Merge remote-tracking branch 'trac/develop' into t/25090/public/pynor…

…maliz1.17_normaliz3.6.1

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.4.beta4, Release Date: 2018-09-06
+SageMath version 8.4.beta5, Release Date: 2018-09-15

build/bin/sage-download-file

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env sage-system-python
 
 # USAGE:
 #

build/bin/sage-flock

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env sage-system-python
 # vim: set filetype=python:
 
 # USAGE:

build/bin/sage-package

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env sage-system-python
 
 # Script to manage third-party tarballs.
 #

build/bin/sage-pip-install

@@ -35,11 +35,14 @@ if [ "$1" != "." ]; then
 fi
 
 
+# Note: We need to take care to specify the full path to Sage's Python here
+# to emphasize that this command hould use it, and not the system Python;
+# see https://trac.sagemath.org/ticket/18438
 if [ "$SAGE_PYTHON3" = yes ]; then
-    PYTHON=python3
+    PYTHON="$SAGE_LOCAL/bin/python3"
     PIP=pip3
 else
-    PYTHON=python2
+    PYTHON="$SAGE_LOCAL/bin/python2"
     PIP=pip2
 fi
 
@@ -62,12 +65,12 @@ fi
 
 # We should avoid running pip2/3 while uninstalling a package because that
 # is prone to race conditions. Therefore, we use a lockfile while
-# running pip. This is implemented in the Python script pip2/3-lock.
+# running pip. This is implemented in the Python script sage-flock
 LOCK="$SAGE_LOCAL/var/lock/$PIP.lock"
 
 # Keep uninstalling as long as it succeeds
 while true; do
-    out=$(sage-flock -x $LOCK $PIP uninstall --disable-pip-version-check -y "$name" 2>&1)
+    out=$(sage-flock -x $LOCK $PYTHON -m pip uninstall --disable-pip-version-check -y "$name" 2>&1)
     if [ $? -ne 0 ]; then
         # Uninstall failed
         echo >&2 "$out"
@@ -86,7 +89,7 @@ done
 # to apply a shared lock)
 echo "Installing package $name using $PIP"
 
-sage-flock -s $LOCK $PIP install $pip_install_flags .
+sage-flock -s $LOCK $PYTHON -m pip install $pip_install_flags .
 if [ $? -ne 0 ]; then
     echo >&2 "Error: installing with $PIP failed"
     exit 3

build/bin/sage-spkg-uninstall

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env sage-system-python
 
 # usage: sage-spkg-uninstall [-h] PKG [SAGE_LOCAL]
 #

build/bin/sage-system-python

@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+
+# Run the system python.
+#
+# This is primarily for use by the build toolchain so that it can continue
+# using the system Python rather than Sage's Python, preventing conflicts
+# that might otherwise occur, particularly in parallel builds.
+#
+# See https://trac.sagemath.org/ticket/18438
+
+PYTHON="$(PATH="$SAGE_ORIG_PATH" command -v python)"
+
+exec "$PYTHON" "$@"

build/bin/sage-uncompress-spkg

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env sage-system-python
 
 # usage: sage-uncompress-spkg [-h] [-d DIR] PKG [FILE]
 #

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=0fbdda7f9b9a2181f32cd257147f6bd4712697fa
-md5=7a95b74489dc74b49f2a36a68b40ba6b
-cksum=2018224632
+sha1=d37563de2152d075765145f2d50568182972cf94
+md5=df46180857c9b8bb2fbccfaa8405214b
+cksum=492825525

