[arch-commits] Commit in sagemath-doc/trunk (6 files)
Antonio Rojas
arojas at archlinux.org
Sat Mar 25 17:42:56 UTC 2017
Date: Saturday, March 25, 2017 @ 17:42:55
Author: arojas
Revision: 218968
Update to 7.6
Added:
sagemath-doc/trunk/increase-rtol.patch
sagemath-doc/trunk/r-no-readline.patch
sagemath-doc/trunk/sagemath-planarity3.patch
sagemath-doc/trunk/sagemath-singular-4.1.0.p2.patch
sagemath-doc/trunk/sagemath-sphinx-1.5.patch
Modified:
sagemath-doc/trunk/PKGBUILD
----------------------------------+
PKGBUILD | 45 ++++++-----
increase-rtol.patch | 37 +++++++++
r-no-readline.patch | 11 ++
sagemath-planarity3.patch | 113 ++++++++++++++++++++++++++++
sagemath-singular-4.1.0.p2.patch | 33 ++++++++
sagemath-sphinx-1.5.patch | 149 +++++++++++++++++++++++++++++++++++++
6 files changed, 370 insertions(+), 18 deletions(-)
Modified: PKGBUILD
===================================================================
--- PKGBUILD 2017-03-25 17:32:00 UTC (rev 218967)
+++ PKGBUILD 2017-03-25 17:42:55 UTC (rev 218968)
@@ -3,24 +3,27 @@
pkgbase=sagemath-doc
pkgname=(sagemath-doc sagemath-src)
-pkgver=7.5
-pkgrel=3
+pkgver=7.6
+pkgrel=1
arch=(any)
url="http://www.sagemath.org"
license=(GPL)
-makedepends=(sagemath sage-notebook python2-pyzmq python2-pillow python2-docutils
- python2-jupyter_client python2-pkgconfig cython2 thebe) # python2-sphinx
-makedepends+=(python2-imagesize python2-sphinx-alabaster-theme) # remove when we can use system sphinx again
+makedepends=(sagemath sage-notebook python2-pyzmq python2-pillow python2-docutils tachyon
+ python2-jupyter_client python2-pkgconfig cython2 thebe python2-sphinx python2-ipywidgets)
source=("$pkgbase-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz"
- "https://pypi.io/packages/source/S/Sphinx/Sphinx-1.4.9.tar.gz"
- package.patch disable-fes.patch docbuild_main.patch is-package-installed.patch ecm-7.patch)
-md5sums=('bff1fb8793ebc2934d14cf1efdcfbea3'
- '6c7472d3630835113ee9cc251cc36c31'
- 'ccfd5b1bc4796f414f1531be52504dd7'
- '06a67e611d10aa2381efe1f08ea4ffd9'
- 'f3bf3fa4e11e5af2bd0573cf2620e1f8'
- '409b0a2c520eb33281b5f262afcb6c76'
- '0c9a57d35de80c2cd418ebec912efbbb')
+ package.patch disable-fes.patch docbuild_main.patch is-package-installed.patch ecm-7.patch increase-rtol.patch
+ r-no-readline.patch sagemath-planarity3.patch sagemath-singular-4.1.0.p2.patch sagemath-sphinx-1.5.patch)
+sha256sums=('e6e0729ab25446e7c922058db0eee4b0b294b32c196e34842e843ea9fae41423'
+ '4a2297e4d9d28f0b3a1f58e1b463e332affcb109eafde44837b1657e309c8212'
+ '7ab53d30b877dabb6835fbe67a208bef65fa0aaf40221b4d0b58e4b7086bc47a'
+ '187b75d3ce202126012ff20b6316277b0a003ffdd7f15b820d3b88459d2753c8'
+ 'd60fb0fbd27991ce9496ca035a54b03334b5b53f244227a8d6e13f3327ce75d2'
+ '65ad84c83d5f956fde8eab961f2caad56d64044324c4abc0e56bcd9f44061cb6'
+ 'be925eefeac3f28e639794ddc20d64e6faafd7181804e29417a510224d19ccc7'
+ 'ef9f401fa84fe1772af9efee6816643534f2896da4c23b809937b19771bdfbbf'
