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
  355. snappy/verify/interval_newton_shapes_engine.py +51 -211
  356. snappy/verify/interval_tree.py +27 -25
  357. snappy/verify/krawczyk_shapes_engine.py +47 -50
  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
  363. snappy/verify/short_slopes.py +41 -42
  364. snappy/verify/{squareExtensions.py → square_extensions.py} +96 -92
  365. snappy/verify/test.py +59 -57
  366. snappy/verify/upper_halfspace/extended_matrix.py +5 -5
  367. snappy/verify/upper_halfspace/finite_point.py +44 -31
  368. snappy/verify/upper_halfspace/ideal_point.py +69 -57
  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
  372. snappy-3.2.dist-info/RECORD +503 -0
  373. {snappy-3.0.3.dist-info → snappy-3.2.dist-info}/WHEEL +1 -1
  374. {snappy-3.0.3.dist-info → snappy-3.2.dist-info}/entry_points.txt +0 -1
  375. {snappy-3.0.3.dist-info → snappy-3.2.dist-info}/top_level.txt +10 -1
  376. snappy/doc/_sources/verify_canon.rst.txt +0 -90
  377. snappy/doc/_static/classic.css +0 -266
  378. snappy/doc/_static/jquery-3.5.1.js +0 -10872
  379. snappy/doc/_static/sidebar.js +0 -159
  380. snappy/doc/_static/underscore-1.13.1.js +0 -2042
  381. snappy/doc/_static/underscore.js +0 -6
  382. snappy/doc/verify_canon.html +0 -283
  383. snappy/ppm_to_png.py +0 -243
  384. snappy/togl/__init__.py +0 -3
  385. snappy/togl/darwin-tk8.6/Togl2.1/LICENSE +0 -28
  386. snappy/togl/darwin-tk8.6/Togl2.1/libTogl2.1.dylib +0 -0
  387. snappy/togl/darwin-tk8.6/Togl2.1/pkgIndex.tcl +0 -5
  388. snappy/togl/linux2-x86_64-tk8.6/Togl2.1/LICENSE +0 -28
  389. snappy/togl/linux2-x86_64-tk8.6/Togl2.1/libTogl2.1.so +0 -0
  390. snappy/togl/linux2-x86_64-tk8.6/Togl2.1/pkgIndex.tcl +0 -5
  391. snappy/togl/win32VC-tk8.6/Togl2.1/LICENSE +0 -28
  392. snappy/togl/win32VC-tk8.6/Togl2.1/Togl21.dll +0 -0
  393. snappy/togl/win32VC-tk8.6/Togl2.1/Togl21.lib +0 -0
  394. snappy/togl/win32VC-tk8.6/Togl2.1/pkgIndex.tcl +0 -6
  395. snappy/togl/win32VC-x86_64-tk8.6/Togl2.1/LICENSE +0 -28
  396. snappy/togl/win32VC-x86_64-tk8.6/Togl2.1/Togl21.dll +0 -0
  397. snappy/togl/win32VC-x86_64-tk8.6/Togl2.1/Togl21.lib +0 -0
  398. snappy/togl/win32VC-x86_64-tk8.6/Togl2.1/pkgIndex.tcl +0 -6
  399. snappy/verify/cuspCrossSection.py +0 -1413
  400. snappy/verify/mathHelpers.py +0 -64
  401. snappy-3.0.3.dist-info/RECORD +0 -360
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+ <li class="toctree-l2"><a class="reference internal" href="#windows">Windows</a></li>
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+ <li class="toctree-l2"><a class="reference internal" href="#linux-app">Linux app</a></li>
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+ <li class="toctree-l2"><a class="reference internal" href="#python-modules-for-macos-or-windows">Python Modules for macOS or Windows</a></li>
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+ <li class="toctree-l2"><a class="reference internal" href="#python-modules-for-linux">Python Modules for Linux</a></li>
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+ <li class="toctree-l2"><a class="reference internal" href="#sagemath">SageMath</a></li>
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+ <li class="toctree-l2"><a class="reference internal" href="#kitchen-sink">Kitchen sink</a></li>
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+ <li class="toctree-l2"><a class="reference internal" href="#conda">Conda</a></li>
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+ <li class="toctree-l2"><a class="reference internal" href="#source-code">Source code</a></li>
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+ </ul>
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+ </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"><a class="reference internal" href="spherogram.html">Links: planar diagrams and invariants</a></li>
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+ <li class="toctree-l1"><a class="reference internal" href="snap.html">Number theory of hyperbolic 3-manifolds</a></li>
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+ <li class="toctree-l1"><a class="reference internal" href="development.html">Development Basics</a></li>
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  <section id="installing-snappy">
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- <h1>Installing SnapPy<a class="headerlink" href="#installing-snappy" title="Permalink to this headline">¶</a></h1>
100
+ <h1>Installing SnapPy<a class="headerlink" href="#installing-snappy" title="Link to this heading"></a></h1>
50
101
  <p>Here are detailed instructions on how to get SnapPy working on a
51
- variety of platforms. The current version is 3.0.3 which was released
52
- on December 2021. If you encounter problems installing SnapPy,
102
+ variety of platforms. The current version is 3.2 which was released
103
+ on January 2025. If you encounter any problems installing SnapPy,
53
104
  <a class="reference internal" href="bugs.html"><span class="doc">please let us know</span></a>.</p>
54
105
  <section id="macos">
55
- <h2>macOS<a class="headerlink" href="#macos" title="Permalink to this headline">¶</a></h2>
106
