Merge branch 'develop' into t/22844/symbolic_limit

Author: rwst

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.0.beta4, Release Date: 2017-04-27
+SageMath version 8.0.beta5, Release Date: 2017-05-04

build/bin/sage-pip-install

@@ -31,8 +31,18 @@ if [ "$1" != "." ]; then
     exit 1
 fi
 
+
+if [ "$SAGE_PYTHON3" = yes ]; then
+    PYTHON=python3
+    PIP=pip3
+else
+    PYTHON=python2
+    PIP=pip2
+fi
+
+
 # Find out the name of the package that we are installing
-name="$(python setup.py --name)"
+name="$($PYTHON setup.py --name)"
 
 if [ $? -ne 0 ]; then
     echo >&2 "Error: could not determine package name"
@@ -46,29 +56,36 @@ if [ $(echo "$name" | wc -l) -gt 1 ]; then
     echo >&2 "line as the package name: $name"
 fi
 
-# We should avoid running pip while uninstalling a package because that
+
+# 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 pip-lock.
+# running pip. This is implemented in the Python script pip2/3-lock.
 
 # Keep uninstalling as long as it succeeds
 while true; do
-    out=$(pip-lock uninstall --disable-pip-version-check -y "$name" 2>&1)
+    out=$($PIP-lock uninstall --disable-pip-version-check -y "$name" 2>&1)
     if [ $? -ne 0 ]; then
         break
     fi
     echo "$out"
 done
 
 # Not ideal, but this is the easiest way to check if the package
-# was not installed to begin with (which pip treats as an error).
+# was not installed to begin with (which pip2/3 treats as an error).
 # If it wasn't, then we proceed quietly; if it was installed show the
 # uninstallation output and error out.
 if [[ "$out" != *"not installed" ]]; then
     echo >&2 "$out"
     exit 1
 fi
 
-# Finally actually do the installation (the "SHARED" tells pip-lock
+# Finally actually do the installation (the "SHARED" tells pip2/3-lock
 # to apply a shared lock)
-echo "Installing package $name using pip"
-exec pip-lock SHARED install $pip_install_flags .
+echo "Installing package $name using $PIP"
+
+$PIP-lock SHARED install $pip_install_flags .
+if [ $? -ne 0 ]; then
+    echo >&2 "Error: installing with $PIP failed"
+    exit 3
+fi
+

build/bin/sage-python23

@@ -0,0 +1,21 @@
+#!/usr/bin/env bash
+
+
+# Run the Python interpreter that we are currently building Sage with
+#
+# An existing Python is a build-time dependency for Sage, but
+# sometimes packages need to specifically run the one in Sage and not
+# just any Python interpreter.
+#
+# This is similar to the sage-pip-install script, which you should be
+# using for installing Python packages if at all possible.
+
+
+if [ "$SAGE_PYTHON3" = yes ]; then
+   PYTHON="$SAGE_LOCAL/bin/python3"
+else
+   PYTHON="$SAGE_LOCAL/bin/python2"
+fi
+
+
+exec $PYTHON "$@"

build/pkgs/brial/spkg-install

@@ -17,6 +17,8 @@ cd src
 # C++11 workaround https://trac.sagemath.org/ticket/20926
 export CXXFLAGS="$CXXFLAGS -std=c++98"
 
+export PYTHON=sage-python23
+
 ./configure \
     --prefix="$SAGE_LOCAL" \
     --libdir="$SAGE_LOCAL/lib" \

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=965fb15ff18f39c5cf38fcc8ff40d7450f70a122
-md5=7b67114fe41bb58afac9386c621d2b88
-cksum=821175052
+sha1=339f2474b789d33051dde8f69d047ae723a36379
+md5=9bb01c255b39648bb19f62a3fa24a80d
+cksum=2072910001

