PyPI - snappy - Versions diffs - 3.0.3__cp38-cp38-macosx_11_0_arm64.whl → 3.2__cp38-cp38-macosx_11_0_arm64.whl - Mend

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

Files changed (401) hide show

snappy/CyOpenGL.cpython-38-darwin.so +0 -0
snappy/SnapPy.cpython-38-darwin.so +0 -0
snappy/SnapPyHP.cpython-38-darwin.so +0 -0
snappy/__init__.py +373 -426
snappy/app.py +240 -75
snappy/app_menus.py +93 -78
snappy/browser.py +87 -63
snappy/cache.py +5 -8
snappy/canonical.py +249 -0
snappy/{verify/cusp_shapes.py → cusps/__init__.py} +11 -19
snappy/cusps/cusp_area_matrix.py +101 -0
snappy/{verify/cusp_areas.py → cusps/cusp_areas_from_matrix.py} +39 -54
snappy/cusps/maximal_cusp_area_matrix.py +136 -0
snappy/cusps/test.py +21 -0
snappy/cusps/trig_cusp_area_matrix.py +63 -0
snappy/database.py +40 -31
snappy/db_utilities.py +13 -14
snappy/decorated_isosig.py +377 -133
snappy/dev/extended_ptolemy/complexVolumesClosed.py +42 -9
snappy/dev/extended_ptolemy/extended.py +32 -25
snappy/dev/extended_ptolemy/giac_rur.py +23 -8
snappy/dev/extended_ptolemy/phc_wrapper.py +10 -10
snappy/dev/vericlosed/computeApproxHyperbolicStructureOrb.py +2 -1
snappy/dev/vericlosed/gimbalLoopFinder.py +5 -5
snappy/dev/vericlosed/hyperbolicStructure.py +3 -3
snappy/dev/vericlosed/oneVertexTruncatedComplex.py +2 -2
snappy/dev/vericlosed/truncatedComplex.py +3 -2
snappy/dev/vericlosed/verifyHyperbolicStructureEngine.py +4 -3
snappy/doc/_images/geodesics.jpg +0 -0
snappy/doc/_images/m004_paper_plane_on_systole.jpg +0 -0
snappy/doc/_images/m125_paper_plane.jpg +0 -0
snappy/doc/_images/o9_00000_systole_paper_plane.jpg +0 -0
snappy/doc/_images/o9_00000_systole_paper_plane_closer.jpg +0 -0
snappy/doc/_sources/additional_classes.rst.txt +1 -0
snappy/doc/_sources/credits.rst.txt +6 -1
snappy/doc/_sources/development.rst.txt +69 -50
snappy/doc/_sources/index.rst.txt +101 -66
snappy/doc/_sources/installing.rst.txt +148 -165
snappy/doc/_sources/news.rst.txt +136 -32
snappy/doc/_sources/ptolemy.rst.txt +1 -1
snappy/doc/_sources/ptolemy_examples1.rst.txt +9 -8
snappy/doc/_sources/ptolemy_examples2.rst.txt +3 -3
snappy/doc/_sources/ptolemy_examples3.rst.txt +14 -14
snappy/doc/_sources/ptolemy_prelim.rst.txt +1 -1
snappy/doc/_sources/snap.rst.txt +2 -2
snappy/doc/_sources/snappy.rst.txt +1 -1
snappy/doc/_sources/triangulation.rst.txt +3 -2
snappy/doc/_sources/verify.rst.txt +89 -29
snappy/doc/_sources/verify_internals.rst.txt +5 -16
snappy/doc/_static/SnapPy-horizontal-128.png +0 -0
snappy/doc/_static/SnapPy.ico +0 -0
snappy/doc/_static/_sphinx_javascript_frameworks_compat.js +123 -0
snappy/doc/_static/basic.css +47 -27
snappy/doc/_static/css/badge_only.css +1 -0
snappy/doc/_static/css/fonts/Roboto-Slab-Bold.woff +0 -0
snappy/doc/_static/css/fonts/Roboto-Slab-Bold.woff2 +0 -0
snappy/doc/_static/css/fonts/Roboto-Slab-Regular.woff +0 -0
snappy/doc/_static/css/fonts/Roboto-Slab-Regular.woff2 +0 -0
snappy/doc/_static/css/fonts/fontawesome-webfont.eot +0 -0
snappy/doc/_static/css/fonts/fontawesome-webfont.svg +2671 -0
snappy/doc/_static/css/fonts/fontawesome-webfont.ttf +0 -0
snappy/doc/_static/css/fonts/fontawesome-webfont.woff +0 -0
snappy/doc/_static/css/fonts/fontawesome-webfont.woff2 +0 -0
snappy/doc/_static/css/fonts/lato-bold-italic.woff +0 -0
snappy/doc/_static/css/fonts/lato-bold-italic.woff2 +0 -0
snappy/doc/_static/css/fonts/lato-bold.woff +0 -0
snappy/doc/_static/css/fonts/lato-bold.woff2 +0 -0
snappy/doc/_static/css/fonts/lato-normal-italic.woff +0 -0
snappy/doc/_static/css/fonts/lato-normal-italic.woff2 +0 -0
snappy/doc/_static/css/fonts/lato-normal.woff +0 -0
snappy/doc/_static/css/fonts/lato-normal.woff2 +0 -0
snappy/doc/_static/css/theme.css +4 -0
snappy/doc/_static/doctools.js +107 -274
snappy/doc/_static/documentation_options.js +6 -5
snappy/doc/_static/fonts/Lato/lato-bold.eot +0 -0
snappy/doc/_static/fonts/Lato/lato-bold.ttf +0 -0
snappy/doc/_static/fonts/Lato/lato-bold.woff +0 -0
snappy/doc/_static/fonts/Lato/lato-bold.woff2 +0 -0
snappy/doc/_static/fonts/Lato/lato-bolditalic.eot +0 -0
snappy/doc/_static/fonts/Lato/lato-bolditalic.ttf +0 -0
snappy/doc/_static/fonts/Lato/lato-bolditalic.woff +0 -0
snappy/doc/_static/fonts/Lato/lato-bolditalic.woff2 +0 -0
snappy/doc/_static/fonts/Lato/lato-italic.eot +0 -0
snappy/doc/_static/fonts/Lato/lato-italic.ttf +0 -0
snappy/doc/_static/fonts/Lato/lato-italic.woff +0 -0
snappy/doc/_static/fonts/Lato/lato-italic.woff2 +0 -0
snappy/doc/_static/fonts/Lato/lato-regular.eot +0 -0
snappy/doc/_static/fonts/Lato/lato-regular.ttf +0 -0
snappy/doc/_static/fonts/Lato/lato-regular.woff +0 -0
snappy/doc/_static/fonts/Lato/lato-regular.woff2 +0 -0
snappy/doc/_static/fonts/RobotoSlab/roboto-slab-v7-bold.eot +0 -0
snappy/doc/_static/fonts/RobotoSlab/roboto-slab-v7-bold.ttf +0 -0
snappy/doc/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff +0 -0
snappy/doc/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff2 +0 -0
snappy/doc/_static/fonts/RobotoSlab/roboto-slab-v7-regular.eot +0 -0
snappy/doc/_static/fonts/RobotoSlab/roboto-slab-v7-regular.ttf +0 -0
snappy/doc/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff +0 -0
snappy/doc/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff2 +0 -0
snappy/doc/_static/jquery.js +2 -2
snappy/doc/_static/js/badge_only.js +1 -0
snappy/doc/_static/js/theme.js +1 -0
snappy/doc/_static/js/versions.js +228 -0
snappy/doc/_static/language_data.js +3 -101
snappy/doc/_static/pygments.css +1 -0
snappy/doc/_static/searchtools.js +489 -398
snappy/doc/_static/snappy_furo.css +33 -0
snappy/doc/_static/snappy_sphinx_rtd_theme.css +42 -0
snappy/doc/_static/sphinx_highlight.js +154 -0
snappy/doc/additional_classes.html +688 -263
snappy/doc/bugs.html +107 -94
snappy/doc/censuses.html +155 -127
snappy/doc/credits.html +115 -104
snappy/doc/development.html +184 -146
snappy/doc/genindex.html +287 -204
snappy/doc/index.html +189 -150
snappy/doc/installing.html +259 -266
snappy/doc/manifold.html +1626 -592
snappy/doc/manifoldhp.html +119 -105
snappy/doc/news.html +198 -104
snappy/doc/objects.inv +0 -0
snappy/doc/other.html +117 -105
snappy/doc/platonic_census.html +161 -114
snappy/doc/plink.html +113 -105
snappy/doc/ptolemy.html +131 -108
snappy/doc/ptolemy_classes.html +242 -223
snappy/doc/ptolemy_examples1.html +144 -130
snappy/doc/ptolemy_examples2.html +141 -129
snappy/doc/ptolemy_examples3.html +148 -132
snappy/doc/ptolemy_examples4.html +131 -111
snappy/doc/ptolemy_prelim.html +162 -138
snappy/doc/py-modindex.html +104 -69
snappy/doc/screenshots.html +117 -108
snappy/doc/search.html +115 -84
snappy/doc/searchindex.js +1 -1
snappy/doc/snap.html +109 -96
snappy/doc/snappy.html +134 -97
snappy/doc/spherogram.html +259 -187
snappy/doc/todo.html +107 -94
snappy/doc/triangulation.html +1380 -111
snappy/doc/tutorial.html +107 -94
snappy/doc/verify.html +194 -125
snappy/doc/verify_internals.html +248 -686
snappy/drilling/__init__.py +456 -0
snappy/drilling/barycentric.py +103 -0
snappy/drilling/constants.py +5 -0
snappy/drilling/crush.py +270 -0
snappy/drilling/cusps.py +125 -0
snappy/drilling/debug.py +242 -0
snappy/drilling/epsilons.py +6 -0
snappy/drilling/exceptions.py +55 -0
snappy/drilling/moves.py +620 -0
snappy/drilling/peripheral_curves.py +210 -0
snappy/drilling/perturb.py +188 -0
snappy/drilling/shorten.py +36 -0
snappy/drilling/subdivide.py +274 -0
snappy/drilling/test.py +23 -0
snappy/drilling/test_cases.py +126 -0
snappy/drilling/tracing.py +351 -0
snappy/exceptions.py +23 -3
snappy/export_stl.py +20 -14
snappy/exterior_to_link/__init__.py +2 -0
snappy/exterior_to_link/barycentric_geometry.py +463 -0
snappy/exterior_to_link/exceptions.py +6 -0
snappy/exterior_to_link/geodesic_map.json +14408 -0
snappy/exterior_to_link/hyp_utils.py +112 -0
snappy/exterior_to_link/link_projection.py +323 -0
snappy/exterior_to_link/main.py +197 -0
snappy/exterior_to_link/mcomplex_with_expansion.py +261 -0
snappy/exterior_to_link/mcomplex_with_link.py +687 -0
snappy/exterior_to_link/mcomplex_with_memory.py +162 -0
snappy/exterior_to_link/pl_utils.py +491 -0
snappy/exterior_to_link/put_in_S3.py +156 -0
snappy/exterior_to_link/rational_linear_algebra.py +123 -0
snappy/exterior_to_link/rational_linear_algebra_wrapped.py +135 -0
snappy/exterior_to_link/simplify_to_base_tri.py +114 -0
snappy/exterior_to_link/stored_moves.py +475 -0
snappy/exterior_to_link/test.py +31 -0
snappy/geometric_structure/__init__.py +212 -0
snappy/geometric_structure/cusp_neighborhood/__init__.py +3 -0
snappy/geometric_structure/cusp_neighborhood/complex_cusp_cross_section.py +697 -0
snappy/geometric_structure/cusp_neighborhood/cusp_cross_section_base.py +484 -0
snappy/geometric_structure/cusp_neighborhood/exceptions.py +42 -0
snappy/geometric_structure/cusp_neighborhood/real_cusp_cross_section.py +298 -0
snappy/geometric_structure/cusp_neighborhood/tiles_for_cusp_neighborhood.py +159 -0
snappy/geometric_structure/cusp_neighborhood/vertices.py +32 -0
snappy/geometric_structure/geodesic/__init__.py +0 -0
snappy/geometric_structure/geodesic/add_core_curves.py +152 -0
snappy/geometric_structure/geodesic/avoid_core_curves.py +369 -0
snappy/geometric_structure/geodesic/canonical_keys.py +52 -0
snappy/geometric_structure/geodesic/check_away_from_core_curve.py +60 -0
