Merge remote-tracking branch 'origin/develop' into depr_alias

Conflicts:
	src/sage/numerical/mip.pyx

VERSION.txt

@@ -1 +1 @@
-Sage version 6.3.beta6, released 2014-07-19
+Sage version 6.4.beta1, released 2014-08-20

build/deps

@@ -31,6 +31,7 @@ all-sage: \
      $(INST)/$(CDDLIB) \
      $(INST)/$(CEPHES) \
      $(INST)/$(CLIQUER) \
+     $(INST)/$(COMBINATORIAL_DESIGNS) \
      $(INST)/$(CONWAY) \
      $(INST)/$(CVXOPT) \
      $(INST)/$(CYTHON) \
@@ -163,12 +164,15 @@ $(INST)/prereq: ../configure
 	    fi; )
 	touch $@
 
+$(INST)/$(PATCH):
+	+$(PIPE) "$(SAGE_SPKG) $(PATCH) 2>&1" "tee -a $(SAGE_LOGS)/$(PATCH).log"
+
+$(INST)/$(PKGCONF): $(INST)/$(PATCH)
+	+$(PIPE) "$(SAGE_SPKG) $(PKGCONF) 2>&1" "tee -a $(SAGE_LOGS)/$(PKGCONF).log"
+
 $(INST)/$(BZIP2): $(INST)/prereq $(INST)/$(PKGCONF)
 	+$(PIPE) "$(SAGE_SPKG) $(BZIP2) 2>&1" "tee -a $(SAGE_LOGS)/$(BZIP2).log"
 
-$(INST)/$(PATCH): $(INST)/$(BZIP2)
-	+$(PIPE) "$(SAGE_SPKG) $(PATCH) 2>&1" "tee -a $(SAGE_LOGS)/$(PATCH).log"
-
 ###############################################################################
 # Building normal packages
 ###############################################################################
@@ -185,6 +189,9 @@ $(INST)/$(BOOST_CROPPED):
 $(INST)/$(CLIQUER):
 	+$(PIPE) "$(SAGE_SPKG) $(CLIQUER) 2>&1" "tee -a $(SAGE_LOGS)/$(CLIQUER).log"
 
+$(INST)/$(COMBINATORIAL_DESIGNS):
+	+$(PIPE) "$(SAGE_SPKG) $(COMBINATORIAL_DESIGNS) 2>&1" "tee -a $(SAGE_LOGS)/$(COMBINATORIAL_DESIGNS).log"
+
 $(INST)/$(NCURSES): $(INST)/$(PKGCONF)
 	+$(PIPE) "$(SAGE_SPKG) $(NCURSES) 2>&1" "tee -a $(SAGE_LOGS)/$(NCURSES).log"
 
@@ -471,6 +478,7 @@ $(INST)/sage: \
 		 $(INST)/$(IML) \
 		 $(INST)/$(JINJA2) \
 		 $(INST)/$(LCALC) \
+		 $(INST)/$(LRCALC) \
 		 $(INST)/$(LIBGAP) \
 		 $(INST)/$(LIBPNG) \
 		 $(INST)/$(LINBOX) \
@@ -521,9 +529,6 @@ $(INST)/$(GCC): $(INST)/$(MPIR) $(INST)/$(MPFR) $(INST)/$(MPC) \
 $(INST)/$(PILLOW): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
 	+$(PIPE) "$(SAGE_SPKG) $(PILLOW) 2>&1" "tee -a $(SAGE_LOGS)/$(PILLOW).log"
 
-$(INST)/$(PKGCONF): 
-	+$(PIPE) "$(SAGE_SPKG) $(PKGCONF) 2>&1" "tee -a $(SAGE_LOGS)/$(PKGCONF).log"
-
 $(INST)/$(PKGCONFIG): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
 	+$(PIPE) "$(SAGE_SPKG) $(PKGCONFIG) 2>&1" "tee -a $(SAGE_LOGS)/$(PKGCONFIG).log"
 

build/install

@@ -324,6 +324,7 @@ BZIP2=`newest_version bzip2`
 CDDLIB=`newest_version cddlib`
 CEPHES=`newest_version cephes`
 CLIQUER=`newest_version cliquer`
+COMBINATORIAL_DESIGNS=`newest_version combinatorial_designs`
 CONWAY=`newest_version conway_polynomials`
 CVXOPT=`newest_version cvxopt`
 CYTHON=`newest_version cython`

