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Merge branch 'develop' into t/12521/evaluate_log_gamma_for_complex_input
* develop: (569 commits) Updated Sage version to 6.4.beta2 Trac 16886: fixed documentation, added one doctest. trac #16890 added doctest trac #16890 - Fixed wrong argument name in FreeQuadraticModule_submodule_with_basis_field Trac 16886: Added pari's idealchinese function. #16852: update eclib to 20140805 trac #16739 reviewer patch, minor changes Remved unnecessary check for _freegroup_ Trac #14684: make conversion between free groups aware of generator names Line wrap update. trac #16875: set the cache when we call difference_matrix trac #16875: move imports Fix incorrect help for reinstalling a package Change of code/doc to make it conform to layout conventions. Corrected indentation for seealso block. Updated docstrings to match ::/: indentation, added REFERENCE and SEEALSO. trac #16868: Mb was initialized twice trac #16881: fix documentation issue changelog update the obvious updates ... Conflicts: src/sage/libs/pari/gen.pyx
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‎VERSION.txt

+1-1
Original file line numberDiff line numberDiff line change
@@ -1 +1 @@
1-
Sage version 6.3, released 2014-08-10
1+
Sage version 6.4.beta2, released 2014-08-28

‎build/deps

+7-6
Original file line numberDiff line numberDiff line change
@@ -164,12 +164,15 @@ $(INST)/prereq: ../configure
164164
fi; )
165165
touch $@
166166

167+
$(INST)/$(PATCH):
168+
+$(PIPE) "$(SAGE_SPKG) $(PATCH) 2>&1" "tee -a $(SAGE_LOGS)/$(PATCH).log"
169+
170+
$(INST)/$(PKGCONF): $(INST)/$(PATCH)
171+
+$(PIPE) "$(SAGE_SPKG) $(PKGCONF) 2>&1" "tee -a $(SAGE_LOGS)/$(PKGCONF).log"
172+
167173
$(INST)/$(BZIP2): $(INST)/prereq $(INST)/$(PKGCONF)
168174
+$(PIPE) "$(SAGE_SPKG) $(BZIP2) 2>&1" "tee -a $(SAGE_LOGS)/$(BZIP2).log"
169175

170-
$(INST)/$(PATCH): $(INST)/$(BZIP2)
171-
+$(PIPE) "$(SAGE_SPKG) $(PATCH) 2>&1" "tee -a $(SAGE_LOGS)/$(PATCH).log"
172-
173176
###############################################################################
174177
# Building normal packages
175178
###############################################################################
@@ -475,6 +478,7 @@ $(INST)/sage: \
475478
$(INST)/$(IML) \
476479
$(INST)/$(JINJA2) \
477480
$(INST)/$(LCALC) \
481+
$(INST)/$(LRCALC) \
478482
$(INST)/$(LIBGAP) \
479483
$(INST)/$(LIBPNG) \
480484
$(INST)/$(LINBOX) \
@@ -525,9 +529,6 @@ $(INST)/$(GCC): $(INST)/$(MPIR) $(INST)/$(MPFR) $(INST)/$(MPC) \
525529
$(INST)/$(PILLOW): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
526530
+$(PIPE) "$(SAGE_SPKG) $(PILLOW) 2>&1" "tee -a $(SAGE_LOGS)/$(PILLOW).log"
527531

528-
$(INST)/$(PKGCONF):
529-
+$(PIPE) "$(SAGE_SPKG) $(PKGCONF) 2>&1" "tee -a $(SAGE_LOGS)/$(PKGCONF).log"
530-
531532
$(INST)/$(PKGCONFIG): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
532533
+$(PIPE) "$(SAGE_SPKG) $(PKGCONFIG) 2>&1" "tee -a $(SAGE_LOGS)/$(PKGCONFIG).log"
533534

