Merge branch 'develop' into t/22364/upgrade_to_pynac_0_7_5

VERSION.txt

@@ -1 +1 @@
-SageMath version 7.6.beta3, Release Date: 2017-02-08
+SageMath version 7.6.beta4, Release Date: 2017-02-14

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=c8b257c6c7ba8a0f8e7e144a49a0a02ff14e4e99
-md5=c85146aac9de29bbedbca378b53e62e7
-cksum=235842247
+sha1=f217d9ec85b7d0e8b6d6b8c9879b027e5e983709
+md5=5e76dd251dd6ad8fa2465b1d590173eb
+cksum=3094273803

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-205
+206

build/pkgs/giac/patches/autotools/ticket-22315-autotools.patch

@@ -0,0 +1,48 @@
+diff -ruN a/Makefile.am b/Makefile.am
+--- a/Makefile.am	2017-02-06 16:01:16.484367300 +0100
++++ b/Makefile.am	2017-02-06 16:06:28.013569300 +0100
+@@ -8,18 +8,18 @@
+ ## FIXME: installing autoconf-generated config.h is just PLAIN WRONG.
+
+ install-exec-hook:
+-	cp config.h $(DESTDIR)/$(includedir)/giac
+-	./mkinstalldirs $(DESTDIR)/$(prefix)/share/
+-	./mkinstalldirs $(DESTDIR)/$(prefix)/share/pixmaps
+-	cp xcas.xpm $(DESTDIR)/$(prefix)/share/pixmaps/xcas.xpm
+-	./mkinstalldirs $(DESTDIR)/$(prefix)/share/applications
+-	cp xcas.desktop $(DESTDIR)/$(prefix)/share/applications/xcas.desktop
+-	./mkinstalldirs $(DESTDIR)/$(prefix)/share/application-registry
+-	cp xcas.applications $(DESTDIR)/$(prefix)/share/application-registry/xcas.applications
+-	./mkinstalldirs $(DESTDIR)/$(prefix)/share/icons/
+-	./mkinstalldirs $(DESTDIR)/$(prefix)/share/icons/hicolor
+-	for SIZE in 256 128 64 32 16; do ./mkinstalldirs $(DESTDIR)/$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE} && ./mkinstalldirs $(DESTDIR)/$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/apps && cp icons/xcas_$${SIZE}.png $(DESTDIR)/$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/apps/xcas.png; done
+-	for SIZE in 256 128 64 32 16; do ./mkinstalldirs $(DESTDIR)/$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/mimetypes && cp icons/x-xcas_$${SIZE}.png $(DESTDIR)/$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/mimetypes/application-x-xcas.png;  done
++	cp config.h $(DESTDIR)$(includedir)/giac
++	./mkinstalldirs $(DESTDIR)$(prefix)/share/
++	./mkinstalldirs $(DESTDIR)$(prefix)/share/pixmaps
++	cp xcas.xpm $(DESTDIR)$(prefix)/share/pixmaps/xcas.xpm
++	./mkinstalldirs $(DESTDIR)$(prefix)/share/applications
++	cp xcas.desktop $(DESTDIR)$(prefix)/share/applications/xcas.desktop
++	./mkinstalldirs $(DESTDIR)$(prefix)/share/application-registry
++	cp xcas.applications $(DESTDIR)$(prefix)/share/application-registry/xcas.applications
++	./mkinstalldirs $(DESTDIR)$(prefix)/share/icons/
++	./mkinstalldirs $(DESTDIR)$(prefix)/share/icons/hicolor
++	for SIZE in 256 128 64 32 16; do ./mkinstalldirs $(DESTDIR)$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE} && ./mkinstalldirs $(DESTDIR)$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/apps && cp icons/xcas_$${SIZE}.png $(DESTDIR)$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/apps/xcas.png; done
++	for SIZE in 256 128 64 32 16; do ./mkinstalldirs $(DESTDIR)$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/mimetypes && cp icons/x-xcas_$${SIZE}.png $(DESTDIR)$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/mimetypes/application-x-xcas.png;  done
+
+ ACLOCAL_AMFLAGS = -I m4
+
+diff -ruN a/src/Makefile.am b/src/Makefile.am
+--- a/src/Makefile.am	2017-02-06 16:01:51.663379800 +0100
++++ b/src/Makefile.am	2017-02-06 16:01:25.730657700 +0100
+@@ -85,8 +85,8 @@
+ bin_SCRIPTS = pgiac
+
+ install-exec-hook:
+-	rm -f $(DESTDIR)$(bindir)/cas_help
+-	mv $(DESTDIR)/$(bindir)/aide$(EXEEXT) $(DESTDIR)$(bindir)/cas_help
++	rm -f $(DESTDIR)$(bindir)/cas_help$(EXEEXT)
++	mv $(DESTDIR)$(bindir)/aide$(EXEEXT) $(DESTDIR)$(bindir)/cas_help
+ 	ln -sf cas_help $(DESTDIR)$(bindir)/en_cas_help
+ 	ln -sf cas_help $(DESTDIR)$(bindir)/es_cas_help
+ 	ln -sf cas_help $(DESTDIR)$(bindir)/fr_cas_help