snappy/geometric_structure/geodesic/constants.py +6 -0
snappy/geometric_structure/geodesic/exceptions.py +22 -0
snappy/geometric_structure/geodesic/fixed_points.py +93 -0
snappy/geometric_structure/geodesic/geodesic_start_point_info.py +435 -0
snappy/geometric_structure/geodesic/graph_trace_helper.py +67 -0
snappy/geometric_structure/geodesic/line.py +30 -0
snappy/geometric_structure/geodesic/multiplicity.py +127 -0
snappy/geometric_structure/geodesic/tiles_for_geodesic.py +101 -0
snappy/geometric_structure/test.py +22 -0
snappy/gui.py +36 -36
snappy/horoviewer.py +50 -48
snappy/hyperboloid/__init__.py +212 -0
snappy/hyperboloid/distances.py +245 -0
snappy/hyperboloid/horoball.py +19 -0
snappy/hyperboloid/line.py +35 -0
snappy/hyperboloid/point.py +9 -0
snappy/hyperboloid/triangle.py +29 -0
snappy/{infodialog.py → infowindow.py} +32 -33
snappy/isometry_signature.py +382 -0
snappy/len_spec/__init__.py +596 -0
snappy/len_spec/geodesic_info.py +110 -0
snappy/len_spec/geodesic_key_info_dict.py +117 -0
snappy/len_spec/geodesic_piece.py +143 -0
snappy/len_spec/geometric_structure.py +182 -0
snappy/len_spec/geometry.py +80 -0
snappy/len_spec/length_spectrum_geodesic_info.py +170 -0
snappy/len_spec/spine.py +206 -0
snappy/len_spec/test.py +24 -0
snappy/len_spec/test_cases.py +69 -0
snappy/len_spec/tile.py +275 -0
snappy/len_spec/word.py +86 -0
snappy/manifolds/__init__.py +1 -1
snappy/math_basics.py +176 -0
snappy/matrix.py +525 -0
snappy/number.py +97 -21
snappy/numeric_output_checker.py +37 -27
snappy/pari.py +30 -69
snappy/phone_home.py +25 -20
snappy/polyviewer.py +39 -37
snappy/ptolemy/__init__.py +4 -6
snappy/ptolemy/component.py +14 -12
snappy/ptolemy/coordinates.py +312 -295
snappy/ptolemy/fieldExtensions.py +14 -12
snappy/ptolemy/findLoops.py +43 -31
snappy/ptolemy/geometricRep.py +24 -26
snappy/ptolemy/homology.py +12 -7
snappy/ptolemy/manifoldMethods.py +69 -70
snappy/ptolemy/matrix.py +65 -26
snappy/ptolemy/numericalSolutionsToGroebnerBasis.py +18 -14
snappy/ptolemy/polynomial.py +125 -119
snappy/ptolemy/processComponents.py +36 -30
snappy/ptolemy/processFileBase.py +79 -18
snappy/ptolemy/processFileDispatch.py +13 -14
snappy/ptolemy/processMagmaFile.py +44 -39
snappy/ptolemy/processRurFile.py +18 -11
snappy/ptolemy/ptolemyGeneralizedObstructionClass.py +20 -17
snappy/ptolemy/ptolemyObstructionClass.py +13 -17
snappy/ptolemy/ptolemyVariety.py +190 -121
snappy/ptolemy/ptolemyVarietyPrimeIdealGroebnerBasis.py +20 -19
snappy/ptolemy/reginaWrapper.py +25 -29
snappy/ptolemy/rur.py +6 -14
snappy/ptolemy/solutionsToPrimeIdealGroebnerBasis.py +27 -22
snappy/ptolemy/test.py +247 -188
snappy/ptolemy/utilities.py +41 -43
snappy/raytracing/__init__.py +64 -0
snappy/raytracing/additional_horospheres.py +64 -0
snappy/raytracing/additional_len_spec_choices.py +63 -0
snappy/raytracing/cohomology_fractal.py +10 -6
snappy/raytracing/eyeball.py +123 -0
snappy/raytracing/finite_raytracing_data.py +48 -38
snappy/raytracing/finite_viewer.py +218 -210
snappy/raytracing/geodesic_tube_info.py +174 -0
snappy/raytracing/geodesics.py +246 -0
snappy/raytracing/geodesics_window.py +258 -0
snappy/raytracing/gui_utilities.py +152 -40
snappy/raytracing/hyperboloid_navigation.py +102 -52
snappy/raytracing/hyperboloid_utilities.py +114 -261
snappy/raytracing/ideal_raytracing_data.py +256 -179
snappy/raytracing/inside_viewer.py +522 -253
snappy/raytracing/pack.py +22 -0
snappy/raytracing/raytracing_data.py +46 -34
snappy/raytracing/raytracing_view.py +190 -109
snappy/raytracing/shaders/Eye.png +0 -0
snappy/raytracing/shaders/NonGeometric.png +0 -0
snappy/raytracing/shaders/__init__.py +60 -4
snappy/raytracing/shaders/fragment.glsl +575 -148
snappy/raytracing/test.py +29 -0
snappy/raytracing/tooltip.py +146 -0
snappy/raytracing/upper_halfspace_utilities.py +98 -0
snappy/raytracing/view_scale_controller.py +98 -0
snappy/raytracing/zoom_slider/__init__.py +32 -29
snappy/raytracing/zoom_slider/test.py +2 -0
snappy/sage_helper.py +69 -123
snappy/{preferences.py → settings.py} +167 -145
snappy/shell.py +4 -0
snappy/snap/__init__.py +12 -8
snappy/snap/character_varieties.py +24 -18
snappy/snap/find_field.py +35 -34
snappy/snap/fundamental_polyhedron.py +99 -85
snappy/snap/generators.py +6 -8
snappy/snap/interval_reps.py +18 -6
snappy/snap/kernel_structures.py +8 -3
snappy/snap/mcomplex_base.py +1 -2
snappy/snap/nsagetools.py +107 -53
snappy/snap/peripheral/__init__.py +1 -1
snappy/snap/peripheral/dual_cellulation.py +15 -7
snappy/snap/peripheral/link.py +20 -16
snappy/snap/peripheral/peripheral.py +22 -14
snappy/snap/peripheral/surface.py +47 -50
snappy/snap/peripheral/test.py +8 -8
snappy/snap/polished_reps.py +65 -40
snappy/snap/shapes.py +41 -22
snappy/snap/slice_obs_HKL.py +64 -25
snappy/snap/t3mlite/arrow.py +88 -51
snappy/snap/t3mlite/corner.py +5 -6
snappy/snap/t3mlite/edge.py +32 -21
snappy/snap/t3mlite/face.py +7 -9
snappy/snap/t3mlite/files.py +31 -23
snappy/snap/t3mlite/homology.py +14 -10
snappy/snap/t3mlite/linalg.py +158 -56
snappy/snap/t3mlite/mcomplex.py +739 -291
snappy/snap/t3mlite/perm4.py +236 -84
snappy/snap/t3mlite/setup.py +9 -10
snappy/snap/t3mlite/simplex.py +65 -48
snappy/snap/t3mlite/spun.py +42 -30
snappy/snap/t3mlite/surface.py +45 -45
snappy/snap/t3mlite/test.py +3 -0
snappy/snap/t3mlite/test_vs_regina.py +17 -13
snappy/snap/t3mlite/tetrahedron.py +25 -24
snappy/snap/t3mlite/vertex.py +8 -13
snappy/snap/test.py +45 -52
snappy/snap/utilities.py +66 -65
snappy/test.py +155 -158
snappy/test_cases.py +263 -0
snappy/testing.py +131 -0
snappy/tiling/__init__.py +2 -0
snappy/tiling/canonical_key_dict.py +59 -0
snappy/tiling/dict_based_set.py +79 -0
snappy/tiling/floor.py +49 -0
snappy/tiling/hyperboloid_dict.py +54 -0
snappy/tiling/iter_utils.py +78 -0
snappy/tiling/lifted_tetrahedron.py +22 -0
snappy/tiling/lifted_tetrahedron_set.py +54 -0
snappy/tiling/real_hash_dict.py +164 -0
snappy/tiling/test.py +23 -0
snappy/tiling/tile.py +215 -0
snappy/tiling/triangle.py +33 -0
snappy/tkterminal.py +313 -203
snappy/twister/main.py +1 -8
snappy/twister/twister_core.cpython-38-darwin.so +0 -0
snappy/upper_halfspace/__init__.py +146 -0
snappy/upper_halfspace/ideal_point.py +26 -0
snappy/verify/__init__.py +4 -8
snappy/verify/{verifyCanonical.py → canonical.py} +114 -97
snappy/verify/complex_volume/__init__.py +3 -2
snappy/verify/complex_volume/adjust_torsion.py +13 -11
snappy/verify/complex_volume/closed.py +29 -24
snappy/verify/complex_volume/compute_ptolemys.py +8 -6
snappy/verify/complex_volume/cusped.py +10 -9
snappy/verify/complex_volume/extended_bloch.py +14 -12
snappy/verify/{cuspTranslations.py → cusp_translations.py} +15 -14
snappy/verify/edge_equations.py +80 -0
snappy/verify/exceptions.py +23 -56
snappy/verify/{verifyHyperbolicity.py → hyperbolicity.py} +19 -15
snappy/verify/interval_newton_shapes_engine.py +51 -211
snappy/verify/interval_tree.py +27 -25
snappy/verify/krawczyk_shapes_engine.py +47 -50
snappy/verify/maximal_cusp_area_matrix/__init__.py +17 -86
snappy/verify/maximal_cusp_area_matrix/cusp_tiling_engine.py +58 -48
snappy/verify/maximal_cusp_area_matrix/cusp_translate_engine.py +53 -57
snappy/verify/{realAlgebra.py → real_algebra.py} +26 -20
snappy/verify/shapes.py +10 -7
snappy/verify/short_slopes.py +41 -42
snappy/verify/{squareExtensions.py → square_extensions.py} +96 -92
snappy/verify/test.py +59 -57
snappy/verify/upper_halfspace/extended_matrix.py +5 -5
snappy/verify/upper_halfspace/finite_point.py +44 -31
snappy/verify/upper_halfspace/ideal_point.py +69 -57
snappy/verify/volume.py +15 -12
snappy/version.py +2 -3
{snappy-3.0.3.dist-info → snappy-3.2.dist-info}/METADATA +14 -12
snappy-3.2.dist-info/RECORD +503 -0
{snappy-3.0.3.dist-info → snappy-3.2.dist-info}/WHEEL +1 -1
{snappy-3.0.3.dist-info → snappy-3.2.dist-info}/entry_points.txt +0 -1
{snappy-3.0.3.dist-info → snappy-3.2.dist-info}/top_level.txt +10 -1
snappy/doc/_sources/verify_canon.rst.txt +0 -90
snappy/doc/_static/classic.css +0 -266
snappy/doc/_static/jquery-3.5.1.js +0 -10872
snappy/doc/_static/sidebar.js +0 -159
snappy/doc/_static/underscore-1.13.1.js +0 -2042
snappy/doc/_static/underscore.js +0 -6
snappy/doc/verify_canon.html +0 -283
snappy/ppm_to_png.py +0 -243
snappy/togl/__init__.py +0 -3
snappy/togl/darwin-tk8.6/Togl2.1/LICENSE +0 -28
snappy/togl/darwin-tk8.6/Togl2.1/libTogl2.1.dylib +0 -0
snappy/togl/darwin-tk8.6/Togl2.1/pkgIndex.tcl +0 -5
snappy/togl/linux2-x86_64-tk8.6/Togl2.1/LICENSE +0 -28
snappy/togl/linux2-x86_64-tk8.6/Togl2.1/libTogl2.1.so +0 -0
snappy/togl/linux2-x86_64-tk8.6/Togl2.1/pkgIndex.tcl +0 -5
snappy/togl/win32VC-tk8.6/Togl2.1/LICENSE +0 -28
snappy/togl/win32VC-tk8.6/Togl2.1/Togl21.dll +0 -0
snappy/togl/win32VC-tk8.6/Togl2.1/Togl21.lib +0 -0
snappy/togl/win32VC-tk8.6/Togl2.1/pkgIndex.tcl +0 -6
snappy/togl/win32VC-x86_64-tk8.6/Togl2.1/LICENSE +0 -28
snappy/togl/win32VC-x86_64-tk8.6/Togl2.1/Togl21.dll +0 -0
snappy/togl/win32VC-x86_64-tk8.6/Togl2.1/Togl21.lib +0 -0
snappy/togl/win32VC-x86_64-tk8.6/Togl2.1/pkgIndex.tcl +0 -6
snappy/verify/cuspCrossSection.py +0 -1413
snappy/verify/mathHelpers.py +0 -64
snappy-3.0.3.dist-info/RECORD +0 -360

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+           <div itemprop="articleBody">
