sage: 8.4.beta0 -> 8.4.beta1

4 files changed, 0 insertions, 200 deletions

diff --git a/pkgs/applications/science/math/sage/patches/dochtml-optional.patch b/pkgs/applications/science/math/sage/patches/dochtml-optional.patch
deleted file mode 100644
index a51e30312ed9..000000000000
--- a/pkgs/applications/science/math/sage/patches/dochtml-optional.patch
+++ /dev/null
@@ -1,127 +0,0 @@
-diff --git a/src/doc/common/conf.py b/src/doc/common/conf.py
-index 25f94f7b7d..9f6139ea4a 100644
---- a/src/doc/common/conf.py
-+++ b/src/doc/common/conf.py
-@@ -622,9 +622,9 @@ def call_intersphinx(app, env, node, contnode):
-     Check that the link from the thematic tutorials to the reference
-     manual is relative, see :trac:`20118`::
- 
--        sage: from sage.env import SAGE_DOC
--        sage: thematic_index = os.path.join(SAGE_DOC, "html", "en", "thematic_tutorials", "index.html")
--        sage: for line in open(thematic_index).readlines():
-+        sage: from sage.env import SAGE_DOC  # optional - dochtml
-+        sage: thematic_index = os.path.join(SAGE_DOC, "html", "en", "thematic_tutorials", "index.html")  # optional - dochtml
-+        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 ...)"><span>Introduction to the -adics</span></a></li>
-diff --git a/src/sage/doctest/control.py b/src/sage/doctest/control.py
-index 4236fd05e0..8e499cbaf7 100644
---- a/src/sage/doctest/control.py
-+++ b/src/sage/doctest/control.py
-@@ -87,7 +87,7 @@ class DocTestDefaults(SageObject):
-         self.sagenb = False
-         self.long = False
-         self.warn_long = None
--        self.optional = set(['sage']) | auto_optional_tags
-+        self.optional = set(['sage', 'dochtml']) | auto_optional_tags
-         self.randorder = None
-         self.global_iterations = 1  # sage-runtests default is 0
-         self.file_iterations = 1    # sage-runtests default is 0
-@@ -343,7 +343,8 @@ class DocTestController(SageObject):
-                     if not optionaltag_regex.search(o):
-                         raise ValueError('invalid optional tag {!r}'.format(o))
- 
--                options.optional |= auto_optional_tags
-+                if "sage" in options.optional:
-+                    options.optional |= auto_optional_tags
- 
-         self.options = options
-         self.files = args
-@@ -741,7 +742,7 @@ class DocTestController(SageObject):
-             sage: DC = DocTestController(DD, [dirname])
-             sage: DC.expand_files_into_sources()
-             sage: sorted(DC.sources[0].options.optional)  # abs tol 1
--            ['guava', 'magma', 'py3']
-+            ['guava', 'magma']
- 
-         We check that files are skipped appropriately::
- 
-@@ -968,7 +969,7 @@ class DocTestController(SageObject):
-             sage: from sage.doctest.control import DocTestDefaults, DocTestController
-             sage: DC = DocTestController(DocTestDefaults(), [])
-             sage: DC._optional_tags_string()
--            'sage'
-+            'dochtml,sage'
-             sage: DC = DocTestController(DocTestDefaults(optional="all,and,some,more"), [])
-             sage: DC._optional_tags_string()
-             'all'
-diff --git a/src/sage/misc/sagedoc.py b/src/sage/misc/sagedoc.py
-index 9255aa848f..cc4712d3ec 100644
---- a/src/sage/misc/sagedoc.py
-+++ b/src/sage/misc/sagedoc.py
-@@ -18,9 +18,9 @@ TESTS:
- Check that argspecs of extension function/methods appear correctly,
- see :trac:`12849`::
- 
--    sage: from sage.env import SAGE_DOC
--    sage: docfilename = os.path.join(SAGE_DOC, 'html', 'en', 'reference', 'calculus', 'sage', 'symbolic', 'expression.html')
--    sage: with open(docfilename) as fobj:
-+    sage: from sage.env import SAGE_DOC  # optional - dochtml