+ 'a1c562ebe4538d672404ca3ac2e954a3c955afeb7463f7b4fe6eaa6fa74fe5c7'
+ 'e1912afec58b834fac3b9161c2d5a1794bb618126c6bd7a4be85c834231360e7'
+ '0ffbccdd65ba8dfe84222e62d9e43663735d4f33276f7ec7b2e44ed53d1f24d0')
prepare() {
cd sage-$pkgver
@@ -30,6 +33,14 @@
patch -p0 -i ../package.patch
# fix regressions with ECM 7
patch -p1 -i ../ecm-7.patch
+# increase numerical tolerance, needed by scipy 0.18
+ patch -p1 -i ../increase-rtol.patch
+# fix freezes in R interface with readline 7 (Debian)
+ patch -p1 -i ../r-no-readline.patch
+# fix build with planarity 3 (Debian)
+ patch -p2 -i ../sagemath-planarity3.patch
+# fix build with Singular 4.1.0-p2
+ patch -p0 -i ../sagemath-singular-4.1.0.p2.patch
# Upstream patches
# fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209
@@ -38,12 +49,11 @@
patch -p0 -i ../disable-fes.patch
# replace is_package_installed usage http://trac.sagemath.org/ticket/20377
patch -p1 -i ../is-package-installed.patch
+# fix doc build with sphinx 1.5 https://trac.sagemath.org/ticket/22252
+ patch -p1 -i ../sagemath-sphinx-1.5.patch
# fix relative imports
patch -p0 -i ../docbuild_main.patch
-# fix thebe.js link
- rm src/doc/common/themes/sage/static/thebe.js
- ln -s /usr/share/thebe/thebe.js src/doc/common/themes/sage/static/thebe.js
# use python2
sed -e 's|cython %s %s|cython2 %s %s|' -e 's|python setup.py|python2 setup.py|' -i src/sage/misc/cython.py
@@ -50,7 +60,6 @@
mkdir -p local-python
ln -sr src/sage_setup local-python
- cp -r "$srcdir"/Sphinx-1.4.9/* local-python
}
build() {
Added: increase-rtol.patch
===================================================================
--- increase-rtol.patch (rev 0)
+++ increase-rtol.patch 2017-03-25 17:42:55 UTC (rev 218968)
@@ -0,0 +1,37 @@
+diff -ru sage-7.3.orig/src/sage/coding/code_bounds.py sage-7.3/src/sage/coding/code_bounds.py
+--- sage-7.3.orig/src/sage/coding/code_bounds.py 2016-08-05 20:26:10.033204091 +0200
++++ sage-7.3/src/sage/coding/code_bounds.py 2016-08-05 20:32:27.276579565 +0200
+@@ -554,7 +554,7 @@
+ if q < 2: # Here we check that q is actually at least 2
+ raise ValueError("The value q must be an integer greater than 1")
+
+- eps = 4.5e-16 # find_root has about this as the default xtol
++ eps = 4.5e-15 # find_root has about this as the default xtol
+ ymax = 1 - 1/q
+ if x <= eps:
+ return 0
+diff -ru sage-7.3.orig/src/sage/numerical/optimize.py sage-7.3/src/sage/numerical/optimize.py
+--- sage-7.3.orig/src/sage/numerical/optimize.py 2016-08-05 20:26:10.816536625 +0200
++++ sage-7.3/src/sage/numerical/optimize.py 2016-08-05 20:32:21.449907130 +0200
+@@ -15,7 +15,7 @@
+ from sage.rings.real_double import RDF
+
+
+-def find_root(f, a, b, xtol=10e-13, rtol=4.5e-16, maxiter=100, full_output=False):
++def find_root(f, a, b, xtol=10e-13, rtol=4.5e-15, maxiter=100, full_output=False):
+ """
+ Numerically find a root of ``f`` on the closed interval `[a,b]`
+ (or `[b,a]`) if possible, where ``f`` is a function in the one variable.