   <section id="classes">
-<h1>Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h1>
+<h1>Classes<a class="headerlink" href="#classes" title="Link to this heading"></a></h1>
 <section id="ptolemyvariety">
-<h2>PtolemyVariety<a class="headerlink" href="#ptolemyvariety" title="Permalink to this headline">¶</a></h2>
+<h2>PtolemyVariety<a class="headerlink" href="#ptolemyvariety" title="Link to this heading"></a></h2>
 <dl class="py class">
 <dt class="sig sig-object py" id="snappy.ptolemy.ptolemyVariety.PtolemyVariety">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">snappy.ptolemy.ptolemyVariety.</span></span><span class="sig-name descname"><span class="pre">PtolemyVariety</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">manifold</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">N</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">obstruction_class</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simplify</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">eliminate_fixed_ptolemys</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.ptolemyVariety.PtolemyVariety" title="Permalink to this definition">¶</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">snappy.ptolemy.ptolemyVariety.</span></span><span class="sig-name descname"><span class="pre">PtolemyVariety</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">manifold</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">N</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">obstruction_class</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simplify</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">eliminate_fixed_ptolemys</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.ptolemyVariety.PtolemyVariety" title="Link to this definition"></a></dt>
 <dd><p>Holds a reduced Ptolemy variety.</p>
 <p>=== Examples ===</p>
 <p>To generate such a variety, call:</p>
@@ -98,7 +157,7 @@ python section by py_eval_variable_dict().)</p>
 </div>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.ptolemyVariety.PtolemyVariety.compute_decomposition">
-<span class="sig-name descname"><span class="pre">compute_decomposition</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">engine</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">memory_limit</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">750000000</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">directory</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">verbose</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">template_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'magma/default.magma_template'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.ptolemyVariety.PtolemyVariety.compute_decomposition" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">compute_decomposition</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">engine</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">memory_limit</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">750000000</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">directory</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">verbose</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">template_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'magma/default.magma_template'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.ptolemyVariety.PtolemyVariety.compute_decomposition" title="Link to this definition"></a></dt>
 <dd><p>Starts an engine such as magma to compute the
 radical decomposition of the Ptolemy variety.</p>
 <p>If started in sage, uses sage, otherwise, uses magma.</p>
@@ -111,7 +170,7 @@ verbose — print extra information</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.ptolemyVariety.PtolemyVariety.compute_solutions">
-<span class="sig-name descname"><span class="pre">compute_solutions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">engine</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">numerical</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">template_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'magma/default.magma_template'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">memory_limit</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">750000000</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">directory</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">verbose</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="#snappy.ptolemy.ptolemyVariety.PtolemyVariety.compute_solutions" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">compute_solutions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">engine</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">numerical</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">template_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'magma/default.magma_template'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">memory_limit</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">750000000</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">directory</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">verbose</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="#snappy.ptolemy.ptolemyVariety.PtolemyVariety.compute_solutions" title="Link to this definition"></a></dt>
 <dd><p>Starts an engine such as magma to compute the
 radical decomposition of the ideal and computes exact solutions.</p>
 <p>If started in sage, uses sage, otherwise, uses magma.</p>
@@ -125,7 +184,7 @@ verbose — print extra information</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.ptolemyVariety.PtolemyVariety.degree_to_shapes">
-<span class="sig-name descname"><span class="pre">degree_to_shapes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.ptolemyVariety.PtolemyVariety.degree_to_shapes" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">degree_to_shapes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.ptolemyVariety.PtolemyVariety.degree_to_shapes" title="Link to this definition"></a></dt>
 <dd><p>In general, there can be d different solutions to the (reduced) Ptolemy
 variety for each solution to the gluing equations (with peripheral
 equations). This method computes d which is also the number of elements
@@ -157,7 +216,7 @@ Thus the following call returns 2 = 4 / 2</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.ptolemyVariety.PtolemyVariety.filename_base">
-<span class="sig-name descname"><span class="pre">filename_base</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.ptolemyVariety.PtolemyVariety.filename_base" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">filename_base</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.ptolemyVariety.PtolemyVariety.filename_base" title="Link to this definition"></a></dt>
 <dd><p>Preferred filename base for writing out this Ptolemy variety</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">snappy</span> <span class="kn">import</span> <span class="o">*</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">M</span> <span class="o">=</span> <span class="n">Manifold</span><span class="p">(</span><span class="s1">&#39;4_1&#39;</span><span class="p">)</span>
@@ -175,7 +234,7 @@ Thus the following call returns 2 = 4 / 2</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.ptolemyVariety.PtolemyVariety.py_eval_section">
-<span class="sig-name descname"><span class="pre">py_eval_section</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.ptolemyVariety.PtolemyVariety.py_eval_section" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">py_eval_section</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.ptolemyVariety.PtolemyVariety.py_eval_section" title="Link to this definition"></a></dt>
 <dd><p>Returns a string that can be evaluated in python and contains extra
 information needed to recover solutions from a simplified Ptolemy
 variety.</p>
@@ -187,7 +246,7 @@ variety.</p>
 <p>Get extra information</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">eval_section</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">py_eval_section</span><span class="p">()</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="nb">print</span><span class="p">(</span><span class="n">eval_section</span><span class="p">)</span>
-<span class="go">{&#39;variable_dict&#39; : </span>
+<span class="go">{&#39;variable_dict&#39; :</span>
 <span class="go">     (lambda d: {</span>
 <span class="go">    ...</span>
 </pre></div>
@@ -219,7 +278,7 @@ Ptolemy variety to a full solution.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.ptolemyVariety.PtolemyVariety.to_magma">
-<span class="sig-name descname"><span class="pre">to_magma</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">template_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'magma/default.magma_template'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.ptolemyVariety.PtolemyVariety.to_magma" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">to_magma</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">template_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'magma/default.magma_template'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.ptolemyVariety.PtolemyVariety.to_magma" title="Link to this definition"></a></dt>