-+    sage: docfilename = os.path.join(SAGE_DOC, 'html', 'en', 'reference', 'calculus', 'sage', 'symbolic', 'expression.html')  # optional - dochtml
-+    sage: with open(docfilename) as fobj:  # optional - dochtml
-     ....:     for line in fobj:
-     ....:         if "#sage.symbolic.expression.Expression.numerical_approx" in line:
-     ....:             print(line)
-@@ -790,11 +790,12 @@ def _search_src_or_doc(what, string, extra1='', extra2='', extra3='',
- 
-     ::
- 
--        sage: len(_search_src_or_doc('src', r'matrix\(', 'incidence_structures', 'self', 'combinat', interact=False).splitlines()) > 1
-+        sage: from sage.misc.sagedoc import _search_src_or_doc  # optional - dochtml
-+        sage: len(_search_src_or_doc('src', r'matrix\(', 'incidence_structures', 'self', 'combinat', interact=False).splitlines()) > 1  # optional - dochtml
-         True
--        sage: 'abvar/homology' in _search_src_or_doc('doc', 'homology', 'variety', interact=False)  # long time (4s on sage.math, 2012)
-+        sage: 'abvar/homology' in _search_src_or_doc('doc', 'homology', 'variety', interact=False)  # optional - dochtml, long time (4s on sage.math, 2012)
-         True
--        sage: 'divisors' in _search_src_or_doc('src', '^ *def prime', interact=False)
-+        sage: 'divisors' in _search_src_or_doc('src', '^ *def prime', interact=False)  # optional - dochtml
-         True
-     """
-     # process keywords
-@@ -1160,9 +1161,9 @@ def search_doc(string, extra1='', extra2='', extra3='', extra4='',
-     counting the length of ``search_doc('tree',
-     interact=False).splitlines()`` gives the number of matches. ::
- 
--        sage: len(search_doc('tree', interact=False).splitlines()) > 4000  # long time
-+        sage: len(search_doc('tree', interact=False).splitlines()) > 4000  # optional - dochtml, long time
-         True
--        sage: len(search_doc('tree', whole_word=True, interact=False).splitlines()) < 2000  # long time
-+        sage: len(search_doc('tree', whole_word=True, interact=False).splitlines()) < 2000  # optional - dochtml, long time
-         True
-     """
-     return _search_src_or_doc('doc', string, extra1=extra1, extra2=extra2,
-@@ -1332,9 +1333,9 @@ class _sage_doc:
- 
-     EXAMPLES::
- 
--        sage: browse_sage_doc._open("reference", testing=True)[0]  # indirect doctest
-+        sage: browse_sage_doc._open("reference", testing=True)[0]  # optional - dochtml, indirect doctest
-         'http://localhost:8000/doc/live/reference/index.html'
--        sage: browse_sage_doc(identity_matrix, 'rst')[-107:-47]
-+        sage: browse_sage_doc(identity_matrix, 'rst')[-107:-47]  # optional - dochtml
-         'Full MatrixSpace of 3 by 3 sparse matrices over Integer Ring'
-     """
-     def __init__(self):
-@@ -1494,9 +1495,9 @@ class _sage_doc:
- 
-         EXAMPLES::
- 
--            sage: browse_sage_doc._open("reference", testing=True)[0]
-+            sage: browse_sage_doc._open("reference", testing=True)[0]  # optional - dochtml
-             'http://localhost:8000/doc/live/reference/index.html'
--            sage: browse_sage_doc._open("tutorial", testing=True)[1]
-+            sage: browse_sage_doc._open("tutorial", testing=True)[1]  # optional - dochtml
-             '.../html/en/tutorial/index.html'
-         """
-         url = self._base_url + os.path.join(name, "index.html")
diff --git a/pkgs/applications/science/math/sage/patches/eclib-20180710.patch b/pkgs/applications/science/math/sage/patches/eclib-20180710.patch
index d06e1e6cedf2..986ae42aeb62 100644
--- a/pkgs/applications/science/math/sage/patches/eclib-20180710.patch
+++ b/pkgs/applications/science/math/sage/patches/eclib-20180710.patch
@@ -14,27 +14,3 @@ index 4417b59276..ae57ca2991 100644
      """
      global instances
      try:
-diff --git a/src/sage/libs/eclib/wrap.cpp b/src/sage/libs/eclib/wrap.cpp