+diff -ru sage-7.3.orig/src/sage/symbolic/expression.pyx sage-7.3/src/sage/symbolic/expression.pyx
+--- sage-7.3.orig/src/sage/symbolic/expression.pyx 2016-08-05 20:26:11.333202767 +0200
++++ sage-7.3/src/sage/symbolic/expression.pyx 2016-08-05 20:32:14.236566826 +0200
+@@ -10884,7 +10884,7 @@
+ ret = ret[0]
+ return ret
+
+- def find_root(self, a, b, var=None, xtol=10e-13, rtol=4.5e-16, maxiter=100, full_output=False):
++ def find_root(self, a, b, var=None, xtol=10e-13, rtol=4.5e-15, maxiter=100, full_output=False):
+ """
+ Numerically find a root of self on the closed interval [a,b] (or
+ [b,a]) if possible, where self is a function in the one variable.
+
Added: r-no-readline.patch
===================================================================
--- r-no-readline.patch (rev 0)
+++ r-no-readline.patch 2017-03-25 17:42:55 UTC (rev 218968)
@@ -0,0 +1,11 @@
+--- a/src/sage/interfaces/r.py
++++ b/src/sage/interfaces/r.py
+@@ -331,7 +331,7 @@
+ prompt = '> ', #default, later comes the change
+
+ # This is the command that starts up your program
+- command = "R --vanilla --quiet",
++ command = "R --no-readline --vanilla --quiet",
+
+ server=server,
+ server_tmpdir=server_tmpdir,
Added: sagemath-planarity3.patch
===================================================================
--- sagemath-planarity3.patch (rev 0)
+++ sagemath-planarity3.patch 2017-03-25 17:42:55 UTC (rev 218968)
@@ -0,0 +1,113 @@
+Author: Ximin Luo <infinity0 at debian.org>
+Bug: https://trac.sagemath.org/ticket/21774
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- a/sage/src/sage/graphs/planarity.pyx
++++ b/sage/src/sage/graphs/planarity.pyx
+@@ -3,13 +3,19 @@
+ """
+
+ cdef extern from "planarity/graph.h":
+- ctypedef struct graphNode:
+- int v
++ ctypedef struct vertexRec:
+ int link[2]
+- ctypedef graphNode * graphNodeP
++ int index
++ ctypedef vertexRec * vertexRecP
++
++ ctypedef struct edgeRec:
++ int link[2]
++ int neighbor
++ ctypedef edgeRec * edgeRecP
+
+ ctypedef struct BM_graph:
+- graphNodeP G
++ vertexRecP V
++ edgeRecP E
+ int N
+ ctypedef BM_graph * graphP
+
+@@ -93,15 +99,16 @@
+ g._pos = { u: [0,0], v: [0,1] }
+ return (True, None) if kuratowski else True
+
+- # create to and from mappings to relabel vertices to the set {0,...,n-1}
++ # create to and from mappings to relabel vertices to the set {1,...,n}
++ # (planarity 3 uses 1-based array indexing, with 0 representing NIL)
+ cdef int i
+ listto = g.vertices()
+ ffrom = {}
+ for vvv in listto:
+- ffrom[vvv] = listto.index(vvv)
++ ffrom[vvv] = listto.index(vvv) + 1
+ to = {}
+ for i from 0 <= i < len(listto):
+- to[i] = listto[i]
++ to[i + 1] = listto[i]
+ g.relabel(ffrom)
+
+ cdef graphP theGraph
+@@ -125,7 +132,7 @@
+ status = gp_Embed(theGraph, EMBEDFLAGS_PLANAR)
+ gp_SortVertices(theGraph)
+
+- # use to and from mappings to relabel vertices back from the set {0,...,n-1}
++ # use to and from mappings to relabel vertices back from the set {1,...,n}
+ g.relabel(to)
+
+ if status == NOTOK:
+@@ -134,12 +141,12 @@
+ # Kuratowski subgraph isolator
+ g_dict = {}
+ from sage.graphs.graph import Graph
