Merge tag '8.7' into u/dkrenn/joint-spectral-radius

SageMath version 8.7, Release Date: 2019-03-23

* tag '8.7': (943 commits)
  Updated SageMath version to 8.7
  Updated SageMath version to 8.7.rc0
  Trac sagemath#27490: Moved the alternate build_many implementation into a sage_setup.docbuild.utils module.
  Trac sagemath#27490: Further fixes in use of os.wait()
  Trac sagemath#27214: Patch GAP to allocate its memory pool using MAP_NORESERVE on Cygwin
  Trac sagemath#27490: Address some review comments and other cleanup:
  A little bit of import cleanup
  Trac sagemath#27490: Simplistic multiprocessing.Pool replacement for parallel docbuild on older Cygwin
  Fix alarm() test when cysignals was compiled with debugging
  Trac sagemath#27485: Use sdh_cmake in the spkg-install for primecount.
  Trac sagemath#27484: Add shd_cmake helper for running cmake with the correct flags for building Sage SPKGs.
  cysignals should be a normal dependency
  Upgrade to Cysignals 1.10.2
  Upgrade to notebook-5.7.6
  Trac sagemath#27461: Add abs tol on this test to account for minor numerical difference on Cygwin due to libm differences.
  Replacing None < infinity comparison with equivalent code.
  Some last little tidbits for uniformity.
  Removing some code duplication for __pth_root (changed to _pth_root_func).
  One more xderinv added.
  trac 27474: move some references to the master bibliography file.
  ...

Makefile

@@ -53,11 +53,10 @@ build/make/Makefile: configure build/make/deps build/make/Makefile.in build/pkgs
 		fi; )
 
 # This is used to monitor progress towards Python 3 and prevent
-# regressions. The target "build" should be upgraded to reflect the
-# level of Python 3 support that is known to work.
+# regressions.
 buildbot-python3: configure
 	./configure --with-python=3
-	$(MAKE) build
+	$(MAKE)
 
 # Preemptively download all standard upstream source tarballs.
 download:
@@ -144,6 +143,7 @@ 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
@@ -189,6 +189,9 @@ ptestoptional: all
 ptestoptionallong: all
 	$(PTESTALL) --long --logfile=logs/ptestoptionallong.log
 
+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
 
@@ -209,4 +212,4 @@ 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
 
@@ -148,45 +149,73 @@ 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`.
 
-   To start the build, type `make`.
+1. 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: If you want to build the PDF version of the documentation,
+    run `make doc-pdf` (this requires LaTeX to be installed).
 
 1. Optional: You might install optional packages of interest to you: type
    `./sage --optional` to get a list.
@@ -335,7 +364,7 @@ source tree goes something like this:
 
 1. `make python2`
 1. run `./bootstrap` if `configure` does not exist
-1. run `./configure` if `build/make/Makefile` doe not exist
+1. run `./configure` if `build/make/Makefile` does not exist
 1. `cd` into `build/make` and run the `install` script--this is little more
    than a front-end to running `make -f build/make/Makefile python2`, which
    sets some necessary environment variables and logs some information

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.6, Release Date: 2019-01-15
+SageMath version 8.7, Release Date: 2019-03-23

bootstrap

@@ -47,13 +47,15 @@ SAGE_SPKG_CONFIGURE_$(echo ${pkgname} | tr '[a-z]' '[A-Z]')"
     case $st in
         0) true;; # Success
 
-        63|127)  # Autotools not installed or version too old
+        16|63|127)  # no m4 for pkg-config, or autotools not installed, or version too old
             if [ $DOWNLOAD = yes ]; then
                 echo >&2 "Bootstrap failed, downloading required files instead."
                 bootstrap-download || exit $?
             else
                 if [ $st -eq 127 ]; then
                     verb="install"
+                elif [ $st -eq 16 ]; then
+                    verb="install pkg-config m4 macros for"
                 else
                     verb="upgrade"
                 fi

build/bin/sage-spkg

@@ -715,7 +715,7 @@ __EOF__
 }
 
 
-WRAPPED_SCRIPTS="build install check postinst legacy-uninstall prerm postrm"
+WRAPPED_SCRIPTS="build install check preinst postinst legacy-uninstall prerm postrm"
 INSTALLED_SCRIPTS="prerm postrm"
 
 
@@ -850,6 +850,15 @@ if [ "$KEEP_EXISTING" != "yes" ]; then
     sage-spkg-uninstall "$PKG_BASE"
 fi
 
+# Run the pre-install script, if any
+if [ -f spkg-preinst ]; then
+    echo "Running pre-install script for $PKG_NAME."
+    time $SAGE_SUDO ./spkg-preinst
+    if [ $? -ne 0 ]; then
+        error_msg "Error running the preinst script for $PKG_NAME."
+        exit 1
+    fi
+fi
 
 if [ -f spkg-build ]; then
     # Package has both spkg-build and spkg-install; execute the latter with SAGE_SUDO
@@ -976,7 +985,15 @@ if [ "$SAGE_CHECK" = "yes" ]; then
     fi
 fi
 