+ <h2>macOS<a class="headerlink" href="#macos" title="Link to this heading"></a></h2>
56
107
  <p>Simply download <a class="reference external" href="https://github.com/3-manifolds/SnapPy/releases/latest/download/SnapPy.dmg">SnapPy.dmg</a>
57
108
  and copy SnapPy.app to the Applications folder. Double-click to start
58
- it, just like any other application. Works with macOS/OS X 10.9 and
59
- newer. Earlier releases <a class="reference external" href="https://github.com/3-manifolds/SnapPy/releases/">can be found here</a>.</p>
109
+ it, just like any other application. The current version works with macOS 10.14 and
110
+ newer and earlier releases <a class="reference external" href="https://github.com/3-manifolds/SnapPy/releases/">can be found here</a>.</p>
60
111
  </section>
61
112
  <section id="windows">
62
- <h2>Windows<a class="headerlink" href="#windows" title="Permalink to this headline">¶</a></h2>
113
+ <h2>Windows<a class="headerlink" href="#windows" title="Link to this heading"></a></h2>
63
114
  <p>Simply download and run <a class="reference external" href="https://github.com/3-manifolds/SnapPy/releases/latest/download/InstallSnapPy.exe">InstallSnapPy.exe</a>.
64
115
  Earlier releases <a class="reference external" href="https://github.com/3-manifolds/SnapPy/releases/">can be found here</a>.</p>
65
116
  </section>
66
- <section id="linux">
67
- <h2>Linux<a class="headerlink" href="#linux" title="Permalink to this headline">¶</a></h2>
68
- <p>Here are short recipes which work on most Linux systems, specifically
69
- those that run a 64-bit kernel and have Python 3.6 or newer. These
70
- instructions assume you have system administrator (superuser)
71
- privileges to install software packages from your Linux distribution
72
- but want to install SnapPy (and its various Python dependencies) just
73
- in your own user directory, specifically <code class="docutils literal notranslate"><span class="pre">~/.local</span></code>. For other
74
- Linux systems, try the one closest to yours below, and if that fails,
75
- follow the instructions for <a class="reference internal" href="#generic-unix">generic Unix</a>.</p>
76
- <ul>
77
- <li><p><strong>Ubuntu/Debian/Mint</strong>: Tested on Ubuntu 20.04:</p>
78
- <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">apt</span><span class="o">-</span><span class="n">get</span> <span class="n">install</span> <span class="n">python3</span><span class="o">-</span><span class="n">tk</span> <span class="n">python3</span><span class="o">-</span><span class="n">pip</span>
79
- <span class="c1"># Note no &quot;sudo&quot; on the next one!</span>
80
- <span class="n">python3</span> <span class="o">-</span><span class="n">m</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">upgrade</span> <span class="o">--</span><span class="n">user</span> <span class="n">snappy</span>
117
+ <section id="linux-app">
118
+ <h2>Linux app<a class="headerlink" href="#linux-app" title="Link to this heading"></a></h2>
119
+ <p>Starting with SnapPy 3.2, a completely self-contained SnapPy <a class="reference external" href="https://docs.appimage.org/introduction/quickstart.html#ref-quickstart">AppImage</a>
120
+ is available that should work on any Linux system from the last 5
121
+ years. This AppImage contains its own private copy of Python, so if
122
+ you plan to use SnapPy in your own Python programs, skip ahead to
123
+ <a class="reference internal" href="#python-modules-for-linux">Python Modules for Linux</a>. Here is the recipe for installing the
124
+ AppImage in <code class="docutils literal notranslate"><span class="pre">~/bin</span></code> after you have downloaded the file
125
+ <a class="reference external" href="https://github.com/3-manifolds/SnapPy/releases/latest/download/SnapPy-x86_64.AppImage.">SnapPy-x86_64.AppImage</a>:</p>
126
+ <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mkdir</span> <span class="o">-</span><span class="n">p</span> <span class="o">~/</span><span class="nb">bin</span>
127
+ <span class="n">mv</span> <span class="o">~/</span><span class="n">Downloads</span><span class="o">/</span><span class="n">SnapPy</span><span class="o">-</span><span class="n">x86_64</span><span class="o">.</span><span class="n">AppImage</span> <span class="o">~/</span><span class="nb">bin</span>
128
+ <span class="n">chmod</span> <span class="o">+</span><span class="n">x</span> <span class="o">~/</span><span class="nb">bin</span><span class="o">/</span><span class="n">SnapPy</span><span class="o">-</span><span class="n">x86_64</span><span class="o">.</span><span class="n">AppImage</span>
129
+ <span class="n">ln</span> <span class="o">-</span><span class="n">s</span> <span class="o">-</span><span class="n">f</span> <span class="o">~/</span><span class="nb">bin</span><span class="o">/</span><span class="n">SnapPy</span><span class="o">-</span><span class="n">x86_64</span><span class="o">.</span><span class="n">AppImage</span> <span class="o">~/</span><span class="nb">bin</span><span class="o">/</span><span class="n">SnapPy</span>
130
+ <span class="o">~/</span><span class="nb">bin</span><span class="o">/</span><span class="n">SnapPy</span><span class="o">-</span><span class="n">x86_64</span><span class="o">.</span><span class="n">AppImage</span> <span class="o">--</span><span class="n">install</span>
