Merge branch 'develop' into t/23782/fricas_output_and_sage_conversion…

…_bug

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.1.beta5, Release Date: 2017-09-11
+SageMath version 8.1.beta6, Release Date: 2017-09-21

build/bin/sage-spkg

@@ -220,7 +220,7 @@ while true; do
         -s)
             export SAGE_KEEP_BUILT_SPKGS=yes;;
         -c|--check)
-            SAGE_CHECK_PACKAGES=x  # nonempty, so not set to '!python2' later
+            SAGE_CHECK_PACKAGES=x  # nonempty, so not set to default later
             export SAGE_CHECK=yes;;
         -*)
             echo >&2 "Error: unknown option '$1'"
@@ -767,7 +767,7 @@ fi
 # Since Python's self-tests seem to fail on all platforms, we disable
 # its test suite by default.
 if [ -z "$SAGE_CHECK_PACKAGES" ]; then
-    SAGE_CHECK_PACKAGES='!python2'
+    SAGE_CHECK_PACKAGES='!python2,!python3'
 fi
 # Allow spaces, commas, or colons as separator (the documentation suggests commas).
 if echo ",$SAGE_CHECK_PACKAGES," | grep -i "[ ,:]\!$PKG_BASE[ ,:]" > /dev/null ; then

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=c063b3ecf3e5b7b4669670f40d960231d0cc9470
-md5=76d19d3a4f35085009a2a0a398259d74
-cksum=2616315576
+sha1=f97d37995518571ade4ec3ba1004fb8f2e60eb72
+md5=09a7668e2d53c68bb22c25c70a9fe8c7
+cksum=2353275698

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-237
+238

build/pkgs/fricas/checksums.ini

@@ -1,4 +1,4 @@
 tarball=fricas-VERSION-full.tar.bz2
-sha1=f476a535ba189658cbc6055a951867c0c23787e4
-md5=1850f25249ed238203b9519c522d1795
-cksum=2721391206
+sha1=8fc3e850a9890eac21cd9f391dd58000b3537067
+md5=0d3af65758ce93b1cc52c2511e73e674
+cksum=1048748907

build/pkgs/fricas/package-version.txt

@@ -1 +1 @@
-1.2.7
+1.3.2

build/pkgs/frobby/SPKG.txt

@@ -30,7 +30,7 @@ Frobby source distribution.
 == Changelog ==
 
 === frobby-0.9.0.p2 (Dima Pasechnik, Jun 30, 2016) ===
- * convertion to new-style package
+ * conversion to new-style package
  * integration of Macaulay2 patches
  * fix linking (rpath)
 

build/pkgs/numpy/package-version.txt

@@ -1 +1 @@
-1.12.1
+1.12.1.p0

build/pkgs/numpy/patches/PEP_3141.patch

@@ -0,0 +1,39 @@
+See https://github.com/numpy/numpy/pull/9691
+
+commit 409e78dd851f5413338f8ce22e50d1a11aa0391a
+Author: Jeroen Demeyer <jdemeyer@cage.ugent.be>
+Date:   Fri Sep 15 12:22:51 2017 +0200
+
+    PEP 3141 numbers should be considered scalars
+
+diff --git a/numpy/core/numeric.py b/numpy/core/numeric.py
+index fde0849..647a9dd 100644
+--- a/numpy/core/numeric.py
++++ b/numpy/core/numeric.py
+@@ -5,6 +5,7 @@ import itertools
+ import operator
+ import sys
+ import warnings
++import numbers
+
+ import numpy as np
+ from . import multiarray
+@@ -2161,12 +2162,14 @@ def isscalar(num):
+     True
+     >>> np.isscalar('numpy')
+     True
++    >>> from fractions import Fraction
++    >>> isscalar(Fraction())
++    True
+
+     """
+-    if isinstance(num, generic):
+-        return True
+-    else:
+-        return type(num) in ScalarType
++    return (isinstance(num, generic)
++            or type(num) in ScalarType
++            or isinstance(num, numbers.Number))
+
+
+ def binary_repr(num, width=None):

