diff options
| -rw-r--r-- | .SRCINFO | 8 | ||||
| -rw-r--r-- | PKGBUILD | 18 | ||||
| -rw-r--r-- | sagemath-matplotlib-3.2.patch | 86 | ||||
| -rw-r--r-- | sagemath-no-dict-sorting.patch | 103 | ||||
| -rw-r--r-- | sagemath-sphinx-3.patch | 272 |
5 files changed, 422 insertions, 65 deletions
@@ -1,6 +1,6 @@ pkgbase = sagemath-git pkgdesc = Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab - pkgver = 9.1.rc0.r0.g10ed24e3ed + pkgver = 9.1.rc1.r0.g249fc90389 pkgrel = 1 url = http://www.sagemath.org arch = x86_64 @@ -108,6 +108,7 @@ pkgbase = sagemath-git source = sagemath-matplotlib-3.2.patch source = sagemath-pari-2.11.3.patch source = sagemath-jedi-0.16.patch + source = sagemath-sphinx-3.patch sha256sums = SKIP sha256sums = b1112875776635b4f33bc13c8aaedfbbaed8f62a1dac986f7b8faa7565d6abae sha256sums = 6a5470d7044a50a35a6478f57c19adf72fe54aefebeea8a095915b63f9e219ac @@ -115,14 +116,15 @@ pkgbase = sagemath-git sha256sums = 937074fa7a8a4e2aba9ea77ec622fe937985a1a9176c48460d51325ee877a4f5 sha256sums = 408e193c96a466cfe0134fe44a28e93659916d1d28bd4ea89460aec7fefe8657 sha256sums = e44bbde87f3312548faad75b7383ef21fade55be251ab5804de41cd3842ca8a0 - sha256sums = 0ef047e671ddd288e07e9f544f646a9a0bd908accfe6b96dcaf4ee52fa6037e7 + sha256sums = 54de32de6f5b71b102aa3df2f6c177d81f4a9fd1076079d412e3e3393155566b sha256sums = fc28ca3aa1a656bfb451181d5086b3041238f24bf462cc69626d3cd603a246df sha256sums = e5aa663c7f76d737ea697a805094734ab8e06eab35bbeadcb4dcab89998d7b31 sha256sums = 5e6d1aa34959bd4369bd08a80648a5c7bc2d38e72c97e9a5f986e91f8a7aca07 sha256sums = 588d831b44ec28ca18540d5649e8af518500b82431a59542f3daa92d6c3007cd - sha256sums = 979777363001cca87f73128dd4db5f372fc9e4f1079805a20af01df47797468f + sha256sums = 4947a86264622dffebb58b802f0616f0fb47b5784d95346f44ee426cb2e541fc sha256sums = 1f41b35c916df74fc943949ccde1155e59e7bbbee220c845c9afdf4e0f76bfbc sha256sums = 30e15715cdc90639d7cbd34e76bbadae2e6d8bab6241617a386aed9513207b8a + sha256sums = eeeafd1a74c8c43c369569c8ea1dbae8fd9fcfdf0e6609471c030e9738b97ce5 pkgname = sagemath-git optdepends = cython: to compile cython code @@ -7,7 +7,7 @@ pkgbase=sagemath-git pkgname=(sagemath-git sagemath-jupyter-git) -pkgver=9.1.rc0.r0.g10ed24e3ed +pkgver=9.1.rc1.r0.g249fc90389 pkgrel=1 pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab" arch=(x86_64) @@ -48,7 +48,8 @@ source=(git://git.sagemath.org/sage.git#branch=develop sagemath-gap-4.11.patch sagemath-matplotlib-3.2.patch sagemath-pari-2.11.3.patch - sagemath-jedi-0.16.patch) + sagemath-jedi-0.16.patch + sagemath-sphinx-3.patch) sha256sums=('SKIP' 'b1112875776635b4f33bc13c8aaedfbbaed8f62a1dac986f7b8faa7565d6abae' '6a5470d7044a50a35a6478f57c19adf72fe54aefebeea8a095915b63f9e219ac' @@ -56,14 +57,15 @@ sha256sums=('SKIP' '937074fa7a8a4e2aba9ea77ec622fe937985a1a9176c48460d51325ee877a4f5' '408e193c96a466cfe0134fe44a28e93659916d1d28bd4ea89460aec7fefe8657' 'e44bbde87f3312548faad75b7383ef21fade55be251ab5804de41cd3842ca8a0' - '0ef047e671ddd288e07e9f544f646a9a0bd908accfe6b96dcaf4ee52fa6037e7' + '54de32de6f5b71b102aa3df2f6c177d81f4a9fd1076079d412e3e3393155566b' 'fc28ca3aa1a656bfb451181d5086b3041238f24bf462cc69626d3cd603a246df' 'e5aa663c7f76d737ea697a805094734ab8e06eab35bbeadcb4dcab89998d7b31' '5e6d1aa34959bd4369bd08a80648a5c7bc2d38e72c97e9a5f986e91f8a7aca07' '588d831b44ec28ca18540d5649e8af518500b82431a59542f3daa92d6c3007cd' - '979777363001cca87f73128dd4db5f372fc9e4f1079805a20af01df47797468f' + '4947a86264622dffebb58b802f0616f0fb47b5784d95346f44ee426cb2e541fc' '1f41b35c916df74fc943949ccde1155e59e7bbbee220c845c9afdf4e0f76bfbc' - '30e15715cdc90639d7cbd34e76bbadae2e6d8bab6241617a386aed9513207b8a') + '30e15715cdc90639d7cbd34e76bbadae2e6d8bab6241617a386aed9513207b8a' + 'eeeafd1a74c8c43c369569c8ea1dbae8fd9fcfdf0e6609471c030e9738b97ce5') pkgver() { cd sage @@ -92,8 +94,6 @@ prepare(){ sed -e 's|mathjax|mathjax2|g' -i src/sage/env.py # Fix gap.version() and doctests with GAP 4.11 patch -p1 -i ../sagemath-gap-4.11.patch -# Fix warnings with matplotlib 3.2 - patch -p1 -i ../sagemath-matplotlib-3.2.patch # Fix doctests with pari 2.11.3 patch -p1 -i ../sagemath-pari-2.11.3.patch # Fix deprecation warnings on autocompletion with jedi 0.16 @@ -106,6 +106,10 @@ prepare(){ patch -p1 -i ../sagemath-singular-4.1.2.patch # Fix SIGFPE crashes with ecl 16.1.3 https://trac.sagemath.org/ticket/22191 