 <dd><p>Returns a string with the ideal that can be used as input for magma.</p>
 <p>The advanced user can provide a template string to write own magma
 code to process the equations.</p>
@@ -239,7 +298,7 @@ True</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.ptolemyVariety.PtolemyVariety.to_magma_file">
-<span class="sig-name descname"><span class="pre">to_magma_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">template_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'magma/default.magma_template'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.ptolemyVariety.PtolemyVariety.to_magma_file" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">to_magma_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">template_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'magma/default.magma_template'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.ptolemyVariety.PtolemyVariety.to_magma_file" title="Link to this definition"></a></dt>
 <dd><div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">os</span><span class="o">,</span> <span class="nn">tempfile</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">snappy</span> <span class="kn">import</span> <span class="n">Manifold</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">handle</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">mkstemp</span><span class="p">()</span>
@@ -254,10 +313,10 @@ True</p>
 </section>
 <section id="ptolemycoordinates">
-<h2>PtolemyCoordinates<a class="headerlink" href="#ptolemycoordinates" title="Permalink to this headline">¶</a></h2>
+<h2>PtolemyCoordinates<a class="headerlink" href="#ptolemycoordinates" title="Link to this heading"></a></h2>
 <dl class="py class">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">snappy.ptolemy.coordinates.</span></span><span class="sig-name descname"><span class="pre">PtolemyCoordinates</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">d</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">is_numerical=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">py_eval_section=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifold_thunk=&lt;function</span> <span class="pre">PtolemyCoordinates.&lt;lambda&gt;&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">non_trivial_generalized_obstruction_class=False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates" title="Permalink to this definition">¶</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">snappy.ptolemy.coordinates.</span></span><span class="sig-name descname"><span class="pre">PtolemyCoordinates</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">d</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">is_numerical=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">py_eval_section=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifold_thunk=&lt;function</span> <span class="pre">PtolemyCoordinates.&lt;lambda&gt;&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">non_trivial_generalized_obstruction_class=False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates" title="Link to this definition"></a></dt>
 <dd><p>Represents a solution of a Ptolemy variety as python dictionary.</p>
 <p>=== Examples ===</p>
 <p>Construct solution from magma output:</p>
@@ -349,13 +408,13 @@ according to SnapPy convention, see help(solution.cross_ratios):</p>
 </div>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates.N">
-<span class="sig-name descname"><span class="pre">N</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.N" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">N</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.N" title="Link to this definition"></a></dt>
 <dd><p>Get the <em>N</em> where these coordinates are for SL/PSL(<em>N</em>, <strong>C</strong>)-representations.</p>
 </dd></dl>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates.check_against_manifold">
-<span class="sig-name descname"><span class="pre">check_against_manifold</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">M</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">epsilon</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.check_against_manifold" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">check_against_manifold</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">M</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">epsilon</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.check_against_manifold" title="Link to this definition"></a></dt>
 <dd><p>Checks that the given solution really is a solution to the Ptolemy
 variety of a manifold. See help(ptolemy.PtolemyCoordinates) for
 more example.</p>
@@ -369,7 +428,7 @@ None for exact comparison.</p></li>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates.complex_volume_numerical">
-<span class="sig-name descname"><span class="pre">complex_volume_numerical</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">drop_negative_vols</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">with_modulo</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="#snappy.ptolemy.coordinates.PtolemyCoordinates.complex_volume_numerical" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">complex_volume_numerical</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">drop_negative_vols</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">with_modulo</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="#snappy.ptolemy.coordinates.PtolemyCoordinates.complex_volume_numerical" title="Link to this definition"></a></dt>
 <dd><p>Turn into (Galois conjugate) numerical solutions and compute complex
 volumes. If already numerical, return the volume.</p>
 <p>Complex volume is defined up to i*pi**2/6.</p>
@@ -379,7 +438,7 @@ argument, only return complex volumes with non-negative real part.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates.cross_ratios">
-<span class="sig-name descname"><span class="pre">cross_ratios</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.cross_ratios" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">cross_ratios</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.cross_ratios" title="Link to this definition"></a></dt>
 <dd><p>Compute cross ratios from Ptolemy coordinates. The cross ratios are
 according to the SnapPy convention, so we have:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">z</span> <span class="o">=</span> <span class="mi">1</span> <span class="o">-</span> <span class="mi">1</span><span class="o">/</span><span class="n">zp</span><span class="p">,</span> <span class="n">zp</span> <span class="o">=</span> <span class="mi">1</span> <span class="o">-</span> <span class="mi">1</span><span class="o">/</span><span class="n">zpp</span><span class="p">,</span> <span class="n">zpp</span> <span class="o">=</span> <span class="mi">1</span> <span class="o">-</span> <span class="mi">1</span><span class="o">/</span><span class="n">z</span>
@@ -391,10 +450,10 @@ according to the SnapPy convention, so we have:</p>
 <span class="n">zpp</span> <span class="ow">is</span> <span class="n">at</span> <span class="n">the</span> <span class="n">edge</span> <span class="mi">03</span> <span class="ow">and</span> <span class="n">equal</span> <span class="n">to</span>   <span class="n">s0</span> <span class="o">*</span> <span class="n">s3</span> <span class="o">*</span> <span class="p">(</span><span class="n">c_1100</span> <span class="o">*</span> <span class="n">c_0011</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="n">c_0101</span> <span class="o">*</span> <span class="n">c_1010</span><span class="p">)</span><span class="o">.</span>
 </pre></div>
 </div>
-<p>Note that this is different from the convention used in
+<p>Note that this is different from the convention used in
 Garoufalidis, Goerner, Zickert:
-Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
-<a class="reference external" href="http://arxiv.org/abs/1207.6711">http://arxiv.org/abs/1207.6711</a></p>
+Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
+<a class="reference external" href="https://arxiv.org/abs/1207.6711">https://arxiv.org/abs/1207.6711</a></p>
 <p>Take an exact solution:</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">snappy.ptolemy.processMagmaFile</span> <span class="kn">import</span> <span class="n">_magma_output_for_4_1__sl3</span><span class="p">,</span> <span class="n">solutions_from_magma</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">solutions</span> <span class="o">=</span> <span class="n">solutions_from_magma</span><span class="p">(</span><span class="n">_magma_output_for_4_1__sl3</span><span class="p">)</span>
@@ -428,26 +487,26 @@ Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates.cross_ratios_numerical">
-<span class="sig-name descname"><span class="pre">cross_ratios_numerical</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.cross_ratios_numerical" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">cross_ratios_numerical</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.cross_ratios_numerical" title="Link to this definition"></a></dt>
 <dd><p>Turn exact solutions into numerical and then compute cross ratios.
