Merge branch 'develop' of git://git.sagemath.org/sage into t/26625/up…

…date_maxima_to_5_42_1

.gitignore

@@ -1,5 +1,4 @@
 *.pyc
-/.BUILDSTART
 /dist
 /local
 /logs
@@ -15,6 +14,8 @@
 /config.status
 /configure
 
+/m4/sage_spkg_configures.m4
+
 ###################
 # Temporary Files #
 ###################

Makefile

@@ -84,7 +84,6 @@ misc-clean:
 	rm -f aclocal.m4 config.log config.status confcache
 	rm -rf autom4te.cache
 	rm -f build/make/Makefile build/make/Makefile-auto
-	rm -f .BUILDSTART
 
 bdist-clean: clean
 	$(MAKE) misc-clean
@@ -145,6 +144,7 @@ fast-rebuild-clean: misc-clean bdist-clean
 
 TESTALL = ./sage -t --all
 PTESTALL = ./sage -t -p --all
+PTEST_PYTHON3 = cat src/ext/doctest/python3-known-passing.txt | xargs ./sage -t --long -p
 
 # Flags for ./sage -t --all.
 # By default, include all tests marked 'dochtml' -- see
@@ -190,7 +190,10 @@ ptestoptional: all
 ptestoptionallong: all
 	$(PTESTALL) --long --logfile=logs/ptestoptionallong.log
 
-configure: configure.ac src/bin/sage-version.sh m4/*.m4
+ptest-python3: buildbot-python3
+	$(PTEST_PYTHON3) --logfile=logs/ptest_python3.log
+
+configure: configure.ac src/bin/sage-version.sh m4/*.m4 build/pkgs/*/spkg-configure.m4
 	./bootstrap -d
 
 install: all
@@ -210,4 +213,4 @@ list:
 	misc-clean bdist-clean distclean bootstrap-clean maintainer-clean \
 	test check testoptional testall testlong testoptionallong testallong \
 	ptest ptestoptional ptestall ptestlong ptestoptionallong ptestallong \
-	buildbot-python3 list
+	buildbot-python3 ptest-python3 list

README.md

@@ -17,9 +17,10 @@ and functions list the authors.
 Getting Started
 ---------------
 
-If you downloaded a [binary](http://www.sagemath.org/download.html),
-you just need open a terminal in the directory where you extracted the binary
-archive and type:
+If you downloaded a [binary](http://www.sagemath.org/download.html)
+(i.e. a version of SageMath prepared for a specific operating system),
+Sage is ready to start -- just open a terminal in the directory where
+you extracted the binary archive and type:
 
     ./sage
 
@@ -148,51 +149,75 @@ More Detailed Instructions to Build from Source
    gas/as, gld/ld, gnm/nm. On most platforms, these are automatically
    installed when you install the programs listed above.
 
-1. Extract the Sage source tarball and cd into a directory with no
-   spaces in it. If you have a machine with 4 processors, say, type
-   `export MAKE="make -j4"` the following to configure the build script to
-   perform a parallel compilation of Sage using 4 jobs.
-   (With 4 processors, you might also consider `-j5` or `-j6` --
-   building with more jobs than CPU cores can speed things up.)
+1. Extract the Sage source tarball into a directory, making sure
+   there are no spaces in the path to the resulting directory.
+
+   Note that moving the directory after Sage has been built will
+   require to build Sage again.
+
+1. Change to the Sage directory using `cd`.
+
+1. Optional: set some environment variables to customize the build.
+
+   For example, the `MAKE` environment variable controls whether to run
+   several jobs in parallel, while the `SAGE_CHECK` environment variable
+   controls whether to perform more tests during the installation.  For
+   an in-depth discussion of environment variables for building Sage, see
+   [the installation guide](http://doc.sagemath.org/html/en/installation/source.html#environment-variables).
+
+   On a machine with 4 processors, say, typing `export MAKE="make -j4"`
+   will configure the build script to perform a parallel compilation of
+   Sage using 4 jobs. You might even consider `-j5` or `-j6`, as
+   building with more jobs than CPU cores can speed things up further.
    You might in addition pass a `-l` [load flag](https://www.gnu.org/software/make/manual/make.html#Options-Summary)
-   to "make": this sets a load limit, so for example if you execute
+   to `make`: this sets a load limit, so for example if you execute
    `export MAKE="make -j4 -l5.5"` then "make" won't start more than one
    job at a time if the system load average is above 5.5, see
    the [make documentation](https://www.gnu.org/software/make/manual/make.html#Parallel).
 