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-218
+219

build/pkgs/cvxopt/spkg-check

@@ -41,7 +41,7 @@ for di in "$CUR"/src/examples/doc/chap* ; do
     cd "$di"
     for i in `ls | grep -v bin` ; do
         echo "Testing $i ..."
-        python $i
+        sage-python23 $i
         if [ $? -ne 0 ]; then
             echo >&2 "Error: test $di/$i failed"
             exit 1

build/pkgs/gambit/spkg-install

@@ -21,7 +21,7 @@ if [ $? -ne 0 ]; then
 fi
 
 cd src/python
-python setup.py --no-user-cfg build install
+sage-python23 setup.py --no-user-cfg build install
 
 if [ $? -ne 0 ]; then
     echo "Error installing Python API"

build/pkgs/gap_jupyter/SPKG.txt

@@ -0,0 +1,16 @@
+= jupyter-kernel-gap =
+
+== Description ==
+
+Jupyter kernel for GAP
+
+This wrapper-kernel is a Jupyter kernel for the GAP Computer Algebra System
+based on the same ideas as the bash wrapper kernel.
+
+== License ==
+
+3-Clause BSD License
+
+== Upstream Contact ==
+
+* https://github.com/gap-packages/jupyter-gap

build/pkgs/gap_jupyter/checksums.ini

@@ -0,0 +1,4 @@
+tarball=jupyter-kernel-gap-VERSION.tar.gz
+sha1=9536aa352c6dee815ae5179e3971bfb9216f8eda
+md5=f5853cc8cd62ce495be8d3c8bdb2500f
+cksum=3578940226

build/pkgs/gap_jupyter/dependencies

@@ -0,0 +1 @@
+$(PYTHON) | pip ipython gap

build/pkgs/gap_jupyter/package-version.txt

@@ -0,0 +1 @@
+0.9

build/pkgs/gap_jupyter/spkg-install

@@ -0,0 +1,3 @@
+#!/usr/bin/env bash
+
+cd src && $PIP_INSTALL .

build/pkgs/gap_jupyter/type

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

build/pkgs/gmpy2/spkg-check

@@ -1,3 +1,3 @@
 #!/usr/bin/env bash
 
-cd src/test && python runtests.py
+cd src/test && sage-python23 runtests.py

build/pkgs/libhomfly/checksums.ini

@@ -1,4 +1,4 @@
 tarball=libhomfly-VERSION.tar.gz
-sha1=65c1ffc5814061323534e79d9ea5d523adb3ec57
-md5=1d56c477a1f5e4f934c3fccf5d560948
-cksum=233275648
+sha1=e6824c228c1313c7bd22ec68e1fcbb2a227e0edf
+md5=767dcfbccf17d5d076361d9633bb9e8e
+cksum=973275567

build/pkgs/libhomfly/package-version.txt

@@ -1 +1 @@
-1.0
+1.0r2

build/pkgs/matplotlib/make-setup-config.py

@@ -1,7 +1,10 @@
-from six.moves import configparser as ConfigParser
+try:
+    from configparser import SafeConfigParser   # Python 3
+except ImportError:
+    from ConfigParser import SafeConfigParser   # Python 2
 import os
 
-config = ConfigParser.SafeConfigParser()
+config = SafeConfigParser()
 
 config.add_section('directories')
 config.set('directories', 'basedirlist', os.environ['SAGE_LOCAL'])

build/pkgs/matplotlib/spkg-install

@@ -24,9 +24,3 @@ if [ $? -ne 0 ]; then
     echo "Error installing matplotlib package."
     exit 1
 fi
-
-# Print value of MPLCONFIGDIR
-VERSION=`python -c 'import pkg_resources; print(pkg_resources.get_distribution("matplotlib").version)'`
-echo
-echo "When Sage runs, MPLCONFIGDIR will be set to '\$DOT_SAGE/matplotlib-$VERSION'."
-echo

