/lato-bold.woff +0 -0
  67. snappy/doc/_static/css/fonts/lato-bold.woff2 +0 -0
  68. snappy/doc/_static/css/fonts/lato-normal-italic.woff +0 -0
  69. snappy/doc/_static/css/fonts/lato-normal-italic.woff2 +0 -0
  70. snappy/doc/_static/css/fonts/lato-normal.woff +0 -0
  71. snappy/doc/_static/css/fonts/lato-normal.woff2 +0 -0
  72. snappy/doc/_static/css/theme.css +4 -0
  73. snappy/doc/_static/doctools.js +107 -274
  74. snappy/doc/_static/documentation_options.js +6 -5
  75. snappy/doc/_static/fonts/Lato/lato-bold.eot +0 -0
  76. snappy/doc/_static/fonts/Lato/lato-bold.ttf +0 -0
  77. snappy/doc/_static/fonts/Lato/lato-bold.woff +0 -0
  78. snappy/doc/_static/fonts/Lato/lato-bold.woff2 +0 -0
  79. snappy/doc/_static/fonts/Lato/lato-bolditalic.eot +0 -0
  80. snappy/doc/_static/fonts/Lato/lato-bolditalic.ttf +0 -0
  81. snappy/doc/_static/fonts/Lato/lato-bolditalic.woff +0 -0
  82. snappy/doc/_static/fonts/Lato/lato-bolditalic.woff2 +0 -0
  83. snappy/doc/_static/fonts/Lato/lato-italic.eot +0 -0
  84. snappy/doc/_static/fonts/Lato/lato-italic.ttf +0 -0
  85. snappy/doc/_static/fonts/Lato/lato-italic.woff +0 -0
  86. snappy/doc/_static/fonts/Lato/lato-italic.woff2 +0 -0
  87. snappy/doc/_static/fonts/Lato/lato-regular.eot +0 -0
  88. snappy/doc/_static/fonts/Lato/lato-regular.ttf +0 -0
  89. snappy/doc/_static/fonts/Lato/lato-regular.woff +0 -0
  90. snappy/doc/_static/fonts/Lato/lato-regular.woff2 +0 -0
  91. snappy/doc/_static/fonts/RobotoSlab/roboto-slab-v7-bold.eot +0 -0
  92. snappy/doc/_static/fonts/RobotoSlab/roboto-slab-v7-bold.ttf +0 -0
  93. snappy/doc/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff +0 -0
  94. snappy/doc/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff2 +0 -0
  95. snappy/doc/_static/fonts/RobotoSlab/roboto-slab-v7-regular.eot +0 -0
  96. snappy/doc/_static/fonts/RobotoSlab/roboto-slab-v7-regular.ttf +0 -0
  97. snappy/doc/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff +0 -0
  98. snappy/doc/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff2 +0 -0
  99. snappy/doc/_static/jquery.js +2 -2
  100. snappy/doc/_static/js/badge_only.js +1 -0
  101. snappy/doc/_static/js/theme.js +1 -0
  102. snappy/doc/_static/js/versions.js +228 -0
  103. snappy/doc/_static/language_data.js +3 -101
  104. snappy/doc/_static/pygments.css +1 -0
  105. snappy/doc/_static/searchtools.js +489 -398
  106. snappy/doc/_static/snappy_furo.css +33 -0
  107. snappy/doc/_static/snappy_sphinx_rtd_theme.css +42 -0
  108. snappy/doc/_static/sphinx_highlight.js +154 -0
  109. snappy/doc/additional_classes.html +688 -263
  110. snappy/doc/bugs.html +107 -94
  111. snappy/doc/censuses.html +155 -127
  112. snappy/doc/credits.html +115 -104
  113. snappy/doc/development.html +184 -146
  114. snappy/doc/genindex.html +287 -204
  115. snappy/doc/index.html +189 -150
  116. snappy/doc/installing.html +259 -266
  117. snappy/doc/manifold.html +1626 -592
  118. snappy/doc/manifoldhp.html +119 -105
  119. snappy/doc/news.html +198 -104
  120. snappy/doc/objects.inv +0 -0
  121. snappy/doc/other.html +117 -105
  122. snappy/doc/platonic_census.html +161 -114
  123. snappy/doc/plink.html +113 -105
  124. snappy/doc/ptolemy.html +131 -108
  125. snappy/doc/ptolemy_classes.html +242 -223
  126. snappy/doc/ptolemy_examples1.html +144 -130
  127. snappy/doc/ptolemy_examples2.html +141 -129
  128. snappy/doc/ptolemy_examples3.html +148 -132
  129. snappy/doc/ptolemy_examples4.html +131 -111
  130. snappy/doc/ptolemy_prelim.html +162 -138
  131. snappy/doc/py-modindex.html +104 -69
  132. snappy/doc/screenshots.html +117 -108
  133. snappy/doc/search.html +115 -84
  134. snappy/doc/searchindex.js +1 -1
  135. snappy/doc/snap.html +109 -96
  136. snappy/doc/snappy.html +134 -97
  137. snappy/doc/spherogram.html +259 -187
  138. snappy/doc/todo.html +107 -94
  139. snappy/doc/triangulation.html +1380 -111
  140. snappy/doc/tutorial.html +107 -94
  141. snappy/doc/verify.html +194 -125
  142. snappy/doc/verify_internals.html +248 -686
  143. snappy/drilling/__init__.py +456 -0
  144. snappy/drilling/barycentric.py +103 -0
  145. snappy/drilling/constants.py +5 -0
  146. snappy/drilling/crush.py +270 -0
  147. snappy/drilling/cusps.py +125 -0
  148. snappy/drilling/debug.py +242 -0
  149. snappy/drilling/epsilons.py +6 -0
  150. snappy/drilling/exceptions.py +55 -0
  151. snappy/drilling/moves.py +620 -0
  152. snappy/drilling/peripheral_curves.py +210 -0
  153. snappy/drilling/perturb.py +188 -0
  154. snappy/drilling/shorten.py +36 -0
  155. snappy/drilling/subdivide.py +274 -0
  156. snappy/drilling/test.py +23 -0
  157. snappy/drilling/test_cases.py +126 -0
  158. snappy/drilling/tracing.py +351 -0
  159. snappy/exceptions.py +23 -3
  160. snappy/export_stl.py +20 -14
  161. snappy/exterior_to_link/__init__.py +2 -0
  162. snappy/exterior_to_link/barycentric_geometry.py +463 -0
  163. snappy/exterior_to_link/exceptions.py +6 -0
  164. snappy/exterior_to_link/geodesic_map.json +14408 -0
  165. snappy/exterior_to_link/hyp_utils.py +112 -0
  166. snappy/exterior_to_link/link_projection.py +323 -0
  167. snappy/exterior_to_link/main.py +197 -0
  168. snappy/exterior_to_link/mcomplex_with_expansion.py +261 -0
  169. snappy/exterior_to_link/mcomplex_with_link.py +687 -0
  170. snappy/exterior_to_link/mcomplex_with_memory.py +162 -0
  171. snappy/exterior_to_link/pl_utils.py +491 -0
  172. snappy/exterior_to_link/put_in_S3.py +156 -0
  173. snappy/exterior_to_link/rational_linear_algebra.py +123 -0
  174. snappy/exterior_to_link/rational_linear_algebra_wrapped.py +135 -0
  175. snappy/exterior_to_link/simplify_to_base_tri.py +114 -0
  176. snappy/exterior_to_link/stored_moves.py +475 -0
  177. snappy/exterior_to_link/test.py +31 -0
  178. snappy/geometric_structure/__init__.py +212 -0
  179. snappy/geometric_structure/cusp_neighborhood/__init__.py +3 -0
  180. snappy/geometric_structure/cusp_neighborhood/complex_cusp_cross_section.py +697 -0
  181. snappy/geometric_structure/cusp_neighborhood/cusp_cross_section_base.py +484 -0
  182. snappy/geometric_structure/cusp_neighborhood/exceptions.py +42 -0
  183. snappy/geometric_structure/cusp_neighborhood/real_cusp_cross_section.py +298 -0
  184. snappy/geometric_structure/cusp_neighborhood/tiles_for_cusp_neighborhood.py +159 -0
  185. snappy/geometric_structure/cusp_neighborhood/vertices.py +32 -0
  186. snappy/geometric_structure/geodesic/__init__.py +0 -0
  187. snappy/geometric_structure/geodesic/add_core_curves.py +152 -0
  188. snappy/geometric_structure/geodesic/avoid_core_curves.py +369 -0
  189. snappy/geometric_structure/geodesic/canonical_keys.py +52 -0
  190. snappy/geometric_structure/geodesic/check_away_from_core_curve.py +60 -0
  191. snappy/geometric_structure/geodesic/constants.py +6 -0
  192. snappy/geometric_structure/geodesic/exceptions.py +22 -0
  193. snappy/geometric_structure/geodesic/fixed_points.py +93 -0
  194. snappy/geometric_structure/geodesic/geodesic_start_point_info.py +435 -0
  195. snappy/geometric_structure/geodesic/graph_trace_helper.py +67 -0
  196. snappy/geometric_structure/geodesic/line.py +30 -0
  197. snappy/geometric_structure/geodesic/multiplicity.py +127 -0
  198. snappy/geometric_structure/geodesic/tiles_for_geodesic.py +101 -0
  199. snappy/geometric_structure/test.py +22 -0
  200. snappy/gui.py +36 -36
  201. snappy/horoviewer.py +50 -48
  202. snappy/hyperboloid/__init__.py +212 -0
  203. snappy/hyperboloid/distances.py +245 -0
  204. snappy/hyperboloid/horoball.py +19 -0
  205. snappy/hyperboloid/line.py +35 -0
  206. snappy/hyperboloid/point.py +9 -0
  207. snappy/hyperboloid/triangle.py +29 -0
  208. snappy/{infodialog.py → infowindow.py} +32 -33
  209. snappy/isometry_signature.py +382 -0
  210. snappy/len_spec/__init__.py +596 -0
  211. snappy/len_spec/geodesic_info.py +110 -0
  212. snappy/len_spec/geodesic_key_info_dict.py +117 -0
  213. snappy/len_spec/geodesic_piece.py +143 -0
  214. snappy/len_spec/geometric_structure.py +182 -0
  215. snappy/len_spec/geometry.py +80 -0
  216. snappy/len_spec/length_spectrum_geodesic_info.py +170 -0
  217. snappy/len_spec/spine.py +206 -0
  218. snappy/len_spec/test.py +24 -0
  219. snappy/len_spec/test_cases.py +69 -0
  220. snappy/len_spec/tile.py +275 -0
  221. snappy/len_spec/word.py +86 -0
  222. snappy/manifolds/__init__.py +1 -1
  223. snappy/math_basics.py +176 -0
  224. snappy/matrix.py +525 -0
  225. snappy/number.py +97 -21
  226. snappy/numeric_output_checker.py +37 -27
  227. snappy/pari.py +30 -69
  228. snappy/phone_home.py +25 -20
  229. snappy/polyviewer.py +39 -37
  230. snappy/ptolemy/__init__.py +4 -6
  231. snappy/ptolemy/component.py +14 -12
  232. snappy/ptolemy/coordinates.py +312 -295
  233. snappy/ptolemy/fieldExtensions.py +14 -12
  234. snappy/ptolemy/findLoops.py +43 -31
  235. snappy/ptolemy/geometricRep.py +24 -26
  236. snappy/ptolemy/homology.py +12 -7
  237. snappy/ptolemy/manifoldMethods.py +69 -70
  238. snappy/ptolemy/matrix.py +65 -26
  239. snappy/ptolemy/numericalSolutionsToGroebnerBasis.py +18 -14
  240. snappy/ptolemy/polynomial.py +125 -119
  241. snappy/ptolemy/processComponents.py +36 -30
  242. snappy/ptolemy/processFileBase.py +79 -18
  243. snappy/ptolemy/processFileDispatch.py +13 -14
  244. snappy/ptolemy/processMagmaFile.py +44 -39
  245. snappy/ptolemy/processRurFile.py +18 -11
  246. snappy/ptolemy/ptolemyGeneralizedObstructionClass.py +20 -17
  247. snappy/ptolemy/ptolemyObstructionClass.py +13 -17
  248. snappy/ptolemy/ptolemyVariety.py +190 -121
  249. snappy/ptolemy/ptolemyVarietyPrimeIdealGroebnerBasis.py +20 -19
  250. snappy/ptolemy/reginaWrapper.py +25 -29
  251. snappy/ptolemy/rur.py +6 -14
  252. snappy/ptolemy/solutionsToPrimeIdealGroebnerBasis.py +27 -22
  253. snappy/ptolemy/test.py +247 -188
  254. snappy/ptolemy/utilities.py +41 -43
  255. snappy/raytracing/__init__.py +64 -0
  256. snappy/raytracing/additional_horospheres.py +64 -0
  257. snappy/raytracing/additional_len_spec_choices.py +63 -0
  258. snappy/raytracing/cohomology_fractal.py +10 -6
  259. snappy/raytracing/eyeball.py +123 -0
  260. snappy/raytracing/finite_raytracing_data.py +48 -38
  261. snappy/raytracing/finite_viewer.py +218 -210
  262. snappy/raytracing/geodesic_tube_info.py +174 -0
  263. snappy/raytracing/geodesics.py +246 -0
  264. snappy/raytracing/geodesics_window.py +258 -0
  265. snappy/raytracing/gui_utilities.py +152 -40
  266. snappy/raytracing/hyperboloid_navigation.py +102 -52
  267. snappy/raytracing/hyperboloid_utilities.py +114 -261
  268. snappy/raytracing/ideal_raytracing_data.py +256 -179
  269. snappy/raytracing/inside_viewer.py +522 -253
  270. snappy/raytracing/pack.py +22 -0
  271. snappy/raytracing/raytracing_data.py +46 -34
  272. snappy/raytracing/raytracing_view.py +190 -109
  273. snappy/raytracing/shaders/Eye.png +0 -0
  274. snappy/raytracing/shaders/NonGeometric.png +0 -0
  275. snappy/raytracing/shaders/__init__.py +60 -4
  276. snappy/raytracing/shaders/fragment.glsl +575 -148
  277. snappy/raytracing/test.py +29 -0
  278. snappy/raytracing/tooltip.py +146 -0
  279. snappy/raytracing/upper_halfspace_utilities.py +98 -0
  280. snappy/raytracing/view_scale_controller.py +98 -0
  281. snappy/raytracing/zoom_slider/__init__.py +32 -29
  282. snappy/raytracing/zoom_slider/test.py +2 -0
  283. snappy/sage_helper.py +69 -123
  284. snappy/{preferences.py → settings.py} +167 -145
  285. snappy/shell.py +4 -0
  286. snappy/snap/__init__.py +12 -8
  287. snappy/snap/character_varieties.py +24 -18
  288. snappy/snap/find_field.py +35 -34
  289. snappy/snap/fundamental_polyhedron.py +99 -85
  290. snappy/snap/generators.py +6 -8
  291. snappy/snap/interval_reps.py +18 -6
  292. snappy/snap/kernel_structures.py +8 -3
  293. snappy/snap/mcomplex_base.py +1 -2
  294. snappy/snap/nsagetools.py +107 -53
  295. snappy/snap/peripheral/__init__.py +1 -1
  296. snappy/snap/peripheral/dual_cellulation.py +15 -7
  297. snappy/snap/peripheral/link.py +20 -16
  298. snappy/snap/peripheral/peripheral.py +22 -14
  299. snappy/snap/peripheral/surface.py +47 -50
  300. snappy/snap/peripheral/test.py +8 -8
  301. snappy/snap/polished_reps.py +65 -40
  302. snappy/snap/shapes.py +41 -22
  303. snappy/snap/slice_obs_HKL.py +64 -25
  304. snappy/snap/t3mlite/arrow.py +88 -51
  305. snappy/snap/t3mlite/corner.py +5 -6
  306. snappy/snap/t3mlite/edge.py +32 -21
  307. snappy/snap/t3mlite/face.py +7 -9
  308. snappy/snap/t3mlite/files.py +31 -23
  309. snappy/snap/t3mlite/homology.py +14 -10
  310. snappy/snap/t3mlite/linalg.py +158 -56
  311. snappy/snap/t3mlite/mcomplex.py +739 -291
  312. snappy/snap/t3mlite/perm4.py +236 -84
  313. snappy/snap/t3mlite/setup.py +9 -10
  314. snappy/snap/t3mlite/simplex.py +65 -48
  315. snappy/snap/t3mlite/spun.py +42 -30
  316. snappy/snap/t3mlite/surface.py +45 -45
  317. snappy/snap/t3mlite/test.py +3 -0
  318. snappy/snap/t3mlite/test_vs_regina.py +17 -13
  319. snappy/snap/t3mlite/tetrahedron.py +25 -24
  320. snappy/snap/t3mlite/vertex.py +8 -13
  321. snappy/snap/test.py +45 -52
  322. snappy/snap/utilities.py +66 -65
  323. snappy/test.py +155 -158
  324. snappy/test_cases.py +263 -0
  325. snappy/testing.py +131 -0
  326. snappy/tiling/__init__.py +2 -0
  327. snappy/tiling/canonical_key_dict.py +59 -0
  328. snappy/tiling/dict_based_set.py +79 -0
  329. snappy/tiling/floor.py +49 -0
  330. snappy/tiling/hyperboloid_dict.py +54 -0
  331. snappy/tiling/iter_utils.py +78 -0
  332. snappy/tiling/lifted_tetrahedron.py +22 -0
  333. snappy/tiling/lifted_tetrahedron_set.py +54 -0
  334. snappy/tiling/real_hash_dict.py +164 -0
  335. snappy/tiling/test.py +23 -0
  336. snappy/tiling/tile.py +215 -0
  337. snappy/tiling/triangle.py +33 -0
  338. snappy/tkterminal.py +313 -203
  339. snappy/twister/main.py +1 -8
  340. snappy/twister/twister_core.cpython-38-darwin.so +0 -0
  341. snappy/upper_halfspace/__init__.py +146 -0
  342. snappy/upper_halfspace/ideal_point.py +26 -0
  343. snappy/verify/__init__.py +4 -8
  344. snappy/verify/{verifyCanonical.py → canonical.py} +114 -97
  345. snappy/verify/complex_volume/__init__.py +3 -2
  346. snappy/verify/complex_volume/adjust_torsion.py +13 -11
  347. snappy/verify/complex_volume/closed.py +29 -24
  348. snappy/verify/complex_volume/compute_ptolemys.py +8 -6
  349. snappy/verify/complex_volume/cusped.py +10 -9
  350. snappy/verify/complex_volume/extended_bloch.py +14 -12
  351. snappy/verify/{cuspTranslations.py → cusp_translations.py} +15 -14
  352. snappy/verify/edge_equations.py +80 -0
  353. snappy/verify/exceptions.py +23 -56
  354. snappy/verify/{verifyHyperbolicity.py → hyperbolicity.py} +19 -15
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  356. snappy/verify/interval_tree.py +27 -25