build/pkgs/combinatorial_designs/SPKG.txt

@@ -0,0 +1,29 @@
+= Combinatorial Designs =
+
+== Description ==
+
+Data for Combinatorial Designs. Current content:
+
+- The table of MOLS (10 000 integers) from the Handbook of Combinatorial
+  Designs, 2ed.
+
+== SPKG Maintainers ==
+
+ * Nathann Cohen
+
+== License ==
+
+Public domain.
+
+== Upstream Contact ==
+
+ None
+
+== Dependencies ==
+
+N/A
+
+== Changelog ==
+
+== designs-20140630 (Nathann Cohen, 2014-06-30) ==
+ * #16541: Table of MOLS

build/pkgs/combinatorial_designs/checksums.ini

@@ -0,0 +1,4 @@
+tarball=combinatorial_designs-VERSION.tar.bz2
+sha1=353ba24217f9b7920890a784fd75dc59175f7196
+md5=f345a6918b1bcf34fcd71c2f26d10de0
+cksum=131472289

build/pkgs/combinatorial_designs/package-version.txt

@@ -0,0 +1 @@
+20140630

build/pkgs/combinatorial_designs/spkg-install

@@ -0,0 +1,4 @@
+#!/bin/sh
+
+mkdir -p "$SAGE_SHARE"/combinatorial_designs
+mv src/* "$SAGE_SHARE"/combinatorial_designs

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=3265062e02ba06ebe5897596eea08fb04cb3c554
-md5=f3a75a886044f86dab6565b399141bde
-cksum=666076577
+sha1=80f834dff7baffd5306b4269dffe547df264a72a
+md5=90e5cd2fef68232a20ac565f8efea235
+cksum=3340757205

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-36
+45

build/pkgs/graphs/spkg-install

@@ -1,6 +1,4 @@
 #!/bin/sh
 
-rm -rf "$SAGE_SHARE"/graphs
-
-mkdir -p "$SAGE_SHARE"
-mv src "$SAGE_SHARE"/graphs
+mkdir -p "$SAGE_SHARE"/graphs
+cp src/* "$SAGE_SHARE"/graphs/

build/pkgs/libgap/spkg-install

@@ -44,6 +44,7 @@ done
 echo "Configuring libGAP..."
 ./configure --disable-static \
     CFLAGS="$CFLAGS" CXXFLAGS="$CXXFLAGS" CPPFLAGS="$CPPFLAGS" \
+    --libdir="$SAGE_LOCAL/lib" \
     --with-gap_system_arch="$GAParch_system" \
     --with-sage="$SAGE_LOCAL" --with-gmp="$SAGE_LOCAL" --prefix="$SAGE_LOCAL"
 if [ $? -ne 0 ]; then

build/pkgs/maxima/SPKG.txt

@@ -69,6 +69,10 @@ The following patches are applied:
 
  * infodir.patch: Correct the path to the Info directory.
 
+ * limit-replace-logs.patch: Fix for Maxima bug #2621 (gamma limit
+   error).  Introduced in Trac #15033 (Wrong limit value of expression
+   involving gamma function).
+
  * matrixexp.patch: Fix matrixexp(matrix([%i*%pi])), which broke after
    Maxima 5.29.1.  Introduced in Trac #13973.
 