patch -p1 -i ../sagemath-ecl-sigfpe.patch +# Fix doc build with sphinx 3 https://trac.sagemath.org/ticket/28856 + patch -p1 -i ../sagemath-sphinx-3.patch +# Fix warnings with matplotlib 3.2 https://trac.sagemath.org/ticket/29547 + patch -p1 -i ../sagemath-matplotlib-3.2.patch sed -e 's|sage-python23|python|' -i src/bin/* sed -e 's|$SAGE_PYTHON3|yes|' -i src/bin/sage diff --git a/sagemath-matplotlib-3.2.patch b/sagemath-matplotlib-3.2.patch index c8f542ca5bd5..97baa4ea92aa 100644 --- a/sagemath-matplotlib-3.2.patch +++ b/sagemath-matplotlib-3.2.patch @@ -1,18 +1,35 @@ -diff --git a/src/sage/plot/contour_plot.py b/src/sage/plot/contour_plot.py -index a7533fa3d9..12a2b1f670 100644 ---- a/src/sage/plot/contour_plot.py -+++ b/src/sage/plot/contour_plot.py -@@ -223,7 +223,7 @@ class ContourPlot(GraphicPrimitive): - cb.add_lines(CS) +diff --git a/src/sage/combinat/root_system/root_lattice_realizations.py b/src/sage/combinat/root_system/root_lattice_realizations.py +index f55c24f..16d3ca5 100644 +--- a/src/sage/combinat/root_system/root_lattice_realizations.py ++++ b/src/sage/combinat/root_system/root_lattice_realizations.py +@@ -3131,8 +3131,8 @@ class RootLatticeRealizations(Category_over_base_ring): + sage: L = RootSystem(['A',2]).ambient_space() + sage: C = crystals.Tableaux(['A',2], shape=[2,1]) +- sage: L.plot_crystal(C) +- Graphics object consisting of 16 graphics primitives ++ sage: L.plot_crystal(C, plot_labels='multiplicities') ++ Graphics object consisting of 15 graphics primitives + sage: C = crystals.Tableaux(['A',2], shape=[8,4]) + sage: p = L.plot_crystal(C, plot_labels='circles') + sage: p.show(figsize=15) +diff --git a/src/sage/interacts/test_jupyter.rst b/src/sage/interacts/test_jupyter.rst +index ed2bcb5..3f307d2 100644 +--- a/src/sage/interacts/test_jupyter.rst ++++ b/src/sage/interacts/test_jupyter.rst +@@ -281,9 +281,7 @@ Test all interacts from the Sage interact library:: + Interactive function <function coin at ...> with 2 widgets + n: IntSlider(value=1000, description=u'Number of Tosses', max=10000, min=2, step=100) + interval: IntRangeSlider(value=(0, 0), description=u'Plotting range (y)', max=1) +- doctest:...: UserWarning: Attempting to set identical bottom==top results +- in singular transformations; automatically expanding. +- bottom=0.0, top=0.0 ++ doctest:...: UserWarning: Attempting to set identical bottom == top == 0.0 results in singular transformations; automatically expanding. + + Test matrix control (see :trac:`27735`):: --@suboptions('colorbar', orientation='vertical', format=None, spacing=None) -+@suboptions('colorbar', orientation='vertical', format=None, spacing='uniform') - @suboptions('label', fontsize=9, colors='blue', inline=None, inline_spacing=3, - fmt="%1.2f") - @options(plot_points=100, fill=True, contours=None, linewidths=None, diff --git a/src/sage/plot/colors.py b/src/sage/plot/colors.py -index 1860b6c948..af6fc7ec64 100644 +index 1860b6c..da3c9c3 100644 --- a/src/sage/plot/colors.py +++ b/src/sage/plot/colors.py @@ -20,7 +20,7 @@ comprises the "official" W3C CSS3_ / SVG_ colors. @@ -47,7 +64,7 @@ index 1860b6c948..af6fc7ec64 100644 0 sage: maps.load_maps() - sage: len(maps.maps)>130 -+ sage: len(maps.maps)>65 ++ sage: len(maps.maps)>60 True """ global cm @@ -56,7 +73,48 @@ index 1860b6c948..af6fc7ec64 100644 sage: from sage.plot.colors import Colormaps sage: maps = Colormaps() - sage: len(maps)>130 -+ sage: len(maps)>65 ++ sage: len(maps)>60 True """ self.load_maps() +diff --git a/src/sage/plot/contour_plot.py b/src/sage/plot/contour_plot.py +index a7533fa..12a2b1f 100644 +--- a/src/sage/plot/contour_plot.py ++++ b/src/sage/plot/contour_plot.py +@@ -223,7 +223,7 @@ class ContourPlot(GraphicPrimitive): + cb.add_lines(CS) + + +-@suboptions('colorbar', orientation='vertical', format=None, spacing=None) ++@suboptions('colorbar', orientation='vertical', format=None, spacing='uniform') + @suboptions('label', fontsize=9, colors='blue', inline=None, inline_spacing=3, + fmt="%1.2f") + @options(plot_points=100, fill=True, contours=None, linewidths=None, +diff --git a/src/sage/plot/multigraphics.py b/src/sage/plot/multigraphics.py +index 3135ceb..184a97c 100644 +--- a/src/sage/plot/multigraphics.py ++++ b/src/sage/plot/multigraphics.py +@@ -1295,15 +1295,15 @@ class GraphicsArray(MultiGraphics): + sage: g2 = circle((0,1), 