build/pkgs/openblas/patches/openblas-0.2.19-cygwin.patch

@@ -0,0 +1,67 @@
+diff -ruN a/exports/Makefile b/exports/Makefile
+--- a/exports/Makefile	2017-09-07 12:40:36.504486400 +0200
++++ b/exports/Makefile	2017-09-07 13:28:39.665869200 +0200
+@@ -89,13 +89,13 @@
+ # in their import table.  By instead using a stable name it is possible to
+ # upgrade between library versions, without needing to re-link an application.
+ # For more details see: https://github.com/xianyi/OpenBLAS/issues/127.
+-../$(LIBDLLNAME) : ../$(LIBNAME) libopenblas.def dllinit.$(SUFFIX)
++../$(LIBDLLNAME) : ../$(LIBNAME) $(LIBPREFIX).def dllinit.$(SUFFIX)
+ 	$(RANLIB) ../$(LIBNAME)
+-	$(CC) $(CFLAGS) $(LDFLAGS) libopenblas.def dllinit.$(SUFFIX) \
+-	-shared -o ../$(LIBDLLNAME) -Wl,--out-implib,../$(LIBDLLNAME).a \
++	$(CC) $(CFLAGS) $(LDFLAGS) $(LIBPREFIX).def dllinit.$(SUFFIX) \
++	-shared -o ../$(LIBDLLNAME) -Wl,--out-implib,../$(IMPLIBNAME) \
+ 	-Wl,--whole-archive ../$(LIBNAME) -Wl,--no-whole-archive $(FEXTRALIB) $(EXTRALIB)
+
+-libopenblas.def : gensymbol
++$(LIBPREFIX).def : gensymbol
+ 	perl ./gensymbol win2k    $(ARCH) dummy $(EXPRECISION) $(NO_CBLAS) $(NO_LAPACK) $(NO_LAPACKE) $(NEED2UNDERSCORES) $(ONLY_CBLAS) "$(SYMBOLPREFIX)" "$(SYMBOLSUFFIX)" $(BUILD_LAPACK_DEPRECATED) > $(@F)
+
+ libgoto_hpl.def : gensymbol
+diff -ruN a/Makefile.install b/Makefile.install
+--- a/Makefile.install	2017-09-07 12:40:50.166767100 +0200
++++ b/Makefile.install	2017-09-07 13:28:29.265353000 +0200
+@@ -88,10 +88,11 @@
+ endif
+ ifeq ($(OSNAME), WINNT)
+ 	@-cp $(LIBDLLNAME) "$(DESTDIR)$(OPENBLAS_BINARY_DIR)"
+-	@-cp $(LIBDLLNAME).a "$(DESTDIR)$(OPENBLAS_LIBRARY_DIR)"
++	@-cp $(IMPLIBNAME) "$(DESTDIR)$(OPENBLAS_LIBRARY_DIR)"
+ endif
+ ifeq ($(OSNAME), CYGWIN_NT)
+-	@-cp $(LIBDLLNAME) $(OPENBLAS_BINARY_DIR)
++	@-cp $(LIBDLLNAME) "$(DESTDIR)$(OPENBLAS_BINARY_DIR)"
++	@-cp $(IMPLIBNAME) "$(DESTDIR)$(OPENBLAS_LIBRARY_DIR)"
+ endif
+ endif
+ #Generating OpenBLASConfig.cmake
+diff -ruN a/Makefile.system b/Makefile.system
+--- a/Makefile.system	2017-09-07 12:40:47.348982600 +0200
++++ b/Makefile.system	2017-09-07 13:29:01.062873600 +0200
+@@ -904,9 +904,15 @@
+ endif
+
+ ifndef LIBNAMESUFFIX
+-LIBPREFIX = lib$(SYMBOLPREFIX)openblas$(SYMBOLSUFFIX)
++LIBNAMEBASE = $(SYMBOLPREFIX)openblas$(SYMBOLSUFFIX)
+ else
+-LIBPREFIX = lib$(SYMBOLPREFIX)openblas$(SYMBOLSUFFIX)_$(LIBNAMESUFFIX)
++LIBNAMEBASE = $(SYMBOLPREFIX)openblas$(SYMBOLSUFFIX)_$(LIBNAMESUFFIX)
++endif
++
++ifeq ($(OSNAME), CYGWIN_NT)
++LIBPREFIX = cyg$(LIBNAMEBASE)
++else
++LIBPREFIX = lib$(LIBNAMEBASE)
+ endif
+
+ KERNELDIR	= $(TOPDIR)/kernel/$(ARCH)
+@@ -1065,6 +1071,7 @@
+
+
+ LIBDLLNAME   = $(LIBPREFIX).dll
++IMPLIBNAME   = lib$(LIBNAMEBASE).dll.a
+ LIBSONAME    = $(LIBNAME:.$(LIBSUFFIX)=.so)
+ LIBDYNNAME   = $(LIBNAME:.$(LIBSUFFIX)=.dylib)
+ LIBDEFNAME   = $(LIBNAME:.$(LIBSUFFIX)=.def)