build/pkgs/maxima/package-version.txt

@@ -1 +1 @@
-5.33.0.p0
+5.33.0.p1

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

@@ -0,0 +1,54 @@
+diff --git a/src/limit.lisp b/src/limit.lisp
+index 86492cc..a56569a 100644
+--- a/src/limit.lisp
++++ b/src/limit.lisp
+@@ -3160,6 +3160,26 @@ ignoring dummy variables and array indices."
+ 		    omega))
+     (cons exp logw)))
+
++;;; if log w(x) = h(x), rewrite all subexpressions of the form
++;;; log(f(x)) as log(w^-c f(x)) + c h(x) with c the unique constant
++;;; such that w^-c f(x) is strictly less rapidly varying than w.
++(defun mrv-rewrite-logs (exp wsym logw)
++  (cond ((atom exp) exp)
++	((and (mlogp exp)
++	      (not (freeof wsym exp)))
++	 (let* ((f (cadr exp))
++		(c ($lopow (calculate-series f wsym)
++			   wsym)))
++	   (m+ (list (car exp)
++		     (m* (m^ wsym (m- c))
++			 (mrv-rewrite-logs f wsym logw)))
++	       (m* c logw))))
++	(t
++	 (cons (car exp)
++	       (mapcar (lambda (e)
++			 (mrv-rewrite-logs e wsym logw))
++		       (cdr exp))))))
++
+ ;; returns list of two elements: coeff and exponent of leading term of exp,
+ ;; after rewriting exp in term of its MRV set omega.
+ (defun mrv-leadterm (exp var omega)
+@@ -3181,7 +3201,8 @@ ignoring dummy variables and array indices."
+ 			     lo
+ 			     coef
+ 			     ((f . logw) (mrv-rewrite exp omega var wsym))
+-			     (series (calculate-series f wsym)))
++			     (series (calculate-series (mrv-rewrite-logs f wsym logw)
++						       wsym)))
+ 			    (setq series (maxima-substitute logw `((%log) ,wsym) series))
+ 			    (setq lo ($lopow series wsym))
+ 			    (when (or (not ($constantp lo))
+diff --git a/tests/rtest_limit.mac b/tests/rtest_limit.mac
+index b255d40..80ec53a 100644
+--- a/tests/rtest_limit.mac
++++ b/tests/rtest_limit.mac
+@@ -625,3 +625,8 @@ limit(log(-1/3125*((-1/2*sqrt(5) + 1/2)^n - (1/2*sqrt(5) +
+ limit(x^2*exp(-%i*x - x), x, inf);
+ 0;
+
++/* bug #2621 gamma limit error */
++
++limit(gamma(x+1/2)/(sqrt(x)*gamma(x)), x, inf);
++1;
++

build/pkgs/nose/SPKG.txt

@@ -0,0 +1,39 @@
+= nose =
+
+== Description ==
+
+nose extends the test loading and running features of unittest, making
+it easier to write, find and run tests.
+
+== License ==
+
+GNU LGPL
+
+== SPKG Maintainers ==
+
+John H. Palmieri <palmieri@math.washington.edu>
+Martin W.-Raum <martin@raum-brother.eu>
+
+== Upstream Contact ==
+
+Author: Jason Pellerin
+Home Page: http://readthedocs.org/docs/nose/
+  see also https://github.com/nose-devs/nose
+
+== Dependencies ==
+
+ * setuptools / distribute
+ * Python
+ * GNU patch (shipped with Sage)
+
+== Special Update/Build Instructions ==
+
+Remove any .pyc files by running the spkg-src script.
+
+== Changelog ==
+
+=== nose-1.1.2 (John H. Palmieri, June 14, 2012) ===
+ * #9921: initial version.
+
+=== nose-1.3.3 (Martin W.-Raum, Juli 21, 2014) ===
+ * #??: Updated

build/pkgs/nose/checksums.ini

@@ -0,0 +1,4 @@
+tarball=nose-VERSION.tar.bz2
+sha1=b3177ffaa32eb169e1d775d02c8a361d0d76808e
+md5=aab52d77de9845d58ad717016f48668f
+cksum=2069758669

build/pkgs/nose/package-version.txt

@@ -0,0 +1 @@
+1.3.3

build/pkgs/nose/spkg-check

@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+
+if [ -z "$SAGE_LOCAL" ]; then
+    echo "SAGE_LOCAL undefined - exiting..."
+    echo "Maybe run 'sage -sh'?"
+    exit 1
+fi
+
+cd src
+
+nosetests functional_tests
+if [ $? -ne 0 ]; then
+    echo "Error running functional_tests."
+    exit 1
+fi
+nosetests unit_tests
+if [ $? -ne 0 ]; then
+    echo "Error running unit_tests."
+    exit 1
+fi

build/pkgs/nose/spkg-install

@@ -0,0 +1,36 @@
+#!/usr/bin/env bash
+
+if [ -z "$SAGE_LOCAL" ]; then
+    echo "SAGE_LOCAL undefined - exiting..."
+    echo "Maybe run 'sage -sh'?"
+    exit 1
+fi
+
+# Helper functions
+success() {
+    if [ $? -ne 0 ]; then
+        echo "Error: '$1'"
+        exit 1
+    fi
+}
+
+CUR=`pwd`
+
+cd src
+
+# Build new version
+echo "Building nose..."
+python setup.py build
+success 'Error building nose'
+echo
+
+echo "Removing old version of nose..."
+rm -rf "$SAGE_LOCAL"/lib/python/site-packages/Nose-*
+success 'Error deleting previous version'
+echo
+
+# Install new version
+echo "Installing nose..."
+python setup.py install
+success 'Error installing nose'
+echo

build/pkgs/patch/SPKG.txt

@@ -37,30 +37,5 @@ None
 In the event patches ever need to be made to this package, the method of
 applying the patches should not rely on the 'patch' existing on the system.
 