‎build/pkgs/configure/checksums.ini

+3-3
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
11
tarball=configure-VERSION.tar.gz
2-
sha1=66707652c9fc87fa6d0fdc92a305a3844e4299ea
3-
md5=ab1dcf6477ff8b1a65e2f5c6abc97a16
4-
cksum=615729644
2+
sha1=9f52b9a8917273a8b29a40c8e517ebb099cc0537
3+
md5=adfa272430f561682954687258364d5d
4+
cksum=3677976078

‎build/pkgs/configure/package-version.txt

+1-1
Original file line numberDiff line numberDiff line change
@@ -1 +1 @@
1-
43
1+
46

‎build/pkgs/cvxopt/SPKG.txt

+3
Original file line numberDiff line numberDiff line change
@@ -54,6 +54,9 @@ GNU Lesser General Public License, v2.1. See src/LICENSE for more details.
5454

5555
== Changelog ==
5656

57+
=== cvxopt-1.1.7 (Dima Pasechnik, 24 Aug 2014) ===
58+
* #16874: upgrade to version 1.1.7.
59+
5760
=== cvxopt-1.1.6.p0 (Volker Braun, Jeroen Demeyer, 15 May 2013) ===
5861
* #12832: upgrade to version 1.1.6.
5962
* Remove undocumented patch changing int_t to int.

‎build/pkgs/cvxopt/checksums.ini

+4-4
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
tarball=cvxopt-VERSION.tar.bz2
2-
sha1=ded19c9acfa3c256e6cbd738fbaf5a155c7dbc96
3-
md5=7114b6952d0428da51d237b974ab64bd
4-
cksum=2074500616
1+
tarball=cvxopt-VERSION.tar.gz
2+
sha1=199ae22f7175be8e46b277993eea7c39e30da1f1
3+
md5=3073a5da23cb5a77d3bc143edde1e4f1
4+
cksum=708245817

‎build/pkgs/cvxopt/package-version.txt

+1-1
Original file line numberDiff line numberDiff line change
@@ -1 +1 @@
1-
1.1.6.p0
1+
1.1.7

‎build/pkgs/cvxopt/patches/setup.py.patch

+8-7
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,9 @@
1-
diff -ru src/setup.py b/setup.py
2-
--- src/setup.py 2013-04-22 08:44:28.000000000 +0200
3-
+++ b/setup.py 2013-05-15 10:43:21.332392968 +0200
4-
@@ -2,26 +2,38 @@
5-
from glob import glob
1+
diff --git a/setup.py b/setup.py
2+
index 20670f7..62e82c5 100644
3+
--- a/setup.py
4+
+++ b/setup.py
5+
@@ -7,26 +7,38 @@ from glob import glob
6+
import os
67

78
# Modifiy this if BLAS and LAPACK libraries are not in /usr/lib.
89
-BLAS_LIB_DIR = '/usr/lib'
@@ -45,7 +46,7 @@ diff -ru src/setup.py b/setup.py
4546

4647
# Set to 1 if you are installing the fftw module.
4748
BUILD_FFTW = 0
48-
@@ -33,13 +45,13 @@
49+
@@ -38,13 +50,13 @@ FFTW_LIB_DIR = '/usr/lib'
4950
FFTW_INC_DIR = '/usr/include'
5051

5152
# Set to 1 if you are installing the glpk module.
@@ -62,7 +63,7 @@ diff -ru src/setup.py b/setup.py
6263

6364
# Set to 1 if you are installing the DSDP module.
6465
BUILD_DSDP = 0
65-
@@ -77,7 +89,7 @@
66+
@@ -103,7 +115,7 @@ if BUILD_FFTW:
6667
extmods += [fftw];
6768

6869
if BUILD_GLPK:

‎build/pkgs/eclib/checksums.ini

+3-3
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
11
tarball=eclib-VERSION.tar.bz2
2-
sha1=1210d69f679f6d70c378cb78231980f28e18a0af
3-
md5=87773eb30baaa7f413afa01a5c251265
4-
cksum=4230857238
2+
sha1=d868342a9d763787dfecd7d07ffacead8d04be73
3+
md5=5ee8cc313b5383dc463ed13f4b147edc
4+
cksum=420082920

