[arch-commits] Commit in sagemath/trunk (5 files)
Antonio Rojas
arojas at archlinux.org
Mon May 7 20:54:11 UTC 2018
Date: Monday, May 7, 2018 @ 20:54:10
Author: arojas
Revision: 319415
Fix env patch, update networkx 2 patch
Added:
sagemath/trunk/sagemath-ignore-warnings.patch
(from rev 319414, sagemath/trunk/pari-stackwarn.patch)
Modified:
sagemath/trunk/PKGBUILD
sagemath/trunk/sagemath-env.patch
sagemath/trunk/sagemath-networkx2.patch
Deleted:
sagemath/trunk/pari-stackwarn.patch
--------------------------------+
PKGBUILD | 14 +++++++-------
pari-stackwarn.patch | 23 -----------------------
sagemath-env.patch | 20 +++++++++++++++++---
sagemath-ignore-warnings.patch | 25 +++++++++++++++++++++++++
sagemath-networkx2.patch | 10 ++++++++++
5 files changed, 59 insertions(+), 33 deletions(-)
Modified: PKGBUILD
===================================================================
--- PKGBUILD 2018-05-07 20:42:22 UTC (rev 319414)
+++ PKGBUILD 2018-05-07 20:54:10 UTC (rev 319415)
@@ -9,7 +9,7 @@
pkgbase=sagemath
pkgname=(sagemath sagemath-jupyter)
pkgver=8.2
-pkgrel=1
+pkgrel=2
pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab"
arch=(x86_64)
url="http://www.sagemath.org"
@@ -36,12 +36,12 @@
mcqd coxeter bliss-graphs tdlib python2-pkgconfig shared_meataxe libfes)
source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz"
sagemath-env.patch package.patch latte-count.patch jupyter-path.patch sagemath-python3-notebook.patch test-optional.patch
- r-no-readline.patch fes02.patch sagemath-threejs.patch pari-stackwarn.patch
+ r-no-readline.patch fes02.patch sagemath-threejs.patch sagemath-ignore-warnings.patch
sagemath-detect-igraph.patch sagemath-networkx2.patch sagemath-scipy-1.0.patch sagemath-lrs.patch
sagemath-singular-4.1.1.patch sagemath-lcalc-c++11.patch
pari-ratpoints.patch::"https://github.com/sagemath/sage/commit/83458400.patch")
sha256sums=('41ba2c2dde7a02e1bb6880ae875d37ab058567cc26e760efe87eeb12188cd65b'
- 'ad1ce89c624b848c5908e34851e4b765d1ba85819bb3626eedfd0cab6157c5e4'
+ '6f95ef6960acb3b368bc6245783d88fcadaa63537e1bf9f41d8d91b28e95ddf9'
'c41ae665499c6cd775d40bbe178f8786830b0931ee26bf11ee02f7d83bcc8107'
'0b680e674c11c47afa86162d8b49645620b8912722e08133d23357c29ca9310a'
'2cad308f8adbb6c54e6603fa22b2f0eb60f6f09248d5d015000c3932ac14f646'
@@ -50,9 +50,9 @@
'afd0952b9bb8f52fd428eae36cf719a58ff85a894baae88cbb2124e043768cc7'
'7fcb52e96935dccb0f958d37c2f4e3918392480b9af53e08562f6cba6c68cb94'
'2d13b15ad2d1511bb3d752a261497060a8901882b1c2fa9813219781b7a71d83'
- 'eaf252b2c9b397a0db8fb8cbf45f0b56a21910b5f632d59709f41eff30c5eaab'
+ 'a4a6c87b46ff23b89608aca66d00427334502e8bfb5dfe68b94497d19be1c7ae'
'bfe49f0168fe0824f0eaf4ea793b08d5b3e43c4e3634eb5f664c70644a793a59'
- '54bb6de642cbc07c24904016546f42de5d5aa040e67014884cbfa20e35e52cbd'
+ '8253730940687992dd29d90d95bea7e2685bb4854db004090c8196ce92859b64'
'17397b8e1843b013ef5d2e083369109f0719651edd8ef0c8493cb49e2bc4324a'
'c0f65534a845ba802de6196229159fe67fcc3f72f0cb1ce57d4ae5c9fe10282c'
'369f1483e0364031d73d43d9e63b7bf2b0929c8a1d470c1596f98f9f1aa80750'
@@ -88,8 +88,8 @@