build/pkgs/pynac/checksums.ini

@@ -1,4 +1,4 @@
 tarball=pynac-VERSION.tar.bz2
-sha1=613108dd2f74a277ec401c86a369d8521d352ae6
-md5=2d4dd3aa493a80c97de9afc8bbadb464
-cksum=2175259532
+sha1=4a451caec15ac10387b722ca42f5fd6baf5f4d6d
+md5=36dfabf9c1ecc39eda3d34b4393fbb9f
+cksum=4008480479

build/pkgs/pynac/package-version.txt

@@ -1 +1 @@
-0.7.10
+0.7.11

build/pkgs/pynac/patches/mixed-sqrt.patch

@@ -0,0 +1,26 @@
+diff --git a/ginac/power.cpp b/ginac/power.cpp
+index 74dc725..ca504f1 100644
+--- a/ginac/power.cpp
++++ b/ginac/power.cpp
+@@ -744,12 +744,15 @@ ex power::eval(int level) const
+                                                 outex = outer[0];
+                                         else
+                                                 outex = mul(outer).hold();
+-                                        if (inner.size() == 1)
+-                                                innex = inner[0];
+-                                        else
+-                                                innex = mul(inner).hold();
+-                                        ex p = power(innex, eexponent).hold();
+-                                        return (new mul(outex, p))->setflag(status_flags::dynallocated | status_flags::evaluated);
++                                        if (inner.size() > 0) {
++                                                if (inner.size() == 1)
++                                                        innex = inner[0];
++                                                else
++                                                        innex = mul(inner).hold();
++                                                ex p = power(innex, eexponent).hold();
++                                                return (new mul(outex, p))->setflag(status_flags::dynallocated | status_flags::evaluated);
++                                        }
++                                        return outex;
+                                 }
+                         }
+                 }

build/pkgs/sphinx/package-version.txt

@@ -1 +1 @@
-1.6.3.p0
+1.6.3.p1

build/pkgs/sphinx/patches/unpickle_error.patch

@@ -0,0 +1,24 @@
+commit f4c8115a7e5f1a5d9ba10279b5a7634f63c18526
+Author: Jeroen Demeyer <jdemeyer@cage.ugent.be>
+Date:   Fri Sep 8 11:42:35 2017 +0200
+
+    Turn any environment unpickling error into IOError
+
+diff --git a/sphinx/environment/__init__.py b/sphinx/environment/__init__.py
+index 536aa95..a3a3e3a 100644
+--- a/sphinx/environment/__init__.py
++++ b/sphinx/environment/__init__.py
+@@ -110,7 +110,12 @@ class BuildEnvironment(object):
+     @staticmethod
+     def load(f, app=None):
+         # type: (IO, Sphinx) -> BuildEnvironment
+-        env = pickle.load(f)
++        try:
++            env = pickle.load(f)
++        except Exception as exc:
++            # This can happen for example when the pickle is from a
++            # different version of Sphinx.
++            raise IOError(exc)
+         if env.version != ENV_VERSION:
+             raise IOError('build environment version not current')
+         if app:

src/bin/sage-banner

@@ -1,5 +1,5 @@
 ┌────────────────────────────────────────────────────────────────────┐
-│ SageMath version 8.1.beta5, Release Date: 2017-09-11               │
+│ SageMath version 8.1.beta6, Release Date: 2017-09-21               │
 │ 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='8.1.beta5'
-SAGE_RELEASE_DATE='2017-09-11'
+SAGE_VERSION='8.1.beta6'
+SAGE_RELEASE_DATE='2017-09-21'