-index 5fd5693b53..d12468faa8 100644
---- a/src/sage/libs/eclib/wrap.cpp
-+++ b/src/sage/libs/eclib/wrap.cpp
-@@ -133,8 +133,8 @@ char* Curvedata_isogeny_class(struct Curvedata* E, int verbose)
- 
- 
- int mw_process(struct Curvedata* curve, struct mw* m,
--                      const struct bigint* x, const struct bigint* y,
--                      const struct bigint* z, int sat)
-+                      const bigint* x, const bigint* y,
-+                      const bigint* z, int sat)
- {
-   Point P(*curve, *x, *y, *z);
-   if (!P.isvalid())
-@@ -188,7 +188,7 @@ int mw_rank(struct mw* m)
- }
- 
- /* Returns index and unsat long array, which user must deallocate */
--int mw_saturate(struct mw* m, struct bigint* index, char** unsat,
-+int mw_saturate(struct mw* m, bigint* index, char** unsat,
-                        long sat_bd, int odd_primes_only)
- {
-   vector<long> v;
diff --git a/pkgs/applications/science/math/sage/patches/pari-no-threads.patch b/pkgs/applications/science/math/sage/patches/pari-no-threads.patch
deleted file mode 100644
index 13b47dbdd31b..000000000000
--- a/pkgs/applications/science/math/sage/patches/pari-no-threads.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-diff --git a/src/sage/libs/pari/__init__.py b/src/sage/libs/pari/__init__.py
-index e451766474..77eda66097 100644
---- a/src/sage/libs/pari/__init__.py
-+++ b/src/sage/libs/pari/__init__.py
-@@ -205,6 +205,13 @@ def _get_pari_instance():
-     # messages in Sage.
-     P.default("debugmem", 0)
- 
-+    # Make sure pari doesn't use threads, regardless of how it was compiled.
-+    # Threads cause some doctest failures (memory issues). Those could probably
-+    # be solved without disabling threads. But that would require figuring out
-+    # some sensible values for `threadsizemax`. See
-+    # https://pari.math.u-bordeaux.fr/dochtml/html/GP_defaults.html
-+    P.default("nbthreads", 1)
-+
-     return P
- 
- pari = _get_pari_instance()
diff --git a/pkgs/applications/science/math/sage/patches/test-in-tmpdir.patch b/pkgs/applications/science/math/sage/patches/test-in-tmpdir.patch
deleted file mode 100644
index febab3702771..000000000000
--- a/pkgs/applications/science/math/sage/patches/test-in-tmpdir.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-diff --git a/src/sage/repl/ipython_kernel/install.py b/src/sage/repl/ipython_kernel/install.py
-index aa23c8405d..8a87de0591 100644
---- a/src/sage/repl/ipython_kernel/install.py
-+++ b/src/sage/repl/ipython_kernel/install.py
-@@ -112,7 +112,7 @@ class SageKernelSpec(object):
-         EXAMPLES::
- 
-             sage: from sage.repl.ipython_kernel.install import SageKernelSpec
--            sage: spec = SageKernelSpec()
-+            sage: spec = SageKernelSpec(prefix = tmp_dir())
-             sage: spec.use_local_mathjax()
-             sage: mathjax = os.path.join(spec.nbextensions_dir, 'mathjax')
-             sage: os.path.isdir(mathjax)
-@@ -129,7 +129,7 @@ class SageKernelSpec(object):
-         EXAMPLES::
- 
-             sage: from sage.repl.ipython_kernel.install import SageKernelSpec
--            sage: spec = SageKernelSpec()
-+            sage: spec = SageKernelSpec(prefix = tmp_dir())
-             sage: spec.use_local_jsmol()
-             sage: jsmol = os.path.join(spec.nbextensions_dir, 'jsmol')
-             sage: os.path.isdir(jsmol)
-@@ -146,7 +146,7 @@ class SageKernelSpec(object):
-         EXAMPLES::
- 
-             sage: from sage.repl.ipython_kernel.install import SageKernelSpec
--            sage: spec = SageKernelSpec()
-+            sage: spec = SageKernelSpec(prefix = tmp_dir())
-             sage: spec.use_local_threejs()
-             sage: threejs = os.path.join(spec.nbextensions_dir, 'threejs')
-             sage: os.path.isdir(threejs)