1.) + sage: G = graphics_array([g1, g2]) + sage: G.position(0) # tol 1.0e-13 +- (0.028906249999999998, +- 0.038541666666666696, +- 0.45390624999999996, +- 0.9229166666666667) ++ (0.023437500000000003, ++ 0.03415488992713045, ++ 0.4627803348994754, ++ 0.9345951100728696) + sage: G.position(1) # tol 1.0e-13 +- (0.5171874999999999, +- 0.038541666666666696, +- 0.45390624999999996, +- 0.9229166666666667) ++ (0.5136230468749999, ++ 0.19293222169724827, ++ 0.46278033489947534, ++ 0.617040446532634) + + """ + if not self._positions: diff --git a/sagemath-no-dict-sorting.patch b/sagemath-no-dict-sorting.patch index d0b06bee6dcc..b5bfecfd1b64 100644 --- a/sagemath-no-dict-sorting.patch +++ b/sagemath-no-dict-sorting.patch @@ -390,7 +390,7 @@ index cc2b504296..119d5e37d3 100644 TESTS:: diff --git a/src/sage/categories/finite_dimensional_algebras_with_basis.py b/src/sage/categories/finite_dimensional_algebras_with_basis.py -index 7b14ee25c1..f4a34aace0 100644 +index 754d26276e..ec51907106 100644 --- a/src/sage/categories/finite_dimensional_algebras_with_basis.py +++ b/src/sage/categories/finite_dimensional_algebras_with_basis.py @@ -1276,9 +1276,9 @@ class FiniteDimensionalAlgebrasWithBasis(CategoryWithAxiom_over_base_ring): @@ -421,7 +421,7 @@ index 91598d3cd4..5d04074012 100644 '_repr_type_str': None} """ diff --git a/src/sage/categories/morphism.pyx b/src/sage/categories/morphism.pyx -index 391422bdf5..ef824b9777 100644 +index dec8b00b74..9322833836 100644 --- a/src/sage/categories/morphism.pyx +++ b/src/sage/categories/morphism.pyx @@ -601,11 +601,11 @@ cdef class SetMorphism(Morphism): @@ -550,7 +550,7 @@ index dc27b10920..2fefa65d8c 100644 (2*a + 2, 2*a + 2): (2*a + 2, 2*a + 2, 0)} """ diff --git a/src/sage/combinat/cluster_algebra_quiver/cluster_seed.py b/src/sage/combinat/cluster_algebra_quiver/cluster_seed.py -index fcb53e3ac3..b1d988632d 100644 +index aec20b0687..7483c67e0b 100644 --- a/src/sage/combinat/cluster_algebra_quiver/cluster_seed.py +++ b/src/sage/combinat/cluster_algebra_quiver/cluster_seed.py @@ -2735,119 +2735,119 @@ class ClusterSeed(SageObject): @@ -2091,10 +2091,10 @@ index 94e2928525..cb461c07f8 100644 return self._orig_args diff --git a/src/sage/geometry/polyhedron/base.py b/src/sage/geometry/polyhedron/base.py -index ef3ad4d644..b83588c249 100644 +index d8609bdfe4..4f07456b3e 100644 --- a/src/sage/geometry/polyhedron/base.py +++ b/src/sage/geometry/polyhedron/base.py -@@ -6063,20 +6063,20 @@ class Polyhedron_base(Element): +@@ -6126,20 +6126,20 @@ class Polyhedron_base(Element): sage: P = polytopes.twenty_four_cell() sage: P.flag_f_vector() {(-1,): 1, @@ -2123,7 +2123,7 @@ index ef3ad4d644..b83588c249 100644 (3,): 24, (4,): 1} -@@ -6106,18 +6106,18 @@ class Polyhedron_base(Element): +@@ -6169,18 +6169,18 @@ class Polyhedron_base(Element): sage: P = (Polyhedron(lines=[[1]]) * polytopes.cross_polytope(3)) sage: P.flag_f_vector() {(-1,): 1, @@ -2147,7 +2147,7 @@ index ef3ad4d644..b83588c249 100644 (2,): 12, (3,): 8, 4: 1} -@@ -6157,22 +6157,22 @@ class Polyhedron_base(Element): +@@ -6220,22 +6220,22 @@ class Polyhedron_base(Element): sage: polytopes.hypercube(4)._flag_f_vector() {(-1,): 1, @@ -2238,10 +2238,10 @@ index 969c9f86db..25843ea25a 100644 poly = self.face_lattice().flag_f_polynomial() variables = poly.variables() diff --git a/src/sage/geometry/polyhedron/ppl_lattice_polytope.py b/src/sage/geometry/polyhedron/ppl_lattice_polytope.py -index 4281de7bf0..8bc045a34b 100644 +index 4287f9ed56..78d30d8f75 100644 --- a/src/sage/geometry/polyhedron/ppl_lattice_polytope.py +++ b/src/sage/geometry/polyhedron/ppl_lattice_polytope.py -@@ -1231,15 +1231,15 @@ class LatticePolytope_PPL_class(C_Polyhedron): +@@ -1229,15 +1229,15 @@ class LatticePolytope_PPL_class(C_Polyhedron): sage: polygon.embed_in_reflexive_polytope('polytope') A 2-dimensional lattice polytope in ZZ^2 with 3 vertices sage: polygon.embed_in_reflexive_polytope('points') @@ -2265,7 +2265,7 @@ index 4281de7bf0..8bc045a34b 100644 sage: LatticePolytope_PPL((0,0), (4,0), (0,4)).embed_in_reflexive_polytope() Traceback (most recent call last): diff --git a/src/sage/geometry/triangulation/element.py b/src/sage/geometry/triangulation/element.py -index 6f8222d07c..1c94998e15 100644 +index ba053e7139..d354b5c19b 100644 --- a/src/sage/geometry/triangulation/element.py +++ b/src/sage/geometry/triangulation/element.py @@ -605,32 +605,32 @@ class Triangulation(Element): @@ -2273,14 +2273,14 @@ index 6f8222d07c..1c94998e15 100644 sage: triangulation = polytopes.hypercube(2).triangulate(engine='internal') sage: triangulation._boundary_simplex_dictionary() - {(0, 1): ((0, 1, 3),), -- (0, 2): ((0, 2, 3),), -+ {(1, 3): ((0, 1, 3),), - (0, 3): ((0, 1, 3), (0, 2, 3)), -- (1, 3): ((0, 1, 3),), -- (2, 3): ((0, 2, 3),)} ++ {(1, 3): ((0, 1, 3), (1, 2, 3)), + (0, 3): ((0, 1, 3),), +- (1, 2): ((1, 2, 3),), +- (1, 3): ((0, 1, 3), (1, 2, 3)), +- (2, 3): ((1, 2, 3),)} + (0, 1): ((0, 1, 3),), -+ (2, 3): ((0, 2, 3),), -+ (0, 2): ((0, 2, 3),)} ++ (2, 3): ((1, 2, 3),), ++ (1, 2): ((1, 2, 3),)} sage: triangulation = polytopes.cube().triangulate(engine='internal') sage: triangulation._boundary_simplex_dictionary() @@ -2318,6 +2318,21 @@ index 6f8222d07c..1c94998e15 100644 """ result = dict() for simplex in self: +@@ -750,12 +750,10 @@ class Triangulation(Element): + (-1, 0, 0, -1), + ( 0, 1, 0, -1), + ( 0, -1, 0, 1) +- in Ambient free module of rank 4 +- over the principal ideal domain Integer Ring ++ in Ambient free module of rank 4 over the principal ideal domain Integer Ring + sage: N.dual().rays() + (1, -1, 1, -1) +- in Ambient free module of rank 4 +- over the principal ideal domain Integer Ring ++ in Ambient free module of rank 4 over the principal ideal domain Integer Ring + + TESTS:: + diff --git a/src/sage/graphs/base/boost_graph.pyx b/src/sage/graphs/base/boost_graph.pyx index 6ba0a44c9a..c50374c542 100644 --- a/src/sage/graphs/base/boost_graph.pyx @@ -2451,10 +2466,10 @@ index 802d4a8f6e..aa5efb8dac 100644 TESTS: diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py -index c369e3723a..50edd704b2 100644 +index 23ed1da506..bd9733a9b2 100644 --- a/src/sage/graphs/generic_graph.py +++ b/src/sage/graphs/generic_graph.py -@@ -5211,7 +5211,7 @@ class GenericGraph(GenericGraph_pyx): +@@ -5209,7 +5209,7 @@ class GenericGraph(GenericGraph_pyx): This method is deprecated since Sage-4.4.1.alpha2. Please use instead: sage: g.layout(layout = "planar", save_pos = True) @@ -2463,7 +2478,7 @@ index c369e3723a..50edd704b2 100644 """ deprecation(24494, 'This method is replaced by the method layout. ' 'Please use layout(layout="planar", save_pos=True) ' -@@ -5265,16 +5265,16 @@ class GenericGraph(GenericGraph_pyx): +@@ -5263,16 +5263,16 @@ class GenericGraph(GenericGraph_pyx): sage: g = graphs.PathGraph(10) sage: g.layout(layout='planar', save_pos=True, test=True) @@ -2485,7 +2500,7 @@ index c369e3723a..50edd704b2 100644 sage: g = graphs.BalancedTree(3, 4) sage: pos = g.layout(layout='planar', save_pos=True, test=True) sage: pos[0] -@@ -5283,7 +5283,7 @@ class GenericGraph(GenericGraph_pyx): +@@ -5281,7 +5281,7 @@ class GenericGraph(GenericGraph_pyx): [3, 64] sage: g = graphs.CycleGraph(7) sage: g.layout(layout='planar', save_pos=True, test=True) @@ -2494,7 +2509,7 @@ index c369e3723a..50edd704b2 100644 sage: g = graphs.CompleteGraph(5) sage: g.layout(layout='planar', save_pos=True, test=True, set_embedding=True) Traceback (most recent call last): -@@ -5294,9 +5294,9 @@ class GenericGraph(GenericGraph_pyx): +@@ -5292,9 +5292,9 @@ class GenericGraph(GenericGraph_pyx): sage: g = graphs.CompleteGraph(4) sage: g.layout(layout='planar', external_face=(0,1)) @@ -2506,7 +2521,7 @@ index c369e3723a..50edd704b2 100644 TESTS:: -@@ -16514,7 +16514,26 @@ class GenericGraph(GenericGraph_pyx): +@@ -16512,7 +16512,26 @@ class GenericGraph(GenericGraph_pyx): sage: D = graphs.DodecahedralGraph() sage: D.shortest_paths(0) @@ -2534,7 +2549,7 @@ index c369e3723a..50edd704b2 100644 All these paths are obviously induced graphs:: -@@ -16524,7 +16543,16 @@ class GenericGraph(GenericGraph_pyx): +@@ -16522,7 +16541,16 @@ class GenericGraph(GenericGraph_pyx): :: sage: D.shortest_paths(0, cutoff=2) @@ -2552,7 +2567,7 @@ index c369e3723a..50edd704b2 100644 sage: G = Graph( { 0: {1: 1}, 1: {2: 1}, 2: {3: 1}, 3: {4: 2}, 4: {0: 2} }, sparse=True) sage: G.plot(edge_labels=True).show() # long time sage: G.shortest_paths(0, by_weight=True) -@@ -16534,7 +16562,7 @@ class GenericGraph(GenericGraph_pyx): +@@ -16532,7 +16560,7 @@ class GenericGraph(GenericGraph_pyx): sage: D = DiGraph([(0,1,1),(1,2,3),(0,2,5)]) sage: D.shortest_paths(0) @@ -2561,7 +2576,7 @@ index c369e3723a..50edd704b2 100644 sage: D.shortest_paths(0, by_weight=True) {0: [0], 1: [0, 1], 2: [0, 1, 2]} -@@ -16783,7 +16811,26 @@ class GenericGraph(GenericGraph_pyx): +@@ -16781,7 +16809,26 @@ class GenericGraph(GenericGraph_pyx): sage: D = graphs.DodecahedralGraph() sage: D.shortest_path_lengths(0) @@ -2589,7 +2604,7 @@ index c369e3723a..50edd704b2 100644 Weighted case:: -@@ -18909,18 +18956,18 @@ class GenericGraph(GenericGraph_pyx): +@@ -18900,18 +18947,18 @@ class GenericGraph(GenericGraph_pyx): '#00ff00': [((1,3,2,4), (1,4)(2,3), 3), ...], '#ff0000': [((1,3,2,4), (1,3)(2,4), 1), ...]