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  358. snappy/verify/maximal_cusp_area_matrix/__init__.py +17 -86
  359. snappy/verify/maximal_cusp_area_matrix/cusp_tiling_engine.py +58 -48
  360. snappy/verify/maximal_cusp_area_matrix/cusp_translate_engine.py +53 -57
  361. snappy/verify/{realAlgebra.py → real_algebra.py} +26 -20
  362. snappy/verify/shapes.py +10 -7
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  366. snappy/verify/upper_halfspace/extended_matrix.py +5 -5
  367. snappy/verify/upper_halfspace/finite_point.py +44 -31
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  369. snappy/verify/volume.py +15 -12
  370. snappy/version.py +2 -3
  371. {snappy-3.0.3.dist-info → snappy-3.2.dist-info}/METADATA +14 -12
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  373. {snappy-3.0.3.dist-info → snappy-3.2.dist-info}/WHEEL +1 -1
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  375. {snappy-3.0.3.dist-info → snappy-3.2.dist-info}/top_level.txt +10 -1
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- <h1>Links: planar diagrams and invariants<a class="headerlink" href="#links-planar-diagrams-and-invariants" title="Permalink to this headline">¶</a></h1>
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+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
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+ <ul class="current">
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+ <li class="toctree-l1"><a class="reference internal" href="installing.html">Installing SnapPy</a></li>
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+ <li class="toctree-l1"><a class="reference internal" href="screenshots.html">Screenshots: SnapPy in action</a></li>
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+ <li class="toctree-l1"><a class="reference internal" href="tutorial.html">Tutorial</a></li>
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+ <li class="toctree-l1"><a class="reference internal" href="snappy.html">The snappy module and its classes</a></li>
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+ <li class="toctree-l1"><a class="reference internal" href="plink.html">Using SnapPy’s link editor</a></li>
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+ <li class="toctree-l1 current"><a class="current reference internal" href="#">Links: planar diagrams and invariants</a><ul>
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+ <li class="toctree-l2"><a class="reference internal" href="#tutorial">Tutorial</a></li>
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+ <li class="toctree-l2"><a class="reference internal" href="#random-links">Random Links</a><ul>
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+ <li class="toctree-l3"><a class="reference internal" href="#spherogram.random_link"><code class="docutils literal notranslate"><span class="pre">random_link()</span></code></a></li>
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+ </ul>
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+ </li>
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+ <li class="toctree-l2"><a class="reference internal" href="#the-link-class">The Link class</a><ul>
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+ <li class="toctree-l3"><a class="reference internal" href="#spherogram.Link"><code class="docutils literal notranslate"><span class="pre">Link</span></code></a><ul>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.DT_code"><code class="docutils literal notranslate"><span class="pre">Link.DT_code()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.KLPProjection"><code class="docutils literal notranslate"><span class="pre">Link.KLPProjection()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.PD_code"><code class="docutils literal notranslate"><span class="pre">Link.PD_code()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.alexander_matrix"><code class="docutils literal notranslate"><span class="pre">Link.alexander_matrix()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.alexander_poly"><code class="docutils literal notranslate"><span class="pre">Link.alexander_poly()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.alexander_polynomial"><code class="docutils literal notranslate"><span class="pre">Link.alexander_polynomial()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.all_crossings_oriented"><code class="docutils literal notranslate"><span class="pre">Link.all_crossings_oriented()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.alternating"><code class="docutils literal notranslate"><span class="pre">Link.alternating()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.backtrack"><code class="docutils literal notranslate"><span class="pre">Link.backtrack()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.black_graph"><code class="docutils literal notranslate"><span class="pre">Link.black_graph()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.braid_word"><code class="docutils literal notranslate"><span class="pre">Link.braid_word()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.connected_sum"><code class="docutils literal notranslate"><span class="pre">Link.connected_sum()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.copy"><code class="docutils literal notranslate"><span class="pre">Link.copy()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.crossing_entries"><code class="docutils literal notranslate"><span class="pre">Link.crossing_entries()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.crossing_strands"><code class="docutils literal notranslate"><span class="pre">Link.crossing_strands()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.deconnect_sum"><code class="docutils literal notranslate"><span class="pre">Link.deconnect_sum()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.determinant"><code class="docutils literal notranslate"><span class="pre">Link.determinant()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.digraph"><code class="docutils literal notranslate"><span class="pre">Link.digraph()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.dual_graph"><code class="docutils literal notranslate"><span class="pre">Link.dual_graph()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.exterior"><code class="docutils literal notranslate"><span class="pre">Link.exterior()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.faces"><code class="docutils literal notranslate"><span class="pre">Link.faces()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.goeritz_matrix"><code class="docutils literal notranslate"><span class="pre">Link.goeritz_matrix()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.is_alternating"><code class="docutils literal notranslate"><span class="pre">Link.is_alternating()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.is_planar"><code class="docutils literal notranslate"><span class="pre">Link.is_planar()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.jones_polynomial"><code class="docutils literal notranslate"><span class="pre">Link.jones_polynomial()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.knot_floer_homology"><code class="docutils literal notranslate"><span class="pre">Link.knot_floer_homology()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.knot_group"><code class="docutils literal notranslate"><span class="pre">Link.knot_group()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.linking_matrix"><code class="docutils literal notranslate"><span class="pre">Link.linking_matrix()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.linking_number"><code class="docutils literal notranslate"><span class="pre">Link.linking_number()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.mirror"><code class="docutils literal notranslate"><span class="pre">Link.mirror()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.morse_diagram"><code class="docutils literal notranslate"><span class="pre">Link.morse_diagram()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.morse_number"><code class="docutils literal notranslate"><span class="pre">Link.morse_number()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.optimize_overcrossings"><code class="docutils literal notranslate"><span class="pre">Link.optimize_overcrossings()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.sage_link"><code class="docutils literal notranslate"><span class="pre">Link.sage_link()</span></code></a></li>
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+ <li class="toctree-l4"><a class="reference internal" href="#spherogram.Link.seifert_matrix"><code class="docutils literal notranslate"><span class="pre">Link.seifert_matrix()</span></code></a></li>
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+ <li class="toctree-l1"><a class="reference internal" href="other.html">Other components</a></li>
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+ <li class="breadcrumb-item active">Links: planar diagrams and invariants</li>
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+ <span id="module-spherogram"></span><h1>Links: planar diagrams and invariants<a class="headerlink" href="#links-planar-diagrams-and-invariants" title="Link to this heading"></a></h1>
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  <p>SnapPy includes the <a class="reference external" href="https://github.com/3-manifolds/Spherogram">Spherogram</a> module which allows one to
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  create links programmatically. The graphical conventions used are
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  <a class="reference external" href="https://github.com/3-manifolds/Spherogram/raw/master/spherogram_src/links/doc.pdf">summarized here</a>.</p>
@@ -113,10 +214,10 @@ basic link invariants, including the Jones polynomial. See the
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  complete list of Link methods below.</p>
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  <dt class="sig sig-object py" id="spherogram.random_link">
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- <span class="sig-prename descclassname"><span class="pre">spherogram.</span></span><span class="sig-name descname"><span class="pre">random_link</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">crossings</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_components</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'any'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">initial_map_gives_link</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alternating</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">consistent_twist_regions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simplify</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'basic'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prime_decomposition</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_all_pieces</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_tries</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.random_link" title="Permalink to this definition">¶</a></dt>
220
+ <span class="sig-prename descclassname"><span class="pre">spherogram.</span></span><span class="sig-name descname"><span class="pre">random_link</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">crossings</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_components</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'any'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">initial_map_gives_link</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alternating</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">consistent_twist_regions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simplify</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'basic'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prime_decomposition</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_all_pieces</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_tries</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.random_link" title="Link to this definition"></a></dt>
120
221
  <dd><p>Generates a random link from a model that starts with a random
121
222
  4-valent planar graph sampled with the uniform distribution by
122
223
  Schaeffer’s <a class="reference external" href="http://www.lix.polytechnique.fr/~schaeffe/PagesWeb/PlanarMap/index-en.html">PlanarMap program.</a></p>
@@ -145,12 +246,12 @@ set this argument to <code class="docutils literal notranslate"><span class="pre
145
246
  </li>
146
247
  <li><p>The 4-valent vertices of G are turned into crossings by flipping a
147
248
  fair coin. If you want the unique alternating diagram associated to
148
- G, pass <code class="docutils literal notranslate"><span class="pre">alternating</span> <span class="pre">=</span> <span class="pre">True</span></code>. If you want there to be no
249
+ G, pass <code class="docutils literal notranslate"><span class="pre">alternating=True</span></code>. If you want there to be no
149
250
  obvious Type II Reidemeister moves, pass
150
- <code class="docutils literal notranslate"><span class="pre">consistent_twist_regions</span> <span class="pre">=</span> <span class="pre">False</span></code>.</p></li>
251
+ <code class="docutils literal notranslate"><span class="pre">consistent_twist_regions=True</span></code>.</p></li>
151
252
  <li><p><code class="docutils literal notranslate"><span class="pre">simplify</span></code>: Whether and how to try to reduce the number of
152
253
  crossings of the link via Reidemeister moves using the method
153
- <code class="docutils literal notranslate"><span class="pre">Link.simplify</span></code>. For no simplification, set <code class="docutils literal notranslate"><span class="pre">simplify</span> <span class="pre">=</span> <span class="pre">None</span></code>;
254
+ <code class="docutils literal notranslate"><span class="pre">Link.simplify</span></code>. For no simplification, set <code class="docutils literal notranslate"><span class="pre">simplify=None</span></code>;
154
255
  otherwise set <code class="docutils literal notranslate"><span class="pre">simplify</span></code> to be the appropriate mode for
155
256
  <code class="docutils literal notranslate"><span class="pre">Link.simplify</span></code>, for example <code class="docutils literal notranslate"><span class="pre">basic</span></code> (the default), <code class="docutils literal notranslate"><span class="pre">level</span></code>,
156
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  or <code class="docutils literal notranslate"><span class="pre">global</span></code>.</p></li>
@@ -183,10 +284,10 @@ can have fewer components than the link as a whole.</p>
183
284
 