81
131
  </pre></div>
82
132
  </div>
83
- <p>Users of Ubuntu 18.04 or older should do:</p>
84
- <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">apt</span><span class="o">-</span><span class="n">get</span> <span class="n">install</span> <span class="n">python3</span><span class="o">-</span><span class="n">tk</span> <span class="n">python3</span><span class="o">-</span><span class="n">pip</span>
85
- <span class="c1"># Note no &quot;sudo&quot; on the next two</span>
86
- <span class="n">python3</span> <span class="o">-</span><span class="n">m</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">upgrade</span> <span class="o">--</span><span class="n">user</span> <span class="n">pip</span> <span class="n">wheel</span>
87
- <span class="n">python3</span> <span class="o">-</span><span class="n">m</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">upgrade</span> <span class="o">--</span><span class="n">user</span> <span class="n">snappy</span>
133
+ <p>The last command registers the SnapPy app with your desktop system and
134
+ starts it. Next time, you can start SnapPy by using the desktop
135
+ search tool with GNOME or the main menu with KDE. You can pin also the icon
136
+ to your dash or task bar for easy access. From a terminal window, you
137
+ can also start the app by typing <code class="docutils literal notranslate"><span class="pre">SnapPy</span></code> provided <code class="docutils literal notranslate"><span class="pre">~/bin</span></code> is in
138
+ your <a class="reference external" href="https://opensource.com/article/17/6/set-path-linux">$PATH</a>.</p>
139
+ </section>
140
+ <section id="python-modules-for-macos-or-windows">
141
+ <h2>Python Modules for macOS or Windows<a class="headerlink" href="#python-modules-for-macos-or-windows" title="Link to this heading"></a></h2>
142
+ <p>If you write Python programs on macOS or Windows, you may wish to
143
+ install SnapPy as a Python module into your own copy of Python. We
144
+ support Python 3.9 and up. (On macOS, use a Python downloaded from
145
+ <a class="reference external" href="http://python.org">Python.org</a> and not the one provided by Apple.)
146
+ After installing Python, you may install a SnapPy module from your
147
+ Terminal application or Command Prompt with the command:</p>
148
+ <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python3</span> <span class="o">-</span><span class="n">m</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">upgrade</span> <span class="o">--</span><span class="n">user</span> <span class="n">snappy</span> <span class="n">snappy_15_knots</span>
88
149
  </pre></div>
89
150
  </div>
90
- </li>
91
- <li><p><strong>Fedora</strong>: Tested on Fedora 30:</p>
92
- <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">yum</span> <span class="n">install</span> <span class="n">python3</span><span class="o">-</span><span class="n">tkinter</span> <span class="n">python3</span><span class="o">-</span><span class="n">pip</span>
93
- <span class="c1"># Note no &quot;sudo&quot; on the next one!</span>
94
- <span class="n">python3</span> <span class="o">-</span><span class="n">m</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">upgrade</span> <span class="o">--</span><span class="n">user</span> <span class="n">snappy</span>
151
+ <p>If you do not want the larger version of HTLinkExteriors that includes
152
+ the 15 crossing knots (it uses 110M of disk space), omit
153
+ <code class="docutils literal notranslate"><span class="pre">snappy_15_knots</span></code> from the command.</p>
154
+ </section>
155
+ <section id="python-modules-for-linux">
156
+ <h2>Python Modules for Linux<a class="headerlink" href="#python-modules-for-linux" title="Link to this heading"></a></h2>
157
+ <p>You can also use SnapPy with your Linux system’s version of Python,
158
+ for example if you want to incorporate SnapPy in your own Python
159
+ scripts. These instructions assume you have system administrator
160
+ (superuser) privileges to install software packages from your Linux
161
+ distribution. (If you’re not a superuser, use either the
162
+ <a class="reference internal" href="#linux-app">Linux app</a> or <a class="reference internal" href="#conda">conda</a>.)</p>
163
+ <p>The first step is to install Python and other requirements; here’s how
164
+ to do that on the most popular Linux distributions:</p>
165
+ <ul>
166
+ <li><p><strong>Ubuntu/Debian/Mint/MX Linux/Elementary:</strong> Tested on Ubuntu 24.04:</p>
167
+ <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">apt</span> <span class="n">install</span> <span class="n">python3</span><span class="o">-</span><span class="n">pip</span> <span class="n">python3</span><span class="o">-</span><span class="n">tk</span>
95
168
  </pre></div>
96
169
  </div>
97
170
  </li>
98
- <li><p><strong>Red Hat Enterprise Linux/CentOS/SciLinux</strong>: These instructions
99
- are for version 7 or later, and you need to have the <a class="reference external" href="https://fedoraproject.org/wiki/EPEL#How_can_I_use_these_extra_packages.3F">EPEL packages
100
- available</a>.