-   If you want to run the test suite for each individual spkg as it is
-   installed, type `export SAGE_CHECK="yes"` before starting the Sage
-   build. This will run each test suite and will raise an error if any
-   failures occur. Python's test suite has been disabled by default,
-   because it causes failures on most systems. To enable the Python
-   testsuite, set the environment variable `SAGE_CHECK_PACKAGES` to `python`.
+   If you want to run the test suite for each individual Sage package
+   as it gets installed, type `export SAGE_CHECK="yes"`. This will run
+   each test suite, raising an error if any failure occurs. Python's
+   test suite has been disabled by default, because it causes failures
+   on most systems. To enable the Python test suite, set the environment
+   variable `SAGE_CHECK_PACKAGES` to `python`.
+
+1. To start the build, type `make`.
 
-   To start the build, type `make`.
+   Note: to build a Python3-based Sage, instead of typing `make`, type
+
+       make configure
+       ./configure --with-python=3
+       make
+
+   This will build Sage based on Python 3 rather than based on Python 2,
+   which is still the default at this point. The resulting Sage mostly
+   works well, though some features (less of them at each release!) are
+   not yet ready for Python 3. The progress on this is tracked at
+   [Sage Trac ticket 15530: Metaticket: Add support for python 3.6+](https://trac.sagemath.org/ticket/15530).
 
 1. Wait about 20 minutes to 14 days, depending on your computer (it took
    about 2 weeks to build Sage on the T-Mobile G1 Android cell phone).
 
 1. Type `./sage` to try it out.
 
-1. Optional: Type `make ptest` to test all examples in the documentation
+1. Optional: Type `make ptestlong` to test all examples in the documentation
    (over 200,000 lines of input!) -- this takes from 10 minutes to
    several hours. Don't get too disturbed if there are 2 to 3 failures,
-   but always feel free to email the section of `logs/ptest.log` that
+   but always feel free to email the section of `logs/ptestlong.log` that
    contains errors to the [sage-support mailing list](https://groups.google.com/group/sage-support).
    If there are numerous failures, there was a serious problem with your build.
 
+   Note: if you built for Python 3, you can instead run `make ptest-python3`.
+
 1. The HTML version of the [documentation](http://doc.sagemath.org/html/en/index.html)
    is built during the compilation process of Sage and resides in the directory
    `local/share/doc/sage/html/`.
 
-   * Optional: If you want to build the PDF version (requires LaTeX)
-   of the documentation, run `make doc-pdf`.
-
-1. Optional: It is recommended that you install the optional GAP
-   database by typing `./sage -i database_gap`.
+1. Optional: If you want to build the PDF version of the documentation,
+    run `make doc-pdf` (this requires LaTeX to be installed).
 
-   This will download the package and install it. While you're at it,
-   you might install other optional packages of interest to you: type
+1. Optional: You might install optional packages of interest to you: type
    `./sage --optional` to get a list.
 
 1. Optional: It is recommended that you have both LaTeX and the

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.5.beta2, Release Date: 2018-11-01
+SageMath version 8.7.beta3, Release Date: 2019-02-08

bootstrap

@@ -29,6 +29,16 @@ CONFVERSION=`cat $PKG/package-version.txt`
 
 
 bootstrap () {
+    rm -f m4/sage_spkg_configures.m4
+    spkg_configures=""
+    for filename in $(find build/pkgs -type f -name spkg-configure.m4); do
+        pkgname="$(echo $filename | cut -d/ -f3)"
+        echo "m4_sinclude([$filename])" >> m4/sage_spkg_configures.m4
+        spkg_configures="$spkg_configures
+SAGE_SPKG_CONFIGURE_$(echo ${pkgname} | tr '[a-z]' '[A-Z]')"
+    done
+    echo "$spkg_configures" >> m4/sage_spkg_configures.m4
+
     aclocal -I m4 && \
     automake --add-missing --copy build/make/Makefile-auto && \
     autoconf

build/bin/sage-spkg

@@ -170,8 +170,8 @@ if [ -z "$SAGE_BUILD_DIR" ]; then
 fi
 
 
-# Remove '.' from PYTHONPATH, which may also come from SAGE_PATH, to avoid
-# trouble with setuptools / easy_install (cf. #10192, #10176):
+# Remove '.' from PYTHONPATH, to avoid trouble with setuptools / easy_install
+# (cf. #10192, #10176):
 if [ -n "$PYTHONPATH" ]; then
     # We also collapse multiple slashs into a single one (first substitution),
     # remove leading './'s and trailing '/.'s (second and third), and
@@ -892,13 +892,14 @@ if [ -d "$SAGE_DESTDIR" ]; then
 