src/doc/en/developer/git_background.rst

@@ -106,7 +106,7 @@ Using this ``lg`` alias gives you the changelog with a colored ascii graph::
     | * 4aff2a8 - fixed bug 35, and added a test in test_bugfixes (2 weeks ago) [Hugo]
     |/
     * a7ff2e5 - Added notes on discussion/proposal made during Data Array Summit. (2 weeks ago) [Corran Webster]
-    * 68f6752 - Initial implimentation of AxisIndexer - uses 'index_by' which needs to be changed to a call on an Axes object - this is all very sketchy right now. (2 weeks ago) [Corr
+    * 68f6752 - Initial implementation of AxisIndexer - uses 'index_by' which needs to be changed to a call on an Axes object - this is all very sketchy right now. (2 weeks ago) [Corr
     *   376adbd - Merge pull request #46 from terhorst/master (2 weeks ago) [Jonathan Terhorst]
     |\
     | * b605216 - updated joshu example to current api (3 weeks ago) [Jonathan Terhorst]

src/doc/en/installation/source.rst

@@ -967,15 +967,15 @@ Here are some of the more commonly used variables affecting the build process:
   An entry ``package-name`` means to run the test suite for the named package
   regardless of the setting of :envvar:`SAGE_CHECK`.
   An entry ``!package-name`` means to skip its test suite.
-  So if this is set to ``mpir,!python``, then always run the test suite for
-  MPIR, but always skip the test suite for Python.
+  So if this is set to ``mpir,!python2``, then always run the test suite for
+  MPIR, but always skip the test suite for Python 2.
 
   .. note::
 
-     As of this writing (April 2013, Sage 5.8), the test suite for the Python
-     spkg fails on most platforms.
+     As of this writing (September 2017, Sage 8.1), the test suites for the
+     Python 2 and 3 spkgs fail on most platforms.
      So when this variable is empty or unset, Sage uses a default of
-     ``!python``.
+     ``!python2,!python3``.
 
 - :envvar:`SAGE64` - if set to ``yes``, then build a 64-bit binary on platforms
   which default to 32-bit, even though they can build 64-bit binaries.
@@ -1432,4 +1432,4 @@ the directory where you want to install Sage.
 
 
 
-**This page was last updated in February 2017 (Sage 7.6).**
+**This page was last updated in September 2017 (Sage 8.1).**

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

@@ -48,6 +48,7 @@ Named associative algebras
    sage/algebras/iwahori_hecke_algebra
    sage/combinat/posets/incidence_algebras
    sage/algebras/group_algebra
+   sage/combinat/grossman_larson_algebras
    sage/combinat/posets/moebius_algebra
    sage/algebras/nil_coxeter_algebra
    sage/algebras/orlik_solomon

src/doc/en/reference/combinat/module_list.rst

@@ -127,6 +127,7 @@ Comprehensive Module list
     sage/combinat/graph_path
     sage/combinat/gray_codes
     sage/combinat/growth
+    sage/combinat/grossman_larson_algebras
     sage/combinat/hall_polynomial
     sage/combinat/integer_lists/base
     sage/combinat/integer_lists/lists

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

@@ -16,4 +16,24 @@ Discrete dynamics
     - :mod:`sage.combinat.e_one_star`
     - :mod:`sage.combinat.constellation`
 
+
+Arithmetic Dynamical Systems
+----------------------------
+
+.. toctree::
+   :maxdepth: 2
+
+   sage/dynamics/arithmetic_dynamics/generic_ds
+   sage/dynamics/arithmetic_dynamics/affine_ds
+   sage/dynamics/arithmetic_dynamics/projective_ds
+   sage/dynamics/arithmetic_dynamics/product_projective_ds
+   sage/dynamics/arithmetic_dynamics/wehlerK3
+
+
+.. SEEALSO::
+
+    - :mod:`sage.schemes.affine.affine_morphism`
+    - :mod:`sage.schemes.projective.projective_morphism`
+    - :mod:`sage.schemes.product_projective.morphism`
+
 .. include:: ../footer.txt