101
- For CentOS and SciLinux, you can access EPEL packages by doing:</p>
102
- <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">yum</span> <span class="n">install</span> <span class="n">epel</span><span class="o">-</span><span class="n">release</span>
171
+ <li><p><strong>Fedora</strong>: Tested on Fedora 41:</p>
172
+ <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">dnf</span> <span class="n">install</span> <span class="n">python3</span><span class="o">-</span><span class="n">pip</span> <span class="n">python3</span><span class="o">-</span><span class="n">tkinter</span>
103
173
  </pre></div>
104
174
  </div>
105
- <p>Now install via:</p>
106
- <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">yum</span> <span class="n">install</span> <span class="n">python36</span><span class="o">-</span><span class="n">tkinter</span> <span class="n">python36</span><span class="o">-</span><span class="n">pip</span>
107
- <span class="c1"># Note no &quot;sudo&quot; on the next one!</span>
108
- <span class="n">python36</span> <span class="o">-</span><span class="n">m</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">upgrade</span> <span class="o">--</span><span class="n">user</span> <span class="n">snappy</span>
175
+ </li>
176
+ <li><p><strong>Arch/Manjaro/EndeavourOS</strong>: Install via:</p>
177
+ <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">pacman</span> <span class="o">-</span><span class="n">Sy</span> <span class="n">python</span><span class="o">-</span><span class="n">pip</span> <span class="n">tk</span>
109
178
  </pre></div>
110
179
  </div>
111
180
  </li>
112
- <li><p><strong>Arch/Manjaro</strong>: Install via:</p>
113
- <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">pacman</span> <span class="o">-</span><span class="n">Sy</span> <span class="n">python</span><span class="o">-</span><span class="n">pip</span> <span class="n">tk</span>
114
- <span class="c1"># Note no &quot;sudo&quot; on the next one!</span>
115
- <span class="n">python</span> <span class="o">-</span><span class="n">m</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">upgrade</span> <span class="o">--</span><span class="n">user</span> <span class="n">snappy</span>
181
+ <li><p><strong>openSUSE</strong>: For Tumbleweed:</p>
182
+ <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">zypper</span> <span class="n">install</span> <span class="n">python3</span><span class="o">-</span><span class="n">pip</span> <span class="n">python3</span><span class="o">-</span><span class="n">tk</span>
183
+ </pre></div>
184
+ </div>
185
+ <p>For Leap, as of version 15.6 you need to ask for a recent version of
186
+ Python or it will give you Python 3.6 which is too old for SnapPy:</p>
187
+ <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">zypper</span> <span class="n">install</span> <span class="n">python312</span><span class="o">-</span><span class="n">pip</span> <span class="n">python312</span><span class="o">-</span><span class="n">tk</span>
116
188
  </pre></div>
117
189
  </div>
190
+ <p>You will need to replace <code class="docutils literal notranslate"><span class="pre">python3</span></code> by <code class="docutils literal notranslate"><span class="pre">python3.12</span></code> in subsequent
191
+ steps.</p>
118
192
  </li>
119
- <li><p><strong>openSUSE</strong>: Install via:</p>
120
- <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">zypper</span> <span class="n">install</span> <span class="o">-</span><span class="n">y</span> <span class="n">python3</span><span class="o">-</span><span class="n">tk</span> <span class="n">python3</span><span class="o">-</span><span class="n">pip</span>
121
- <span class="c1"># Note no &quot;sudo&quot; on the next one!</span>
122
- <span class="n">python3</span> <span class="o">-</span><span class="n">m</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">upgrade</span> <span class="o">--</span><span class="n">user</span> <span class="n">snappy</span>
193
+ <li><p><strong>Red Hat Enterprise Linux/CentOS/Rocky Linux/AlmaLinux:</strong>: These instructions
194
+ are for version 8 or later; tested on AlmaLinux 8 and 9:</p>
195
+ <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">dnf</span> <span class="n">install</span> <span class="n">python3</span><span class="mf">.11</span><span class="o">-</span><span class="n">pip</span> <span class="n">python3</span><span class="mf">.11</span><span class="o">-</span><span class="n">tkinter</span>
123
196
  </pre></div>
124
197
  </div>
198
+ <p>You will also need to replace <code class="docutils literal notranslate"><span class="pre">python3</span></code> by <code class="docutils literal notranslate"><span class="pre">python3.11</span></code> in subsequent
199
+ steps.</p>
125
200
  </li>
126
201
  </ul>
127
- <p>If you want the larger version of HTLinkExteriors that includes the 15
128
- crossing knots (uses 110M of disk space), also install the Python
129
- package <code class="docutils literal notranslate"><span class="pre">snappy_15_knots</span></code>, e.g. on Ubuntu do:</p>
130
- <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python3</span> <span class="o">-</span><span class="n">m</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">upgrade</span> <span class="o">--</span><span class="n">user</span> <span class="n">snappy_15_knots</span>
202
+ <p>Next, you need to install the SnapPy Python modules. For this, you can
203
+ either use a <em>virtual environment</em> (<code class="docutils literal notranslate"><span class="pre">python</span> <span class="pre">-m</span> <span class="pre">venv</span></code>) or do a <em>user
