Merge branch 'develop' into public/group_theory/improve_iterator_perm…

…_gps-25477

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.4.beta6, Release Date: 2018-09-22
+SageMath version 8.4.beta7, Release Date: 2018-09-30

build/bin/sage-spkg

@@ -881,32 +881,17 @@ if [ -d "$SAGE_DESTDIR" ]; then
     fi
 
     # Generate installed file manifest
-    FILE_LIST=""
-    FIRST=1
-    old_IFS="$IFS"; IFS=$'\n'
-    for filename in $(find "$PREFIX" -type f -o -type l | sort); do
-        filename="${filename#$PREFIX/}"
-        if [ $FIRST -eq 1 ]; then
-            FILE_LIST="\"$filename\""
-            FIRST=0
-        else
-            FILE_LIST="${FILE_LIST},"$'\n        '"\"${filename}\""
-        fi
-        # Copy file from the temp install path into $SAGE_LOCAL
-        if [ ! -d "$SAGE_LOCAL/$(dirname "$filename")" ]; then
-            $SAGE_SUDO mkdir -p "$SAGE_LOCAL/$(dirname "$filename")"
-        fi
-        $SAGE_SUDO mv "$PREFIX/$filename" "${SAGE_LOCAL%/}/$filename"
-        if [ $? -ne 0 ]; then
-            error_msg "Error moving files for $PKG_NAME."
-            exit 1
-        fi
-    done
-    IFS="$old_IFS"
+    FILE_LIST="$(cd "$PREFIX" && find . -type f -o -type l | sed 's|^\./||' | sort)"
 
+    # Copy files into $SAGE_LOCAL
+    $SAGE_SUDO cp -Rp "$PREFIX/." "$SAGE_LOCAL"
+    rm -rf "$SAGE_DESTDIR"
+    if [ $? -ne 0 ]; then
+        error_msg "Error copying files for $PKG_NAME."
+        exit 1
+    fi
     # Remove the $SAGE_DESTDIR entirely once all files have been moved to their
     # final location.
-    rm -rf "$SAGE_DESTDIR"
 fi
 
 
@@ -983,6 +968,7 @@ if [ "$SAGE_CHECK" = "yes" ]; then
     fi
 fi
 
+FILE_LIST="$(echo "$FILE_LIST" | sed 's/^\(.\+\)$/"\1"/; 2,$s/^/        /; $!s/$/,/')"
 
 # Mark that the new package has been installed (and tested, if
 # applicable).

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=00455e50894d088544c9b7e61e20c605696eea0c
-md5=f42fb78fd137874c567f182196dc45c2
-cksum=3977387603
+sha1=585003ab668b8afea5ae14b7fd3f71da3f8f043a
+md5=9058f4a34da70a5f5186b36c076d9a13
+cksum=3490824772

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-283
+284

build/pkgs/ecl/spkg-install

@@ -8,6 +8,13 @@ else
     CXXFLAGS="-g -O2 $CXXFLAGS"
 fi
 
+if [ "$UNAME" = "CYGWIN" ]; then
+    # Some of ECL's sources rely on GNU-isms that are allowed by default on
+    # most glibcs, but not in newlib; https://trac.sagemath.org/ticket/25057
+    CFLAGS="$CFLAGS -D_GNU_SOURCE"
+    CXXFLAGS="$CXXFLAGS -D_GNU_SOURCE"
+fi
+
 export CFLAGS
 export CXXFLAGS
 export LDFLAGS

build/pkgs/fflas_ffpack/spkg-install

@@ -2,20 +2,6 @@ cd src
 
 if [ "$LINBOX_BLAS" != "" ]; then
     echo "Using environment variable LINBOX_BLAS=$LINBOX_BLAS"
-elif [ "$UNAME" = "CYGWIN" ]; then
-    # TODO: we should install a suitable blas.pc on Cygwin
-    echo "Using system-wide Cygwin LAPACK BLAS."
-    if [ ! -f "/usr/lib/libblas.a" ]; then
-        echo >&2 "*************************************************"
-        echo >&2 "*"
-        echo >&2 "* Error: On Cygwin you must install the standard LAPACK Cygwin package"
-        echo >&2 "* via the Cygwin setup.exe program in the 'Math' category."
-        echo >&2 "*"
-        echo >&2 "*************************************************"
-        exit 1
-    fi
-    LINBOX_BLAS="-lblas"
-    LINBOX_BLAS_CFLAGS=""
 else
     LINBOX_BLAS="$(pkg-config --libs cblas)"
     BLAS_CFLAGS="$(pkg-config --cflags cblas)"

build/pkgs/nose/SPKG.txt

@@ -23,12 +23,4 @@ Home Page: http://readthedocs.org/docs/nose/
 
 == 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
+None.