184
285
  </section>
185
286
  <section id="the-link-class">
186
- <h2>The Link class<a class="headerlink" href="#the-link-class" title="Permalink to this headline">¶</a></h2>
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+ <h2>The Link class<a class="headerlink" href="#the-link-class" title="Link to this heading"></a></h2>
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288
  <dl class="py class">
188
289
  <dt class="sig sig-object py" id="spherogram.Link">
189
- <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">spherogram.</span></span><span class="sig-name descname"><span class="pre">Link</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">crossings</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">braid_closure</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">check_planarity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">build</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link" title="Permalink to this definition">¶</a></dt>
290
+ <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">spherogram.</span></span><span class="sig-name descname"><span class="pre">Link</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">crossings</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">braid_closure</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">check_planarity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">build</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link" title="Link to this definition"></a></dt>
190
291
  <dd><p>Links are made from Crossings. The general model is that of the PD
191
292
  diagrams used in <a class="reference external" href="http://katlas.org/wiki/Planar_Diagrams">KnotTheory</a>.</p>
192
293
  <p>See the file “doc.pdf” for the conventions, which can be accessed
@@ -235,7 +336,7 @@ Hoste-Thistlethwaite tables by name.</p>
235
336
  see the documentation for the “sage_link” method for details.</p>
236
337
  <dl class="py method">
237
338
  <dt class="sig sig-object py" id="spherogram.Link.DT_code">
238
- <span class="sig-name descname"><span class="pre">DT_code</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">DT_alpha</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">flips</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.DT_code" title="Permalink to this definition">¶</a></dt>
339
+ <span class="sig-name descname"><span class="pre">DT_code</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">DT_alpha</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">flips</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.DT_code" title="Link to this definition"></a></dt>
239
340
  <dd><p>The Dowker-Thistlethwaite code for the link in either numerical or
240
341
  alphabetical form.</p>
241
342
  <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">L</span> <span class="o">=</span> <span class="n">Link</span><span class="p">(</span><span class="s1">&#39;K8n1&#39;</span><span class="p">)</span>
@@ -252,12 +353,12 @@ each component; subsequent letters describe each crossing with
252
353
 