     # 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
 
 

build/bin/sage-system-python

@@ -15,4 +15,10 @@ fi
 
 PYTHON="$(PATH="$SAGE_ORIG_PATH" command -v python)"
 
+# fallback for systems where only the python3 command is available
+# see https://trac.sagemath.org/ticket/26953
+if [ -z "$PYTHON" ]; then
+    PYTHON="$(PATH="$SAGE_ORIG_PATH" command -v python3)"
+fi
+
 exec "$PYTHON" "$@"

build/make/Makefile.in

@@ -191,6 +191,7 @@ $(1): $$(INST)/$(1)-$(2)
 $(1)-clean:
 	sage-spkg-uninstall $(if $(filter $(1),$(TOOLCHAIN_DEPS)),--keep-files) \
 		$(1) '$(SAGE_LOCAL)'
+
 endef
 
 $(foreach pkgname, $(NORMAL_PACKAGES),\

build/make/deps

@@ -75,13 +75,15 @@ toolchain: $(foreach pkgname,$(TOOLCHAIN),$(inst_$(pkgname)))
 # unconditionally. We still use the dependency checking from $(MAKE),
 # so this will not trigger useless rebuilds.
 # See #14168 and #14232.
-# Note: This list is determined from the dependencies of the TOOLCHAIN
-# packages which include gcc, and optionally ccache; in principle this
-# list is redundant.
-TOOLCHAIN_DEPS = zlib xz $(MP_LIBRARY) mpfr mpc
+#
+# Note: This list consists of only the *runtime* dependencies of the toolchain.
+TOOLCHAIN_DEPS = zlib $(MP_LIBRARY) mpfr mpc
+TOOLCHAIN_DEP_INSTS = \
+	$(foreach pkgname,$(TOOLCHAIN_DEPS),$(inst_$(pkgname)))
+
 toolchain-deps:
-	for pkg in $(TOOLCHAIN_DEPS); do \
-	    $(MAKE) $$pkg; \
+	for target in $(TOOLCHAIN_DEP_INSTS); do \
+	    $(MAKE) $$target; \
 	done
 
 all-toolchain: base-toolchain
@@ -136,6 +138,7 @@ sagelib: \
 		$(inst_ecm) \
 		$(inst_flint) \
 		$(inst_libgd) \
+		$(inst_gap) \
 		$(inst_givaro) \
 		$(inst_glpk) \
 		$(inst_gsl) \
@@ -145,7 +148,6 @@ sagelib: \
 		$(inst_lcalc) \
 		$(inst_lrcalc) \
 		$(inst_libbraiding) \
-		$(inst_libgap) \
 		$(inst_libhomfly) \
 		$(inst_libpng) \
 		$(inst_linbox) \

build/make/install

@@ -30,11 +30,6 @@ export PATH="$SAGE_ROOT/build/bin:$SAGE_SRC/bin:$SAGE_LOCAL/bin:$PATH"
 
 export PYTHONPATH="$SAGE_LOCAL"
 
-# Storing the start time of the build process. The time is stored in
-# seconds since 1970-01-01 in a hidden file called
-# "SAGE_ROOT/.BUILDSTART". See ticket #6744.
-echo `date -u "+%s"` > "$SAGE_ROOT/.BUILDSTART"
-
 ###############################################################################
 # Skip the rest if nothing to do (i.e., to [re]build).
 ###############################################################################

build/pkgs/4ti2/package-version.txt

@@ -1 +1 @@
-1.6.7
+1.6.7.p0

build/pkgs/4ti2/spkg-install

@@ -1,20 +1,7 @@
 cd src/
-
-if [ "$SAGE_LOCAL" = "" ]; then
-   echo "SAGE_LOCAL undefined ... exiting";
-   echo "Maybe run 'sage -sh'?"
-   exit 1
-fi
-
 CFLAGS="-I $SAGE_LOCAL/include -L$SAGE_LOCAL/lib $CFLAGS"
 export CFLAGS
-./configure --prefix=$SAGE_LOCAL --with-gmp=$SAGE_LOCAL --with-glpk=$SAGE_LOCAL --enable-shared=yes --enable-static=no
-
-$MAKE
-$SAGE_SUDO $MAKE install
-
-if [ $? -ne 0 ]; then
-   echo "Error building 4ti2"
-   exit 1
-fi
-
+sdh_configure --with-gmp=$SAGE_LOCAL --with-glpk=$SAGE_LOCAL \
+    --enable-shared=yes --enable-static=no
+sdh_make
+sdh_make_install