build/pkgs/giac/patches/ticket-22315.patch

@@ -0,0 +1,94 @@
+diff -ruN a/Makefile.am b/Makefile.am
+--- a/Makefile.am	2017-02-06 16:01:16.484367300 +0100
++++ b/Makefile.am	2017-02-06 16:06:28.013569300 +0100
+@@ -8,18 +8,18 @@
+ ## FIXME: installing autoconf-generated config.h is just PLAIN WRONG.
+
+ install-exec-hook:
+-	cp config.h $(DESTDIR)/$(includedir)/giac
+-	./mkinstalldirs $(DESTDIR)/$(prefix)/share/
+-	./mkinstalldirs $(DESTDIR)/$(prefix)/share/pixmaps
+-	cp xcas.xpm $(DESTDIR)/$(prefix)/share/pixmaps/xcas.xpm
+-	./mkinstalldirs $(DESTDIR)/$(prefix)/share/applications
+-	cp xcas.desktop $(DESTDIR)/$(prefix)/share/applications/xcas.desktop
+-	./mkinstalldirs $(DESTDIR)/$(prefix)/share/application-registry
+-	cp xcas.applications $(DESTDIR)/$(prefix)/share/application-registry/xcas.applications
+-	./mkinstalldirs $(DESTDIR)/$(prefix)/share/icons/
+-	./mkinstalldirs $(DESTDIR)/$(prefix)/share/icons/hicolor
+-	for SIZE in 256 128 64 32 16; do ./mkinstalldirs $(DESTDIR)/$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE} && ./mkinstalldirs $(DESTDIR)/$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/apps && cp icons/xcas_$${SIZE}.png $(DESTDIR)/$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/apps/xcas.png; done
+-	for SIZE in 256 128 64 32 16; do ./mkinstalldirs $(DESTDIR)/$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/mimetypes && cp icons/x-xcas_$${SIZE}.png $(DESTDIR)/$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/mimetypes/application-x-xcas.png;  done
++	cp config.h $(DESTDIR)$(includedir)/giac
++	./mkinstalldirs $(DESTDIR)$(prefix)/share/
++	./mkinstalldirs $(DESTDIR)$(prefix)/share/pixmaps
++	cp xcas.xpm $(DESTDIR)$(prefix)/share/pixmaps/xcas.xpm
++	./mkinstalldirs $(DESTDIR)$(prefix)/share/applications
++	cp xcas.desktop $(DESTDIR)$(prefix)/share/applications/xcas.desktop
++	./mkinstalldirs $(DESTDIR)$(prefix)/share/application-registry
++	cp xcas.applications $(DESTDIR)$(prefix)/share/application-registry/xcas.applications
++	./mkinstalldirs $(DESTDIR)$(prefix)/share/icons/
++	./mkinstalldirs $(DESTDIR)$(prefix)/share/icons/hicolor
++	for SIZE in 256 128 64 32 16; do ./mkinstalldirs $(DESTDIR)$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE} && ./mkinstalldirs $(DESTDIR)$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/apps && cp icons/xcas_$${SIZE}.png $(DESTDIR)$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/apps/xcas.png; done
++	for SIZE in 256 128 64 32 16; do ./mkinstalldirs $(DESTDIR)$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/mimetypes && cp icons/x-xcas_$${SIZE}.png $(DESTDIR)$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/mimetypes/application-x-xcas.png;  done
+
+ ACLOCAL_AMFLAGS = -I m4
+
+diff -ruN a/Makefile.in b/Makefile.in
+--- a/Makefile.in	2017-02-06 16:01:16.279348700 +0100
++++ b/Makefile.in	2017-02-06 16:07:13.838103600 +0100
+@@ -847,18 +847,18 @@
+ $(PACKAGE)-$(VERSION).tar.gz: dist
+
+ install-exec-hook:
+-	cp config.h $(DESTDIR)/$(includedir)/giac
+-	./mkinstalldirs $(DESTDIR)/$(prefix)/share/
+-	./mkinstalldirs $(DESTDIR)/$(prefix)/share/pixmaps
+-	cp xcas.xpm $(DESTDIR)/$(prefix)/share/pixmaps/xcas.xpm
+-	./mkinstalldirs $(DESTDIR)/$(prefix)/share/applications
+-	cp xcas.desktop $(DESTDIR)/$(prefix)/share/applications/xcas.desktop