253
354
  <dl class="py method">
254
355
  <dt class="sig sig-object py" id="spherogram.Link.KLPProjection">
255
- <span class="sig-name descname"><span class="pre">KLPProjection</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.KLPProjection" title="Permalink to this definition">¶</a></dt>
356
+ <span class="sig-name descname"><span class="pre">KLPProjection</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.KLPProjection" title="Link to this definition"></a></dt>
256
357
  <dd></dd></dl>
257
358
 
258
359
  <dl class="py method">
259
360
  <dt class="sig sig-object py" id="spherogram.Link.PD_code">
260
- <span class="sig-name descname"><span class="pre">PD_code</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">KnotTheory</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_strand_index</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.PD_code" title="Permalink to this definition">¶</a></dt>
361
+ <span class="sig-name descname"><span class="pre">PD_code</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">KnotTheory</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_strand_index</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.PD_code" title="Link to this definition"></a></dt>
261
362
  <dd><p>The planar diagram code for the link. When reconstructing a link
262
363
  from its PD code, it will not change the ordering of the
263
364
  components, and will preserve their orientation except
@@ -274,7 +375,7 @@ possibly for components with only two crossings.</p>
274
375
 
275
376
  <dl class="py method">
276
377
  <dt class="sig sig-object py" id="spherogram.Link.alexander_matrix">
277
- <span class="sig-name descname"><span class="pre">alexander_matrix</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mv</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.alexander_matrix" title="Permalink to this definition">¶</a></dt>
378
+ <span class="sig-name descname"><span class="pre">alexander_matrix</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mv</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.alexander_matrix" title="Link to this definition"></a></dt>
278
379
  <dd><p>Returns the Alexander matrix of the link:</p>
279
380
  <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sage</span><span class="p">:</span> <span class="n">L</span> <span class="o">=</span> <span class="n">Link</span><span class="p">(</span><span class="s1">&#39;3_1&#39;</span><span class="p">)</span>
280
381
  <span class="n">sage</span><span class="p">:</span> <span class="n">A</span> <span class="o">=</span> <span class="n">L</span><span class="o">.</span><span class="n">alexander_matrix</span><span class="p">()</span>
@@ -294,14 +395,15 @@ possibly for components with only two crossings.</p>
294
395
 
295
396
  <dl class="py method">
296
397
  <dt class="sig sig-object py" id="spherogram.Link.alexander_poly">
297
- <span class="sig-name descname"><span class="pre">alexander_poly</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.alexander_poly" title="Permalink to this definition">¶</a></dt>
398
+ <span class="sig-name descname"><span class="pre">alexander_poly</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.alexander_poly" title="Link to this definition"></a></dt>
298
399
  <dd><p>Please use the “alexander_polynomial” method instead.</p>
299
400
  </dd></dl>
300
401
 
301
402
  <dl class="py method">
302
403
  <dt class="sig sig-object py" id="spherogram.Link.alexander_polynomial">
303
- <span class="sig-name descname"><span class="pre">alexander_polynomial</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">multivar</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'no'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'default'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">norm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">factored</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.alexander_polynomial" title="Permalink to this definition">¶</a></dt>
304
- <dd><p>Calculates the Alexander polynomial of the link. For links with one component,
404
+ <span class="sig-name descname"><span class="pre">alexander_polynomial</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">multivar</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'no'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'default'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">norm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">factored</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.alexander_polynomial" title="Link to this definition"></a></dt>
405
+ <dd><p>Calculates the Alexander polynomial of the link.</p>
406
+ <p>For links with one component,
305
407
  can evaluate the alexander polynomial at v:</p>
306
408
  <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sage</span><span class="p">:</span> <span class="n">K</span> <span class="o">=</span> <span class="n">Link</span><span class="p">(</span><span class="s1">&#39;4_1&#39;</span><span class="p">)</span>
307
409
  <span class="n">sage</span><span class="p">:</span> <span class="n">K</span><span class="o">.</span><span class="n">alexander_polynomial</span><span class="p">()</span>
@@ -326,12 +428,12 @@ Wirtinger presentation for the link:</p>
326
428
 
327
429
  <dl class="py method">
328
430
  <dt class="sig sig-object py" id="spherogram.Link.all_crossings_oriented">
329
- <span class="sig-name descname"><span class="pre">all_crossings_oriented</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.all_crossings_oriented" title="Permalink to this definition">¶</a></dt>
431
+ <span class="sig-name descname"><span class="pre">all_crossings_oriented</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.all_crossings_oriented" title="Link to this definition"></a></dt>
330
432
  <dd></dd></dl>
331
433
 
332
434
  <dl class="py method">
333
435
  <dt class="sig sig-object py" id="spherogram.Link.alternating">
334
- <span class="sig-name descname"><span class="pre">alternating</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.alternating" title="Permalink to this definition">¶</a></dt>
436
+ <span class="sig-name descname"><span class="pre">alternating</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.alternating" title="Link to this definition"></a></dt>
335
437
  <dd><p>Returns the alternating link with the same planar graph. No attempt
336
438
  is made to preserve the order of the link components or ensure
337
439
  that the DT code of the result has all positive entries (as
@@ -346,7 +448,7 @@ opposed to all negative).</p>
346
448
 
347
449
  <dl class="py method">
348
450
  <dt class="sig sig-object py" id="spherogram.Link.backtrack">
349
- <span class="sig-name descname"><span class="pre">backtrack</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">steps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prob_type_1</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prob_type_2</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.3</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.backtrack" title="Permalink to this definition">¶</a></dt>
451
+ <span class="sig-name descname"><span class="pre">backtrack</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">steps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prob_type_1</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prob_type_2</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.3</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.backtrack" title="Link to this definition"></a></dt>
350
452
  <dd><p>Performs a sequence of Reidemeister moves which increase or maintain
351
453
  the number of crossings in a diagram. The number of such
352
454
  moves is the parameter steps. The diagram is modified in place.</p>
@@ -365,11 +467,12 @@ moves is the parameter steps. The diagram is modified in place.</p>
365
467
 
366
468
  <dl class="py method">
367
469
  <dt class="sig sig-object py" id="spherogram.Link.black_graph">
368
- <span class="sig-name descname"><span class="pre">black_graph</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.black_graph" title="Permalink to this definition">¶</a></dt>
369
- <dd><p>Returns the black graph of K. If the black graph is disconnected
370
- (which can only happen for a split link diagram), returns one
371
- connected component. The edges are labeled by the crossings
372
- they correspond to. Example:</p>
470
+ <span class="sig-name descname"><span class="pre">black_graph</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.black_graph" title="Link to this definition"></a></dt>
471
+ <dd><p>Returns the black graph of K.</p>
472
+ <p>If the black graph is disconnected (which can only happen for
473
+ a split link diagram), returns one connected component. The
474
+ edges are labeled by the crossings they correspond to.</p>
475
+ <p>Example:</p>
373
476
  <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sage</span><span class="p">:</span> <span class="n">K</span><span class="o">=</span><span class="n">Link</span><span class="p">(</span><span class="s1">&#39;5_1&#39;</span><span class="p">)</span>
374
477
  <span class="n">sage</span><span class="p">:</span> <span class="n">K</span><span class="o">.</span><span class="n">black_graph</span><span class="p">()</span>
375
478
  <span class="n">Subgraph</span> <span class="n">of</span> <span class="p">():</span> <span class="n">Multi</span><span class="o">-</span><span class="n">graph</span> <span class="n">on</span> <span class="mi">2</span> <span class="n">vertices</span>
@@ -382,7 +485,7 @@ expected way.</p>
382
485
 