204
+ install</em> (<code class="docutils literal notranslate"><span class="pre">pip</span> <span class="pre">install</span> <span class="pre">--user</span></code>). The former will work on any
205
+ version of Linux, whereas the latter is now strongly discouraged on
206
+ many systems (e.g. Ubuntu 24.04). If you have not previously
207
+ installed SnapPy on this computer, we recommend using a virtual
208
+ environment, but suggest a user install if you are upgrading an
209
+ existing version of SnapPy that was installed in that manner.</p>
210
+ <dl>
211
+ <dt>Virtual environment</dt><dd><p>Here is the <a class="reference external" href="https://docs.python.org/3/tutorial/venv.html">official tutorial</a> on using virtual
212
+ environments in Python and an <a class="reference external" href="https://realpython.com/python-virtual-environments-a-primer/">in-depth article</a>. A
213
+ recipe is:</p>
214
+ <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python3</span> <span class="o">-</span><span class="n">m</span> <span class="n">venv</span> <span class="n">snappy_venv</span>
215
+ <span class="c1"># Switch to snappy_venv&#39;s Python</span>
216
+ <span class="n">source</span> <span class="n">snappy_venv</span><span class="o">/</span><span class="nb">bin</span><span class="o">/</span><span class="n">activate</span>
217
+ <span class="n">pip</span> <span class="n">install</span> <span class="n">snappy</span> <span class="n">snappy_15_knots</span>
218
+ <span class="c1"># Start the SnapPy app!</span>
219
+ <span class="n">SnapPy</span>
220
+ <span class="c1"># Return to system Python</span>
221
+ <span class="n">deactivate</span>
131
222
  </pre></div>
132
223
  </div>
133
- <p>Once you have installed SnapPy, do the following to start it:</p>
134
- <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">~/.</span><span class="n">local</span><span class="o">/</span><span class="nb">bin</span><span class="o">/</span><span class="n">SnapPy</span>
224
+ <p>If you always want to use the <code class="docutils literal notranslate"><span class="pre">snappy_venv</span></code> Python, adjust your
225
+ <a class="reference external" href="https://opensource.com/article/17/6/set-path-linux">$PATH</a> to
226
+ <strong>start</strong> with <code class="docutils literal notranslate"><span class="pre">snappy_venv/bin</span></code>.</p>
227
+ </dd>
228
+ <dt>User install</dt><dd><p>To do a user install with pip, try:</p>
229
+ <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># Note no &quot;sudo&quot; below!</span>
230
+ <span class="n">python3</span> <span class="o">-</span><span class="n">m</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">upgrade</span> <span class="o">--</span><span class="n">user</span> <span class="n">snappy</span> <span class="n">snappy_15_knots</span>
135
231
  </pre></div>
136
232
  </div>
137
- <p>You may get a message about creating a “.ipython” directory; this is
138
- normal, just hit return to continue. There should also now be a
139
- command “SnapPy” which does the same thing. To make it so that you
140
- can start SnapPy with just the command <code class="docutils literal notranslate"><span class="pre">SnapPy</span></code>, make sure
141
- <code class="docutils literal notranslate"><span class="pre">~/.local/bin</span></code> is in <a class="reference external" href="https://opensource.com/article/17/6/set-path-linux">in your path</a>.</p>
142
- </section>
143
- <section id="python-modules-for-macintosh-or-windows">
144
- <h2>Python Modules for Macintosh or Windows<a class="headerlink" href="#python-modules-for-macintosh-or-windows" title="Permalink to this headline">¶</a></h2>
145
- <p>If you write Python programs on a Macintosh or Windows system, you may
146
- wish to install SnapPy as a Python module into your own copy of
147
- Python. We support Python 3.6 and up. (On macOS, use a Python
148
- downloaded from <a class="reference external" href="http://python.org">Python.org</a> and not the one
149
- provided by Apple.) After installing Python, you may install a SnapPy
150
- module from your Terminal application or Command Prompt with the
151
- commands:</p>
152
- <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python3</span> <span class="o">-</span><span class="n">m</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">upgrade</span> <span class="o">--</span><span class="n">user</span> <span class="n">snappy</span>
233
+ <p>If you get a long error message that starts:</p>
234
+ <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">error</span><span class="p">:</span> <span class="n">externally</span><span class="o">-</span><span class="n">managed</span><span class="o">-</span><span class="n">environment</span>
153
235
  </pre></div>
154
236
  </div>
155
- <p>If you want the larger version of HTLinkExteriors that includes the 15
156
- crossing knots (uses 110M of disk space), do:</p>
157
- <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python3</span> <span class="o">-</span><span class="n">m</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">upgrade</span> <span class="o">--</span><span class="n">user</span> <span class="n">snappy_15_knots</span>
237
+ <p>you should probably use a virtual environment; however,
238
+ you can force pip to do a user install via:</p>
239
+ <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># Note no &quot;sudo&quot; below!</span>
240