build/pkgs/ntl/checksums.ini

@@ -1,4 +1,4 @@
 tarball=ntl-VERSION.tar.gz
-sha1=1ab5908743079103eeca4a4c6ff7de85042c28e9
-md5=16b3449335163a753d45b5f1231bee23
-cksum=368444531
+sha1=ab2e7853a73e01227316215903073ebce54760ed
+md5=b682166b8652e4437c86154698b9831e
+cksum=2237621894

build/pkgs/ntl/package-version.txt

@@ -1 +1 @@
-10.1.0
+10.3.0

build/pkgs/numpy/checksums.ini

@@ -1,4 +1,4 @@
 tarball=numpy-VERSION.tar.gz
-sha1=5fbfde55b1d4b07cc449b10395472ffa41ec00c1
-md5=2f44a895a8104ffac140c3a70edbd450
-cksum=4092335543
+sha1=8eb0e29bf93c2f283d7691587b6322686d5baf0d
+md5=2abe6efb8ea0ac1716d1fc5fa90cbacf
+cksum=1617766273

build/pkgs/numpy/package-version.txt

@@ -1 +1 @@
-1.11.1.p1
+1.12.1

build/pkgs/numpy/patches/numpy-1.10.1-asarray_conversion.patch

@@ -36,7 +36,7 @@ else
     export LDFLAGS="${LDFLAGS} -shared"
 fi
 
-python ../lapack_conf.py
+sage-python23 ../lapack_conf.py
 
 # Make sure that the fortran objects are compiled with -fPIC
 export FFLAGS="$FFLAGS -fPIC"
@@ -48,7 +48,7 @@ export NUMPY_FCONFIG="config_fc --noopt --noarch"
 
 rm -rf "$SAGE_LOCAL/lib/python*/site-packages/numpy"
 
-python setup.py \
+sage-python23 setup.py \
         --no-user-cfg \
        install \
        --single-version-externally-managed \
@@ -58,7 +58,7 @@ python setup.py \
 # Touch all includes such that dependency checking works properly:
 # the timestamp of the includes should be *now*, not the time when
 # the numpy package was created.
-python <<EOF
+sage-python23 <<EOF
 import os
 os.chdir(os.environ["SAGE_ROOT"])  # Import numpy from safe location
 import numpy

build/pkgs/numpy/spkg-install

@@ -1,4 +1,4 @@
-tarball=ore_algebra-VERSION.tar.gz
-sha1=5083b94a3429f92acc79a043302adf107bd57a63
-md5=48b6a6c4613981fb033ca2188f12f802
-cksum=3887839116
+tarball=ore_algebra-VERSION.tgz
+sha1=0c7ba5bc7b8f6e988e10011ea45af39b78014f27
+md5=584adda6ae7b715fa3b1f9f5d91c6e63
+cksum=1732945549

build/pkgs/ore_algebra/checksums.ini

@@ -1 +1 @@
-0.2.p0
+0.3

build/pkgs/ore_algebra/package-version.txt

@@ -9,11 +9,13 @@ fi
 cd src
 
 # Delete old version
-site_packages="$SAGE_LOCAL/lib/python*/site-packages"
-rm -rf "$site_packages"/PIL "$site_packages"/PIL-*.egg* "$site_packages"/Pillow-*.egg*
+rm -rf \
+   "$SAGE_LOCAL"/lib/python*/site-packages/PIL \
+   "$SAGE_LOCAL"/lib/python*/site-packages/PIL-*.egg* \
+   "$SAGE_LOCAL"/lib/python*/site-packages/Pillow-*.egg*
 
 # Note: Avoid shared libraries inside egg files, Trac #19467
-python setup.py \
+sage-python23 setup.py \
        --no-user-cfg \
        build_ext \
        --disable-jpeg \

build/pkgs/pillow/spkg-install

@@ -1,4 +1,4 @@
-$(PYTHON) setuptools
+python2 python3 setuptools
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/pip/dependencies