build/pkgs/alabaster/checksums.ini

@@ -1,4 +1,4 @@
 tarball=alabaster-VERSION.tar.gz
-sha1=dba599faf1ca5541ef35ab251eb2b365ae2f25c7
-md5=7934dccf38801faa105f6e7b4784f493
-cksum=3227702678
+sha1=36c11bd5d8e99e2009b643b7f6e91bf2a0fd573b
+md5=3591827fde96d1dd23970fb05410ed04
+cksum=3567264444

build/pkgs/alabaster/package-version.txt

@@ -1 +1 @@
-0.7.10
+0.7.12

build/pkgs/arb/checksums.ini

@@ -1,5 +1,4 @@
 tarball=arb-VERSION.tar.gz
-sha1=94680f32c3ccd40cc8ef417cc18d7b74b0c6c522
-md5=8f9a8d57417466080cfd1358bbb41efd
-cksum=3846267256
-
+sha1=42c4720675d7fc40d2f6af9de06407c00775b8f2
+md5=35855176fc2c2e69e4b4c3cde004c070
+cksum=745812142

build/pkgs/arb/package-version.txt

@@ -1 +1 @@
-2.14.0
+2.15.1

build/pkgs/atlas/configuration.py

@@ -5,7 +5,12 @@
 
 from __future__ import print_function
 
-import platform, os, sys, time, shutil, glob, subprocess
+import platform
+import os
+import sys
+import shutil
+import glob
+import subprocess
 
 
 # this dictionary will hold all configuration information

build/pkgs/atlas/spkg-install.py

@@ -164,8 +164,9 @@ def is_atlas_lib_path(path, libs):
         sys.exit(2)
 
     for fname in os.listdir(ATLAS_LIB):
-        if fname.startswith(prefix+'f77blas'):
+        if fname.startswith(prefix + 'f77blas'):
             f77blas = os.path.join(ATLAS_LIB, fname)
+            break
     else:
         f77blas = None
     if f77blas is not None:

build/pkgs/babel/checksums.ini

@@ -1,4 +1,4 @@
 tarball=Babel-VERSION.tar.gz
-sha1=9adbd49864392713c6a3080aeb0a9e6432577277
-md5=60228b3ce93a203357158b909afe8ae1
-cksum=2035941902
+sha1=6aed99e4fb8a2a75de7815599f610cdcbb81e3c2
+md5=c384ac03026e8fe6f9b90f55201f1bff
+cksum=3805303136

build/pkgs/babel/package-version.txt

@@ -1 +1 @@
-2.5.1
+2.6.0

build/pkgs/backports_functools_lru_cache/checksums.ini

@@ -1,4 +1,4 @@
 tarball=backports.functools_lru_cache-VERSION.tar.gz
-sha1=8a546e7887e961c2873c9b053f4e2cd2a96bd71d
-md5=b954e7d5e2ca0f0f66ad2ed12ba800e5
-cksum=2013684405
+sha1=35a5895d22875cd024694d3c7393a793e9fd653d
+md5=20f53f54cd3f04b3346ce75a54959754
+cksum=4241725171

build/pkgs/backports_functools_lru_cache/package-version.txt

@@ -1 +1 @@
-1.4
+1.5

build/pkgs/barvinok/SPKG.txt

@@ -0,0 +1,15 @@
+= barvinok =
+
+== Description ==
+
+barvinok is a library for counting the number of integer points
+in parametric and non-parametric polytopes as well as projections
+of such sets.
+
+== License ==
+
+GPL v2
+
+== Upstream Contact ==
+
+ * http://groups.google.com/group/isl-development

build/pkgs/barvinok/checksums.ini

@@ -0,0 +1,4 @@
+tarball=barvinok-VERSION.tar.bz2
+sha1=31c50d4b2a4cebe049072fd54c6e41ccece5ec1d
+md5=60082222a73b2d4fd430da7b770a4072
+cksum=355377045