+ <span class="n">python3</span> <span class="o">-</span><span class="n">m</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">upgrade</span> <span class="o">--</span><span class="n">user</span> <span class="o">--</span><span class="k">break</span><span class="o">-</span><span class="n">system</span><span class="o">-</span><span class="n">packages</span> <span class="n">snappy</span> <span class="n">snappy_15_knots</span>
158
241
  </pre></div>
159
242
  </div>
160
- <p>If you use Python 2 rather than Python 3, replace <code class="docutils literal notranslate"><span class="pre">python3</span></code> with
161
- <code class="docutils literal notranslate"><span class="pre">python</span></code> in the above. If your Python lacks the pip module, <a class="reference external" href="https://pip.pypa.io/en/stable/installing/">get it
162
- here</a>.</p>
243
+ <p>Despite the scary name, provided you don’t use <code class="docutils literal notranslate"><span class="pre">sudo</span></code>, this will
244
+ not actually modify the system packages, but rather install
245
+ <code class="docutils literal notranslate"><span class="pre">snappy</span></code> into the subdirectory
246
+ <code class="docutils literal notranslate"><span class="pre">~/.local/share/python3.*/site-packages</span></code> of your home directory.</p>
247
+ <p>After a user install, you run the following command to start
248
+ the app:</p>
249
+ <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">~/.</span><span class="n">local</span><span class="o">/</span><span class="nb">bin</span><span class="o">/</span><span class="n">SnapPy</span>
250
+ </pre></div>
251
+ </div>
252
+ <p>So that you can start SnapPy with just the command <code class="docutils literal notranslate"><span class="pre">SnapPy</span></code>, make
253
+ sure <code class="docutils literal notranslate"><span class="pre">~/.local/bin</span></code> is in <a class="reference external" href="https://opensource.com/article/17/6/set-path-linux">in your path</a>.</p>
254
+ </dd>
255
+ </dl>
163
256
  </section>
164
257
  <section id="sagemath">
165
- <h2>SageMath<a class="headerlink" href="#sagemath" title="Permalink to this headline">¶</a></h2>
258
+ <h2>SageMath<a class="headerlink" href="#sagemath" title="Link to this heading"></a></h2>
166
259
  <p>SnapPy has some special features when used within <a class="reference external" href="http://sagemath.org">SageMath</a>, the universal mathematics software based on
167
260
  Python. This section describes how to install SnapPy into your
168
- existing copy of SageMath, but you may find it easier to use the
169
- <a class="reference internal" href="#kitchen-sink">kitchen sink</a> approach instead. You can install it as a Sage
170
- optional package via the following if using Sage 6.4 or newer:</p>
171
- <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sage</span> <span class="o">-</span><span class="n">pip</span> <span class="n">install</span> <span class="n">snappy</span>
172
- <span class="n">sage</span> <span class="o">-</span><span class="n">pip</span> <span class="n">install</span> <span class="n">snappy_15_knots</span> <span class="c1"># Larger version of HTLinkExteriors</span>
261
+ existing copy of SageMath:</p>
262
+ <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sage</span> <span class="o">-</span><span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">upgrade</span> <span class="n">snappy</span> <span class="n">snappy_15_knots</span>
173
263
  </pre></div>
174
264
  </div>
175
- <p>If you are on macOS, we recommend use <a class="reference external" href="https://github.com/3-manifolds/Sage_macOS/releases">this binary</a>.</p>
176
265
  <p>Alternatively, SageMath on <a class="reference external" href="https://cocalc.com/">CoCalc</a> (formerly
177
266
  the SageMathCloud) also has SnapPy preinstalled, and the graphics
178
267
  features even work via the <a class="reference external" href="http://blog.sagemath.com/cocalc/2018/11/05/x11.html">X11 interface</a>, see the
179
268
  bottom of that page for more.</p>
180
- <p>If you previously installed SnapPy into SageMath and want to upgrade
181
- SnapPy to the latest version, do:</p>
182
- <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sage</span> <span class="o">-</span><span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">upgrade</span> <span class="n">snappy</span>
183
- </pre></div>
184
- </div>
185
- <p>If it has trouble when compiling CyOpenGL, you are probably missing
186
- the <cite>“gl.h” headers &lt;openglmesa&gt;</cite>. The graphical features may or may
187
- not work, depending on how Tkinter was configured within Sage, and may
188
- seem to “hang” when you try to start them. To deal with the latter
189
- issue type “%gui tk” at the Sage prompt; please note that doing so may
190
- break Sage’s “attach” feature.</p>
269
+ <p>The graphical features may or may not work, depending on how Tkinter
270
+ was configured within Sage. (There is no problem on macOS if you use
271
+ this <a class="reference external" href="https://github.com/3-manifolds/Sage_macOS/releases">SageMath binary</a>.) If the
272
+ graphical features seem to “hang” when you try to start them, type
273
+ <code class="docutils literal notranslate"><span class="pre">%gui</span> <span class="pre">tk</span></code> at the Sage prompt; please note that doing so may break
274
+ Sage’s “attach” feature.</p>
191
275
  </section>
192
276
  <section id="kitchen-sink">
193
- <h2>Kitchen sink<a class="headerlink" href="#kitchen-sink" title="Permalink to this headline">¶</a></h2>
277
+ <h2>Kitchen sink<a class="headerlink" href="#kitchen-sink" title="Link to this heading"></a></h2>
194
278
  <p>SnapPy gains extra features when used in <a class="reference external" href="http://sagemath.org">SageMath</a> and one can use