@@ -3,6 +3,20 @@
 cd src
 
 # pip can install itself!
-# need to use --upgrade or else pip, which is importing itself, will think
-# itself is already installed
-python -m pip install --verbose --no-index --upgrade --isolated .
+#
+# need to use --upgrade or --ignore-installed; Otherwise pip, which is
+# importing itself, will think itself is already installed
+#
+# Install pip3 first so pip2 overwrites local/bin/pip
+
+python3 -m pip install --verbose --no-index --ignore-installed --isolated .
+if [ $? -ne 0 ]; then
+    echo "Error building / installing pip3"
+    exit 1
+fi
+
+python2 -m pip install --verbose --no-index --ignore-installed --isolated .
+if [ $? -ne 0 ]; then
+    echo "Error building / installing pip2"
+    exit 1
+fi

build/pkgs/pip/spkg-install

@@ -9,7 +9,7 @@ fi
 cd src
 
 echo "PyCrypto will now be tested"
-python setup.py test
+sage-python23 setup.py test
 if [ $? -ne 0 ]; then
     echo >&2 "Error: PyCrypto failed to pass its test suite."
     exit 1

build/pkgs/pycrypto/spkg-check

@@ -118,19 +118,18 @@ rm -f "$SAGE_LOCAL/lib/python"
 
 build
 
-PYTHON_VERSION=$("$SAGE_LOCAL/bin/python2" -c 'import sys; print("%d.%d" % sys.version_info[:2])')
-
 # On OS X with XCode 4, the presence of
 # $SAGE_LOCAL/lib/python2.*/config/libpython2.x.a causes problems with
 # GiNaC -- see #11967.  It is easiest to test the version of OS X; we
 # delete this file if using OS X 10.6 or later (so `uname -r` returns
 # x.y.z with x >= 10).
 if [ "$UNAME" = "Darwin" ] && \
+    PYTHON_VERSION=$("$SAGE_LOCAL/bin/python2" -c 'import sys; print("%d.%d" % sys.version_info[:2])')
     [ `uname -r | cut '-d.' -f1` -gt 9 ]; then
     rm -f "$SAGE_LOCAL/lib/python$PYTHON_VERSION/config/libpython${PYTHON_VERSION}.a"
 elif [ "$UNAME" = "CYGWIN" ]; then
     # See http://trac.sagemath.org/ticket/20437
-    ln -sf "python/config/libpython${PYTHON_VERSION}.dll.a" "$SAGE_LOCAL/lib/libpython${PYTHON_VERSION}.dll.a"
+    ln -sf "python$PYTHON_VERSION/config/libpython${PYTHON_VERSION}.dll.a" "$SAGE_LOCAL/lib/libpython${PYTHON_VERSION}.dll.a"
 fi
 
 # Make sure extension modules were built correctly.

build/pkgs/python2/spkg-install

@@ -1,4 +1,4 @@
-zlib readline sqlite libpng | bzip2
+zlib readline sqlite libpng xz | bzip2
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/python3/dependencies

@@ -1 +1 @@
-3.5.1
+3.5.1.p0

build/pkgs/python3/package-version.txt

@@ -0,0 +1,23 @@
+--- a/Include/pyport.h	2017-04-07 13:26:39.000000000 -0700
++++ b/Include/pyport.h	2017-04-07 13:27:54.000000000 -0700
+@@ -688,6 +688,12 @@
+ #endif
+ 
+ #ifdef _PY_PORT_CTYPE_UTF8_ISSUE
++#ifndef __cplusplus
++   /* The workaround below is unsafe in C++ because
++    * the <locale> defines these symbols as real functions,
++    * with a slightly different signature.
++    * See issue #10910
++    */
+ #include <ctype.h>
+ #include <wctype.h>
+ #undef isalnum
+@@ -705,6 +711,7 @@
+ #undef toupper
+ #define toupper(c) towupper(btowc(c))
+ #endif
++#endif
+ 
+ 
+ /* Declarations for symbol visibility.