build/pkgs/nose/checksums.ini

@@ -1,4 +1,4 @@
-tarball=nose-VERSION.tar.bz2
-sha1=b3177ffaa32eb169e1d775d02c8a361d0d76808e
-md5=aab52d77de9845d58ad717016f48668f
-cksum=2069758669
+tarball=nose-VERSION.tar.gz
+sha1=97f2a04c9d43b29ddf4794a1a1d1ba803f1074c6
+md5=4d3ad0ff07b61373d2cefc89c5d0b20b
+cksum=3318391794

build/pkgs/nose/package-version.txt

@@ -1 +1 @@
-1.3.3.p0
+1.3.7

build/pkgs/pycosat/SPKG.txt

@@ -0,0 +1,28 @@
+= pycosat =
+
+== Description ==
+
+PicoSAT is a popular SAT solver written by Armin Biere in pure C. This package
+provides efficient Python bindings to picosat on the C level, i.e. when
+importing pycosat, the picosat solver becomes part of the Python process itself.
+For ease of deployment, the picosat source (namely picosat.c and picosat.h) is
+included in this project. These files have been extracted from the picosat
+source.
+
+== License ==
+
+MIT
+
+== Upstream Contact ==
+
+PicoSAT: http://fmv.jku.at/picosat/
+pycosat: https://github.com/ContinuumIO/pycosat
+
+== Dependencies ==
+
+None.
+
+== Special Update/Build Instructions ==
+
+None.
+

build/pkgs/pycosat/checksums.ini

@@ -0,0 +1,4 @@
+tarball=pycosat-VERSION.tar.gz
+sha1=1c2243fcc52491db8aa11558d4df626f28311757
+md5=08e378db1c15dc1668bc62897bd325a5
+cksum=2006887185

build/pkgs/pycosat/dependencies

@@ -0,0 +1,5 @@
+$(PYTHON) | pip
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.

build/pkgs/pycosat/package-version.txt

@@ -0,0 +1 @@
+0.6.3

build/pkgs/pycosat/spkg-check

@@ -0,0 +1,15 @@
+if [ "$SAGE_LOCAL" = "" ]; then
+   echo >&2 "Error: SAGE_LOCAL undefined - exiting..."
+   echo >&2 "Maybe run 'sage -sh'?"
+   exit 1
+fi
+
+echo "Testing pycosat..."
+
+cd src
+python test_pycosat.py
+
+if [ $? -ne 0 ]; then
+    echo >&2 "Error running self tests."
+    exit 1
+fi

build/pkgs/pycosat/spkg-install

@@ -0,0 +1,15 @@
+if [ "$SAGE_LOCAL" = "" ]; then
+   echo "SAGE_LOCAL undefined ... exiting";
+   echo "Maybe run 'sage -sh'?"
+   exit 1
+fi
+
+cd src
+
+sdh_pip_install .
+
+if [ $? -ne 0 ]; then
+    echo "Error installing pycosat ... exiting"
+    exit 1
+fi
+

build/pkgs/pycosat/type

@@ -0,0 +1 @@
+optional

src/bin/sage-version.sh

@@ -1,5 +1,5 @@
 # Sage version information for shell scripts
 # This file is auto-generated by the sage-update-version script, do not edit!
-SAGE_VERSION='8.4.beta6'
-SAGE_RELEASE_DATE='2018-09-22'
-SAGE_VERSION_BANNER='SageMath version 8.4.beta6, Release Date: 2018-09-22'
+SAGE_VERSION='8.4.beta7'
+SAGE_RELEASE_DATE='2018-09-30'
+SAGE_VERSION_BANNER='SageMath version 8.4.beta7, Release Date: 2018-09-30'

src/doc/en/developer/coding_basics.rst

@@ -870,7 +870,7 @@ written.
       sage: print "not like that"
       Traceback (most recent call last):
       ...
-      SyntaxError: invalid syntax
+      SyntaxError: ...
       sage: print("but like this")
       but like this
 