-Versions 2.6 and 2.6.1 seem to be broken on OS X 10.4 (and supposedly also
-Solaris too). So do NOT update the package to those versions.
-
-Version 2.6.1 had some self-tests, so assuming the OS X & Solaris bugs get
-fixed at some point, a spkg-check file should be added.
-
-== Changelog ==
-
-=== patch-2.5.9.p3 (Jean-Pierre Flori, 5 January 2013) ===
- * #13844: Install manifest file on Cygwin for Windows 7.
-
-=== patch-2.5.9.p2 (Jeroen Demeyer, 16 August 2011) ===
- * #11232: Make all files in src/ owner-writable.
-
-=== patch-2.5.9.p1 (Dima Pasechnik, 21nd March 2011)  ===
- * #11232 We should not build patch on Cygwin, and rely on Cygwin-supplied
-   one.
-
-=== patch-2.5.9.p0 (David Kirkby, 22nd March 2011)  ===
- * #10979 Disable debugging information on AIX, by adding -g0
-  to CFLAGS otherwise there are link errors with GNU patch and
-  many other programs. See these threads.
-  http://www.ibm.com/developerworks/forums/thread.jspa?threadID=348558
-  http://gcc.gnu.org/bugzilla/show_bug.cgi?id=46072
-
-=== patch-2.5.9 (David Kirkby, Jeroen Demeyer, 16th november 2010)  ===
- * Initial version.
+Since bzip2 may (actually, does) depend on patch indirectly the patch
+tarball must be in gzip format.

build/pkgs/patch/checksums.ini

@@ -1,4 +1,4 @@
-tarball=patch-VERSION.tar.bz2
-sha1=b0858023f34c87028cbdbeab6c4a797258ea1be1
-md5=e0871f9e39c6625b2ec05cf79a959830
-cksum=1913387126
+tarball=patch-VERSION.tar.gz
+sha1=4ac0fc1a636365be9db252c9340aba7209c60bbe
+md5=95dd8d7e41dcbcecdd5cd88ef915378d
+cksum=3799073743

build/pkgs/patch/package-version.txt

@@ -1 +1 @@
-2.5.9.p3
+2.7.1

build/pkgs/patch/spkg-install

@@ -59,7 +59,7 @@ fi
 
 # Sanity check that we have the correct version of patch
 # in our PATH.
-if ! patch --version | grep >/dev/null 'patch 2\.5\.9'; then
+if ! patch --version | grep >/dev/null 'patch 2\.7\.1'; then
     echo >&2 "Cannot find the patch program we just installed"
     exit 1
 fi

build/pkgs/pip/SPKG.txt

@@ -0,0 +1,28 @@
+= pip =
+
+== Description ==
+
+This package installs pip, the tool for installing and managing Python packages,
+such as those found in the Python Package Index. It’s a replacement for
+easy_install.
+
+== License ==
+
+MIT
+
+== SPKG Maintainers ==
+
+* Vincent Delecroix
+
+== Upstream Contact ==
+
+Project Page: https://github.com/pypa/pip
+Install howto: https://pip.pypa.io/en/latest/installing.html
+Changelog: https://pip.pypa.io/en/latest/news.html
+Bug Tracking: https://github.com/pypa/pip/issues
+Mailing list: http://groups.google.com/group/python-virtualenv
+Docs: https://pip.pypa.io/
+
+== Dependencies ==
+
+* python

build/pkgs/pip/checksums.ini

@@ -0,0 +1,4 @@
+tarball=pip-VERSION.tar.gz
+sha1=e6cd9e6f2fd8d28c9976313632ef8aa8ac31249e
+md5=01026f87978932060cc86c1dc527903e
+cksum=3140729302

build/pkgs/pip/package-version.txt

@@ -0,0 +1 @@
+1.5.6