} sage: G._color_by_label() # py3 @@ -2612,7 +2627,7 @@ index c369e3723a..50edd704b2 100644 TESTS: -@@ -19065,8 +19112,8 @@ class GenericGraph(GenericGraph_pyx): +@@ -19056,8 +19103,8 @@ class GenericGraph(GenericGraph_pyx): sage: g.layout(layout="acyclic_dummy", save_pos=True) {('0', 0): [0.3..., 0], @@ -2622,7 +2637,7 @@ index c369e3723a..50edd704b2 100644 ('1', 1): [0.6..., 1]} sage: D3 = g.layout(dim=3); D3 # random -@@ -19202,10 +19249,10 @@ class GenericGraph(GenericGraph_pyx): +@@ -19193,10 +19240,10 @@ class GenericGraph(GenericGraph_pyx): sage: g = graphs.LadderGraph(3) sage: g.layout_ranked(heights={i: (i, i+3) for i in range(3)}) {0: [0.668..., 0], @@ -2635,7 +2650,7 @@ index c369e3723a..50edd704b2 100644 5: [1.33..., 2]} sage: g = graphs.LadderGraph(7) sage: g.plot(layout="ranked", heights={i: (i, i+7) for i in range(7)}) -@@ -19389,13 +19436,13 @@ class GenericGraph(GenericGraph_pyx): +@@ -19380,13 +19427,13 @@ class GenericGraph(GenericGraph_pyx): sage: G = graphs.BalancedTree(2, 2) sage: G.layout_tree(tree_root=0) @@ -2654,7 +2669,7 @@ index c369e3723a..50edd704b2 100644 sage: G = graphs.BalancedTree(2, 4) sage: G.plot(layout="tree", tree_root=0, tree_orientation="up") -@@ -19407,15 +19454,15 @@ class GenericGraph(GenericGraph_pyx): +@@ -19398,15 +19445,15 @@ class GenericGraph(GenericGraph_pyx): sage: T.set_embedding({0: [1, 6, 3], 1: [2, 5, 0], 2: [1], 3: [4, 7, 8, 0], ....: 4: [3], 5: [1], 6: [0], 7: [3], 8: [3]}) sage: T.layout_tree() @@ -2677,7 +2692,7 @@ index c369e3723a..50edd704b2 100644 sage: T.plot(layout="tree", tree_root=3) Graphics object consisting of 18 graphics primitives -@@ -23574,7 +23621,8 @@ class GenericGraph(GenericGraph_pyx): +@@ -23560,7 +23607,8 @@ class GenericGraph(GenericGraph_pyx): sage: G = DiGraph({1: [10], 2:[10,11], 3:[10,11], 4:[], 5:[11, 4], 6:[11], 7:[10,11], 8:[10,11], 9:[10], 10:[11, 5, 8], 11:[6]}) sage: G.katz_centrality(.85) @@ -2687,7 +2702,7 @@ index c369e3723a..50edd704b2 100644 2: 0.000000000000000, 3: 0.000000000000000, 4: 16.7319819819820, -@@ -23583,7 +23631,6 @@ class GenericGraph(GenericGraph_pyx): +@@ -23569,7 +23617,6 @@ class GenericGraph(GenericGraph_pyx): 7: 0.000000000000000, 8: 18.6846846846847, 9: 0.000000000000000, @@ -2695,7 +2710,7 @@ index c369e3723a..50edd704b2 100644 11: 202.778914049184} -@@ -23603,7 +23650,7 @@ class GenericGraph(GenericGraph_pyx): +@@ -23589,7 +23636,7 @@ class GenericGraph(GenericGraph_pyx): sage: graphs.PathGraph(4).katz_centrality(1/20,3) 21/379 sage: (graphs.PathGraph(3) + graphs.PathGraph(4)).katz_centrality(1/20) @@ -2705,7 +2720,7 @@ index c369e3723a..50edd704b2 100644 """ n = self.order() diff --git a/src/sage/graphs/graph.py b/src/sage/graphs/graph.py -index e76003f23c..d1ec1a9e05 100644 +index c46dde0a40..6043454e5f 100644 --- a/src/sage/graphs/graph.py +++ b/src/sage/graphs/graph.py @@ -3820,7 +3820,7 @@ class Graph(GenericGraph): @@ -3757,7 +3772,7 @@ index ad2dba4fbc..1cd1fa7ba4 100644 """ return self._nproc diff --git a/src/sage/plot/graphics.py b/src/sage/plot/graphics.py -index 931661d26c..cfd152e992 100644 +index 8a1917dc5a..8197b189d3 100644 --- a/src/sage/plot/graphics.py +++ b/src/sage/plot/graphics.py @@ -1297,8 +1297,8 @@ class Graphics(WithEqualityById, SageObject): @@ -4501,21 +4516,27 @@ index ce311014d3..799cd00aa7 100644 gens = self.gens() names = self.variable_names() diff --git a/src/sage/rings/ring_extension.pyx b/src/sage/rings/ring_extension.pyx -index 754b8c2ca6..291ae46fe6 100644 +index 754b8c2ca6..eef5fe247a 100644 --- a/src/sage/rings/ring_extension.pyx +++ b/src/sage/rings/ring_extension.pyx -@@ -379,8 +379,8 @@ class RingExtensionFactory(UniqueFactory): +@@ -377,10 +377,12 @@ class RingExtensionFactory(UniqueFactory): + ((Ring morphism: + From: Integer