383
486
  <dl class="py method">
384
487
  <dt class="sig sig-object py" id="spherogram.Link.braid_word">
385
- <span class="sig-name descname"><span class="pre">braid_word</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">as_sage_braid</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.braid_word" title="Permalink to this definition">¶</a></dt>
488
+ <span class="sig-name descname"><span class="pre">braid_word</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">as_sage_braid</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.braid_word" title="Link to this definition"></a></dt>
386
489
  <dd><p>Return a list of integers which defines a braid word whose closure is the
387
490
  given link. The natural numbers 1, 2, 3, etc are the generators and the
388
491
  negatives are the inverses.</p>
@@ -407,7 +510,7 @@ braids, a new algorithm”.</p>
407
510
 
408
511
  <dl class="py method">
409
512
  <dt class="sig sig-object py" id="spherogram.Link.connected_sum">
410
- <span class="sig-name descname"><span class="pre">connected_sum</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other_knot</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.connected_sum" title="Permalink to this definition">¶</a></dt>
513
+ <span class="sig-name descname"><span class="pre">connected_sum</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other_knot</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.connected_sum" title="Link to this definition"></a></dt>
411
514
  <dd><p>Returns the connected sum of two knots.</p>
412
515
  <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">fig8</span> <span class="o">=</span> <span class="p">[(</span><span class="mi">1</span><span class="p">,</span><span class="mi">7</span><span class="p">,</span><span class="mi">2</span><span class="p">,</span><span class="mi">6</span><span class="p">),</span> <span class="p">(</span><span class="mi">5</span><span class="p">,</span><span class="mi">3</span><span class="p">,</span><span class="mi">6</span><span class="p">,</span><span class="mi">2</span><span class="p">),</span> <span class="p">(</span><span class="mi">7</span><span class="p">,</span><span class="mi">4</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">5</span><span class="p">),</span> <span class="p">(</span><span class="mi">3</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">4</span><span class="p">,</span><span class="mi">1</span><span class="p">)]</span>
413
516
  <span class="gp">&gt;&gt;&gt; </span><span class="n">K</span> <span class="o">=</span> <span class="n">Link</span><span class="p">(</span><span class="n">fig8</span><span class="p">)</span>
@@ -419,7 +522,7 @@ braids, a new algorithm”.</p>
419
522
 
420
523
  <dl class="py method">
421
524
  <dt class="sig sig-object py" id="spherogram.Link.copy">
422
- <span class="sig-name descname"><span class="pre">copy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">recursively</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.copy" title="Permalink to this definition">¶</a></dt>
525
+ <span class="sig-name descname"><span class="pre">copy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">recursively</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.copy" title="Link to this definition"></a></dt>
423
526
  <dd><p>Returns a copy of the link.</p>
424
527
  <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">K</span> <span class="o">=</span> <span class="n">Link</span><span class="p">(</span><span class="s1">&#39;L14n467&#39;</span><span class="p">)</span>
425
528
  <span class="gp">&gt;&gt;&gt; </span><span class="n">copy</span> <span class="o">=</span> <span class="n">K</span><span class="o">.</span><span class="n">copy</span><span class="p">();</span> <span class="n">copy</span>
@@ -432,17 +535,17 @@ braids, a new algorithm”.</p>
432
535
 
433
536
  <dl class="py method">
434
537
  <dt class="sig sig-object py" id="spherogram.Link.crossing_entries">
435
- <span class="sig-name descname"><span class="pre">crossing_entries</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.crossing_entries" title="Permalink to this definition">¶</a></dt>
538
+ <span class="sig-name descname"><span class="pre">crossing_entries</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.crossing_entries" title="Link to this definition"></a></dt>
436
539
  <dd></dd></dl>
437
540
 
438
541
  <dl class="py method">
439
542
  <dt class="sig sig-object py" id="spherogram.Link.crossing_strands">
440
- <span class="sig-name descname"><span class="pre">crossing_strands</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.crossing_strands" title="Permalink to this definition">¶</a></dt>
543
+ <span class="sig-name descname"><span class="pre">crossing_strands</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.crossing_strands" title="Link to this definition"></a></dt>
441
544
  <dd></dd></dl>
442
545
 
443
546
  <dl class="py method">
444
547
  <dt class="sig sig-object py" id="spherogram.Link.deconnect_sum">
445
- <span class="sig-name descname"><span class="pre">deconnect_sum</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">destroy_original</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.deconnect_sum" title="Permalink to this definition">¶</a></dt>
548
+ <span class="sig-name descname"><span class="pre">deconnect_sum</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">destroy_original</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.deconnect_sum" title="Link to this definition"></a></dt>
446
549
  <dd><p>Undoes all connect sums that are diagramatically obvious,
447
550
  i.e. those where there is a circle which meets the projection
448
551
  in two points.</p>
@@ -458,7 +561,7 @@ in two points.</p>
458
561
 
459
562
  <dl class="py method">
460
563
  <dt class="sig sig-object py" id="spherogram.Link.determinant">
461
- <span class="sig-name descname"><span class="pre">determinant</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'goeritz'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.determinant" title="Permalink to this definition">¶</a></dt>
564
+ <span class="sig-name descname"><span class="pre">determinant</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'goeritz'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.determinant" title="Link to this definition"></a></dt>
462
565
  <dd><p>Returns the determinant of the link, a non-negative integer.</p>
463
566
  <p>Possible methods are ‘wirt’, using the Wirtinger presentation; ‘goeritz’,
464
567
  using the Goeritz matrix, and ‘color’, using the ‘colorability matrix’, or
@@ -472,13 +575,13 @@ anything else, to compute the Alexander polynomial at -1. Example:</p>
472
575
 
473
576
  <dl class="py method">
474
577
  <dt class="sig sig-object py" id="spherogram.Link.digraph">
475
- <span class="sig-name descname"><span class="pre">digraph</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.digraph" title="Permalink to this definition">¶</a></dt>
578
+ <span class="sig-name descname"><span class="pre">digraph</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.digraph" title="Link to this definition"></a></dt>
476
579
  <dd><p>The underlying directed graph for the link diagram.</p>
477
580
  </dd></dl>
478
581
 
479
582
  <dl class="py method">
480
583
  <dt class="sig sig-object py" id="spherogram.Link.dual_graph">
481
- <span class="sig-name descname"><span class="pre">dual_graph</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.dual_graph" title="Permalink to this definition">¶</a></dt>
584
+ <span class="sig-name descname"><span class="pre">dual_graph</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.dual_graph" title="Link to this definition"></a></dt>
482
585
  <dd><p>The dual graph to a link diagram D, whose vertices correspond to
483
586
  complementary regions (faces) of D and whose edges are dual to the
484
587
  edges of D.</p>
@@ -486,7 +589,7 @@ edges of D.</p>
486
589
 
487
590
  <dl class="py method">
488
591
  <dt class="sig sig-object py" id="spherogram.Link.exterior">
489
- <span class="sig-name descname"><span class="pre">exterior</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">with_hyperbolic_structure</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_finite_vertices</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.exterior" title="Permalink to this definition">¶</a></dt>
592
+ <span class="sig-name descname"><span class="pre">exterior</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">with_hyperbolic_structure</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_finite_vertices</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.exterior" title="Link to this definition"></a></dt>
490
593
  <dd><p>The exterior or complement of the link L, that is, S^3 minus L.</p>
491
594
  <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">K</span> <span class="o">=</span> <span class="n">Link</span><span class="p">(</span><span class="s1">&#39;4_1&#39;</span><span class="p">)</span>
492
595
  <span class="gp">&gt;&gt;&gt; </span><span class="n">M</span> <span class="o">=</span> <span class="n">K</span><span class="o">.</span><span class="n">exterior</span><span class="p">()</span>
@@ -508,7 +611,7 @@ projection plane, set the flag remove_finite_vertices to False.</p>
508
611
 
509
612
  <dl class="py method">
510
613
  <dt class="sig sig-object py" id="spherogram.Link.faces">
511
- <span class="sig-name descname"><span class="pre">faces</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.faces" title="Permalink to this definition">¶</a></dt>
614
+ <span class="sig-name descname"><span class="pre">faces</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.faces" title="Link to this definition"></a></dt>
512
615
  <dd><p>The faces are the complementary regions of the link diagram. Each face
513
616
  is given as a list of corners of crossings as one goes around
514
617
  <em>clockwise</em>. These corners are recorded as CrossingStrands,
@@ -520,7 +623,7 @@ as the <em>heads</em> of the oriented edges of the face.</p>
520
623
 
521
624
  <dl class="py method">
522
625
  <dt class="sig sig-object py" id="spherogram.Link.goeritz_matrix">
523
- <span class="sig-name descname"><span class="pre">goeritz_matrix</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">return_graph</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.goeritz_matrix" title="Permalink to this definition">¶</a></dt>
626
+ <span class="sig-name descname"><span class="pre">goeritz_matrix</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">return_graph</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.goeritz_matrix" title="Link to this definition"></a></dt>
524
627
  <dd><p>Call self.white_graph() and return the Goeritz matrix of the result.
525
628
  If the return_graph flag is set, also return the graph:</p>
526
629
  <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sage</span><span class="p">:</span> <span class="n">K</span><span class="o">=</span><span class="n">Link</span><span class="p">(</span><span class="s1">&#39;4_1&#39;</span><span class="p">)</span>
@@ -532,7 +635,7 @@ If the return_graph flag is set, also return the graph:</p>
532
635
 
533
636
  <dl class="py method">
534
637
  <dt class="sig sig-object py" id="spherogram.Link.is_alternating">
535
- <span class="sig-name descname"><span class="pre">is_alternating</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.is_alternating" title="Permalink to this definition">¶</a></dt>
638
+ <span class="sig-name descname"><span class="pre">is_alternating</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.is_alternating" title="Link to this definition"></a></dt>
536
639
  <dd><p>Returns whether or not this link diagram is alternating.</p>
537
640
  <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">K</span> <span class="o">=</span> <span class="n">Link</span><span class="p">(</span><span class="s1">&#39;K9a1&#39;</span><span class="p">)</span>
538
641
  <span class="gp">&gt;&gt;&gt; </span><span class="n">L</span> <span class="o">=</span> <span class="n">Link</span><span class="p">(</span><span class="s1">&#39;K10n1&#39;</span><span class="p">)</span>
@@ -555,9 +658,9 @@ class. Here is the Hopf link with two silly extra crossings:</p>
555
658
 
