Merge branch 'develop' into DGA

VERSION.txt

@@ -1 +1 @@
-Sage version 6.3.rc1, released 2014-08-06
+Sage version 6.4.beta1, released 2014-08-20

build/deps

@@ -164,12 +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
 ###############################################################################
@@ -475,6 +478,7 @@ $(INST)/sage: \
 		 $(INST)/$(IML) \
 		 $(INST)/$(JINJA2) \
 		 $(INST)/$(LCALC) \
+		 $(INST)/$(LRCALC) \
 		 $(INST)/$(LIBGAP) \
 		 $(INST)/$(LIBPNG) \
 		 $(INST)/$(LINBOX) \
@@ -525,9 +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/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=e4216daaf501fd22541cd68c58236bfb6d878d7c
-md5=823e501492778f7fa0615b7672accbb3
-cksum=418482624
+sha1=80f834dff7baffd5306b4269dffe547df264a72a
+md5=90e5cd2fef68232a20ac565f8efea235
+cksum=3340757205

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-42
+45

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/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

build/pkgs/pip/spkg-install

@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+
+cd src
+
+python setup.py install

build/pkgs/pyparsing/spkg-install

@@ -10,7 +10,8 @@ cd src
 
 for patch in ../patches/*.patch; do
     [ -f "$patch" ] || continue
-    patch -p1 <"$patch"
+    # Apply patch as binary since source has incorrect line endings
+    patch -p1 --binary <"$patch"
     if [ $? -ne 0 ]; then
         echo >&2 "Error applying '$patch'"
         exit 1

build/pkgs/sage_mode/checksums.ini

@@ -1,4 +1,4 @@
 tarball=sage_mode-VERSION.tar.bz2
-sha1=83abb4de8724543bf67dba05c37d8e8400d811e6
-md5=c1c9fad76db2314b7576765f10ae254c
-cksum=409763902
+sha1=116148dad9ba4e421b2cefe8fdd8a23a5ef75780
+md5=9c35650fa58caab7e5c42710deb15dcc
+cksum=1189123393

build/pkgs/sage_mode/package-version.txt

@@ -1 +1 @@
-0.11
+0.12

src/bin/sage

@@ -163,6 +163,7 @@ usage_advanced() {
     echo "                           --failed - only test files that failed last test"
     echo "                           --sagenb - test all sagenb files"
     echo "                           --help - show all testing options"
+    echo "                           --warn-long [timeout] - warning if doctest is slow"
     echo "  -tp <N> [...]       -- like -t above, but tests in parallel using N threads"
     echo "                         with 0 interpreted as a sensible default"
     echo "  -testall [options]  -- test all source files, docs, and examples.  options"

src/bin/sage-banner

@@ -1,5 +1,5 @@
 ┌────────────────────────────────────────────────────────────────────┐
-│ Sage Version 6.3.rc1, Release Date: 2014-08-06                     │
+│ Sage Version 6.4.beta1, Release Date: 2014-08-20                   │
 │ Type "notebook()" for the browser-based notebook interface.        │
 │ Type "help()" for help.                                            │
 └────────────────────────────────────────────────────────────────────┘

src/bin/sage-version.sh

@@ -1,4 +1,4 @@
 # Sage version information for shell scripts
 # This file is auto-generated by the sage-update-version script, do not edit!
-SAGE_VERSION='6.3.rc1'
-SAGE_RELEASE_DATE='2014-08-06'
+SAGE_VERSION='6.4.beta1'
+SAGE_RELEASE_DATE='2014-08-20'

src/doc/en/bordeaux_2008/nf_galois_groups.rst

@@ -309,7 +309,7 @@ ideal classes containing :math:`(5,\sqrt{-30})` and
     Class group of order 4 with structure C2 x C2 of Number Field
     in a with defining polynomial x^2 + 30
     sage: category(C)
-    Category of groups
+    Category of finite commutative groups
     sage: C.gens()
     (Fractional ideal class (5, a), Fractional ideal class (3, a))
 

src/doc/en/developer/doctesting.rst

@@ -669,13 +669,22 @@ Optional Arguments
 Run Long Tests
 --------------
 
-Use the ``--long`` flag to run doctests that have been marked with
-the comment ``# long time``.
+Ideally, doctests should not take any noticeable amount of time. If
+you really need longer-running doctests (anything beyond about one
+second) then you should mark them as::
 
-No doctest should take longer than a second or so, and longer doctests
-(taking up to 30-60 seconds) should be marked as ``# long time``.
-These tests are normally skipped in order to reduce the time spent
-running tests::
+    sage: my_long_test()  # long time
+
+Even then, long doctests should ideally complete in 5 seconds or
+less. We know that you (the author) want to show off the capabilities
+of your code, but this is not the place to do so. Long-running tests
+will sooner or later hurt our ability to run the testsuite. Really,
+doctests should be as fast as possible while providing coverage for
+the code.
+
+Use the ``--long`` flag to run doctests that have been marked with the
+comment ``# long time``. These tests are normally skipped in order to
+reduce the time spent running tests::
 