Ring To: Rational Field - Defn: 1 |--> 1, (), ()), - {'constructors': [(<type 'sage.rings.ring_extension.RingExtension_generic'>, +- Defn: 1 |--> 1, (), ()), +- {'constructors': [(<type 'sage.rings.ring_extension.RingExtension_generic'>, - {'is_backend_exposed': True, - 'print_options': {'print_elements_as': None, 'print_parent_as': None}})]}) ++ Defn: 1 |--> 1, ++ (), ++ ()), ++ {'constructors': [(<class 'sage.rings.ring_extension.RingExtension_generic'>, + {'print_options': {'print_parent_as': None, 'print_elements_as': None}, + 'is_backend_exposed': True})]}) sage: RingExtension.create_key_and_extra_args(GF(5^4), GF(5^2), names=('a',)) ((Ring morphism: -@@ -388,7 +388,7 @@ class RingExtensionFactory(UniqueFactory): +@@ -388,7 +390,7 @@ class RingExtensionFactory(UniqueFactory): To: Finite Field in z4 of size 5^4 Defn: z2 |--> z4^3 + z4^2 + z4 + 3, (z4,), ('a',)), {'constructors': [(<type 'sage.rings.ring_extension.RingExtensionWithGen'>, diff --git a/sagemath-sphinx-3.patch b/sagemath-sphinx-3.patch new file mode 100644 index 000000000000..3ff48e16bc2b --- /dev/null +++ b/sagemath-sphinx-3.patch @@ -0,0 +1,272 @@ +diff --git a/src/doc/en/thematic_tutorials/structures_in_coding_theory.rst b/src/doc/en/thematic_tutorials/structures_in_coding_theory.rst +index 13f1a83..4726bce 100644 +--- a/src/doc/en/thematic_tutorials/structures_in_coding_theory.rst ++++ b/src/doc/en/thematic_tutorials/structures_in_coding_theory.rst +@@ -721,8 +721,6 @@ derive from the one that follows. + + .. CODE-BLOCK:: python + +- :class:`sage.coding.repetition_code.BinaryRepetitionCode <sage.coding.repetition_code.BinaryRepetitionCode>` +- #the line above creates a link to the class in the html documentation of coding theory library + from sage.coding.repetition_code import BinaryRepetitionCode + + ``encoders_catalog.py`` (continued): +diff --git a/src/sage/combinat/permutation.py b/src/sage/combinat/permutation.py +index a68d673..ae644cf 100644 +--- a/src/sage/combinat/permutation.py ++++ b/src/sage/combinat/permutation.py +@@ -415,9 +415,6 @@ class Permutation(CombinatorialElement): + [] + sage: Permutation( [[], []] ) + [] +- +- .. automethod:: Permutation.left_action_product +- .. automethod:: Permutation.right_action_product + """ + @staticmethod + def __classcall_private__(cls, l, check_input = True): +diff --git a/src/sage/docs/conf.py b/src/sage/docs/conf.py +index a1212f5..c4941f0 100644 +--- a/src/sage/docs/conf.py ++++ b/src/sage/docs/conf.py +@@ -8,6 +8,7 @@ from docutils import nodes + from docutils.transforms import Transform + from sphinx.ext.doctest import blankline_re + from sphinx import highlighting ++import sphinx.ext.intersphinx as intersphinx + from IPython.lib.lexers import IPythonConsoleLexer, IPyLexer + + # If your extensions are in another directory, add it here. +@@ -173,13 +174,8 @@ todo_include_todos = True + + # Cross-links to other project's online documentation. + python_version = sys.version_info.major +-intersphinx_mapping = { +- 'python': ('https://docs.python.org/', +- os.path.join(SAGE_DOC_SRC, "common", +- "python{}.inv".format(python_version))), +- 'pplpy': (PPLPY_DOCS, None)} + +-def set_intersphinx_mappings(app): ++def set_intersphinx_mappings(app, config): + """ + Add precompiled inventory (the objects.inv) + """ +@@ -190,7 +186,11 @@ def set_intersphinx_mappings(app): + app.config.intersphinx_mapping = {} + return + +- app.config.intersphinx_mapping = intersphinx_mapping ++ app.config.intersphinx_mapping = { ++ 'python': ('https://docs.python.org/', ++ os.path.join(SAGE_DOC_SRC, "common", ++ "python{}.inv".format(python_version))), ++ 'pplpy': (PPLPY_DOCS, None)} + + # Add master intersphinx mapping + dst = os.path.join(invpath, 'objects.inv') +@@ -205,6 +205,7 @@ def set_intersphinx_mappings(app): + dst = os.path.join(invpath, directory, 'objects.inv') + app.config.intersphinx_mapping[src] = dst + ++ intersphinx.normalize_intersphinx_mapping(app, config) + + # By default document are not master. + multidocs_is_master = True +@@ -669,11 +670,11 @@ def call_intersphinx(app, env, node, contnode): + sage: for line in open(thematic_index).readlines(): # optional - dochtml + ....: if "padics" in line: + ....: _ = sys.stdout.write(line) +- <li><a class="reference external" href="../reference/padics/sage/rings/padics/tutorial.html#sage-rings-padics-tutorial" title="(in Sage... Reference Manual: p-Adics v...)"