556
659
  <dl class="py method">
557
660
  <dt class="sig sig-object py" id="spherogram.Link.is_planar">
558
- <span class="sig-name descname"><span class="pre">is_planar</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.is_planar" title="Permalink to this definition">¶</a></dt>
559
- <dd><p>Whether the 4-valent graph underlying the link projection is planar.
560
- Should always be True for any actual Link.</p>
661
+ <span class="sig-name descname"><span class="pre">is_planar</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.is_planar" title="Link to this definition"></a></dt>
662
+ <dd><p>Whether the 4-valent graph underlying the link projection is planar.</p>
663
+ <p>Should always be <code class="docutils literal notranslate"><span class="pre">True</span></code> for any actual Link.</p>
561
664
  <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">c</span> <span class="o">=</span> <span class="n">Crossing</span><span class="p">()</span>
562
665
  <span class="gp">&gt;&gt;&gt; </span><span class="n">c</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">c</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">c</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">c</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="c1"># Punctured torus gluing</span>
563
666
  <span class="gp">&gt;&gt;&gt; </span><span class="n">bad</span> <span class="o">=</span> <span class="n">Link</span><span class="p">([</span><span class="n">c</span><span class="p">],</span> <span class="n">check_planarity</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
@@ -589,7 +692,7 @@ False
589
692
 
590
693
  <dl class="py method">
591
694
  <dt class="sig sig-object py" id="spherogram.Link.jones_polynomial">
592
- <span class="sig-name descname"><span class="pre">jones_polynomial</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">variable</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">new_convention</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.jones_polynomial" title="Permalink to this definition">¶</a></dt>
695
+ <span class="sig-name descname"><span class="pre">jones_polynomial</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">variable</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">new_convention</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.jones_polynomial" title="Link to this definition"></a></dt>
593
696
  <dd><p>Returns the Jones polynomial of the link, following the
594
697
  conventions of <a class="reference external" href="https://arxiv.org/abs/math/0201043">https://arxiv.org/abs/math/0201043</a></p>
595
698
  <p>In particular, it obeys the oriented skein relation:</p>
@@ -623,7 +726,7 @@ can recover the old conventions as illustrated below:</p>
623
726
 
624
727
  <dl class="py method">
625
728
  <dt class="sig sig-object py" id="spherogram.Link.knot_floer_homology">
626
- <span class="sig-name descname"><span class="pre">knot_floer_homology</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">prime</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complex</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.knot_floer_homology" title="Permalink to this definition">¶</a></dt>
729
+ <span class="sig-name descname"><span class="pre">knot_floer_homology</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">prime</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complex</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.knot_floer_homology" title="Link to this definition"></a></dt>
627
730
  <dd><p>Uses Zoltán Szabó’s HFK Calculator to compute the knot Floer
628
731
  homology. This also gives the Seifert genus, whether the knot
629
732
  fibers, etc:</p>
@@ -677,23 +780,23 @@ is recorded.)</p></li>
677
780
  </ul>
678
781
  <p>For example, to compute the vertical differential, whose homology
679
782
  is HFhat(S^3), you can do:</p>
680
- <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">data</span> <span class="o">=</span> <span class="n">L</span><span class="o">.</span><span class="n">knot_floer_homology</span><span class="p">(</span><span class="n">prime</span><span class="o">=</span><span class="mi">31991</span><span class="p">,</span> <span class="nb">complex</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
681
- <span class="gp">&gt;&gt;&gt; </span><span class="n">gens</span><span class="p">,</span> <span class="n">diff</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="s1">&#39;generators&#39;</span><span class="p">],</span> <span class="n">data</span><span class="p">[</span><span class="s1">&#39;differentials&#39;</span><span class="p">]</span>
682
- <span class="gp">&gt;&gt;&gt; </span><span class="n">vert</span> <span class="o">=</span> <span class="p">{(</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">):</span><span class="n">diff</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span> <span class="ow">in</span> <span class="n">diff</span>
683
- <span class="gp">... </span> <span class="k">if</span> <span class="n">gens</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="n">gens</span><span class="p">[</span><span class="n">j</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="mi">1</span><span class="p">}</span>
783
+ <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sage</span><span class="p">:</span> <span class="n">data</span> <span class="o">=</span> <span class="n">L</span><span class="o">.</span><span class="n">knot_floer_homology</span><span class="p">(</span><span class="n">prime</span><span class="o">=</span><span class="mi">31991</span><span class="p">,</span> <span class="nb">complex</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
784
+ <span class="n">sage</span><span class="p">:</span> <span class="n">gens</span><span class="p">,</span> <span class="n">diff</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="s1">&#39;generators&#39;</span><span class="p">],</span> <span class="n">data</span><span class="p">[</span><span class="s1">&#39;differentials&#39;</span><span class="p">]</span>
785
+ <span class="n">sage</span><span class="p">:</span> <span class="n">vert</span> <span class="o">=</span> <span class="p">{(</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">):</span><span class="n">diff</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">j</span> <span class="ow">in</span> <span class="n">diff</span>
786
+ <span class="o">...</span> <span class="k">if</span> <span class="n">gens</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="n">gens</span><span class="p">[</span><span class="n">j</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="mi">1</span><span class="p">}</span>
787
+ <span class="n">sage</span><span class="p">:</span> <span class="kn">from</span> <span class="nn">sage.all</span> <span class="kn">import</span> <span class="n">matrix</span><span class="p">,</span> <span class="n">GF</span>
788
+ <span class="n">sage</span><span class="p">:</span> <span class="n">M</span> <span class="o">=</span> <span class="n">matrix</span><span class="p">(</span><span class="n">GF</span><span class="p">(</span><span class="mi">31991</span><span class="p">),</span> <span class="nb">len</span><span class="p">(</span><span class="n">gens</span><span class="p">),</span> <span class="nb">len</span><span class="p">(</span><span class="n">gens</span><span class="p">),</span> <span class="n">vert</span><span class="p">,</span> <span class="n">sparse</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
789
+ <span class="n">sage</span><span class="p">:</span> <span class="n">M</span><span class="o">*</span><span class="n">M</span> <span class="o">==</span> <span class="mi">0</span>
790
+ <span class="kc">True</span>
791
+ <span class="n">sage</span><span class="p">:</span> <span class="n">M</span><span class="o">.</span><span class="n">right_kernel</span><span class="p">()</span><span class="o">.</span><span class="n">rank</span><span class="p">()</span> <span class="o">-</span> <span class="n">M</span><span class="o">.</span><span class="n">rank</span><span class="p">()</span>
792
+ <span class="mi">1</span>
684
793
  </pre></div>
685
794
  </div>
686
- <p>sage: from sage.all import matrix, GF
687
- sage: M = matrix(GF(31991), len(gens), len(gens), vert, sparse=True)
688
- sage: M*M == 0
689
- True
690
- sage: M.right_kernel().rank() - M.rank()
691
- 1</p>
692
795
  </dd></dl>
693
796
 
694
797
  <dl class="py method">
695
798
  <dt class="sig sig-object py" id="spherogram.Link.knot_group">
696
- <span class="sig-name descname"><span class="pre">knot_group</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.knot_group" title="Permalink to this definition">¶</a></dt>
799
+ <span class="sig-name descname"><span class="pre">knot_group</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.knot_group" title="Link to this definition"></a></dt>
697
800
  <dd><p>Computes the knot group using the Wirtinger presentation.</p>
698
801
  <p>Returns a finitely presented group:</p>
699
802
  <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>sage: K = Link(&#39;3_1&#39;)
@@ -706,7 +809,7 @@ sage: type(G)
706
809
 
707
810
  <dl class="py method">
708
811
  <dt class="sig sig-object py" id="spherogram.Link.linking_matrix">
709
- <span class="sig-name descname"><span class="pre">linking_matrix</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.linking_matrix" title="Permalink to this definition">¶</a></dt>
812
+ <span class="sig-name descname"><span class="pre">linking_matrix</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.linking_matrix" title="Link to this definition"></a></dt>
710
813
  <dd><p>Calculates the linking number for each pair of link components.</p>
711
814
  <p>Returns a linking matrix, in which the (i,j)th component is the
712
815
  linking number of the ith and jth link components.</p>
@@ -714,7 +817,7 @@ linking number of the ith and jth link components.</p>
714
817
 
715
818
  <dl class="py method">
716
819
  <dt class="sig sig-object py" id="spherogram.Link.linking_number">
717
- <span class="sig-name descname"><span class="pre">linking_number</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.linking_number" title="Permalink to this definition">¶</a></dt>
820
+ <span class="sig-name descname"><span class="pre">linking_number</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.linking_number" title="Link to this definition"></a></dt>
718
821
  <dd><p>Returns the linking number of self if self has two components;
719
822
  or the sum of the linking numbers of all pairs of components
720
823
  in general.</p>
@@ -722,14 +825,14 @@ in general.</p>
722
825
 
723
826
  <dl class="py method">
724
827
  <dt class="sig sig-object py" id="spherogram.Link.mirror">
725
- <span class="sig-name descname"><span class="pre">mirror</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.mirror" title="Permalink to this definition">¶</a></dt>
828
+ <span class="sig-name descname"><span class="pre">mirror</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.mirror" title="Link to this definition"></a></dt>
726
829
  <dd><p>Returns the mirror image of the link, preserving link orientations and
727
830
  component order.</p>
728
831
  </dd></dl>
729
832
 
