path: root/sagemath-sphinx-3.patch

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 = []