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-281
+282

build/pkgs/flint/package-version.txt

@@ -1 +1 @@
-2.5.2.p2
+2.5.2.p3

build/pkgs/flint/patches/Makefile.subdirs.patch

@@ -0,0 +1,13 @@
+diff --git a/Makefile.subdirs b/Makefile.subdirs
+index ec05fb0..0a54772 100644
+--- a/Makefile.subdirs
++++ b/Makefile.subdirs
+@@ -85,7 +85,7 @@ $(BUILD_DIR)/test/%$(EXEEXT): test/%.c $(BUILD_DIR)/../../test_helpers.o
+ 	$(QUIET_CC) $(CC) $(CFLAGS) $(INCS) $< $(BUILD_DIR)/../../test_helpers.o -o $@ $(LIBS) -MMD -MP -MF [email protected] -MT "$@" -MT "[email protected]"
+
+ $(BUILD_DIR)/test/%$(EXEEXT): test/%.cpp $(BUILD_DIR)/../../test_helpers.o
+-	$(QUIET_CC) $(CXX) $(CFLAGS) $(INCS) $< $(BUILD_DIR)/../../test_helpers.o -o $@ $(LIBS) -MMD -MP -MF [email protected] -MT "$@" -MT "[email protected]"
++	$(QUIET_CC) $(CXX) $(CXXFLAGS) $(INCS) $< $(BUILD_DIR)/../../test_helpers.o -o $@ $(LIBS) -MMD -MP -MF [email protected] -MT "$@" -MT "[email protected]"
+
+ %_RUN: %
+ 	@$<

build/pkgs/rubiks/package-version.txt

@@ -1 +1 @@
-20070912.p19
+20070912.p20

build/pkgs/rubiks/patches/Makefile.patch

@@ -0,0 +1,18 @@
+diff -ruN rubiks-20070912/Makefile rubiks-20070912.new/Makefile
+--- rubiks-20070912/Makefile	2018-09-10 18:20:18.923991000 +0100
++++ rubiks-20070912.new/Makefile	2018-09-10 18:20:33.203529000 +0100
+@@ -5,12 +5,12 @@
+
+ all clean:
+ 	for dir in $(DIRS); do \
+-		(cd $${dir} && make $@)\
++		(cd $${dir} && $(MAKE) $@)\
+ 	done
+
+ distclean: clean
+ 	for dir in $(DIRS); do \
+-		(cd $${dir} && make distclean)\
++		(cd $${dir} && $(MAKE) distclean)\
+ 	done
+
+ install: all

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.beta4'
-SAGE_RELEASE_DATE='2018-09-06'
-SAGE_VERSION_BANNER='SageMath version 8.4.beta4, Release Date: 2018-09-06'
+SAGE_VERSION='8.4.beta5'
+SAGE_RELEASE_DATE='2018-09-15'
+SAGE_VERSION_BANNER='SageMath version 8.4.beta5, Release Date: 2018-09-15'

src/doc/ca/intro/index.rst

@@ -201,8 +201,10 @@ Per exemple::
     sage: C = Set(S)
     sage: S
     [121, 49, 25, 9, 9, 25, 49, 121]
-    sage: C
+    sage: C    # random
     {121, 9, 49, 25}
+    sage: sorted(C)
+    [9, 25, 49, 121]
 
 La `i`-èssima entrada d'una seqüència (o d'un conjunt) `C`
 és ``C[i]``. Però compte perquè Sage
@@ -257,7 +259,7 @@ de la manera següent::
 
 Podem aplicar una funció a tots els elements d'una llista de la manera següent::
 
-    sage: map(cos, [0,pi..6*pi])
+    sage: [cos(t) for t in [0,pi..6*pi]]
     [1, -1, 1, -1, 1, -1, 1]
 
 

src/doc/de/tutorial/programming.rst

@@ -544,7 +544,8 @@ nichtnegativen ganzen Zahlen bis :math:`10000000`.
 
 ::
 
-    sage: v = (n^2 for n in xrange(10000000))
+    sage: v = (n^2 for n in xrange(10000000))  # py2
+    sage: v = (n^2 for n in range(10000000))   # py3
     sage: next(v)
     0
     sage: next(v)

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

@@ -17,6 +17,7 @@ Lie Algebras
    sage/algebras/lie_algebras/onsager
    sage/algebras/lie_algebras/poincare_birkhoff_witt
    sage/algebras/lie_algebras/structure_coefficients
+   sage/algebras/lie_algebras/subalgebra
    sage/algebras/lie_algebras/verma_module
    sage/algebras/lie_algebras/virasoro
 

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

@@ -792,6 +792,9 @@ REFERENCES:
             error-correcting codes from game theory*, IEEE
             Trans. Infor. Theory **32** (1986) 337-348.
 