+-	./mkinstalldirs $(DESTDIR)/$(prefix)/share/application-registry
+-	cp xcas.applications $(DESTDIR)/$(prefix)/share/application-registry/xcas.applications
+-	./mkinstalldirs $(DESTDIR)/$(prefix)/share/icons/
+-	./mkinstalldirs $(DESTDIR)/$(prefix)/share/icons/hicolor
+-	for SIZE in 256 128 64 32 16; do ./mkinstalldirs $(DESTDIR)/$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE} && ./mkinstalldirs $(DESTDIR)/$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/apps && cp icons/xcas_$${SIZE}.png $(DESTDIR)/$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/apps/xcas.png; done
+-	for SIZE in 256 128 64 32 16; do ./mkinstalldirs $(DESTDIR)/$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/mimetypes && cp icons/x-xcas_$${SIZE}.png $(DESTDIR)/$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/mimetypes/application-x-xcas.png;  done
++	cp config.h $(DESTDIR)$(includedir)/giac
++	./mkinstalldirs $(DESTDIR)$(prefix)/share/
++	./mkinstalldirs $(DESTDIR)$(prefix)/share/pixmaps
++	cp xcas.xpm $(DESTDIR)$(prefix)/share/pixmaps/xcas.xpm
++	./mkinstalldirs $(DESTDIR)$(prefix)/share/applications
++	cp xcas.desktop $(DESTDIR)$(prefix)/share/applications/xcas.desktop
++	./mkinstalldirs $(DESTDIR)$(prefix)/share/application-registry
++	cp xcas.applications $(DESTDIR)$(prefix)/share/application-registry/xcas.applications
++	./mkinstalldirs $(DESTDIR)$(prefix)/share/icons/
++	./mkinstalldirs $(DESTDIR)$(prefix)/share/icons/hicolor
++	for SIZE in 256 128 64 32 16; do ./mkinstalldirs $(DESTDIR)$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE} && ./mkinstalldirs $(DESTDIR)$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/apps && cp icons/xcas_$${SIZE}.png $(DESTDIR)$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/apps/xcas.png; done
++	for SIZE in 256 128 64 32 16; do ./mkinstalldirs $(DESTDIR)$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/mimetypes && cp icons/x-xcas_$${SIZE}.png $(DESTDIR)$(prefix)/share/icons/hicolor/$${SIZE}x$${SIZE}/mimetypes/application-x-xcas.png;  done
+
+ # Tell versions [3.59,3.63) of GNU make to not export all variables.
+ # Otherwise a system limit (for SysV at least) may be exceeded.
+diff -ruN a/src/Makefile.am b/src/Makefile.am
+--- a/src/Makefile.am	2017-02-06 16:01:51.663379800 +0100
++++ b/src/Makefile.am	2017-02-06 16:01:25.730657700 +0100
+@@ -85,8 +85,8 @@
+ bin_SCRIPTS = pgiac
+
+ install-exec-hook:
+-	rm -f $(DESTDIR)$(bindir)/cas_help
+-	mv $(DESTDIR)/$(bindir)/aide$(EXEEXT) $(DESTDIR)$(bindir)/cas_help
++	rm -f $(DESTDIR)$(bindir)/cas_help$(EXEEXT)
++	mv $(DESTDIR)$(bindir)/aide$(EXEEXT) $(DESTDIR)$(bindir)/cas_help
+ 	ln -sf cas_help $(DESTDIR)$(bindir)/en_cas_help
+ 	ln -sf cas_help $(DESTDIR)$(bindir)/es_cas_help
+ 	ln -sf cas_help $(DESTDIR)$(bindir)/fr_cas_help
+diff -ruN a/src/Makefile.in b/src/Makefile.in
+--- a/src/Makefile.in	2017-02-06 16:01:52.110694800 +0100
++++ b/src/Makefile.in	2017-02-06 16:01:25.669644700 +0100
+@@ -1030,7 +1030,7 @@
+
+ install-exec-hook:
+ 	rm -f $(DESTDIR)$(bindir)/cas_help
+-	mv $(DESTDIR)/$(bindir)/aide$(EXEEXT) $(DESTDIR)$(bindir)/cas_help
++	mv $(DESTDIR)$(bindir)/aide$(EXEEXT) $(DESTDIR)$(bindir)/cas_help
+ 	ln -sf cas_help $(DESTDIR)$(bindir)/en_cas_help
+ 	ln -sf cas_help $(DESTDIR)$(bindir)/es_cas_help
+ 	ln -sf cas_help $(DESTDIR)$(bindir)/fr_cas_help