 See numerical() and cross_ratios().</p>
 </dd></dl>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates.diamond_coordinate">
-<span class="sig-name descname"><span class="pre">diamond_coordinate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tet</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pt</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.diamond_coordinate" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">diamond_coordinate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tet</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pt</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.diamond_coordinate" title="Link to this definition"></a></dt>
 <dd><p>Returns the diamond coordinate for tetrahedron with index tet
 for the face with vertices v0, v1, v2 (integers between 0 and 3) and
 integral point pt (quadruple adding up to N-2).</p>
 <p>See Definition 10.1:
 Garoufalidis, Goerner, Zickert:
-Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
-<a class="reference external" href="http://arxiv.org/abs/1207.6711">http://arxiv.org/abs/1207.6711</a></p>
+Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
+<a class="reference external" href="https://arxiv.org/abs/1207.6711">https://arxiv.org/abs/1207.6711</a></p>
 </dd></dl>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates.evaluate_word">
-<span class="sig-name descname"><span class="pre">evaluate_word</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">word</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">G</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.evaluate_word" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">evaluate_word</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">word</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">G</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.evaluate_word" title="Link to this definition"></a></dt>
 <dd><p>Given a word in the generators of the fundamental group,
 compute the corresponding matrix. By default, these are the
 generators of the unsimplified presentation of the fundamental
@@ -461,8 +520,8 @@ M.fundamental_group(True).</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates.flattenings_numerical">
-<span class="sig-name descname"><span class="pre">flattenings_numerical</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.flattenings_numerical" title="Permalink to this definition">¶</a></dt>
-<dd><p>Turn into numerical solutions and compute flattenings, see
+<span class="sig-name descname"><span class="pre">flattenings_numerical</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.flattenings_numerical" title="Link to this definition"></a></dt>
+<dd><p>Turn into numerical solutions and compute flattenings, see
 help(snappy.ptolemy.coordinates.Flattenings)
 Also see numerical()</p>
 <p>Get Ptolemy coordinates.</p>
@@ -471,7 +530,7 @@ Also see numerical()</p>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">solution</span> <span class="o">=</span> <span class="n">solutions</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
 </pre></div>
 </div>
-<p>Compute a numerical soluton</p>
+<p>Compute a numerical solution</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">flattenings</span> <span class="o">=</span> <span class="n">solution</span><span class="o">.</span><span class="n">flattenings_numerical</span><span class="p">()</span>
 </pre></div>
 </div>
@@ -480,21 +539,21 @@ Also see numerical()</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates.get_manifold">
-<span class="sig-name descname"><span class="pre">get_manifold</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.get_manifold" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">get_manifold</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.get_manifold" title="Link to this definition"></a></dt>
 <dd><p>Get the manifold for which this structure represents a solution
 to the Ptolemy variety.</p>
 </dd></dl>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates.has_obstruction">
-<span class="sig-name descname"><span class="pre">has_obstruction</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.has_obstruction" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">has_obstruction</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.has_obstruction" title="Link to this definition"></a></dt>
 <dd><p>Whether the Ptolemy variety has legacy obstruction class that
 modifies the Ptolemy relation to</p>
 </dd></dl>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates.is_geometric">
-<span class="sig-name descname"><span class="pre">is_geometric</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">epsilon</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-06</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.is_geometric" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">is_geometric</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">epsilon</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-06</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.is_geometric" title="Link to this definition"></a></dt>
 <dd><p>Returns true if all shapes corresponding to this solution have positive
 imaginary part.</p>
 <p>If the solutions are exact, it returns true if one of the corresponding
@@ -505,15 +564,15 @@ considered positive if it is larger than this epsilon.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates.long_edge">
-<span class="sig-name descname"><span class="pre">long_edge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tet</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.long_edge" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">long_edge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tet</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.long_edge" title="Link to this definition"></a></dt>
 <dd><p>The matrix that labels a long edge from v0 to v1 (integers between 0
 and 3) of a (doubly) truncated simplex corresponding to an ideal
 tetrahedron with index tet.</p>
 <p>This matrix was labeled alpha^{v0v1v2} (v2 does not matter for non
 double-truncated simplex) in Figure 18 of
 Garoufalidis, Goerner, Zickert:
-Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
-<a class="reference external" href="http://arxiv.org/abs/1207.6711">http://arxiv.org/abs/1207.6711</a></p>
+Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
+<a class="reference external" href="https://arxiv.org/abs/1207.6711">https://arxiv.org/abs/1207.6711</a></p>
 <p>It is computed using equation 10.4. Note that the ratio coordinate
 is different from the definition in the paper (see ratio_coordinate).</p>
 <p>The resulting matrix is given as a python list of lists.</p>
@@ -521,22 +580,22 @@ is different from the definition in the paper (see ratio_coordinate).</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates.middle_edge">
-<span class="sig-name descname"><span class="pre">middle_edge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tet</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.middle_edge" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">middle_edge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tet</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.middle_edge" title="Link to this definition"></a></dt>
 <dd><p>The matrix that labels a middle edge on the face v0, v1, v2 (integers
 between 0 and 3) of a doubly truncated simplex (or a short edge of the
 truncated simplex) corresponding to an ideal tetrahedron with index
 tet.</p>
 <p>This matrix was labeled beta^{v0v1v2} in Figure 18 of
 Garoufalidis, Goerner, Zickert:
-Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
-<a class="reference external" href="http://arxiv.org/abs/1207.6711">http://arxiv.org/abs/1207.6711</a></p>
+Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
+<a class="reference external" href="https://arxiv.org/abs/1207.6711">https://arxiv.org/abs/1207.6711</a></p>
 <p>It is computed using equation 10.4.</p>
 <p>The resulting matrix is given as a python list of lists.</p>
 </dd></dl>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates.multiply_and_simplify_terms_in_RUR">
-<span class="sig-name descname"><span class="pre">multiply_and_simplify_terms_in_RUR</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.multiply_and_simplify_terms_in_RUR" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">multiply_and_simplify_terms_in_RUR</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.multiply_and_simplify_terms_in_RUR" title="Link to this definition"></a></dt>
 <dd><p>If a Ptolemy coordinate is given as Rational Univariate Representation
 with numerator and denominator being a product, multiply the terms,
 reduce the fraction and return the result.</p>
@@ -547,7 +606,7 @@ factorised.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates.multiply_terms_in_RUR">
-<span class="sig-name descname"><span class="pre">multiply_terms_in_RUR</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.multiply_terms_in_RUR" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">multiply_terms_in_RUR</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.multiply_terms_in_RUR" title="Link to this definition"></a></dt>
 <dd><p>If a Ptolemy coordinate is given as Rational Univariate Representation
 with numerator and denominator being a product, multiply the terms and
 return the result.</p>
@@ -558,20 +617,20 @@ factorised.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates.num_tetrahedra">
-<span class="sig-name descname"><span class="pre">num_tetrahedra</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.num_tetrahedra" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">num_tetrahedra</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.num_tetrahedra" title="Link to this definition"></a></dt>
 <dd><p>The number of tetrahedra for which we have Ptolemy coordinates.</p>
 </dd></dl>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates.number_field">
-<span class="sig-name descname"><span class="pre">number_field</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.number_field" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">number_field</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.number_field" title="Link to this definition"></a></dt>
 <dd><p>For an exact solution, return the number_field spanned by the
 Ptolemy coordinates. If number_field is Q, return None.</p>
 </dd></dl>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates.numerical">
-<span class="sig-name descname"><span class="pre">numerical</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.numerical" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">numerical</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.numerical" title="Link to this definition"></a></dt>
 <dd><p>Turn exact solutions into numerical solutions using pari.</p>
 <p>Take an exact solution:</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">snappy.ptolemy.processMagmaFile</span> <span class="kn">import</span> <span class="n">_magma_output_for_4_1__sl3</span><span class="p">,</span> <span class="n">solutions_from_magma</span>
@@ -595,34 +654,34 @@ Ptolemy coordinates. If number_field is Q, return None.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates.ratio_coordinate">
-<span class="sig-name descname"><span class="pre">ratio_coordinate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tet</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pt</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.ratio_coordinate" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">ratio_coordinate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tet</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pt</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.ratio_coordinate" title="Link to this definition"></a></dt>
 <dd><p>Returns the ratio coordinate for tetrahedron with index tet
 for the edge from v0 to v1 (integers between 0 and 3) and integral
 point pt (quadruple adding up N-1) on the edge.</p>
 <p>See Definition 10.2:
 Garoufalidis, Goerner, Zickert:
-Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
-<a class="reference external" href="http://arxiv.org/abs/1207.6711">http://arxiv.org/abs/1207.6711</a></p>
+Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
+<a class="reference external" href="https://arxiv.org/abs/1207.6711">https://arxiv.org/abs/1207.6711</a></p>
 <p>Note that this definition turned out to have the wrong sign. Multiply
 the result by -1 if v1 &lt; v0 and N is even.</p>
 </dd></dl>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates.short_edge">
-<span class="sig-name descname"><span class="pre">short_edge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tet</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.short_edge" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">short_edge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tet</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.short_edge" title="Link to this definition"></a></dt>
 <dd><p>Returns the identity. This is because we can think of the matrices
 given by Ptolemy coordinates of living on truncated simplices which
 can be though of as doubly truncated simplices where all short edges
 are collapsed, hence labeled by the identity.</p>
-<p>See equation 10.4 in
+<p>See equation 10.4 in
 Garoufalidis, Goerner, Zickert:
-Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
-<a class="reference external" href="http://arxiv.org/abs/1207.6711">http://arxiv.org/abs/1207.6711</a></p>
+Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
+<a class="reference external" href="https://arxiv.org/abs/1207.6711">https://arxiv.org/abs/1207.6711</a></p>
 </dd></dl>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates.to_PUR">
-<span class="sig-name descname"><span class="pre">to_PUR</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.to_PUR" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">to_PUR</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.PtolemyCoordinates.to_PUR" title="Link to this definition"></a></dt>
 <dd><p>If any Ptolemy coordinates are given as Rational Univariate
 Representation, convert them to Polynomial Univariate Representation and
 return the result.</p>
@@ -632,7 +691,7 @@ return the result.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.PtolemyCoordinates.volume_numerical">
-<span class="sig-name descname"><span class="pre">volume_numerical</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">drop_negative_vols</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="#snappy.ptolemy.coordinates.PtolemyCoordinates.volume_numerical" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">volume_numerical</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">drop_negative_vols</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="#snappy.ptolemy.coordinates.PtolemyCoordinates.volume_numerical" title="Link to this definition"></a></dt>
 <dd><p>Turn into (Galois conjugate) numerical solutions and compute volumes.