+- for i from 0 <= i < theGraph.N:
++ for i from 0 < i <= theGraph.N:
+ linked_list = []
+- j = theGraph.G[i].link[1]
+- while j >= theGraph.N:
+- linked_list.append(to[theGraph.G[j].v])
+- j = theGraph.G[j].link[1]
++ j = theGraph.V[i].link[1]
++ while j:
++ linked_list.append(to[theGraph.E[j].neighbor])
++ j = theGraph.E[j].link[1]
+ if len(linked_list) > 0:
+ g_dict[to[i]] = linked_list
+ G = Graph(g_dict)
+@@ -153,12 +160,12 @@
+ if set_embedding:
+ emb_dict = {}
+ #for i in range(theGraph.N):
+- for i from 0 <= i < theGraph.N:
++ for i from 0 < i <= theGraph.N:
+ linked_list = []
+- j = theGraph.G[i].link[1]
+- while j >= theGraph.N:
+- linked_list.append(to[theGraph.G[j].v])
+- j = theGraph.G[j].link[1]
++ j = theGraph.V[i].link[1]
++ while j:
++ linked_list.append(to[theGraph.E[j].neighbor])
++ j = theGraph.E[j].link[1]
+ emb_dict[to[i]] = linked_list
+ g._embedding = emb_dict
+ if set_pos:
+@@ -174,12 +181,12 @@
+
+ emb_dict = {}
+ #for i in range(theGraph.N):
+- for i from 0 <= i < theGraph.N:
++ for i from 0 < i <= theGraph.N:
+ linked_list = []
+- j = theGraph.G[i].link[0]
+- while j >= theGraph.N:
+- linked_list.append(to[theGraph.G[j].v])
+- j = theGraph.G[j].link[0]
++ j = theGraph.V[i].link[0]
++ while j:
++ linked_list.append(to[theGraph.E[j].neighbor])
++ j = theGraph.E[j].link[0]
+ emb_dict[to[i]] = linked_list
+ g._embedding = emb_dict
+ gp_Free(&theGraph)
Added: sagemath-singular-4.1.0.p2.patch
===================================================================
--- sagemath-singular-4.1.0.p2.patch (rev 0)
+++ sagemath-singular-4.1.0.p2.patch 2017-03-25 17:42:55 UTC (rev 218968)
@@ -0,0 +1,33 @@
+--- src/sage/libs/singular/decl.pxd.orig 2017-02-21 07:58:27.088118954 +0000
++++ src/sage/libs/singular/decl.pxd 2017-02-21 07:59:01.794846500 +0000
+@@ -484,8 +484,8 @@
+
+ ring *rDefault(int char , int nvars, char **names)
+ ring *rDefault(const n_Procs_s* cf, int nvars, char **names)
+- ring *rDefault(int ch , int nvars, char **names,int ord_size, int *ord, int *block0, int *block1, int **wvhdl)
+- ring *rDefault(const n_Procs_s* cf, int nvars, char **names,int ord_size, int *ord, int *block0, int *block1, int **wvhdl)
++ ring *rDefault(int ch , int nvars, char **names,int ord_size, rRingOrder_t *ord, int *block0, int *block1, int **wvhdl)
++ ring *rDefault(const n_Procs_s* cf, int nvars, char **names,int ord_size, rRingOrder_t *ord, int *block0, int *block1, int **wvhdl)
+
+
+
+--- src/sage/libs/singular/ring.pyx.orig 2017-02-21 07:24:23.197906897 +0000
++++ src/sage/libs/singular/ring.pyx 2017-02-21 07:29:23.731763098 +0000
+@@ -21,7 +21,7 @@
+ from sage.libs.singular.decl cimport number, poly, ring, currRing
+ from sage.libs.singular.decl cimport rChangeCurrRing, rCopy0, rComplete, rDelete, idInit
+ from sage.libs.singular.decl cimport omAlloc0, omStrDup, omAlloc, omAlloc0Bin, sip_sring_bin, rnumber_bin
+-from sage.libs.singular.decl cimport ringorder_dp, ringorder_Dp, ringorder_lp, ringorder_rp, ringorder_ds, ringorder_Ds, ringorder_ls, ringorder_M, ringorder_C, ringorder_wp, ringorder_Wp, ringorder_ws, ringorder_Ws, ringorder_a