730
833
  <dl class="py method">
731
834
  <dt class="sig sig-object py" id="spherogram.Link.morse_diagram">
732
- <span class="sig-name descname"><span class="pre">morse_diagram</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.morse_diagram" title="Permalink to this definition">¶</a></dt>
835
+ <span class="sig-name descname"><span class="pre">morse_diagram</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.morse_diagram" title="Link to this definition"></a></dt>
733
836
  <dd><p>Returns a MorseLinkDiagram of this link diagram, that is a choice
734
837
  of height function which realizes the Morse number:</p>
735
838
  <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sage</span><span class="p">:</span> <span class="n">L</span> <span class="o">=</span> <span class="n">Link</span><span class="p">(</span><span class="s1">&#39;L8n2&#39;</span><span class="p">)</span>
@@ -747,7 +850,7 @@ of height function which realizes the Morse number:</p>
747
850
 
748
851
  <dl class="py method">
749
852
  <dt class="sig sig-object py" id="spherogram.Link.morse_number">
750
- <span class="sig-name descname"><span class="pre">morse_number</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">solver</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'GLPK'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.morse_number" title="Permalink to this definition">¶</a></dt>
853
+ <span class="sig-name descname"><span class="pre">morse_number</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">solver</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'GLPK'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.morse_number" title="Link to this definition"></a></dt>
751
854
  <dd><p>The <em>Morse number</em> of a planar link diagram D is</p>
752
855
  <blockquote>
753
856
  <div><p>m(D) = min { # of maxima of h on D }</p>
@@ -767,7 +870,7 @@ traditional bridge number. Examples:</p>
767
870
 
768
871
  <dl class="py method">
769
872
  <dt class="sig sig-object py" id="spherogram.Link.optimize_overcrossings">
770
- <span class="sig-name descname"><span class="pre">optimize_overcrossings</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.optimize_overcrossings" title="Permalink to this definition">¶</a></dt>
873
+ <span class="sig-name descname"><span class="pre">optimize_overcrossings</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.optimize_overcrossings" title="Link to this definition"></a></dt>
771
874
  <dd><p>Minimizes the number of crossings of a strand which crosses entirely
772
875
  above the diagram by finding the path crossing over the diagram with
773
876
  the least number of overcrossings. It begins with the longest
@@ -791,7 +894,7 @@ reduces the number of crossings. Returns number of crossings removed.</p>
791
894
 
792
895
  <dl class="py method">
793
896
  <dt class="sig sig-object py" id="spherogram.Link.overstrands">
794
- <span class="sig-name descname"><span class="pre">overstrands</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.overstrands" title="Permalink to this definition">¶</a></dt>
897
+ <span class="sig-name descname"><span class="pre">overstrands</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.overstrands" title="Link to this definition"></a></dt>
795
898
  <dd><p>Returns a list of the sequences of overcrossings (which are lists of
796
899
  CrossingEntryPoints), sorted in descending order of length.</p>
797
900
  <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">L</span> <span class="o">=</span> <span class="n">Link</span><span class="p">(</span><span class="s1">&#39;L14n1000&#39;</span><span class="p">)</span>
@@ -803,12 +906,12 @@ CrossingEntryPoints), sorted in descending order of length.</p>
803
906
 
804
907
  <dl class="py method">
805
908
  <dt class="sig sig-object py" id="spherogram.Link.peer_code">
806
- <span class="sig-name descname"><span class="pre">peer_code</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.peer_code" title="Permalink to this definition">¶</a></dt>
909
+ <span class="sig-name descname"><span class="pre">peer_code</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.peer_code" title="Link to this definition"></a></dt>
807
910
  <dd></dd></dl>
808
911
 
809
912
  <dl class="py method">
810
913
  <dt class="sig sig-object py" id="spherogram.Link.sage_link">
811
- <span class="sig-name descname"><span class="pre">sage_link</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.sage_link" title="Permalink to this definition">¶</a></dt>
914
+ <span class="sig-name descname"><span class="pre">sage_link</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.sage_link" title="Link to this definition"></a></dt>
812
915
  <dd><p>Convert to a SageMath Knot or Link:</p>
813
916
  <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sage</span><span class="p">:</span> <span class="n">L</span> <span class="o">=</span> <span class="n">Link</span><span class="p">(</span><span class="s1">&#39;K10n11&#39;</span><span class="p">)</span> <span class="c1"># Spherogram link</span>
814
917
  <span class="n">sage</span><span class="p">:</span> <span class="n">K</span> <span class="o">=</span> <span class="n">L</span><span class="o">.</span><span class="n">sage_link</span><span class="p">();</span> <span class="n">K</span>
@@ -820,23 +923,30 @@ CrossingEntryPoints), sorted in descending order of length.</p>
820
923
  </pre></div>
821
924
  </div>
822
925
  <p>Can also go the other way:</p>
823
- <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sage</span><span class="p">:</span> <span class="n">B</span> <span class="o">=</span> <span class="n">BraidGroup</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span>
824
- <span class="n">sage</span><span class="p">:</span> <span class="n">a</span><span class="p">,</span> <span class="n">b</span><span class="p">,</span> <span class="n">c</span> <span class="o">=</span> <span class="n">B</span><span class="o">.</span><span class="n">gens</span><span class="p">()</span>
825
- <span class="n">sage</span><span class="p">:</span> <span class="n">Link</span><span class="p">(</span><span class="n">braid_closure</span><span class="o">=</span><span class="p">(</span><span class="n">a</span><span class="o">**-</span><span class="mi">3</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">b</span><span class="o">**</span><span class="mi">4</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">c</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span> <span class="o">*</span> <span class="n">a</span> <span class="o">*</span> <span class="n">b</span> <span class="o">*</span> <span class="n">c</span> <span class="p">)</span>
826
- <span class="o">&lt;</span><span class="n">Link</span><span class="p">:</span> <span class="mi">2</span> <span class="n">comp</span><span class="p">;</span> <span class="mi">12</span> <span class="n">cross</span><span class="o">&gt;</span>
827
- <span class="n">sage</span><span class="p">:</span> <span class="n">L</span> <span class="o">=</span> <span class="n">Link</span><span class="p">(</span><span class="n">a</span> <span class="o">*</span> <span class="n">b</span> <span class="o">*</span> <span class="n">c</span><span class="p">);</span> <span class="n">L</span>
828
- <span class="o">&lt;</span><span class="n">Link</span><span class="p">:</span> <span class="mi">1</span> <span class="n">comp</span><span class="p">;</span> <span class="mi">3</span> <span class="n">cross</span><span class="o">&gt;</span>
829
- <span class="n">sage</span><span class="p">:</span> <span class="n">S</span> <span class="o">=</span> <span class="n">L</span><span class="o">.</span><span class="n">sage_link</span><span class="p">();</span> <span class="n">S</span>
830
- <span class="n">Knot</span> <span class="n">represented</span> <span class="n">by</span> <span class="mi">3</span> <span class="n">crossings</span>
831
- <span class="n">sage</span><span class="p">:</span> <span class="n">Link</span><span class="p">(</span><span class="n">S</span><span class="p">)</span>
832
- <span class="o">&lt;</span><span class="n">Link</span><span class="p">:</span> <span class="mi">1</span> <span class="n">comp</span><span class="p">;</span> <span class="mi">3</span> <span class="n">cross</span><span class="o">&gt;</span>
926
+ <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sage</span><span class="p">:</span> <span class="n">L</span> <span class="o">=</span> <span class="n">Link</span><span class="p">(</span><span class="s1">&#39;K11n11&#39;</span><span class="p">)</span>
927
+ <span class="n">sage</span><span class="p">:</span> <span class="n">M</span> <span class="o">=</span> <span class="n">Link</span><span class="p">(</span><span class="n">L</span><span class="o">.</span><span class="n">sage_link</span><span class="p">())</span>
928
+ <span class="n">sage</span><span class="p">:</span> <span class="n">L</span><span class="o">.</span><span class="n">signature</span><span class="p">(),</span> <span class="n">M</span><span class="o">.</span><span class="n">signature</span><span class="p">()</span>
929
+ <span class="p">(</span><span class="o">-</span><span class="mi">2</span><span class="p">,</span> <span class="o">-</span><span class="mi">2</span><span class="p">)</span>
833
930
  </pre></div>
834
931
  </div>
932
+ <p>Can also take a braid group perspective.</p>
933
+ <blockquote>
934
+ <div><p>sage: B = BraidGroup(4)
935
+ sage: a, b, c = B.gens()
936
+ sage: Link(braid_closure=(a**-3) * (b**4) * (c**2) * a * b * c )
937
+ &lt;Link: 2 comp; 12 cross&gt;
938
+ sage: L = Link(a * b * c); L
939
+ &lt;Link: 1 comp; 3 cross&gt;
940
+ sage: S = L.sage_link(); S
941
+ Knot represented by 3 crossings
942
+ sage: Link(S)
943
+ &lt;Link: 1 comp; 3 cross&gt;</p>
944
+ </div></blockquote>
835
945
  </dd></dl>
836
946
 
837
947
  <dl class="py method">
838
948
  <dt class="sig sig-object py" id="spherogram.Link.seifert_matrix">
839
- <span class="sig-name descname"><span class="pre">seifert_matrix</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.seifert_matrix" title="Permalink to this definition">¶</a></dt>
949
+ <span class="sig-name descname"><span class="pre">seifert_matrix</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.seifert_matrix" title="Link to this definition"></a></dt>
840
950
  <dd><p>Returns the Seifert matrix of the link:</p>
841
951
  <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sage</span><span class="p">:</span> <span class="n">L</span> <span class="o">=</span> <span class="n">Link</span><span class="p">(</span><span class="s1">&#39;K10n11&#39;</span><span class="p">)</span>
842
952
  <span class="n">sage</span><span class="p">:</span> <span class="n">A</span> <span class="o">=</span> <span class="n">L</span><span class="o">.</span><span class="n">seifert_matrix</span><span class="p">()</span>
@@ -855,7 +965,7 @@ from a braid representation.” (2007).</p>
855
965
 