@@ -1081,9 +1081,9 @@ framework. Here is a comprehensive list:
   64-bit machines. Note that this particular flag is to be applied on the
   **output** lines, not the input lines::
 
-      sage: hash(-920390823904823094890238490238484)
-      -873977844            # 32-bit
-      6874330978542788722   # 64-bit
+      sage: hash(2^31 + 2^13)
+      -2147475456               # 32-bit
+      2147491840                # 64-bit
 
 Using ``search_src`` from the Sage prompt (or ``grep``), one can
 easily find the aforementioned keywords. In the case of ``todo: not

src/doc/en/faq/faq-usage.rst

@@ -10,14 +10,15 @@ How do I get started?
 
 You can try out Sage without downloading anything:
 
-* **SageMathCloud™:** Go to http://cloud.sagemath.org and set up a free
-  account.
+* **CoCalc™:** Go to https://cocalc.com and set up a free account.
 
   If you log in, you will gain access to the latest version of Sage and to 
   many other programs.
 
+  Note that this website is an independent commercial service.
+
 * **Sage cell:** A "one-off" version of Sage, available for doing one
-  computation at a time. http://sagecell.sagemath.org/
+  computation at a time. https://sagecell.sagemath.org/
 
 To download a **pre-built binary** Sage distribution, visit
 http://sagemath.org/download.html and click on the link for the binary for your
@@ -36,10 +37,6 @@ You can also run it from the command line of sage::
 
     sage: notebook() # not tested
 
-Where can I find more information about using SageMathCloud™?
-"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-Visit the Frequently Asked Questions page for SageMathCloud™ at https://github.com/sagemath/cloud/wiki/FAQ .
 
 What are the prerequisites for installing a copy of Sage on my computer?
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@@ -48,8 +45,8 @@ Most of the dependencies of Sage are shipped with Sage itself. In most
 cases, you can download a pre-built binary and use that without
 installing any dependencies. If you use Windows, you will need to
 install
-`VirtualBox <http://www.virtualbox.org>`_, which can be downloaded
-from the page http://www.virtualbox.org/wiki/Downloads. After
+`VirtualBox <https://www.virtualbox.org>`_, which can be downloaded
+from the page https://www.virtualbox.org/wiki/Downloads. After
 installing VirtualBox, you need to download a VirtualBox distribution
 of Sage available at
 http://www.sagemath.org/download-windows.html. Ensure you follow the
@@ -146,11 +143,17 @@ every change applied to the file simple.py will be automatically updated in Sage
 Can I use SageMath with Python 3.x?
 """""""""""""""""""""""""""""""""""
 
-Currently, no (February 2017). Work in progress aims to allow this in
-the not-so-far future. Until this task is completed, SageMath will continue
-to use Python 2.x.
+Currently, (September 2018) you can build the source code of SageMath with
+Python 3 using the instructions at the bottom of
+https://wiki.sagemath.org/Python3-compatible%20code
+
+Beware that this is still at an experimental stage.
+
+Work in progress aims to allow usage of Python 3 in the not-so-far
+future. Until this task is completed, SageMath will continue to use
+Python 2.x.
 
-See :trac:`15530` for tracking the current progress.
+See :trac:`15530` and :trac:`26212` for tracking the current progress.
 
 I'm seeing an error about "Permission denied" on a file called "sage-flags.txt".
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@@ -209,7 +212,7 @@ from the
 `download page <http://www.sagemath.org/download.html>`_.
 If you would like to help with updating the Debian/Ubuntu version of
 Sage, please email the
-`sage-devel <http://groups.google.com/group/sage-devel>`_
+`sage-devel <https://groups.google.com/group/sage-devel>`_
 mailing list.
 
 
@@ -218,9 +221,9 @@ Should I use the official version or development version?
 