++from sage.libs.singular.decl cimport ringorder_dp, ringorder_Dp, ringorder_lp, ringorder_rp, ringorder_ds, ringorder_Ds, ringorder_ls, ringorder_M, ringorder_C, ringorder_wp, ringorder_Wp, ringorder_ws, ringorder_Ws, ringorder_a, rRingOrder_t
+ from sage.libs.singular.decl cimport p_Copy, prCopyR
+ from sage.libs.singular.decl cimport n_unknown, n_Zp, n_Q, n_R, n_GF, n_long_R, n_algExt,n_transExt,n_long_C, n_Z, n_Zn, n_Znm, n_Z2m, n_CF
+ from sage.libs.singular.decl cimport n_coeffType, cfInitCharProc
+@@ -165,7 +165,7 @@
+ ## q q : GF(q=p^n) *names TRUE (todo)
+
+ _wvhdl = <int **>omAlloc0((nblcks + 2) * sizeof(int *))
+- _order = <int *>omAlloc0((nblcks + 2) * sizeof(int))
++ _order = <rRingOrder_t *>omAlloc0((nblcks + 2) * sizeof(int))
+ _block0 = <int *>omAlloc0((nblcks + 2) * sizeof(int))
+ _block1 = <int *>omAlloc0((nblcks + 2) * sizeof(int))
+
Added: sagemath-sphinx-1.5.patch
===================================================================
--- sagemath-sphinx-1.5.patch (rev 0)
+++ sagemath-sphinx-1.5.patch 2017-03-25 17:42:55 UTC (rev 218968)
@@ -0,0 +1,149 @@
+diff --git a/src/doc/common/conf.py b/src/doc/common/conf.py
+index 564407b..7ec52df 100644
+--- a/src/doc/common/conf.py
++++ b/src/doc/common/conf.py
+@@ -308,6 +308,7 @@ latex_elements['preamble'] = r"""
+ \usepackage{amssymb}
+ \usepackage{textcomp}
+ \usepackage{mathrsfs}
++\usepackage{iftex}
+
+ % Only declare unicode characters when compiling with pdftex; E.g. japanese
+ % tutorial does not use pdftex
+diff --git a/src/sage/homology/simplicial_complex.py b/src/sage/homology/simplicial_complex.py
+index c110648..462d0bf 100644
+--- a/src/sage/homology/simplicial_complex.py
++++ b/src/sage/homology/simplicial_complex.py
+@@ -195,8 +195,8 @@ def lattice_paths(t1, t2, length=None):
+ :param length: if not ``None``, then an integer, the length of the desired
+ path.
+ :type length: integer or ``None``; optional, default ``None``
+- :type t1: tuple, list, other iterable
+- :type t2: tuple, list, other iterable
++ :type t1: list, other iterable
++ :type t2: list, other iterable
+ :return: list of lists of vertices making up the paths as described above
+ :rtype: list of lists
+
+@@ -333,7 +333,7 @@ class Simplex(SageObject):
+ tuple of the vertices.
+
+ :param X: set of vertices
+- :type X: integer or list, tuple, or other iterable
++ :type X: integer, list, other iterable
+ :return: simplex with those vertices
+
+ ``X`` may be a non-negative integer `n`, in which case the
+diff --git a/src/sage_setup/docbuild/__init__.py b/src/sage_setup/docbuild/__init__.py
+index c155b4e..b93e743 100644
+--- a/src/sage_setup/docbuild/__init__.py
++++ b/src/sage_setup/docbuild/__init__.py
+@@ -1578,32 +1578,6 @@ class IntersphinxCache:
+ return i
+
+
+-def patch_domain_init():
+- """
+- Applies a monkey-patch to the __init__ method of the Domain class in
+- Sphinx, in order to work around a bug.
+-
+- See https://trac.sagemath.org/ticket/21044 as well as
+- https://github.com/sphinx-doc/sphinx/pull/2816 for details about that
+- bug.