195
279
  Sage’s Python to interact not just with SnapPy but a range of other
196
280
  computational tools in low-dimensional topology including
@@ -200,76 +284,27 @@ computational tools in low-dimensional topology including
200
284
  <a class="reference external" href="https://github.com/3-manifolds/gridlink">gridlink</a>,
201
285
  and <a class="reference external" href="http://flipper.readthedocs.io">flipper</a>.
202
286
  We offer a <a class="reference external" href="https://hub.docker.com/r/computop/sage/">prepackaged Docker image</a> with all of the above tools
203
- and many more; using this is frequently the easiest way to get a
204
- working setup for such multifaceted computations. For more, watch
287
+ and many more; using this is sometimes the easiest way to get a
288
+ working setup for such multifaceted computations, especially on Windows. For more, watch
205
289
  <a class="reference external" href="https://icerm.brown.edu/video_archive/?play=1992">this demonstration</a>.</p>
206
- <p>We also offer <a class="reference external" href="https://github.com/unhyperbolic/condaForSnapPy">conda environments</a> with SnapPy and
207
- optionally Sage (only on Mac OS and Linux). While it has none of the
208
- other aforementioned tools, it has the advantage that the GUI elements
209
- such as the link editor and the browser can be used directly.</p>
210
290
  </section>
211
- <section id="generic-unix">
212
- <h2>Generic Unix<a class="headerlink" href="#generic-unix" title="Permalink to this headline">¶</a></h2>
213
- <p>If you use a Unix other than OS X or Linux, or if the prebuilt
214
- packages don’t work for you, you’ll need to build SnapPy from source.
215
- Here are some detailed instructions.</p>
216
- <p>Things you’ll need:</p>
217
- <ul>
218
- <li><p>Python 3 with Tkinter: You’ll need to have <a class="reference external" href="http://python.org">Python</a> (version 3.6 or newer) and <a class="reference external" href="http://tcl.tk">Tk</a> (at least version 8.5) with <a class="reference external" href="http://wiki.python.org/moin/TkInter">Tkinter</a> to connect them, including
219
- the header files. For instance, on Debian or Ubuntu, install the
220
- packages “python3-tk”, “python3-pip”, and “python3-dev”. On Fedora,
221
- you’ll want e.g. “python3-tkinter”, “python3-pip”, and
222
- “python3-devel”, and “python3-wheel”.</p></li>
223
- <li><p>Test that Python is in order by installing PLink from source:</p>
224
- <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python3</span> <span class="o">-</span><span class="n">m</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">user</span> <span class="n">plink</span>
225
- <span class="n">python3</span> <span class="o">-</span><span class="n">m</span> <span class="n">plink</span><span class="o">.</span><span class="n">app</span> <span class="c1"># Should start the link editor!</span>
226
- </pre></div>
227
- </div>
228
- </li>
229
- </ul>
230
- <ul id="openglmesa">
231
- <li><p>Support for OpenGL (3D graphics): This is built in on OS X and the
232
- most installations of Fedora and Ubuntu. But you’ll need the <a class="reference external" href="http://www.mesa3d.org/">MESA</a> header files “gl.h” and “glu.h” to compile
233
- SnapPy. On Debian and Ubuntu, install “libglu1-mesa-dev”; On Fedora install
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- “mesa-libGLU-devel”.</p></li>
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- <li><p><a class="reference external" href="http://cython.org">Cython</a>, which you can install via:</p>
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- <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python3</span> <span class="o">-</span><span class="n">m</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">user</span> <span class="n">cython</span>
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- </pre></div>
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- </div>
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- </li>
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- <li><p>The gcc C++ compiler, g++.</p></li>
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- <li><p><a class="reference external" href="https://pypi.python.org/pypi/cypari/">CyPari</a>: a stand-alone version of
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- <a class="reference external" href="http://sagemath.org">Sage’s</a> Python interface to the
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- <a class="reference external" href="http://pari.math.u-bordeaux.fr/PARI">PARI</a> number theory
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- library. Usually, you can install this with:</p>
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- <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python3</span> <span class="o">-</span><span class="n">m</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">user</span> <span class="n">cypari</span>
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- </pre></div>
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- </div>
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- </li>
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- </ul>
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- <p>Now download the <a class="reference internal" href="#source-code">source code</a> listed below, for instance</p>
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- <pre class="literal-block">wget <a class="reference external" href="https://pypi.python.org/packages/source/s/snappy/">https://pypi.python.org/packages/source/s/snappy/</a>snappy-3.0.3.tar.gz