><span>Introduction to the p-adics</span></a></li> ++ <li><p><a class="reference external" href="../reference/padics/sage/rings/padics/tutorial.html#sage-rings-padics-tutorial" title="(in Sage... Reference Manual: p-Adics v...)"><span>Introduction to the p-adics</span></a></p></li> + """ + debug_inf(app, "???? Trying intersphinx for %s" % node['reftarget']) + builder = app.builder +- res = sphinx.ext.intersphinx.missing_reference( ++ res = intersphinx.missing_reference( + app, env, node, contnode) + if res: + # Replace absolute links to $SAGE_DOC by relative links: this +@@ -856,11 +857,10 @@ def setup(app): + if app.srcdir.startswith(SAGE_DOC_SRC): + app.add_config_value('intersphinx_mapping', {}, False) + app.add_config_value('intersphinx_cache_limit', 5, False) ++ app.connect('config-inited', set_intersphinx_mappings) ++ app.connect('builder-inited', intersphinx.load_mappings) + # We do *not* fully initialize intersphinx since we call it by hand + # in find_sage_dangling_links. + # app.connect('missing-reference', missing_reference) + app.connect('missing-reference', find_sage_dangling_links) +- import sphinx.ext.intersphinx +- app.connect('builder-inited', set_intersphinx_mappings) +- app.connect('builder-inited', sphinx.ext.intersphinx.load_mappings) + app.connect('builder-inited', nitpick_patch_config) +diff --git a/src/sage/misc/sagedoc.py b/src/sage/misc/sagedoc.py +index 85ee764..795dfd3 100644 +--- a/src/sage/misc/sagedoc.py ++++ b/src/sage/misc/sagedoc.py +@@ -24,7 +24,7 @@ see :trac:`12849`:: + ....: for line in fobj: + ....: if "#sage.symbolic.expression.Expression.numerical_approx" in line: + ....: print(line) +- <code class="descname">numerical_approx</code><span class="sig-paren">(</span><em>prec=None</em>, <em>digits=None</em>, <em>algorithm=None</em><span class="sig-paren">)</span>... ++ <code class="sig-name descname">numerical_approx</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">prec</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">digits</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">algorithm</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span>... + + Check that sphinx is not imported at Sage start-up:: + +diff --git a/src/sage_setup/docbuild/__init__.py b/src/sage_setup/docbuild/__init__.py +index 128117b..5aad13c 100644 +--- a/src/sage_setup/docbuild/__init__.py ++++ b/src/sage_setup/docbuild/__init__.py +@@ -817,9 +817,13 @@ class ReferenceSubBuilder(DocBuilder): + + env_pickle = os.path.join(self._doctrees_dir(), 'environment.pickle') + try: +- env = BuildEnvironment.frompickle(env_pickle, FakeApp(self.dir)) +- logger.debug("Opened Sphinx environment: %s", env_pickle) +- return env ++ with open(env_pickle, 'rb') as f: ++ import pickle ++ env = pickle.load(f) ++ env.app = FakeApp(self.dir) ++ env.config.values = env.app.config.values ++ logger.debug("Opened Sphinx environment: %s", env_pickle) ++ return env + except IOError as err: + logger.debug("Failed to open Sphinx environment: %s", err) + +diff --git a/src/sage_setup/docbuild/ext/multidocs.py b/src/sage_setup/docbuild/ext/multidocs.py +index 71a08cd..ffed722 100644 +--- a/src/sage_setup/docbuild/ext/multidocs.py ++++ b/src/sage_setup/docbuild/ext/multidocs.py +@@ -52,27 +52,29 @@ def merge_environment(app, env): + docenv = get_env(app, curdoc) + if docenv is not None: + fixpath = lambda path: os.path.join(curdoc, path) ++ todos = docenv.domaindata['todo'].get('todos', dict()) ++ citations = docenv.domaindata['citation'].get('citations', dict()) ++ indexentries = docenv.domaindata['index'].get('entries', dict()) + logger.info(" %s todos, %s index, %s citations"%( +- len(docenv.todo_all_todos), +- len(docenv.indexentries), +- len(docenv.domaindata["std"]["citations"]) ++ sum(len(t) for t in todos.values()), ++ len(indexentries), ++ len(citations) + ), nonl=1) + + # merge titles + for t in docenv.titles: + env.titles[fixpath(t)] = docenv.titles[t] + # merge the todo links +- for dct in docenv.todo_all_todos: +- dct['docname'] = fixpath(dct['docname']) +- env.todo_all_todos += docenv.todo_all_todos ++ for dct in todos: ++ env.domaindata['todo']['todos'][fixpath(dct)] = todos[dct] + # merge the html index links + newindex = {} +- for ind in docenv.indexentries: ++ for