‎build/pkgs/eclib/package-version.txt

+1-1
Original file line numberDiff line numberDiff line change
@@ -1 +1 @@
1-
20140128
1+
20140805

‎build/pkgs/genus2reduction/checksums.ini

+3-3
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
11
tarball=genus2reduction-VERSION.tar.bz2
2-
sha1=a29ae793b4c2d427ed5ffbecce4f77f5ba5c1e36
3-
md5=550356571d56cb887cc6a7c035e941e5
4-
cksum=649238856
2+
sha1=df358e78da17ce74cd5b63f379e7f7f91c21f08e
3+
md5=46bd298ef0699d7fb7763d08228a3ce1
4+
cksum=2690437212

‎build/pkgs/genus2reduction/package-version.txt

+1-1
Original file line numberDiff line numberDiff line change
@@ -1 +1 @@
1-
0.3.p8
1+
20140211

‎build/pkgs/lcalc/SPKG.txt

+2-2
Original file line numberDiff line numberDiff line change
@@ -82,8 +82,8 @@ http://code.google.com/p/l-calc/
8282
to not redefine the double() cast, thats just fragile and will sooner or
8383
later again fail inside some system headers.
8484

85-
* pari-2.4.4.patch:
86-
Replace obsolete lgeti() by (long)cgeti().
85+
* pari-2.7.patch:
86+
Various changes to port to PARI 2.7.
8787

8888
* init_stack.patch:
8989
Replace obsolete allocatemoremem() by a direct call to the private

‎build/pkgs/lcalc/package-version.txt

+1-1
Original file line numberDiff line numberDiff line change
@@ -1 +1 @@
1-
1.23.p12
1+
1.23.p13

‎build/pkgs/lcalc/patches/pari-2.4.4.patch ‎build/pkgs/lcalc/patches/pari-2.7.patch

+12
Original file line numberDiff line numberDiff line change
@@ -17,3 +17,15 @@
1717

1818
//gaffsg(a1,(GEN) F[1]);
1919
//gaffsg(a2,(GEN) F[2]);
20+
diff -ru src/src/Lcommandline_elliptic.cc b/src/Lcommandline_elliptic.cc
21+
--- src/src/Lcommandline_elliptic.cc 2014-02-10 10:17:11.004419528 +0100
22+
+++ b/src/Lcommandline_elliptic.cc 2014-02-10 10:20:37.757715491 +0100
23+
@@ -139,7 +139,7 @@
24+
gaffect(strtoGEN(a4), (GEN) F[4]);
25+
gaffect(strtoGEN(a6), (GEN) F[5]);
26+
27+
- E = initell(F,BIGDEFAULTPREC);
28+
+ E = ellinit(F, NULL, BIGDEFAULTPREC);
29+
30+
C=globalreduction(E);
31+

‎build/pkgs/maxima/SPKG.txt

+4
Original file line numberDiff line numberDiff line change
@@ -69,6 +69,10 @@ The following patches are applied:
6969

7070
* infodir.patch: Correct the path to the Info directory.
7171

72+
* limit-replace-logs.patch: Fix for Maxima bug #2621 (gamma limit
73+
error). Introduced in Trac #15033 (Wrong limit value of expression
74+
involving gamma function).
75+
7276
* matrixexp.patch: Fix matrixexp(matrix([%i*%pi])), which broke after
7377
Maxima 5.29.1. Introduced in Trac #13973.
7478

‎build/pkgs/maxima/package-version.txt

+1-1
Original file line numberDiff line numberDiff line change
@@ -1 +1 @@
1-
5.33.0.p0
1+
5.33.0.p1