 If already numerical, only return the one volume.
 See numerical().</p>
@@ -644,10 +703,10 @@ only return non-negative volumes.</p>
 </section>
 <section id="crossratios">
-<h2>CrossRatios<a class="headerlink" href="#crossratios" title="Permalink to this headline">¶</a></h2>
+<h2>CrossRatios<a class="headerlink" href="#crossratios" title="Link to this heading"></a></h2>
 <dl class="py class">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.CrossRatios">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">snappy.ptolemy.coordinates.</span></span><span class="sig-name descname"><span class="pre">CrossRatios</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">d</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">is_numerical</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">manifold_thunk</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios" title="Permalink to this definition">¶</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">snappy.ptolemy.coordinates.</span></span><span class="sig-name descname"><span class="pre">CrossRatios</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">d</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">is_numerical</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">manifold_thunk</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios" title="Link to this definition"></a></dt>
 <dd><p>Represents assigned shape parameters/cross ratios as
 dictionary. The cross ratios are according to SnapPy convention, so we
 have:</p>
@@ -660,20 +719,20 @@ have:</p>
 <span class="n">zpp</span> <span class="ow">is</span> <span class="n">at</span> <span class="n">the</span> <span class="n">edge</span> <span class="mi">03</span> <span class="ow">and</span> <span class="n">equal</span> <span class="n">to</span> <span class="n">s0</span> <span class="o">*</span> <span class="n">s3</span> <span class="o">*</span> <span class="p">(</span><span class="n">c_1100</span> <span class="o">*</span> <span class="n">c_0011</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="n">c_0101</span> <span class="o">*</span> <span class="n">c_1010</span><span class="p">)</span><span class="o">.</span>
 </pre></div>
 </div>
-<p>Note that this is different from the convention used in
+<p>Note that this is different from the convention used in
 Garoufalidis, Goerner, Zickert:
-Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
-<a class="reference external" href="http://arxiv.org/abs/1207.6711">http://arxiv.org/abs/1207.6711</a></p>
+Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
+<a class="reference external" href="https://arxiv.org/abs/1207.6711">https://arxiv.org/abs/1207.6711</a></p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.CrossRatios.N">
-<span class="sig-name descname"><span class="pre">N</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.N" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">N</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.N" title="Link to this definition"></a></dt>
 <dd><p>Get the N such that these cross ratios are for
 SL/PSL(N,C)-representations.</p>
 </dd></dl>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.CrossRatios.check_against_manifold">
-<span class="sig-name descname"><span class="pre">check_against_manifold</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">M</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">epsilon</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.check_against_manifold" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">check_against_manifold</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">M</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">epsilon</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.check_against_manifold" title="Link to this definition"></a></dt>
 <dd><p>Checks that the given solution really is a solution to the PGL(N,C) gluing
 equations of a manifold. Usage similar to check_against_manifold of
 PtolemyCoordinates. See help(ptolemy.PtolemtyCoordinates) for example.</p>
@@ -685,7 +744,7 @@ None for exact comparison.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.CrossRatios.evaluate_word">
-<span class="sig-name descname"><span class="pre">evaluate_word</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">word</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">G</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.evaluate_word" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">evaluate_word</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">word</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">G</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.evaluate_word" title="Link to this definition"></a></dt>
 <dd><p>Given a word in the generators of the fundamental group,
 compute the corresponding matrix. By default, these are the
 generators of the unsimplified presentation of the fundamental
@@ -699,7 +758,7 @@ M.fundamental_group(True).</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.CrossRatios.from_snappy_manifold">
-<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_snappy_manifold</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">M</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dec_prec</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">bits_prec</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">intervals</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="#snappy.ptolemy.coordinates.CrossRatios.from_snappy_manifold" title="Permalink to this definition">¶</a></dt>
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_snappy_manifold</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">M</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dec_prec</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">bits_prec</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">intervals</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="#snappy.ptolemy.coordinates.CrossRatios.from_snappy_manifold" title="Link to this definition"></a></dt>
 <dd><p>Constructs an assignment of shape parameters/cross ratios using
 the tetrahehdra_shapes method of a given SnapPy manifold. The optional
 parameters are the same as that of tetrahedra_shapes.</p>
@@ -707,21 +766,21 @@ parameters are the same as that of tetrahedra_shapes.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.CrossRatios.get_manifold">
-<span class="sig-name descname"><span class="pre">get_manifold</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.get_manifold" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">get_manifold</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.get_manifold" title="Link to this definition"></a></dt>
 <dd><p>Get the manifold for which this structure represents a solution
 to the gluing equations.</p>
 </dd></dl>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.CrossRatios.induced_representation">
-<span class="sig-name descname"><span class="pre">induced_representation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">N</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.induced_representation" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">induced_representation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">N</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.induced_representation" title="Link to this definition"></a></dt>
 <dd><p>Given a PSL(2,C) representation constructs the induced representation
 for the given N.
 The induced representation is in SL(N,C) if N is odd and
 SL(N,C) / {+1,-1} if N is even and is described in the Introduction of
 Garoufalidis, Thurston, Zickert
 The Complex Volume of SL(n,C)-Representations of 3-Manifolds
-<a class="reference external" href="http://arxiv.org/abs/1111.2828">http://arxiv.org/abs/1111.2828</a></p>
+<a class="reference external" href="https://arxiv.org/abs/1111.2828">https://arxiv.org/abs/1111.2828</a></p>
 <p>There is a canonical group homomorphism SL(2,C)-&gt;SL(N,C) coming from
 the the natural SL(2,C)-action on the vector space Sym^{N-1}(C^2).
 This homomorphisms decends to a homomorphism from PSL(2,C) if one
@@ -732,7 +791,7 @@ representation.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.CrossRatios.is_geometric">
-<span class="sig-name descname"><span class="pre">is_geometric</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">epsilon</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-06</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.is_geometric" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">is_geometric</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">epsilon</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-06</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.is_geometric" title="Link to this definition"></a></dt>
 <dd><p>Returns true if all shapes corresponding to this solution have positive
 imaginary part.</p>
 <p>If the solutions are exact, it returns true if one of the corresponding
@@ -743,7 +802,7 @@ considered positive if it is larger than this epsilon.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.CrossRatios.is_induced_from_psl2">
-<span class="sig-name descname"><span class="pre">is_induced_from_psl2</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">epsilon</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.is_induced_from_psl2" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">is_induced_from_psl2</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">epsilon</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.is_induced_from_psl2" title="Link to this definition"></a></dt>
 <dd><p>For each simplex and each edges, checks that all cross ratios of that
 simplex that are parallel to that each are the same (maximal absolute
 difference is the epsilon given as argument).
@@ -753,7 +812,7 @@ PSL(2,C) representation.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.CrossRatios.is_pu_2_1_representation">
-<span class="sig-name descname"><span class="pre">is_pu_2_1_representation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">epsilon</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">epsilon2</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.is_pu_2_1_representation" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">is_pu_2_1_representation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">epsilon</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">epsilon2</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.is_pu_2_1_representation" title="Link to this definition"></a></dt>
 <dd><p>Returns True if the representation is also a
 PU(2,1)-representation. This uses Proposition 3.5 and the
 remark following that proposition in <a class="reference internal" href="#fkr2013" id="id1"><span>[FKR2013]</span></a>.</p>
@@ -780,7 +839,7 @@ hold or just because of numerical noise.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.CrossRatios.is_real">
-<span class="sig-name descname"><span class="pre">is_real</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">epsilon</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.is_real" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">is_real</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">epsilon</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.is_real" title="Link to this definition"></a></dt>
 <dd><p>Returns True if all cross ratios are real (have absolute imaginary
 part &lt; epsilon where epsilon is given as argument).