patch -p1 -i ../sagemath-networkx2.patch
# fix three.js plotting backend
patch -p1 -i ../sagemath-threejs.patch
-# don't show PARI stack size increase warnings during doctesting (Debian)
- patch -p1 -i ../pari-stackwarn.patch
+# don't show PARI stack size increase or GLPK warnings during doctesting (Debian)
+ patch -p1 -i ../sagemath-ignore-warnings.patch
# remove deprecated scipy parameters
patch -p1 -i ../sagemath-scipy-1.0.patch
# fix build with Singular 4.1.1
Deleted: pari-stackwarn.patch
===================================================================
--- pari-stackwarn.patch 2018-05-07 20:42:22 UTC (rev 319414)
+++ pari-stackwarn.patch 2018-05-07 20:54:10 UTC (rev 319415)
@@ -1,23 +0,0 @@
-Description: Ignore warnings of PARI increasing the stack size when parsing doctests
- Since we can't patch PARI to not produce the warnings and we don't want to
- patch tons of doctests to expect the warnings, we patch the doctest parser
- to ignore them.
-Author: Tobias Hansen <thansen at debian.org>
---- sage/src/sage/doctest/parsing.py
-+++ sage/src/sage/doctest/parsing.py
-@@ -40,6 +40,7 @@
-
- float_regex = re.compile('\s*([+-]?\s*((\d*\.?\d+)|(\d+\.?))([eE][+-]?\d+)?)')
- optional_regex = re.compile(r'(py2|py3|long time|not implemented|not tested|known bug)|([^ a-z]\s*optional\s*[:-]*((\s|\w)*))')
-+pari_stack_warning_regex = re.compile(r'\s*\*\*\*.*(Warning: increasing stack size to )\d+\.')
- find_sage_prompt = re.compile(r"^(\s*)sage: ", re.M)
- find_sage_continuation = re.compile(r"^(\s*)\.\.\.\.:", re.M)
- random_marker = re.compile('.*random', re.I)
-@@ -935,6 +936,7 @@
- <type 'float'>
- """
- got = self.human_readable_escape_sequences(got)
-+ got = pari_stack_warning_regex.sub('', got)
- if isinstance(want, MarkedOutput):
- if want.random:
- return True
Modified: sagemath-env.patch
===================================================================
--- sagemath-env.patch 2018-05-07 20:42:22 UTC (rev 319414)
+++ sagemath-env.patch 2018-05-07 20:54:10 UTC (rev 319415)
@@ -86,7 +86,7 @@
-export SAGE_SRC="$SAGE_ROOT/src"
-export SAGE_DOC_SRC="$SAGE_SRC/doc"
+export GAP_ROOT_DIR="/usr/lib/gap"
-+export SAGE_SRC="$SAGE_SHARE/sage/source"
++export SAGE_SRC="$SAGE_LOCAL/lib/python2.7/site-packages"
+export SAGE_DOC_SRC="$SAGE_SHARE/doc/sage"
export SAGE_DOC="$SAGE_SHARE/doc/sage"
@@ -121,7 +121,7 @@
# First, figure out the right values for SAGE_NUM_THREADS (default
--- src/sage/env.py.orig 2017-12-07 19:51:25.554281539 +0000
+++ src/sage/env.py 2017-12-07 19:51:42.787654650 +0000
-@@ -117,8 +117,8 @@
+@@ -117,13 +117,13 @@
_add_variable_or_fallback('LOCAL_IDENTIFIER','$HOSTNAME.%s'%os.getpid())
# bunch of sage directories and files
@@ -132,4 +132,18 @@
_add_variable_or_fallback('SAGE_ETC', opj('$SAGE_LOCAL', 'etc'))
_add_variable_or_fallback('SAGE_INC', opj('$SAGE_LOCAL', 'include'))
_add_variable_or_fallback('SAGE_SHARE', opj('$SAGE_LOCAL', 'share'))
-
+
+-_add_variable_or_fallback('SAGE_SRC', opj('$SAGE_ROOT', 'src'))
++_add_variable_or_fallback('SAGE_SRC', opj('$SAGE_LOCAL', 'lib', 'python2.7', 'site-packages'))