+- """
+-
+- from sphinx.domains import Domain
+- import copy
+-
+- orig_init = Domain.__init__
+-
+- def __init__(self, *args, **kwargs):
+- orig_init(self, *args, **kwargs)
+-
+- # Replace the original initial_data class attribute with a new
+- # deep-copy of itself, since the bug will cause the original
+- # initial_data to be modified in-place
+- self.__class__.initial_data = copy.deepcopy(self.initial_data)
+-
+- Domain.__init__ = __init__
+-
+-
+ def main():
+ # Parse the command-line.
+ parser = setup_parser()
+@@ -1653,8 +1627,6 @@ def main():
+
+ ABORT_ON_ERROR = not options.keep_going
+
+- patch_domain_init()
+-
+ # Delete empty directories. This is needed in particular for empty
+ # directories due to "git checkout" which never deletes empty
+ # directories it leaves behind. See Trac #20010.
+diff --git a/src/sage_setup/docbuild/ext/multidocs.py b/src/sage_setup/docbuild/ext/multidocs.py
+index 63dbb71..47b2321 100644
+--- a/src/sage_setup/docbuild/ext/multidocs.py
++++ b/src/sage_setup/docbuild/ext/multidocs.py
+@@ -3,8 +3,6 @@
+ multi documentation in Sphinx
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+- This is a slightly hacked-up version of the Sphinx-multidoc plugin
+-
+ The goal of this extension is to manage a multi documentation in Sphinx.
+ To be able to compile Sage's huge documentation in parallel, the
+ documentation is cut into a bunch of independent documentations called
+@@ -57,7 +55,7 @@ def merge_environment(app, env):
+ app.info(" %s todos, %s index, %s citations"%(
+ len(docenv.todo_all_todos),
+ len(docenv.indexentries),
+- len(docenv.citations)
++ len(docenv.domaindata["std"]["citations"])
+ ), nonl=1)
+
+ # merge titles
+@@ -88,10 +86,10 @@ def merge_environment(app, env):
+ env.metadata[ind] = md
+ # merge the citations
+ newcite = {}
+- for ind, (path, tag) in six.iteritems(docenv.citations):
++ for ind, (path, tag) in six.iteritems(docenv.domaindata["std"]["citations"]):
+ # TODO: Warn on conflicts
+ newcite[ind] = (fixpath(path), tag)
+- env.citations.update(newcite)
++ env.domaindata["std"]["citations"].update(newcite)
+ # merge the py:module indexes
+ newmodules = {}
+ for ind,(modpath,v1,v2,v3) in (
+@@ -102,9 +100,9 @@ def merge_environment(app, env):
+ app.info('... done (%s todos, %s index, %s citations, %s modules)'%(
+ len(env.todo_all_todos),
+ len(env.indexentries),
+- len(env.citations),
++ len(env.domaindata["std"]["citations"]),
+ len(env.domaindata['py']['modules'])))
+- write_citations(app, env.citations)
++ write_citations(app, env.domaindata["std"]["citations"])
+
+ def get_env(app, curdoc):
+ """
+@@ -146,6 +144,10 @@ def merge_js_index(app):
+ titles = app.builder.indexer._titles
+ for (res, title) in six.iteritems(index._titles):
+ titles[fixpath(res)] = title
++ # merge the filenames
++ filenames = app.builder.indexer._filenames
++ for (res, filename) in six.iteritems(index._filenames):
++ filenames[fixpath(res)] = filename
+ # TODO: merge indexer._objtypes, indexer._objnames as well
+
+ # Setup source symbolic links
+@@ -244,7 +246,7 @@ def fetch_citation(app, env):
+ with open(filename, 'rb') as f:
+ cache = cPickle.load(f)
+ app.builder.info("done (%s citations)."%len(cache))
+- cite = env.citations
++ cite = env.domaindata["std"]["citations"]
+ for ind, (path, tag) in six.iteritems(cache):
+ if ind not in cite: # don't override local citation
+ cite[ind]=(os.path.join("..", path), tag)
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