build/pkgs/scipy/spkg-install

@@ -26,6 +26,12 @@ fi
 # Make sure that the fortran objects are compiled with -fPIC
 export FFLAGS="$FFLAGS -fPIC"
 export FCFLAGS="$FCFLAGS -fPIC"
+if [ "$UNAME" = "CYGWIN" -a "$SAGE_DEBUG" = "yes" ]; then
+    # Needed for just one or two modules when compiling in debug mode
+    # Otherwise the debug symbols create too many sections in the binary
+    export CPPFLAGS="$CPPFLAGS -Wa,-mbig-obj"
+fi
+
 
 # This avoids problems on some systems -- until we officially
 # support umfpack (which we will likely do, since cvxopt I think includes it):

src/bin/sage-banner

@@ -1,5 +1,5 @@
 ┌────────────────────────────────────────────────────────────────────┐
-│ SageMath version 7.6.beta3, Release Date: 2017-02-08               │
+│ SageMath version 7.6.beta4, Release Date: 2017-02-14               │
 │ 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='7.6.beta3'
-SAGE_RELEASE_DATE='2017-02-08'
+SAGE_VERSION='7.6.beta4'
+SAGE_RELEASE_DATE='2017-02-14'

src/doc/de/tutorial/programming.rst

@@ -676,18 +676,6 @@ gleichen Typ konvertieren, falls dies möglich ist:
     True
     True
 
-Fast immer können zwei beliebige Objekte verglichen werden. Es gibt
-keine Voraussetzung die besagt, dass die Objekte mit einer totalen Ordnung
-versehen sein müssen.
-
-
-::
-
-    sage: 2 < CC(3.1,1)
-    True
-    sage: 5 < VectorSpace(QQ,3)   # output can be somewhat random
-    True
-
 Nutzen Sie bool für symbolische Ungleichungen:
 
 ::

src/doc/en/constructions/linear_codes.rst

@@ -46,9 +46,9 @@ the four Golay codes
 
 ::
 
-    sage: C = codes.ExtendedTernaryGolayCode()
+    sage: C = codes.GolayCode(GF(3))
     sage: C
-    [12, 6] linear code over GF(3)
+    [12, 6, 6] Extended Golay code over Finite Field of size 3
     sage: C.minimum_distance()
     6
     sage: C.generator_matrix()

src/doc/en/developer/coding_basics.rst

@@ -421,20 +421,21 @@ information. You can use the existing functions of Sage as templates.
 
   For the purposes of removal, A "TESTS" block is a block starting
   with "TEST:" or "TESTS:" (or the same with two colons), on a line on
-  its own, and ending with an unindented line (that is, the same level
-  of indentation as "TESTS") matching one of the following:
+  its own, and ending either with a line indented less than "TESTS",
+  or with a line with the same level of indentation -- not more --
+  matching one of the following:
 
-  - a line which starts with whitespace and then a Sphinx directive
-    of the form ".. FOO:", optionally followed by other text.
+  - a Sphinx directive of the form ".. foo:", optionally followed by
+    other text.
 
-  - a line which starts with whitespace and then text of the form
-    "UPPERCASE:", optionally followed by other text.
+  - text of the form "UPPERCASE:", optionally followed by other
+    text.
 
   - lines which look like a reST header: one line containing
     anything, followed by a line consisting only of whitespace,
-    followed by a string of hyphens, equal signs, or other
-    characters which are valid markers for reST headers:
-    ``- = ` : ' " ~ _ ^ * + # < >``.
+    followed by a string of hyphens, equal signs, or other 
+    characters which are valid markers for reST 
+    headers: ``- = ` : ' " ~ _ ^ * + # < >``.
 