‎build/pkgs/maxima/patches/limit-replace-logs.patch

+54
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,54 @@
1+
diff --git a/src/limit.lisp b/src/limit.lisp
2+
index 86492cc..a56569a 100644
3+
--- a/src/limit.lisp
4+
+++ b/src/limit.lisp
5+
@@ -3160,6 +3160,26 @@ ignoring dummy variables and array indices."
6+
omega))
7+
(cons exp logw)))
8+
9+
+;;; if log w(x) = h(x), rewrite all subexpressions of the form
10+
+;;; log(f(x)) as log(w^-c f(x)) + c h(x) with c the unique constant
11+
+;;; such that w^-c f(x) is strictly less rapidly varying than w.
12+
+(defun mrv-rewrite-logs (exp wsym logw)
13+
+ (cond ((atom exp) exp)
14+
+ ((and (mlogp exp)
15+
+ (not (freeof wsym exp)))
16+
+ (let* ((f (cadr exp))
17+
+ (c ($lopow (calculate-series f wsym)
18+
+ wsym)))
19+
+ (m+ (list (car exp)
20+
+ (m* (m^ wsym (m- c))
21+
+ (mrv-rewrite-logs f wsym logw)))
22+
+ (m* c logw))))
23+
+ (t
24+
+ (cons (car exp)
25+
+ (mapcar (lambda (e)
26+
+ (mrv-rewrite-logs e wsym logw))
27+
+ (cdr exp))))))
28+
+
29+
;; returns list of two elements: coeff and exponent of leading term of exp,
30+
;; after rewriting exp in term of its MRV set omega.
31+
(defun mrv-leadterm (exp var omega)
32+
@@ -3181,7 +3201,8 @@ ignoring dummy variables and array indices."
33+
lo
34+
coef
35+
((f . logw) (mrv-rewrite exp omega var wsym))
36+
- (series (calculate-series f wsym)))
37+
+ (series (calculate-series (mrv-rewrite-logs f wsym logw)
38+
+ wsym)))
39+
(setq series (maxima-substitute logw `((%log) ,wsym) series))
40+
(setq lo ($lopow series wsym))
41+
(when (or (not ($constantp lo))
42+
diff --git a/tests/rtest_limit.mac b/tests/rtest_limit.mac
43+
index b255d40..80ec53a 100644
44+
--- a/tests/rtest_limit.mac
45+
+++ b/tests/rtest_limit.mac
46+
@@ -625,3 +625,8 @@ limit(log(-1/3125*((-1/2*sqrt(5) + 1/2)^n - (1/2*sqrt(5) +
47+
limit(x^2*exp(-%i*x - x), x, inf);
48+
0;
49+
50+
+/* bug #2621 gamma limit error */
51+
+
52+
+limit(gamma(x+1/2)/(sqrt(x)*gamma(x)), x, inf);
53+
+1;
54+
+

‎build/pkgs/pari/SPKG.txt

+2-1
Original file line numberDiff line numberDiff line change
@@ -28,7 +28,8 @@ GPL version 2+
2828
* http://pari.math.u-bordeaux.fr/
2929

3030
== Dependencies ==
31-
* MPIR (in place of GMP)
31+
* Perl
32+
* MPIR or GMP
3233
* Readline
3334
* GNU patch (shipped with Sage)
3435

‎build/pkgs/pari/checksums.ini

+4-4
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
tarball=pari-VERSION.tar.bz2
2-
sha1=3f0838940fcf1cb7748979fe16e4b5cab0d19080
3-
md5=4c54710f7e2d4de7b8781edb9d604c60
4-
cksum=2949888924
1+
tarball=pari-VERSION.tar.gz
2+
sha1=7edec0dfefc5d0c47a7f1c2fb1016cfe313c1652
3+
md5=cdf11f569140343449bda477bea19ddb
4+
cksum=1676608517

‎build/pkgs/pari/package-version.txt

+1-1
Original file line numberDiff line numberDiff line change
@@ -1 +1 @@
1-
2.5.5b.p1
1+
2.7.1.p0