+.. [CS2003] \John E. Cremona and Michael Stoll. On The Reduction Theory of Binary Forms.
+            Journal für die reine und angewandte Mathematik, 565 (2003), 79-99.
+
 .. [Cu1984] \R. Curtis, The Steiner system `S(5,6,12)`, the Mathieu
             group `M_{12}`, and the kitten. *Computational group
             theory*, ed. M. Atkinson, Academic Press, 1984.
@@ -1314,6 +1317,10 @@ REFERENCES:
 
 .. [Gu] GUAVA manual, http://www.gap-system.org/Packages/guava.html
 
+.. [Gut2001] Carsten Gutwenger and Petra Mutzel. *A Linear Time Implementation
+             of SPQR-Trees*, International Symposium on Graph Drawing,
+             (2001) 77-90
+
 .. [GW1999] Frederick M. Goodman and Hans Wenzl. *Crystal bases of quantum
             affine algebras and affine Kazhdan-Lusztig polyonmials*.
             Int. Math. Res. Notices **5** (1999), 251-275.
@@ -1395,6 +1402,9 @@ REFERENCES:
 .. [Hoc] Winfried Hochstaettler, "About the Tic-Tac-Toe Matroid",
          preprint.
 
+.. [Hopcroft1973] J. E. Hopcroft and R. E. Tarjan. *Dividing a Graph into
+                  Triconnected Components*, SIAM J. Comput., 2(3), 135–158
+
 .. [Hopkins2017] Sam Hopkins,
                  *RSK via local transformations*,
                  http://web.mit.edu/~shopkins/docs/rsk.pdf
@@ -2170,6 +2180,9 @@ REFERENCES:
             Number Theory" (ed. Y. Motohashi), London Math. Soc. Lecture Notes
             247 (1997), 313-320, Cambridge Univ. Press.
 
+.. [Mur1983] \G. E. Murphy. *The idempotents of the symmetric group
+             and Nakayama's conjecture*. J. Algebra **81** (1983). 258-265.
+
 .. [MV2010] \D. Micciancio, P. Voulgaris. *A Deterministic Single
             Exponential Time Algorithm for Most Lattice Problems based
             on Voronoi Cell Computations*. Proceedings of the 42nd ACM

src/doc/en/thematic_tutorials/lie/weyl_groups.rst

@@ -83,10 +83,7 @@ construct a list (e.g., using the ``list`` function) or use the method
 