 This means that the corresponding representation is in PSL(N,R).</p>
@@ -788,35 +847,35 @@ This means that the corresponding representation is in PSL(N,R).</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.CrossRatios.long_edge">
-<span class="sig-name descname"><span class="pre">long_edge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tet</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.long_edge" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">long_edge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tet</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.long_edge" title="Link to this definition"></a></dt>
 <dd><p>The matrix that labels a long edge starting at vertex (v0, v1, v2)
 of a doubly truncated simplex corresponding to the ideal tetrahedron
 with index tet.</p>
 <p>This matrix was labeled alpha^{v0v1v2} in Figure 18 of
 Garoufalidis, Goerner, Zickert:
-Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
-<a class="reference external" href="http://arxiv.org/abs/1207.6711">http://arxiv.org/abs/1207.6711</a></p>
+Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
+<a class="reference external" href="https://arxiv.org/abs/1207.6711">https://arxiv.org/abs/1207.6711</a></p>
 <p>It is computed using equation 10.22.</p>
 <p>The resulting matrix is given as a python list of lists.</p>
 </dd></dl>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.CrossRatios.middle_edge">
-<span class="sig-name descname"><span class="pre">middle_edge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tet</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.middle_edge" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">middle_edge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tet</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.middle_edge" title="Link to this definition"></a></dt>
 <dd><p>The matrix that labels a middle edge starting at vertex (v0, v1, v2)
 of a doubly truncated simplex corresponding to the ideal tetrahedron
 with index tet.</p>
 <p>This matrix was labeled beta^{v0v1v2} in Figure 18 of
 Garoufalidis, Goerner, Zickert:
-Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
-<a class="reference external" href="http://arxiv.org/abs/1207.6711">http://arxiv.org/abs/1207.6711</a></p>
+Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
+<a class="reference external" href="https://arxiv.org/abs/1207.6711">https://arxiv.org/abs/1207.6711</a></p>
 <p>It is computed using equation 10.22.</p>
 <p>The resulting matrix is given as a python list of lists.</p>
 </dd></dl>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.CrossRatios.multiply_and_simplify_terms_in_RUR">
-<span class="sig-name descname"><span class="pre">multiply_and_simplify_terms_in_RUR</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.multiply_and_simplify_terms_in_RUR" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">multiply_and_simplify_terms_in_RUR</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.multiply_and_simplify_terms_in_RUR" title="Link to this definition"></a></dt>
 <dd><p>If a cross ratio is given as Rational Univariate Representation
 with numerator and denominator being a product, multiply the terms,
 reduce the fraction and return the result.</p>
@@ -827,7 +886,7 @@ factorised.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.CrossRatios.multiply_terms_in_RUR">
-<span class="sig-name descname"><span class="pre">multiply_terms_in_RUR</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.multiply_terms_in_RUR" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">multiply_terms_in_RUR</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.multiply_terms_in_RUR" title="Link to this definition"></a></dt>
 <dd><p>If a cross ratio is given as Rational Univariate Representation
 with numerator and denominator being a product, multiply the terms and
 return the result.</p>
@@ -838,13 +897,13 @@ factorised.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.CrossRatios.num_tetrahedra">
-<span class="sig-name descname"><span class="pre">num_tetrahedra</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.num_tetrahedra" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">num_tetrahedra</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.num_tetrahedra" title="Link to this definition"></a></dt>
 <dd><p>The number of tetrahedra for which we have cross ratios.</p>
 </dd></dl>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.CrossRatios.numerical">
-<span class="sig-name descname"><span class="pre">numerical</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.numerical" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">numerical</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.numerical" title="Link to this definition"></a></dt>
 <dd><p>Turn exact solutions into numerical solutions using pari. Similar to
 numerical() of PtolemyCoordinates. See help(ptolemy.PtolemyCoordinates)
 for example.</p>
@@ -852,21 +911,21 @@ for example.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.CrossRatios.short_edge">
-<span class="sig-name descname"><span class="pre">short_edge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tet</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.short_edge" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">short_edge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tet</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.short_edge" title="Link to this definition"></a></dt>
 <dd><p>The matrix that labels a long edge starting at vertex (v0, v1, v2)
 of a doubly truncated simplex corresponding to the ideal tetrahedron
 with index tet.</p>
 <p>This matrix was labeled gamma^{v0v1v2} in Figure 18 of
 Garoufalidis, Goerner, Zickert:
-Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
-<a class="reference external" href="http://arxiv.org/abs/1207.6711">http://arxiv.org/abs/1207.6711</a></p>
+Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
+<a class="reference external" href="https://arxiv.org/abs/1207.6711">https://arxiv.org/abs/1207.6711</a></p>
 <p>It is computed using equation 10.22.</p>
 <p>The resulting matrix is given as a python list of lists.</p>
 </dd></dl>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.CrossRatios.to_PUR">
-<span class="sig-name descname"><span class="pre">to_PUR</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.to_PUR" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">to_PUR</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.to_PUR" title="Link to this definition"></a></dt>
 <dd><p>If any Ptolemy coordinates are given as Rational Univariate
 Representation, convert them to Polynomial Univariate Representation and
 return the result.</p>
@@ -876,7 +935,7 @@ return the result.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.CrossRatios.volume_numerical">
-<span class="sig-name descname"><span class="pre">volume_numerical</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">drop_negative_vols</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="#snappy.ptolemy.coordinates.CrossRatios.volume_numerical" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">volume_numerical</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">drop_negative_vols</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="#snappy.ptolemy.coordinates.CrossRatios.volume_numerical" title="Link to this definition"></a></dt>
 <dd><p>Turn into (Galois conjugate) numerical solutions and compute volumes.
 If already numerical, only compute the one volume.
 See numerical().</p>
@@ -886,23 +945,23 @@ only return non-negative volumes.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.CrossRatios.x_coordinate">
-<span class="sig-name descname"><span class="pre">x_coordinate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tet</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pt</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.x_coordinate" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">x_coordinate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tet</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pt</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.CrossRatios.x_coordinate" title="Link to this definition"></a></dt>
 <dd><p>Returns the X-coordinate for the tetrahedron with index tet
 at the point pt (quadruple of integers adding up to N).</p>
 <p>See Definition 10.9:
 Garoufalidis, Goerner, Zickert:
-Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
-<a class="reference external" href="http://arxiv.org/abs/1207.6711">http://arxiv.org/abs/1207.6711</a></p>
+Gluing Equations for PGL(n,C)-Representations of 3-Manifolds
+<a class="reference external" href="https://arxiv.org/abs/1207.6711">https://arxiv.org/abs/1207.6711</a></p>
 </dd></dl>
 </dd></dl>
 </section>
 <section id="flattenings">
-<h2>Flattenings<a class="headerlink" href="#flattenings" title="Permalink to this headline">¶</a></h2>
+<h2>Flattenings<a class="headerlink" href="#flattenings" title="Link to this heading"></a></h2>
 <dl class="py class">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.Flattenings">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">snappy.ptolemy.coordinates.</span></span><span class="sig-name descname"><span class="pre">Flattenings</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">d</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifold_thunk=&lt;function</span> <span class="pre">Flattenings.&lt;lambda&gt;&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">evenN=2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.Flattenings" title="Permalink to this definition">¶</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">snappy.ptolemy.coordinates.</span></span><span class="sig-name descname"><span class="pre">Flattenings</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">d</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manifold_thunk=&lt;function</span> <span class="pre">Flattenings.&lt;lambda&gt;&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">evenN=2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.Flattenings" title="Link to this definition"></a></dt>
 <dd><p>Represents a flattening assigned to each edge of a simplex as dictionary.</p>
 <p>We assign to each pair of parallel edges of each simplex a triple (w, z, p)
 such that:</p>
@@ -912,7 +971,7 @@ such that:</p>
 <p>For N = 2, the three triples belonging to a simplex form a combinatorial
 flattening (w0, w1, w2) as defined in Definition 3.1 in
 Walter D. Neumann, Extended Bloch group and the Cheeger-Chern-Simons class
-<a class="reference external" href="http://arxiv.org/abs/math.GT/0307092">http://arxiv.org/abs/math.GT/0307092</a></p>
+<a class="reference external" href="https://arxiv.org/abs/math.GT/0307092">https://arxiv.org/abs/math.GT/0307092</a></p>
 <p>For N &gt; 2, the three triples form a generalized combinatorial flattening
 (w0, w1, w2) that gives an element in the generalized Extended Bloch group
 which is the Extended Bloch group corresponding to the Riemann surface
@@ -934,17 +993,17 @@ A representation in PSL(n,C) with n odd in the group for N = 2 * n.</p>
 </div>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.Flattenings.N">
-<span class="sig-name descname"><span class="pre">N</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.Flattenings.N" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">N</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.Flattenings.N" title="Link to this definition"></a></dt>
 <dd><p>Get the N such that these cross ratios are for
 SL/PSL(N,C)-representations.</p>
 </dd></dl>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.Flattenings.check_against_manifold">