‎build/pkgs/pari/patches/GCC_PR49330.patch

+11-11
Original file line numberDiff line numberDiff line change
@@ -1,22 +1,22 @@
1-
diff -ru src/src/language/init.c src.patched/src/language/init.c
2-
--- a/src/language/init.c 2012-02-11 10:57:38.000000000 +0100
3-
+++ b/src/language/init.c 2012-03-07 10:24:37.000000000 +0100
4-
@@ -593,14 +593,16 @@
1+
diff -ru src/src/language/init.c b/src/language/init.c
2+
--- src/src/language/init.c 2014-02-01 16:29:48.955825926 +0100
3+
+++ b/src/language/init.c 2014-02-01 16:31:24.612818588 +0100
4+
@@ -612,14 +612,16 @@
55
pari_init_functions(void)
66
{
7-
stack_init(&s_MODULES, sizeof(*MODULES),(void**)&MODULES);
8-
- stack_pushp(&s_MODULES,functions_basic);
9-
stack_init(&s_OLDMODULES, sizeof(*OLDMODULES),(void**)&OLDMODULES);
10-
- stack_pushp(&s_OLDMODULES,oldfonctions);
7+
pari_stack_init(&s_MODULES, sizeof(*MODULES),(void**)&MODULES);
8+
- pari_stack_pushp(&s_MODULES,functions_basic);
9+
pari_stack_init(&s_OLDMODULES, sizeof(*OLDMODULES),(void**)&OLDMODULES);
10+
- pari_stack_pushp(&s_OLDMODULES,oldfonctions);
1111
functions_hash = (entree**) pari_calloc(sizeof(entree*)*functions_tblsz);
1212
pari_fill_hashtable(functions_hash,
1313
new_fun_set? functions_basic: oldfonctions);
1414
defaults_hash = (entree**) pari_calloc(sizeof(entree*)*functions_tblsz);
1515
pari_add_defaults_module(functions_default);
1616
+ /* Move this down to work around GCC bug
1717
+ * http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49330 */
18-
+ stack_pushp(&s_MODULES,functions_basic);
19-
+ stack_pushp(&s_OLDMODULES,oldfonctions);
18+
+ pari_stack_pushp(&s_MODULES,functions_basic);
19+
+ pari_stack_pushp(&s_OLDMODULES,oldfonctions);
2020
}
21-
21+
2222
void

‎build/pkgs/pari/patches/KERNELCFLAGS.patch

+6-6
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,10 @@
11
diff -ru src/config/get_cc b/config/get_cc
2-
--- src/config/get_cc 2012-09-25 23:10:46.000000000 +0200
3-
+++ b/config/get_cc 2013-01-07 16:02:46.607514084 +0100
4-
@@ -122,7 +122,11 @@
5-
case "$__gnuc__" in
6-
2.95.[3-9]*|[3-9].*) OPTFLAGS="$OPTFLAGS -fno-strict-aliasing";;
7-
esac
2+
--- src/config/get_cc 2014-02-01 21:41:54.534348273 +0100
3+
+++ b/config/get_cc 2014-02-01 21:42:50.850930971 +0100
4+
@@ -94,7 +94,11 @@
5+
OPTFLAGS="$OPTFLAGS -fno-strict-aliasing"
6+
fi
7+
rm -f $exe $exe$exe_suff
88
- KERNELCFLAGS=-funroll-loops
99
+ if [ "$SAGE_DEBUG" = yes ]; then
1010
+ KERNELCFLAGS=-O1

‎build/pkgs/pari/patches/README.txt

+2-33
Original file line numberDiff line numberDiff line change
@@ -4,32 +4,17 @@ Current patches to PARI in Sage:
44