     sage: W = WeylGroup("B3",prefix="s")
     sage: ref = W.reflections(); ref
-    Finite family {(1, 0, 0): s1*s2*s3*s2*s1, (0, 1, 1): s3*s2*s3,
-                   (0, 1, -1): s2, (0, 0, 1): s3, (1, -1, 0): s1,
-                   (1, 1, 0): s2*s3*s1*s2*s3*s1*s2, (1, 0, -1): s1*s2*s1,
-                   (1, 0, 1): s3*s1*s2*s3*s1, (0, 1, 0): s2*s3*s2}
+    Finite family {(1, -1, 0): s1, (0, 1, -1): s2, (0, 0, 1): s3, (0, 1, 1): s3*s2*s3, (0, 1, 0): s2*s3*s2, (1, 0, -1): s1*s2*s1, (1, 0, 1): s3*s1*s2*s3*s1, (1, 0, 0): s1*s2*s3*s2*s1, (1, 1, 0): s2*s3*s1*s2*s3*s1*s2}
     sage: [a1,a2,a3] = W.domain().simple_roots()
     sage: a1+a2+a3
     (1, 0, 0)
@@ -103,8 +100,16 @@ and whose values are the roots, you may use the inverse family::
     sage: W = WeylGroup("B3",prefix="s")
     sage: [s1,s2,s3] = W.simple_reflections()
     sage: altref = W.reflections().inverse_family()
-    sage: pprint(altref)
-    Finite family {s3*s2*s3: (0, 1, 1), s2*s3*s2: (0, 1, 0), s1*s2*s3*s2*s1: (1, 0, 0), s1*s2*s1: (1, 0, -1), s1: (1, -1, 0), s2*s3*s1*s2*s3*s1*s2: (1, 1, 0), s2: (0, 1, -1), s3*s1*s2*s3*s1: (1, 0, 1), s3: (0, 0, 1)}
+    sage: altref
+    Finite family {s1*s2*s3*s2*s1: (1, 0, 0),
+     s2*s3*s1*s2*s3*s1*s2: (1, 1, 0),
+     s3*s1*s2*s3*s1: (1, 0, 1),
+     s1*s2*s1: (1, 0, -1),
+     s1: (1, -1, 0),
+     s2*s3*s2: (0, 1, 0),
+     s3*s2*s3: (0, 1, 1),
+     s2: (0, 1, -1),
+     s3: (0, 0, 1)}
     sage: altref[s3*s2*s3]
     (0, 1, 1)
 

src/doc/en/thematic_tutorials/numtheory_rsa.rst

@@ -116,7 +116,7 @@ say, ``/home/mvngu/totient.sage``, organizing it as follows to enhance
 readability. ::
 
     L = []
-    for n in xrange(1, 21):
+    for n in range(1, 21):
         if gcd(n, 20) == 1:
             L.append(n)
     L

src/doc/en/thematic_tutorials/structures_in_coding_theory.rst

@@ -494,7 +494,7 @@ So we only need to override ``transmit_unsafe``! Let us do it::
     ....:     number_err = self.number_errors()
     ....:     V = self.input_space()
     ....:     F = GF(2)
-    ....:     for i in sample(xrange(V.dimension()), number_err):
+    ....:     for i in sample(range(V.dimension()), number_err):
     ....:         w[i] += F.one()
     ....:     return w
 
@@ -699,7 +699,7 @@ derive from the one that follows.
             number_err = self.number_errors()
             V = self.input_space()
             F = GF(2)
-            for i in sample(xrange(V.dimension()), number_err):
+            for i in sample(range(V.dimension()), number_err):
                 w[i] += F.one()
             return w
 

src/doc/en/thematic_tutorials/tutorial-comprehensions.rst

@@ -118,9 +118,11 @@ idioms give the same results; however, the second idiom is much more
 memory efficient (for large examples) as it does not expand any list
 in memory::
 
-    sage: sum( [ binomial(8, i) for i in range(9) ] )
+    sage: sum([binomial(8, i) for i in range(9)])
     256
-    sage: sum( binomial(8, i) for i in xrange(9) )
+    sage: sum(binomial(8, i) for i in xrange(9))  # py2
+    256
+    sage: sum(binomial(8, i) for i in range(9))  # py3
     256
 
 .. TOPIC:: Exercises

src/doc/en/thematic_tutorials/tutorial-programming-python.rst

@@ -262,7 +262,8 @@ be negative. Use range to construct the list `[10, 7, 4, 1, -2]`.
 
 .. SEEALSO::
 
-    - :func:`xrange`: returns an iterator rather than building a list.
+    - :func:`xrange`: returns an iterator rather than building a list,
+      (only for Python2, replaced by range in Python 3).
     - :func:`srange`: like range but with Sage integers; see below.
     - :func:`xsrange`: like xrange but with Sage integers.
 