856
966
  <dl class="py method">
857
967
  <dt class="sig sig-object py" id="spherogram.Link.signature">
858
- <span class="sig-name descname"><span class="pre">signature</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">new_convention</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.signature" title="Permalink to this definition">¶</a></dt>
968
+ <span class="sig-name descname"><span class="pre">signature</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">new_convention</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.signature" title="Link to this definition"></a></dt>
859
969
  <dd><p>Returns the signature of the link, computed from the Goeritz matrix using
860
970
  the algorithm of Gordon and Litherland:</p>
861
971
  <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sage</span><span class="p">:</span> <span class="n">K</span> <span class="o">=</span> <span class="n">Link</span><span class="p">(</span><span class="s1">&#39;4a1&#39;</span><span class="p">)</span>
@@ -884,7 +994,7 @@ recover the previous default by:</p>
884
994
 
885
995
  <dl class="py method">
886
996
  <dt class="sig sig-object py" id="spherogram.Link.simplify">
887
- <span class="sig-name descname"><span class="pre">simplify</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mode</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'basic'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">type_III_limit</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.simplify" title="Permalink to this definition">¶</a></dt>
997
+ <span class="sig-name descname"><span class="pre">simplify</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mode</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'basic'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">type_III_limit</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.simplify" title="Link to this definition"></a></dt>
888
998
  <dd><p>Tries to simplify the link projection. Returns whether it succeeded
889
999
  in reducing the number of crossings. Modifies the link in
890
1000
  place, and unknot components which are also unlinked may be
@@ -940,7 +1050,7 @@ overcrossings (or undercrossings); this has the effect of doing
940
1050
 
941
1051
  <dl class="py method">
942
1052
  <dt class="sig sig-object py" id="spherogram.Link.split_link_diagram">
943
- <span class="sig-name descname"><span class="pre">split_link_diagram</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">destroy_original</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.split_link_diagram" title="Permalink to this definition">¶</a></dt>
1053
+ <span class="sig-name descname"><span class="pre">split_link_diagram</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">destroy_original</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.split_link_diagram" title="Link to this definition"></a></dt>
944
1054
  <dd><p>Breaks the given link diagram into pieces, one for each connected
945
1055
  component of the underlying 4-valent graph.</p>
946
1056
  <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">L</span> <span class="o">=</span> <span class="n">Link</span><span class="p">([(</span><span class="mi">2</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">),</span> <span class="p">(</span><span class="mi">4</span><span class="p">,</span><span class="mi">3</span><span class="p">,</span><span class="mi">3</span><span class="p">,</span><span class="mi">4</span><span class="p">)],</span> <span class="n">check_planarity</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
@@ -952,7 +1062,7 @@ component of the underlying 4-valent graph.</p>
952
1062
 
953
1063
  <dl class="py method">
954
1064
  <dt class="sig sig-object py" id="spherogram.Link.sublink">
955
- <span class="sig-name descname"><span class="pre">sublink</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">components</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.sublink" title="Permalink to this definition">¶</a></dt>
1065
+ <span class="sig-name descname"><span class="pre">sublink</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">components</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.sublink" title="Link to this definition"></a></dt>
956
1066
  <dd><p>Returns the sublink consisting of the specified components; see the
957
1067
  example below for the various accepted forms.</p>
958
1068
  <p>Warnings: Components in the sublink that are both unknotted
@@ -985,7 +1095,7 @@ in the original link.</p>
985
1095
 
986
1096
  <dl class="py method">
987
1097
  <dt class="sig sig-object py" id="spherogram.Link.view">
988
- <span class="sig-name descname"><span class="pre">view</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">viewer</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_crossing_labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.view" title="Permalink to this definition">¶</a></dt>
1098
+ <span class="sig-name descname"><span class="pre">view</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">viewer</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_crossing_labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.view" title="Link to this definition"></a></dt>
989
1099
  <dd><p>Opens a Plink link viewer window displaying the current link.
990
1100
  The strands of the links are unions of edges in the standard
991
1101
  integer grid, following the work of <a class="reference external" href="https://dx.doi.org/10.1137/0216030">Tamassia</a> and <a class="reference external" href="ftp://ftp.cs.brown.edu/pub/techreports/99/cs99-04.pdf">Bridgeman
@@ -994,7 +1104,7 @@ et. al.</a></p>
994
1104
 
995
1105
  <dl class="py method">
996
1106
  <dt class="sig sig-object py" id="spherogram.Link.white_graph">
997
- <span class="sig-name descname"><span class="pre">white_graph</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.white_graph" title="Permalink to this definition">¶</a></dt>
1107
+ <span class="sig-name descname"><span class="pre">white_graph</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.white_graph" title="Link to this definition"></a></dt>
998
1108
  <dd><p>Return the white graph of a non-split link projection.</p>
999
1109
  <p>This method generates a multigraph whose vertices correspond
1000
1110
  to the faces of the diagram, with an edge joining two
@@ -1029,7 +1139,7 @@ expected way.</p>
1029
1139
 
1030
1140
  <dl class="py method">
1031
1141
  <dt class="sig sig-object py" id="spherogram.Link.writhe">
1032
- <span class="sig-name descname"><span class="pre">writhe</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.writhe" title="Permalink to this definition">¶</a></dt>
1142
+ <span class="sig-name descname"><span class="pre">writhe</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.Link.writhe" title="Link to this definition"></a></dt>
1033
1143
  <dd><p>Finds the writhe of a knot.</p>
1034
1144
  <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">K</span> <span class="o">=</span> <span class="n">Link</span><span class="p">(</span> <span class="p">[(</span><span class="mi">4</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">5</span><span class="p">,</span><span class="mi">2</span><span class="p">),</span> <span class="p">(</span><span class="mi">6</span><span class="p">,</span><span class="mi">4</span><span class="p">,</span><span class="mi">7</span><span class="p">,</span><span class="mi">3</span><span class="p">),</span> <span class="p">(</span><span class="mi">8</span><span class="p">,</span><span class="mi">5</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">6</span><span class="p">),</span> <span class="p">(</span><span class="mi">2</span><span class="p">,</span><span class="mi">8</span><span class="p">,</span><span class="mi">3</span><span class="p">,</span><span class="mi">7</span><span class="p">)]</span> <span class="p">)</span> <span class="c1"># Figure 8 knot</span>
1035
1145
  <span class="gp">&gt;&gt;&gt; </span><span class="n">K</span><span class="o">.</span><span class="n">writhe</span><span class="p">()</span>
@@ -1042,13 +1152,13 @@ expected way.</p>
1042
1152
 
1043
1153
  </section>
1044
1154
  <section id="the-closedbraid-class">
1045
- <h2>The ClosedBraid class<a class="headerlink" href="#the-closedbraid-class" title="Permalink to this headline">¶</a></h2>
1155
+ <h2>The ClosedBraid class<a class="headerlink" href="#the-closedbraid-class" title="Link to this heading"></a></h2>
1046
1156
  <p>The ClosedBraid class provides an alternative way to construct links
1047
1157
  as closed braids. It is a subclass of Link, and currently defines
1048
1158
  the same methods and attributes.</p>
1049
1159
  <dl class="py class">
1050
1160
  <dt class="sig sig-object py" id="spherogram.ClosedBraid">
1051
- <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">spherogram.</span></span><span class="sig-name descname"><span class="pre">ClosedBraid</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.ClosedBraid" title="Permalink to this definition">¶</a></dt>
1161
+ <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">spherogram.</span></span><span class="sig-name descname"><span class="pre">ClosedBraid</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#spherogram.ClosedBraid" title="Link to this definition"></a></dt>
1052
1162
  <dd><p>This is a convenience class for constructing closed braids.</p>
1053
1163
  <p>The constructor accepts either a single argument, which should be a list of
1054
1164
  integers to be passed to the Link constructor as the braid_closure
@@ -1068,72 +1178,34 @@ and used as the braid_closure parameter.</p>
1068
1178
  </section>
1069
1179
 
1070
1180
 
1071
- <div class="clearer"></div>
1181
+ </div>
1072
1182
  </div>
1073
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1074
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1075
- <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
1076
- <div class="sphinxsidebarwrapper">
1077
- <h3><a href="index.html">Table of Contents</a></h3>
1078
- <ul>
1079
- <li><a class="reference internal" href="#">Links: planar diagrams and invariants</a><ul>
1080
- <li><a class="reference internal" href="#tutorial">Tutorial</a></li>
1081
- <li><a class="reference internal" href="#random-links">Random Links</a></li>
1082
- <li><a class="reference internal" href="#the-link-class">The Link class</a></li>
1083
- <li><a class="reference internal" href="#the-closedbraid-class">The ClosedBraid class</a></li>
1084
- </ul>
1085
- </li>
1086
- </ul>
1087
-
1088
- <h4>Previous topic</h4>
1089
- <p class="topless"><a href="plink.html"
1090
- title="previous chapter">Using SnapPy’s link editor</a></p>
1091
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1092
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- title="next chapter">Number theory of hyperbolic 3-manifolds</a></p>
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1095
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1096
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1097
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1098
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1099
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1102
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1185
+ <a href="snap.html" class="btn btn-neutral float-right" title="Number theory of hyperbolic 3-manifolds" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
1108
1186
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1109
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1187
+
1188
+ <hr/>
1189
+
1190
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1191
+ <p>&#169; Copyright 2009-2025, by Marc Culler, Nathan Dunfield, Matthias Goerner, Jeffrey Weeks and others.</p>
1192
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1193
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1120
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