55
Patches to configuration files:
66
* get_ld.patch (Carl Witty): Disable -rpath.
7-
* get_tests.patch (John Cremona): Disable testing of ellglobalred in
8-
"make test-all" in spkg-check, since it requires the elldata database
9-
which we do not include since it is about 18MB.
107
* get_config_options.patch (Leif Leonhardy): Catch invalid arguments to
118
"--graphic" (and treat such as an error) since otherwise strange
129
compilation errors might occur (cf. #9722, too).
13-
* get_fltk.patch (Leif Leonhardy): Explicitly link against libstdc++
14-
when using FLTK (for plotting) to support Fedora 13, and do an extra
15-
check for the FLTK include dir (cf. #9722).
16-
* get_X11.patch (Leif Leonhardy): Also search */lib64/* for X11
17-
libraries (since on some systems this is really a separate directory,
18-
i.e. neither a symbolic link to */lib/* nor the target of a symbolic
19-
link */lib/*; cf. #9722, too).
10+
* get_fltk.patch (Leif Leonhardy): do an extra check for the FLTK
11+
include dir (cf. #9722).
2012
* get_dlcflags.patch (Jeroen Demeyer): Add -fno-common to DLCFLAGS on
2113
Darwin. Submitted upstream, but upstream only applied it for PowerPC.
2214
Since this doesn't break anything and only improves performance, add
2315
the flag unconditionally.
24-
* install_doc_no_make.patch (Jeroen Demeyer): Do not *build* the
25-
documentation when doing install-doc or install-docpdf. We must not
26-
build the documentation because that requires tex. On the other hand,
27-
to have ? and ?? work within gp, we must install the .tex files (but
28-
not .dvi files). So simply not doing install-doc doesn't work.
2916
* perl_path.patch (Jeroen Demeyer): change first line of all perl
3017
scripts to "#!/usr/bin/env perl" (#10559).
31-
* cygwin_dll_a.patch (Jean-Pierre Flori): copy libpari.dll.a on Cygwin
32-
(see #13333).
3318
* KERNELCFLAGS.patch (Jeroen Demeyer): when SAGE_DEBUG=yes, compile
3419
kernel files with -O1 instead of -funroll-loops; -O0 gives a
3520
segmentation fault on some OS X systems when doing
@@ -45,22 +30,6 @@ C files:
4530
gcc-4.6.3. Discussed with upstream:
4631
- http://pari.math.u-bordeaux.fr/archives/pari-dev-1203/msg00001.html
4732
- http://pari.math.u-bordeaux.fr/archives/pari-dev-1202/msg00006.html
48-
* trac_13902_determinant.patch (Jeroen Demeyer): patch backported from
49-
upstream git repository based on commits
50-
- 28ea998bc661f5bbde18b6d6b0f50111a10ae16c
51-
- 249432f7088bfa114ed5cd3a5d64ef51ee968e35
52-
* polred.patch (Jeroen Demeyer): Fix polred(), add polredbest()
53-
backported from upstream commits
54-
- 2d00a24fbb1ffe8eba35b9a04763e36eef8a5f7b
55-
- a3596c56f9439144a0dbed4c47bd6ff9485e3fc8
56-
- 1a00ca416de4daebccaab2be1a4b8a061a9f2fde
57-
- ad550d9bbfee8113087407c3262bffc27a020c98
58-
* q_eint1.patch (Jeroen Demeyer): Fix precision of eint1(), backported
59-
from upstream commits
60-
- b894e0171112493bb4945a6a0e4af039b54a1d1f
61-
- 54eb37055167dbd8d4856b1bd698cf7018db561b
62-
and completely backport new algorithm for mpveceint1(). The prefix
63-
q_ in the patch filename is to ensure it comes after polred.patch.
6433
* det_garbage.patch (Jeroen Demeyer, #15654): When computing a
6534
determinant(), only collect garbage once per outer loop iteration.
6635
Better increase PARI stack size instead of collecting garbage too

‎build/pkgs/pari/patches/cygwin_dll_a.patch

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