-FILE_LIST="$(echo "$FILE_LIST" | sed 's/^\(.\+\)$/"\1"/; 2,$s/^/        /; $!s/$/,/')"
+# For each line in $FILE_LIST, enclose in double quotes:
+NEW_LIST=""
+for f in $FILE_LIST; do
+         NEW_LIST+="\"$f\"
+"
+done
+# Now remove the last line (it's blank), indent each line (skipping
+# the first) and append a comma (skipping the last).
+FILE_LIST="$(echo "$NEW_LIST" | sed '$d' | sed '2,$s/^/        /; $!s/$/,/')"
 
 # Mark that the new package has been installed (and tested, if
 # applicable).

build/make/deps

@@ -45,11 +45,8 @@ all-build: toolchain-deps
 
 
 # The 2 preliminary build phases: base and toolchain.
-# During the toolchain build, we export SAGE_BUILD_TOOLCHAIN=yes
-# such that packages can do different things when they are built
-# as prerequisite of GCC.
 base-toolchain: _clean-broken-gcc base
-	env SAGE_BUILD_TOOLCHAIN=yes $(MAKE) toolchain
+	$(MAKE) toolchain
 
 # All targets except for the base packages
 all-sage: \
@@ -127,7 +124,7 @@ base: $(inst_patch) $(inst_pkgconf)
 # dependencies for Cython files (e.g. PARI, NTL, MP_LIBRARY).
 sagelib: \
 		$(inst_arb) \
-		$(BLAS) \
+		$(inst_$(BLAS)) \
 		$(inst_brial) \
 		$(inst_cliquer) \
 		$(inst_cypari) \
@@ -141,6 +138,7 @@ sagelib: \
 		$(inst_gap) \
 		$(inst_givaro) \
 		$(inst_glpk) \
+		$(inst_gmpy2) \
 		$(inst_gsl) \
 		$(inst_iml) \
 		$(inst_jinja2) \
@@ -156,18 +154,18 @@ sagelib: \
 		$(inst_mpc) \
 		$(inst_mpfi) \
 		$(inst_mpfr) \
-		$(MP_LIBRARY) \
+		$(inst_$(MP_LIBRARY)) \
 		$(inst_ntl) \
 		$(inst_numpy) \
 		$(inst_pari) \
 		$(inst_pip) \
 		$(inst_pkgconfig) \
 		$(inst_planarity) \
 		$(inst_ppl) \
+		$(inst_pplpy) \
 		$(inst_pycygwin) \
 		$(inst_pynac) \
-		$(inst_python2) \
-		$(inst_python3) \
+		$(inst_$(PYTHON)) \
 		$(inst_ratpoints) \
 		$(inst_readline) \
 		$(inst_rw) \

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

@@ -1,4 +1,4 @@
 tarball=arb-VERSION.tar.gz
-sha1=42c4720675d7fc40d2f6af9de06407c00775b8f2
-md5=35855176fc2c2e69e4b4c3cde004c070
-cksum=745812142
+sha1=cdbb3d63034a39f22f850def9bd365f7073f620a
+md5=17816f8aa027a5e7fb8b5e62b2b40ce4
+cksum=577630044

build/pkgs/arb/package-version.txt

@@ -1 +1 @@
-2.15.1
+2.16.0.p0

build/pkgs/arb/spkg-install

@@ -5,20 +5,8 @@ cd src
 export EXTRA_SHARED_FLAGS=$LDFLAGS
 
 ./configure --disable-static --prefix="$SAGE_LOCAL" --with-flint="$SAGE_LOCAL" \
-    --with-gmp="$SAGE_LOCAL" --with-mpfr="$SAGE_LOCAL"
-if [ $? -ne 0 ]; then
-    echo >&2 "Error configuring arb."
-    exit 1
-fi
+    --with-gmp="$SAGE_LOCAL" --with-mpfr="$SAGE_LOCAL" || \
+    sdh_die "Error configuring arb."
 
-$MAKE verbose
-if [ $? -ne 0 ]; then
-    echo >&2 "Error building arb."
-    exit 1
-fi
-
-$MAKE install
-if [ $? -ne 0 ]; then
-    echo >&2 "Error installing arb."
-    exit 1
-fi
+sdh_make verbose
+sdh_make_install

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/bleach/checksums.ini

@@ -1,4 +1,4 @@
 tarball=bleach-VERSION.tar.gz
-sha1=ed09e5428b8a47d57e232457ad944119ce9cba06
-md5=47fb1e6a6fd82ca84c0e9fd1023321e6
-cksum=1206011431
+sha1=e7ee75050ccace055d5040010e3fdfb8e2535a3a
+md5=f042c4e8a953824dc8511f535daa20a4
+cksum=3095652578

build/pkgs/bleach/package-version.txt

@@ -1 +1 @@
-2.1.3
+3.0.2