+
+ try:
+ sitepackages_dirs = site.getsitepackages()
+@@ -163,7 +163,7 @@
+ _add_variable_or_fallback('GRAPHS_DATA_DIR', opj('$SAGE_SHARE','graphs'))
+ _add_variable_or_fallback('ELLCURVE_DATA_DIR',opj('$SAGE_SHARE','ellcurves'))
+ _add_variable_or_fallback('POLYTOPE_DATA_DIR',opj('$SAGE_SHARE','reflexive_polytopes'))
+-_add_variable_or_fallback('GAP_ROOT_DIR', opj('$SAGE_LOCAL','gap','latest'))
++_add_variable_or_fallback('GAP_ROOT_DIR', opj('$SAGE_LOCAL','lib','gap'))
+ _add_variable_or_fallback('THEBE_DIR', opj('$SAGE_SHARE','thebe'))
+
+ # locate singular shared object
Copied: sagemath/trunk/sagemath-ignore-warnings.patch (from rev 319414, sagemath/trunk/pari-stackwarn.patch)
===================================================================
--- sagemath-ignore-warnings.patch (rev 0)
+++ sagemath-ignore-warnings.patch 2018-05-07 20:54:10 UTC (rev 319415)
@@ -0,0 +1,25 @@
+Description: Ignore warnings of PARI increasing the stack size when parsing doctests
+ Since we can't patch PARI to not produce the warnings and we don't want to
+ patch tons of doctests to expect the warnings, we patch the doctest parser
+ to ignore them.
+Author: Tobias Hansen <thansen at debian.org>
+--- sage/src/sage/doctest/parsing.py
++++ sage/src/sage/doctest/parsing.py
+@@ -40,6 +40,8 @@
+
+ float_regex = re.compile('\s*([+-]?\s*((\d*\.?\d+)|(\d+\.?))([eE][+-]?\d+)?)')
+ optional_regex = re.compile(r'(py2|py3|long time|not implemented|not tested|known bug)|([^ a-z]\s*optional\s*[:-]*((\s|\w)*))')
++pari_stack_warning_regex = re.compile(r'\s*\*\*\*.*(Warning: increasing stack size to )\d+\.')
++glpk_simplex_warning_regex = re.compile(r'(Long-step dual simplex will be used)')
+ find_sage_prompt = re.compile(r"^(\s*)sage: ", re.M)
+ find_sage_continuation = re.compile(r"^(\s*)\.\.\.\.:", re.M)
+ random_marker = re.compile('.*random', re.I)
+@@ -935,6 +936,8 @@
+ <type 'float'>
+ """
+ got = self.human_readable_escape_sequences(got)
++ got = pari_stack_warning_regex.sub('', got)
++ got = glpk_simplex_warning_regex.sub('', got)
+ if isinstance(want, MarkedOutput):
+ if want.random:
+ return True
Modified: sagemath-networkx2.patch
===================================================================
--- sagemath-networkx2.patch 2018-05-07 20:42:22 UTC (rev 319414)
+++ sagemath-networkx2.patch 2018-05-07 20:54:10 UTC (rev 319415)
@@ -145,6 +145,15 @@
sage: g.matching(algorithm="LP", use_edge_labels=True)
[(1, 2, 999)]
+@@ -4671,7 +4671,7 @@ class Graph(GenericGraph):
+ else:
+ for u, v in L:
+ g.add_edge(u, v)
+- d = networkx.max_weight_matching(g)
++ d = dict(networkx.max_weight_matching(g).union(t[::-1] for t in networkx.max_weight_matching(g)))
+ if value_only:
+ if use_edge_labels:
+ return sum(W[u, v] for u, v in six.iteritems(d) if u < v)
@@ -6305,7 +6305,7 @@ class Graph(GenericGraph):
return networkx.number_of_cliques(self.networkx_graph(copy=False), vertices, cliques)
@@ -163,3 +172,4 @@
@doc_index("Clique-related methods")
def cliques_get_clique_bipartite(self, **kwds):
+
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