-<span class="sig-name descname"><span class="pre">check_against_manifold</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">M</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">epsilon</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-10</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.Flattenings.check_against_manifold" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">check_against_manifold</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">M</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">epsilon</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-10</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.Flattenings.check_against_manifold" title="Link to this definition"></a></dt>
 <dd><p>Checks that the flattening really is a solution to the logarithmic
-PGL(N,C) gluing equations of a manifold. Usage similar to
-check_against_manifold of Ptolemy Coordinates, see
+PGL(N,C) gluing equations of a manifold. Usage similar to
+check_against_manifold of Ptolemy Coordinates, see
 help(ptolemy.Coordinates) for similar examples.</p>
 <p>=== Arguments ===</p>
 <p>M — manifold to check this for
@@ -953,7 +1012,7 @@ epsilon — maximal allowed error when checking the equations</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.Flattenings.complex_volume">
-<span class="sig-name descname"><span class="pre">complex_volume</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">with_modulo</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="#snappy.ptolemy.coordinates.Flattenings.complex_volume" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">complex_volume</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">with_modulo</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="#snappy.ptolemy.coordinates.Flattenings.complex_volume" title="Link to this definition"></a></dt>
 <dd><p>Compute complex volume. The complex volume is defined only up to
 some multiple of m where m = i * pi**2/6 for PSL(2,C) and SL(N,C)
 and m = i * pi**2/18 for PSL(3,C).</p>
@@ -963,7 +1022,7 @@ and m = i * pi**2/18 for PSL(3,C).</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.Flattenings.from_tetrahedra_shapes_of_manifold">
-<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_tetrahedra_shapes_of_manifold</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">M</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.Flattenings.from_tetrahedra_shapes_of_manifold" title="Permalink to this definition">¶</a></dt>
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_tetrahedra_shapes_of_manifold</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">M</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.Flattenings.from_tetrahedra_shapes_of_manifold" title="Link to this definition"></a></dt>
 <dd><p>Takes as argument a manifold and produces (weak) flattenings using
 the tetrahedra_shapes of the manifold M.</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">snappy</span> <span class="kn">import</span> <span class="n">Manifold</span>
@@ -977,13 +1036,13 @@ the tetrahedra_shapes of the manifold M.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.Flattenings.get_manifold">
-<span class="sig-name descname"><span class="pre">get_manifold</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.Flattenings.get_manifold" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">get_manifold</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.Flattenings.get_manifold" title="Link to this definition"></a></dt>
 <dd><p>Get the manifold for which this structure represents a flattening.</p>
 </dd></dl>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.Flattenings.get_order">
-<span class="sig-name descname"><span class="pre">get_order</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.Flattenings.get_order" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">get_order</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.Flattenings.get_order" title="Link to this definition"></a></dt>
 <dd><p>Returns the number N. This flattening represents an element in the
 generalized Extended Bloch group for the Riemann surface given by
 u1 * e^w0 + u2 * e^w1 = 1 where u1^N = u2^N = 1.</p>
@@ -991,17 +1050,17 @@ u1 * e^w0 + u2 * e^w1 = 1 where u1^N = u2^N = 1.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.Flattenings.get_zpq_triple">
-<span class="sig-name descname"><span class="pre">get_zpq_triple</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">key_z</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.Flattenings.get_zpq_triple" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">get_zpq_triple</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">key_z</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.Flattenings.get_zpq_triple" title="Link to this definition"></a></dt>
 <dd><p>Gives a flattening as triple [z;p,q] representing an element
 in the generalized Extended Bloch group similar to the way the
-triple [z;p,q] is used in Lemma 3.2 in
+triple [z;p,q] is used in Lemma 3.2 in
 Walter D. Neumann, Extended Bloch group and the Cheeger-Chern-Simons class
-<a class="reference external" href="http://arxiv.org/abs/math.GT/0307092">http://arxiv.org/abs/math.GT/0307092</a></p>
+<a class="reference external" href="https://arxiv.org/abs/math.GT/0307092">https://arxiv.org/abs/math.GT/0307092</a></p>
 </dd></dl>
 <dl class="py method">
 <dt class="sig sig-object py" id="snappy.ptolemy.coordinates.Flattenings.num_tetrahedra">
-<span class="sig-name descname"><span class="pre">num_tetrahedra</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.Flattenings.num_tetrahedra" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">num_tetrahedra</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.coordinates.Flattenings.num_tetrahedra" title="Link to this definition"></a></dt>
 <dd><p>The number of tetrahedra for which we have cross ratios.</p>
 </dd></dl>
@@ -1009,21 +1068,21 @@ Walter D. Neumann, Extended Bloch group and the Cheeger-Chern-Simons class
 </section>
 <section id="nonzerodimensionalcomponent">
-<h2>NonZeroDimensionalComponent<a class="headerlink" href="#nonzerodimensionalcomponent" title="Permalink to this headline">¶</a></h2>
+<h2>NonZeroDimensionalComponent<a class="headerlink" href="#nonzerodimensionalcomponent" title="Link to this heading"></a></h2>
 <dl class="py class">
 <dt class="sig sig-object py" id="snappy.ptolemy.component.NonZeroDimensionalComponent">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">snappy.ptolemy.component.</span></span><span class="sig-name descname"><span class="pre">NonZeroDimensionalComponent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">witnesses</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dimension</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'unknown'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">free_variables</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">genus</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">p</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.component.NonZeroDimensionalComponent" title="Permalink to this definition">¶</a></dt>
-<dd><p>Represents a non-zero dimensinal component in the
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">snappy.ptolemy.component.</span></span><span class="sig-name descname"><span class="pre">NonZeroDimensionalComponent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">witnesses</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dimension</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'unknown'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">free_variables</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">genus</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">p</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snappy.ptolemy.component.NonZeroDimensionalComponent" title="Link to this definition"></a></dt>
+<dd><p>Represents a non-zero dimensional component in the
 Ptolemy variety. It is a list that can hold points sampled from that
 component (witnesses).</p>
 </dd></dl>
 </section>
 <section id="other-functions">
-<h2>Other functions<a class="headerlink" href="#other-functions" title="Permalink to this headline">¶</a></h2>
+<h2>Other functions<a class="headerlink" href="#other-functions" title="Link to this heading"></a></h2>
 <dl class="py function">
 <dt class="sig sig-object py" id="snappy.ptolemy.solutions_from_magma">
-<span class="sig-prename descclassname"><span class="pre">snappy.ptolemy.</span></span><span class="sig-name descname"><span class="pre">solutions_from_magma</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">numerical</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="#snappy.ptolemy.solutions_from_magma" title="Permalink to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">snappy.ptolemy.</span></span><span class="sig-name descname"><span class="pre">solutions_from_magma</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">numerical</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="#snappy.ptolemy.solutions_from_magma" title="Link to this definition"></a></dt>
 <dd><p>Obsolete, use processFileDispatch.parse_solutions instead.</p>
 <p>Assumes the given string is the output of a magma computation, parses
 it and returns a list of solutions.
@@ -1033,7 +1092,7 @@ NonZeroDimensionalComponent.</p>
 <dl class="py function">
 <dt class="sig sig-object py" id="snappy.ptolemy.solutions_from_magma_file">
-<span class="sig-prename descclassname"><span class="pre">snappy.ptolemy.</span></span><span class="sig-name descname"><span class="pre">solutions_from_magma_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">numerical</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="#snappy.ptolemy.solutions_from_magma_file" title="Permalink to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">snappy.ptolemy.</span></span><span class="sig-name descname"><span class="pre">solutions_from_magma_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">numerical</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="#snappy.ptolemy.solutions_from_magma_file" title="Link to this definition"></a></dt>
 <dd><p>Obsolete, use processFileDispatch.parse_solutions_from_file instead.</p>
 <p>Reads the output from a magma computation from the file with the given
 filename and returns a list of solutions. Also see solutions_from_magma.
@@ -1041,85 +1100,45 @@ A non-zero dimensional component of the variety is reported as
 NonZeroDimensionalComponent.</p>
 </dd></dl>
-<dl class="citation">
-<dt class="label" id="fkr2013"><span class="brackets">FKR2013</span><span class="fn-backref">(<a href="#id1">1</a>,<a href="#id2">2</a>)</span></dt>
-<dd><p>Falbel, Koseleff, Rouillier: Representations of Fundamental Groups of 3-Manifolds into PGL(3,C): Exact Computations in Low Complexity, <a class="reference external" href="http://arxiv.org/abs/1307.6697">http://arxiv.org/abs/1307.6697</a></p>
-</dd>
-</dl>
+<div role="list" class="citation-list">
+<div class="citation" id="fkr2013" role="doc-biblioentry">
+<span class="label"><span class="fn-bracket">[</span>FKR2013<span class="fn-bracket">]</span></span>
+<span class="backrefs">(<a role="doc-backlink" href="#id1">1</a>,<a role="doc-backlink" href="#id2">2</a>)</span>
+<p>Falbel, Koseleff, Rouillier: Representations of Fundamental Groups of 3-Manifolds into PGL(3,C): Exact Computations in Low Complexity, <a class="reference external" href="http://arxiv.org/abs/1307.6697">http://arxiv.org/abs/1307.6697</a></p>
+</div>
+</div>
 </section>
 </section>
-            <div class="clearer"></div>
+           </div>
           </div>
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-      </div>
-      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
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-<li><a class="reference internal" href="#ptolemyvariety">PtolemyVariety</a></li>
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-<li><a class="reference internal" href="#crossratios">CrossRatios</a></li>
-<li><a class="reference internal" href="#flattenings">Flattenings</a></li>
-<li><a class="reference internal" href="#nonzerodimensionalcomponent">NonZeroDimensionalComponent</a></li>
-<li><a class="reference internal" href="#other-functions">Other functions</a></li>
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