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- tar xfz snappy-3.0.3.tar.gz; cd snappy-*</pre>
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- <p>There is one more dependency that may need to be dealt with:</p>
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- <ul class="simple">
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- <li><p><a class="reference external" href="http://togl.sf.net">Togl</a>: a 3d widget for Tk. For OS X and
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- Linux, there are pre-built binaries of this in the snappy
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- subdirectory, e.g. snappy/linux2-tk8.4. For Linux these are built
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- for 64-bit kernels, and should work on most systems. If they don’t,
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- you’ll need to edit or follow “build_togl.sh” to build Togl directly.</p></li>
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- </ul>
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- <p>Finally, compile and install the SnapPy module (which will install
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- certain other dependencies) and test:</p>
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- <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python3</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">build</span>
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- <span class="n">python3</span> <span class="o">-</span><span class="n">m</span> <span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">user</span> <span class="o">.</span>
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- <span class="n">python3</span> <span class="o">-</span><span class="n">m</span> <span class="n">snappy</span><span class="o">.</span><span class="n">test</span>
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- <span class="n">python3</span> <span class="o">-</span><span class="n">m</span> <span class="n">snappy</span><span class="o">.</span><span class="n">app</span>
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+ <section id="conda">
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+ <h2>Conda<a class="headerlink" href="#conda" title="Link to this heading"></a></h2>
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+ <p>Conda can be used to install Python on all platforms and is a
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+ particularly good choice to use SnapPy on the older Linux systems
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+ often found on high-performance clusters. Here is a recipe for
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+ installing SnapPy into a new conda environment on macOS or Linux:</p>
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+ <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">source</span> <span class="o">~/</span><span class="n">miniforge3</span><span class="o">/</span><span class="nb">bin</span><span class="o">/</span><span class="n">activate</span>
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+ <span class="n">mamba</span> <span class="n">create</span> <span class="o">--</span><span class="n">name</span> <span class="n">snappy_env</span> <span class="n">python</span><span class="o">=</span><span class="mf">3.12</span>
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+ <span class="n">conda</span> <span class="n">activate</span> <span class="n">snappy_env</span>
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+ <span class="n">pip</span> <span class="n">install</span> <span class="n">snappy</span>
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+ <span class="n">python</span> <span class="o">-</span><span class="n">m</span> <span class="n">snappy</span><span class="o">.</span><span class="n">app</span>
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  <section id="source-code">
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- <h2>Source code<a class="headerlink" href="#source-code" title="Permalink to this headline">¶</a></h2>
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- <p>The complete source code for all platforms: <a class="reference external" href="https://pypi.python.org/packages/source/s/snappy/snappy-3.0.3.tar.gz">snappy-3.0.3.tar.gz</a></p>
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+ <h2>Source code<a class="headerlink" href="#source-code" title="Link to this heading"></a></h2>
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+ <p>The complete source code for all platforms: <a class="reference external" href="https://pypi.python.org/packages/source/s/snappy/snappy-3.2.tar.gz">snappy-3.2.tar.gz</a></p>
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  <p>You can also browse our <a class="reference external" href="https://github.com/3-manifolds/SnapPy">source code repository</a> or clone it using <a class="reference external" href="https://git-scm.com/">git</a> via:</p>
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  <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">git</span> <span class="n">clone</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="mi">3</span><span class="o">-</span><span class="n">manifolds</span><span class="o">/</span><span class="n">SnapPy</span><span class="o">.</span><span class="n">git</span>
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@@ -278,76 +313,34 @@ certain other dependencies) and test:</p>
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