 You are encouraged to use the latest official version of
 Sage. Development versions are frequently announced on the
-`sage-devel <http://groups.google.com/group/sage-devel>`_
+`sage-devel <https://groups.google.com/group/sage-devel>`_
 and
-`sage-release <http://groups.google.com/group/sage-release>`_
+`sage-release <https://groups.google.com/group/sage-release>`_
 mailing lists. An easy way of helping out with Sage development is to
 download the latest development release, compile it on your system,
 run all doctests, and report any compilation errors or doctest
@@ -242,9 +245,9 @@ by a web search.
 * `Dive into Python <http://www.diveintopython.net>`_ by Mark Pilgrim
 * `How to Think Like a Computer Scientist <http://www.openbookproject.net/thinkCSpy>`_
   by Jeffrey Elkner, Allen B. Downey, and Chris Meyers
-* `Official Python Tutorial <http://docs.python.org/tutorial>`_
+* `Official Python Tutorial <https://docs.python.org/tutorial>`_
 * `Python <http://www.python.org>`_ home page and the
-  `Python standard documentation <http://docs.python.org>`_
+  `Python standard documentation <https://docs.python.org>`_
 
 
 Can I do X in Sage?
@@ -273,7 +276,7 @@ When you type "0.6**2" in Python, it returns something like
 0.35999999999999999. But when you do the same in Sage it returns
 0.360000000000000. To understand why Python behaves as it does, see
 the
-`Python Tutorial <http://docs.python.org/tutorial/floatingpoint.html>`_,
+`Python Tutorial <https://docs.python.org/tutorial/floatingpoint.html>`_,
 especially the chapter "Floating Point Arithmetic: Issues and
 Limitations". What Sage does is "preparse" the input and transforms it
 like this::
@@ -305,7 +308,7 @@ arrow key and then press down arrow key, then the next line in history
 is fetched. This feature allows you to fetch as many successive lines
 in history as you like. However, Sage does not have a similar
 feature. The
-`IPython <http://ipython.scipy.org>`_
+`IPython <https://ipython.org>`_
 command prompt uses the readline library (via pyreadline), which
 evidently does not support this feature. Magma has its own custom
 "readline-like" library, which does support this feature. (Since so
@@ -643,7 +646,7 @@ methods mentioned in the plot documentation, but this one is easiest::
 
 The *reason* this is necessary is that Sage returns complex numbers
 for odd roots of negative numbers when numerically approximated, which
-is a `standard convention <http://en.wikipedia.org/wiki/Cube_root#Complex_numbers>`_.
+is a `standard convention <https://en.wikipedia.org/wiki/Cube_root#Complex_numbers>`_.
 
     sage: N((-1)^(1/3))
     0.500000000000000 + 0.866025403784439*I

src/doc/en/prep/Symbolics-and-Basic-Plotting.rst

@@ -352,7 +352,7 @@ Two of the most useful of these options help in labeling graphs.
 ::
 
     sage: P1 = plot(f,(x,-1,1),axes_labels=['$x$','$y$'],legend_label='$f(x)$')
-    sage: P2 = plot(sin,(x,-1,1),axes_labels=['$x$','$y$'],legend_label='$\sin(x)$',color='red')
+    sage: P2 = plot(sin,(x,-1,1),axes_labels=['$x$','$y$'],legend_label=r'$\sin(x)$',color='red')
     sage: P1+P2
     Graphics object consisting of 2 graphics primitives
 

src/doc/en/reference/algebras/lie_algebras.rst

@@ -6,6 +6,7 @@ Lie Algebras
 
    sage/algebras/lie_algebras/abelian
    sage/algebras/lie_algebras/affine_lie_algebra
+   sage/algebras/lie_algebras/bch
    sage/algebras/lie_algebras/classical_lie_algebra
    sage/algebras/lie_algebras/examples
    sage/algebras/lie_algebras/free_lie_algebra

src/doc/en/reference/function_fields/index.rst

@@ -2,15 +2,17 @@ Algebraic Function Fields
 =========================
 
 Sage allows basic computations with elements and ideals in orders of
-algebraic function fields over arbitrary constant fields.
+algebraic function fields over arbitrary constant fields. Advanced
+computations, like computing the genus or a basis of the Riemann-Roch space of
+a divisor, are available for global function fields.
 
 .. toctree::
    :maxdepth: 1
 
    sage/rings/function_field/function_field
-   sage/rings/function_field/function_field_element
-   sage/rings/function_field/function_field_order
-   sage/rings/function_field/function_field_ideal
+   sage/rings/function_field/element
+   sage/rings/function_field/order
+   sage/rings/function_field/ideal
    sage/rings/function_field/maps
    sage/rings/function_field/constructor