 Sage documentation style
 ^^^^^^^^^^^^^^^^^^^^^^^^

src/doc/en/installation/binary.rst

@@ -30,41 +30,46 @@ in a directory which you have permission to read and write::
 
     tar zxvf sage-x.y.z-x86_64-Linux.tgz
 
-You can move the resulting directory ``sage-x.y.z-x86_64-Linux``
+You can move the resulting directory ``SageMath``
 anywhere and still run ``./sage`` from it, as long as the full path name
-has **no spaces** in it.  You can also copy the file ``sage`` from
-that directory and put it anywhere, e.g., ``/usr/local/bin/``, but
+has **no spaces** in it. The first time you run Sage, you will see a
+message like
+
+::
+
+   Rewriting paths for your new installation directory
+   ===================================================
+
+   This might take a few minutes but only has to be done once.
+
+   patching ...  (long list of files)
+
+At this point, you can no longer move your Sage installation and
+expect Sage to function.
+
+You can also copy the file ``sage`` from
+the ``SageMath`` directory and put it anywhere, e.g., ``/usr/local/bin/``, but
 then you have to edit the ``#SAGE_ROOT=/path/to/sage-version`` line
 at the top of the copied file ``/usr/local/bin/sage``
 (you should not edit the original ``sage`` executable).
 The variable ``SAGE_ROOT`` should point to the directory
-``sage-x.y.z-x86_64-Linux`` of the extracted Sage tarball.
+``SageMath`` of the extracted Sage tarball.
 As long as ``/usr/local/bin`` is in your
 ``$PATH``, you can then type ``sage`` from the command line to run
 Sage.  Another approach is to create a symbolic link, say
-``/usr/local/bin/sage``, pointing to ``sage-x.y.z-x86_64-Linux/sage`` ::
+``/usr/local/bin/sage``, pointing to ``SageMath/sage`` ::
 
-    ln -s /path/to/sage-x.y.z-x86_64-Linux/sage /usr/local/bin/sage
+    ln -s /path/to/SageMath/sage /usr/local/bin/sage
 
 With this approach, there is no need to edit ``/usr/local/bin/sage``,
 the ``SAGE_ROOT`` path will be discovered automatically thanks to the
 symbolic link.
 When you want to install a new version of Sage, just delete the old
 link and create a new one.
 
-Any time you move the Sage directory, you may see a message like
-
-::
-
-    The Sage installation tree may have moved
-    (from /foo to /bar).
-    Changing various hardcoded paths...
-    (Please wait at most a few minutes.)
-    DO NOT INTERRUPT THIS.
-
-We currently distribute ``.dmg`` files for OS X 10.4.x and 10.6.x. But
+We currently distribute ``.dmg`` files for recent versions of OS X, but
 we would like to make Sage more of a native application. Work for that
-is ongoing, but help is always welcome.
+is ongoing, and help is always welcome.
 
 
 Microsoft Windows

src/doc/en/installation/source.rst

@@ -487,10 +487,9 @@ Running Sage from a directory with spaces in its name will also fail.
    fast filesystem, avoiding
    `NFS <http://en.wikipedia.org/wiki/Network_File_System>`_ and the like.
    On personal computers, any subdirectory of your :envvar:`HOME` directory
-   should do.
-   The directory where you built Sage is **NOT** hardcoded.
-   You should be able to safely move or rename that directory.
-   (It's a bug if this is not the case.)
+   should do. Note that once you have built Sage (by running ``make``,
+   as described below), you will not be able to move or rename its
+   directory without likely breaking Sage.
 
 #. Extract the tarfile::
 
@@ -1039,7 +1038,7 @@ Here are some of the more commonly used variables affecting the build process:
   you run ``make``, ``make doc``, or ``make doc-pdf``.
   For example, you can add ``--no-plot`` to this variable to avoid building
   the graphics coming from the ``.. PLOT`` directive within the documentation,
-  or you can add ``--no-tests`` to omit all "TESTS" blocks in the
+  or you can add ``--include-tests-blocks`` to include all "TESTS" blocks in the
   reference manual. Run ``sage --docbuild help`` to see the full list
   of options.
 
@@ -1452,4 +1451,4 @@ would be appropriate if you have a Core i3/5/7 processor with AVX support.
 
 
 
-**This page was last updated in January 2017 (for Sage 7.6).**
+**This page was last updated in February 2017 (Sage 7.6).**