@@ -710,7 +711,7 @@ braces, ``{}``, with comma-separated entries given in the form
 A second method is to use the constructor :class:`dict` which admits a
 list (or actually any iterable) of 2-tuples *(key, value)*::
 
-    sage: dd = dict((i,i^2) for i in xrange(10))
+    sage: dd = dict((i,i^2) for i in range(10))
     sage: dd
     {0: 0, 1: 1, 2: 4, 3: 9, 4: 16, 5: 25, 6: 36, 7: 49, 8: 64, 9: 81}
 

src/doc/en/tutorial/programming.rst

@@ -524,7 +524,8 @@ nonnegative integers up to :math:`10000000`.
 
 ::
 
-    sage: v = (n^2 for n in xrange(10000000))
+    sage: v = (n^2 for n in xrange(10000000))  # py2
+    sage: v = (n^2 for n in range(10000000))  # py3
     sage: next(v)
     0
     sage: next(v)

src/doc/fr/tutorial/programming.rst

@@ -540,7 +540,8 @@ d'entiers positifs jusqu'à :math:`10000000`.
 
 ::
 
-    sage: v = (n^2 for n in xrange(10000000))
+    sage: v = (n^2 for n in xrange(10000000))  # py2
+    sage: v = (n^2 for n in range(10000000))  # py3
     sage: next(v)
     0
     sage: next(v)

src/doc/ja/tutorial/interactive_shell.rst

@@ -423,11 +423,6 @@ IPythonのクイック レファレンスガイドを見たければ， ``%quick
 
 ::
 
-    sage: 3_2
-    Traceback (most recent call last):
-    ...
-    SyntaxError: invalid syntax
-
     sage: EllipticCurve([0,infinity])
     Traceback (most recent call last):
     ...

src/doc/ja/tutorial/programming.rst

@@ -503,7 +503,8 @@ Pythonには集合(set)型が組込まれている．
 
 ::
 
-    sage: v = (n^2 for n in xrange(10000000))
+    sage: v = (n^2 for n in xrange(10000000))  # py2
+    sage: v = (n^2 for n in range(10000000))  # py3
     sage: next(v)
     0
     sage: next(v)

src/doc/pt/tutorial/programming.rst

@@ -547,7 +547,8 @@ sobre o quadrados dos números inteiros até :math:`10000000`.
 
 ::
 
-    sage: v = (n^2 for n in xrange(10000000))
+    sage: v = (n^2 for n in xrange(10000000))  # py2
+    sage: v = (n^2 for n in range(10000000))  # py3
     sage: next(v)
     0
     sage: next(v)

src/doc/ru/tutorial/programming.rst

@@ -508,7 +508,8 @@ http://docs.python.org/lib/typesmapping.html) произвольным объе
 
 ::
 
-    sage: v = (n^2 for n in xrange(10000000))
+    sage: v = (n^2 for n in xrange(10000000))  # py2
+    sage: v = (n^2 for n in range(10000000))  # py3
     sage: next(v)
     0
     sage: next(v)

src/sage/algebras/associated_graded.py

@@ -281,7 +281,7 @@ def algebra_generators(self):
             sage: A = Algebras(QQ).WithBasis().Filtered().example()
             sage: grA = A.graded_algebra()
             sage: grA.algebra_generators()
-            Finite family {'y': bar(U['y']), 'x': bar(U['x']), 'z': bar(U['z'])}
+            Finite family {'x': bar(U['x']), 'y': bar(U['y']), 'z': bar(U['z'])}
         """
         G = self._A.algebra_generators()
         return Family(G.keys(), lambda x: self(G[x]), name="generator")

src/sage/algebras/clifford_algebra.py

@@ -768,7 +768,7 @@ def algebra_generators(self):
             sage: Q = QuadraticForm(ZZ, 3, [1,2,3,4,5,6])
             sage: Cl.<x,y,z> = CliffordAlgebra(Q)
             sage: Cl.algebra_generators()
-            Finite family {'y': y, 'x': x, 'z': z}
+            Finite family {'x': x, 'y': y, 'z': z}
         """
         d = {x: self.gen(i) for i,x in enumerate(self.variable_names())}
         return Family(self.variable_names(), lambda x: d[x])