ind in indexentries: + if ind.startswith('sage/'): +- newindex[fixpath(ind)] = docenv.indexentries[ind] ++ newindex[fixpath(ind)] = indexentries[ind] + else: +- newindex[ind] = docenv.indexentries[ind] +- env.indexentries.update(newindex) ++ newindex[ind] = indexentries[ind] ++ env.domaindata['index']['entries'].update(newindex) + # merge the all_docs links, needed by the js index + newalldoc = {} + for ind in docenv.all_docs: +@@ -86,24 +88,23 @@ def merge_environment(app, env): + env.metadata[ind] = md + # merge the citations + newcite = {} +- citations = docenv.domaindata["std"]["citations"] +- for ind, (path, tag, lineno) in six.iteritems(docenv.domaindata["std"]["citations"]): ++ for ind, (path, tag, lineno) in six.iteritems(citations): + # TODO: Warn on conflicts + newcite[ind] = (fixpath(path), tag, lineno) +- env.domaindata["std"]["citations"].update(newcite) ++ env.domaindata['citation']['citations'].update(newcite) + # merge the py:module indexes + newmodules = {} +- for ind,(modpath,v1,v2,v3) in ( ++ for ind,(modpath,v1,v2,v3,v4) in ( + six.iteritems(docenv.domaindata['py']['modules'])): +- newmodules[ind] = (fixpath(modpath),v1,v2,v3) ++ newmodules[ind] = (fixpath(modpath),v1,v2,v3,v4) + env.domaindata['py']['modules'].update(newmodules) + logger.info(", %s modules"%(len(newmodules))) + logger.info('... done (%s todos, %s index, %s citations, %s modules)'%( +- len(env.todo_all_todos), +- len(env.indexentries), +- len(env.domaindata["std"]["citations"]), ++ sum(len(t) for t in env.domaindata['todo']['todos'].values()), ++ len(env.domaindata['index']['entries']), ++ len(env.domaindata['citation']['citations']), + len(env.domaindata['py']['modules']))) +- write_citations(app, env.domaindata["std"]["citations"]) ++ write_citations(app, env.domaindata['citation']['citations']) + + + def get_env(app, curdoc): +@@ -253,7 +254,7 @@ def fetch_citation(app, env): + with open(filename, 'rb') as f: + cache = cPickle.load(f) + logger.info("done (%s citations)."%len(cache)) +- cite = env.domaindata["std"]["citations"] ++ cite = env.domaindata['citation'].get('citations', dict()) + for ind, (path, tag, lineno) in six.iteritems(cache): + if ind not in cite: # don't override local citation + cite[ind] = (os.path.join("..", path), tag, lineno) +diff --git a/src/sage_setup/docbuild/ext/sage_autodoc.py b/src/sage_setup/docbuild/ext/sage_autodoc.py +index bba274f..179fc25 100644 +--- a/src/sage_setup/docbuild/ext/sage_autodoc.py ++++ b/src/sage_setup/docbuild/ext/sage_autodoc.py +@@ -35,14 +35,15 @@ import sys + from docutils.statemachine import ViewList + + import sphinx +-from sphinx.ext.autodoc.importer import mock, import_object, get_object_members ++from sphinx.ext.autodoc import mock ++from sphinx.ext.autodoc.importer import import_object, get_object_members, get_module_members + from sphinx.locale import _, __ + from sphinx.pycode import ModuleAnalyzer + from sphinx.errors import PycodeError + from sphinx.util import logging + from sphinx.util import rpartition, force_decode + from sphinx.util.docstrings import prepare_docstring +-from sphinx.util.inspect import isdescriptor, safe_getmembers, \ ++from sphinx.util.inspect import isdescriptor, \ + safe_getattr, object_description, is_builtin_class_method, \ + isenumattribute, isclassmethod, isstaticmethod, getdoc + +@@ -536,7 +537,7 @@ class Documenter(object): + + # add content from docstrings + if not no_docstring: +- encoding = self.analyzer and self.analyzer.encoding ++ encoding = self.analyzer and self.analyzer._encoding + docstrings = self.get_doc(encoding) + if not docstrings: + # append at least a dummy docstring, so that the event +@@ -882,7 +883,7 @@ class ModuleDocumenter(Documenter): + if not hasattr(self.object, '__all__'): + # for implicit module members, check __module__ to avoid + # documenting imported objects +- return True, safe_getmembers(self.object) ++ return True, get_module_members(self.object) + else: + memberlist = self.object.__all__ + # Sometimes __all__ is broken... +@@ -893,7 +894,7 @@ class ModuleDocumenter(Documenter): + '(in module %s) -- ignoring __all__' % + (memberlist, self.fullname)) + # fall back to all members +- return True, safe_getmembers(self.object) ++ return True, get_module_members(self.object) + else: + memberlist = self.options.members or [] + ret = [] |