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sage: 8.4.beta0 -> 8.4.beta1

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This commit is contained in:
Timo Kaufmann 2018-08-16 00:17:14 +02:00
parent df97127114
commit 52b9217b50
5 changed files with 2 additions and 234 deletions
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127
pkgs/applications/science/math/sage/patches/dochtml-optional.patch
View file

@ -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")

24
pkgs/applications/science/math/sage/patches/eclib-20180710.patch
View file

@ -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;

18
pkgs/applications/science/math/sage/patches/pari-no-threads.patch
View file

@ -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()

31
pkgs/applications/science/math/sage/patches/test-in-tmpdir.patch
View file

@ -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)

36
pkgs/applications/science/math/sage/sage-src.nix
View file

@ -3,20 +3,17 @@
, fetchpatch
}:
stdenv.mkDerivation rec {
version = "8.4.beta0";
version = "8.4.beta1";
name = "sage-src-${version}";
src = fetchFromGitHub {
owner = "sagemath";
repo = "sage";
rev = version;
sha256 = "1jph4slscpni0smp2fxs3s12282c9r3mdfbgxpyx67gic0d9iya8";
sha256 = "0yk5ndjr1kap7vhd2i6i5bpcfgmr4fhypn6x7myiymiy9s93d37j";
};
nixPatches = [
# https://trac.sagemath.org/ticket/25722
./patches/test-in-tmpdir.patch
# https://trac.sagemath.org/ticket/25358
(fetchpatch {
name = "safe-directory-test-without-patch.patch";
@ -30,21 +27,6 @@ stdenv.mkDerivation rec {
# https://trac.sagemath.org/ticket/25316
# https://github.com/python/cpython/pull/7476
./patches/python-5755-hotpatch.patch
# https://trac.sagemath.org/ticket/25315
(fetchpatch {
name = "find-libraries-in-dyld-library-path.patch";
url = "https://git.sagemath.org/sage.git/patch/?h=20d4593876ce9c6004eac2ab6fd61786d0d96a06";
sha256 = "1k3afq3qlzmgqwx6rzs5wv153vv9dsf5rk8pi61g57l3r3npbjmc";
})
# https://trac.sagemath.org/ticket/25345
# (upstream patch doesn't apply on 8.2 source)
./patches/dochtml-optional.patch
# work with pari with threads enabled at compile time (disable them at runtime)
# https://trac.sagemath.org/ticket/26002
./patches/pari-no-threads.patch
];
packageUpgradePatches = [
@ -96,20 +78,6 @@ stdenv.mkDerivation rec {
url = "https://git.archlinux.org/svntogit/community.git/plain/trunk/sagemath-lcalc-c++11.patch?h=packages/sagemath&id=0e31ae526ab7c6b5c0bfacb3f8b1c4fd490035aa";
sha256 = "0p5wnvbx65i7cp0bjyaqgp4rly8xgnk12pqwaq3dqby0j2bk6ijb";
})
# cddlib 0.94i -> 0.94j
(fetchpatch {
name = "cddlib-0.94j.patch";
url = "https://git.sagemath.org/sage.git/patch/?id=2ab1546b3e21d1d0ab3b4fcd58576848b3a2d888";
sha256 = "1c5gnasq7y9xxj762bn79bis0zi8d9bgg7jzlf64ifixsrc5cymb";
})
# arb 2.13.0 -> 2.14.0
(fetchpatch {
name = "arb-2.14.0.patch";
url = "https://git.sagemath.org/sage.git/patch?id2=8.4.beta0&id=8bef4fd2876a61969b516fe4eb3b8ad7cc076c5e";
sha256 = "00p3hfsfn3w2vxgd9fjd23mz7xfxjfravf8ysjxkyd657jbkpjmk";
})
];
patches = nixPatches ++ packageUpgradePatches ++ [