[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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