     [roed@sage sage-6.0]$ sage -t src/sage/rings/tests.py
     Running doctests with ID 2012-06-21-16-00-13-40835825.
@@ -704,8 +713,9 @@ In order to run the long tests as well, do the following::
         cumulative wall time: 34.7 seconds
 
 To find tests that take longer than the allowed time use the
-``--warn-long`` flag.  Without any options it will cause tests to fail
-if they take longer than 1.0 second::
+``--warn-long`` flag.  Without any options it will cause tests to
+print a warning if they take longer than 1.0 second. Note that this is
+a warning, not an error::
 
     [roed@sage sage-6.0]$ sage -t --warn-long src/sage/rings/factorint.pyx
     Running doctests with ID 2012-07-14-03-27-03-2c952ac1.
@@ -732,13 +742,9 @@ if they take longer than 1.0 second::
         fa(2^4+1)
     Test ran for 2.25 s
     **********************************************************************
-    2 items had failures:
-       1 of   6 in sage.rings.factorint.base_exponent
-       3 of   8 in sage.rings.factorint.factor_aurifeuillian
-        [25 tests, 4 failures, 10.9 s]
-    ------------------------------------------------------------------------
-    sage -t --warn-long src/sage/rings/factorint.pyx # 4 doctests failed
-    ------------------------------------------------------------------------
+    ----------------------------------------------------------------------
+    All tests passed!
+    ----------------------------------------------------------------------
     Total time for all tests: 16.1 seconds
         cpu time: 9.7 seconds
         cumulative wall time: 10.9 seconds
@@ -760,17 +766,17 @@ You can also pass in an explicit amount of time::
         sage.rings.tests.test_random_arith(trials=1000)   # long time (5 seconds?)
     Test ran for 12.42 s
     **********************************************************************
-    2 items had failures:
-       1 of   4 in sage.rings.tests.test_random_arith
-       1 of   4 in sage.rings.tests.test_random_elements
-        [20 tests, 2 failures, 26.3 s]
-    ------------------------------------------------------------------------
-    sage -t --long --warn-long 2.0 tests.py # 2 doctests failed
-    ------------------------------------------------------------------------
+    ----------------------------------------------------------------------
+    All tests passed!
+    ----------------------------------------------------------------------
     Total time for all tests: 27.6 seconds
         cpu time: 24.8 seconds
         cumulative wall time: 26.3 seconds
 
+Finally, you can disable any warnings about long tests with
+``--warn-long 0``.
+
+
 Run Optional Tests
 ------------------
 

src/doc/en/developer/sage_manuals.rst

@@ -185,6 +185,18 @@ In the same vein, you can also add external links of various kinds:
 - MathSciNet: ``:mathscinet:`MR0100971``` adds the link
   :mathscinet:`MR0100971`.
 
+General http-links can be added in a couple of ways. The first method
+is to simply copy and paste the link. ``http://www.sagemath.org`` creates 
+the link http://www.sagemath.org . And if you want to give the link a title 
+you can do this: ```title <http://www.sagemath.org>`_``, which creates the 
+link `title <http://www.sagemath.org>`_.
+
+The latter method in addition to being able to give the link an optional 
+title (just remove the word "title"), lets you put a comma or a period 
+directly after the link, instead of having to put a space between the 
+end of the link and any punctuation that is used after it. The sentence
+above describing the first method was an example of this.
+
 .. note::
 
     Finally, you can check that all links are properly resolved by
@@ -281,8 +293,7 @@ Output Formats
 
 The Sage documentation build system currently supports all of the
 output formats that Sphinx does. For more detailed information, see
-the documentation on builders at http://sphinx.pocoo.org/builders.html
-.
+the documentation on builders at `<http://sphinx.pocoo.org/builders.html>`_.
 
 
 Syntax Highlighting Cython Code

src/doc/en/installation/source.rst

@@ -860,6 +860,11 @@ Here are some of the more commonly used variables affecting the build process:
     These will be notably slower but, for example, make it much easier to
     pinpoint memory allocation problems.
 
+- :envvar:`SAGE_PROFILE` - controls profiling support. If this is set
+  to ``yes``, profiling support is enabled where possible. Note that
+  Python-level profiling is always avaliable; This option enables
+  profiling in Cython modules.
+
 - :envvar:`SAGE_SPKG_LIST_FILES` - if set to ``yes``, then enable verbose
   extraction of tar files, i.e. Sage's spkg files.
   Since some spkgs contain such a huge number of files that the log files