Merge branch 'develop' into t/24889/enumerate_all_genera_of_given_sig…

…nature__determinant_and_bounded_scale_of_a_jordan_block_

Makefile

@@ -9,7 +9,18 @@
 
 default: all
 
-build: all-build
+all: base-toolchain
+	$(MAKE) all-start
+
+build: base-toolchain
+	$(MAKE) all-build
+
+start: base-toolchain
+	$(MAKE) build-start
+
+sageruntime: base-toolchain
+	$(MAKE) all-sageruntime
+
 
 # The --stop flag below is just a random flag to induce graceful
 # breakage with non-GNU versions of make.
@@ -150,8 +161,12 @@ install: all
 	@echo "from https://github.com/sagemath/binary-pkg"
 	@echo "******************************************************************"
 
+list:
+	@$(MAKE) --silent build/make/Makefile >&2
+	@$(MAKE) --silent -f build/make/Makefile SAGE_SPKG_INST=local $@
+
 .PHONY: default build install micro_release \
 	misc-clean bdist-clean distclean bootstrap-clean maintainer-clean \
 	test check testoptional testall testlong testoptionallong testallong \
 	ptest ptestoptional ptestall ptestlong ptestoptionallong ptestallong \
-	buildbot-python3
+	buildbot-python3 list

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.2.beta8, Release Date: 2018-03-10
+SageMath version 8.3.beta0, Release Date: 2018-05-09

build/bin/sage-spkg

@@ -714,7 +714,7 @@ __EOF__
 }
 
 
-for script in build install check; do
+for script in build install check postinst; do
     script="spkg-$script"
     if [ -f "$script" ]; then
         if [ "$USE_LOCAL_SCRIPTS" = "yes" ]; then
@@ -801,6 +801,26 @@ export https_proxy=$http_proxy
 export ftp_proxy=$http_proxy
 export rsync_proxy=$http_proxy
 
+##################################################################
+# We need to run sage-rebase.sh for each package installed, but it
+# can be dangerous to do this while other packages are installing
+# so we need to use a lock to manage when rebase is allowed to
+# run.  Because of this, if multiple sage-spkg runs are waiting on
+# the rebase lock, we can end up with multiple consecutive rebase
+# calls that are redundant, but I don't see an obvious way around
+# that.  This also unfortunately slows down parallel builds since
+# all packages will eventually need to wait for this lock, but
+# again there's no simple way around that.
+##################################################################
+
+if [ "$UNAME" = "CYGWIN" ]; then
+    if [ ! -d "$SAGE_LOCAL/var/lock" ]; then
+        mkdir -p "$SAGE_LOCAL/var/lock"
+    fi
+    exec 200>"$SAGE_LOCAL/var/lock/rebase.lock"
+    sage-flock -s $lock_type 200
+fi
+
 ##################################################################
 # Actually install
 ##################################################################
@@ -810,6 +830,13 @@ export rsync_proxy=$http_proxy
 # this in one place)
 export SAGE_DESTDIR="${SAGE_BUILD_DIR}/${PKG_NAME}/inst"
 
+# The actual prefix where the installation will be staged. This is the
+# directory that you need to work in if you want to change the staged
+# installation tree (before final installation to $SAGE_LOCAL) at the
+# end of spkg-install.
+export SAGE_DESTDIR_LOCAL="${SAGE_DESTDIR}${SAGE_LOCAL}"
+
+
 if [ -f spkg-build ]; then
     # Package has both spkg-build and spkg-install; execute the latter with SAGE_SUDO
     time ./spkg-build
@@ -835,7 +862,7 @@ fi
 # case DESTDIR=$SAGE_DESTDIR installation was not used
 echo "Copying package files from temporary location $SAGE_DESTDIR to $SAGE_LOCAL"
 if [ -d "$SAGE_DESTDIR" ]; then
-    PREFIX="${SAGE_DESTDIR}${SAGE_LOCAL%/}/"
+    PREFIX="${SAGE_DESTDIR_LOCAL%/}/"
 
     rm -f "$PREFIX"lib/*.la
     if [ $? -ne 0 ]; then
@@ -857,9 +884,9 @@ if [ -d "$SAGE_DESTDIR" ]; then
         fi
         # Copy file from the temp install path into $SAGE_LOCAL
         if [ ! -d "$SAGE_LOCAL/$(dirname "$filename")" ]; then
-            mkdir -p "$SAGE_LOCAL/$(dirname "$filename")"
+            $SAGE_SUDO mkdir -p "$SAGE_LOCAL/$(dirname "$filename")"
         fi
-        mv "$PREFIX$filename" "${SAGE_LOCAL%/}/$filename"
+        $SAGE_SUDO mv "$PREFIX$filename" "${SAGE_LOCAL%/}/$filename"
         if [ $? -ne 0 ]; then
             error_msg "Error moving files for $PKG_BASE."
             exit 1
@@ -871,10 +898,29 @@ if [ -d "$SAGE_DESTDIR" ]; then
     rm -rf "$SAGE_DESTDIR"
 fi
 
+# At this stage the path in $SAGE_DESTDIR no longer exists, so the variable
+# should be unset
+unset SAGE_DESTDIR
+unset SAGE_DESTDIR_LOCAL
+
+# Run the post-install script, if any
+if [ -f spkg-postinst ]; then
+    time $SAGE_SUDO ./spkg-postinst
+    if [ $? -ne 0 ]; then
+        error_msg "Error running the postinst script for $PKG_BASE."
+        exit 1
+    fi
+fi
+
 if [ "$UNAME" = "CYGWIN" ]; then
+    # Drop our sage-spkg's shared lock, and try to call sage-rebase.sh
+    # under an exclusive lock
+    sage-flock -u 200
+
     # Rebase after installing each package--in case any packages load this
     # package at build time we need to ensure during the build that no binaries
     # have conflicting address spaces
+    echo "Waiting for rebase lock"
     sage-flock -x "$SAGE_LOCAL/var/lock/rebase.lock" \
         sage-rebase.sh "$SAGE_LOCAL" 2>/dev/null
 fi

build/make/Makefile.in

@@ -125,11 +125,15 @@ $(INST)/.dummy:
 #
 #     $(inst_python2) $(inst_cython) $(inst_pari) | $(inst_pip)
 #
+# If some value in the dependencies list is not a package name (e.g. it is
+# the name of some arbitrary file, or it is the '|' symbol) then it is just
+# used verbatim.
+#
 # Positional arguments:
 #     $(1): package name
 pkg_deps = \
 	$(foreach dep,$(deps_$(1)),\
-        $(if $(findstring |,$(dep)),|,$$(inst_$(dep))))
+        $(if $(value inst_$(dep)),$$(inst_$(dep)),$(dep)))
 
 # ============================= normal packages ==============================
 # Generate build rules for 'normal' packages; this template is used to generate
@@ -253,6 +257,16 @@ $(foreach pkgname,$(SCRIPT_PACKAGES),\
 	$(info $(call SCRIPT_PACKAGE_templ,$(pkgname),$(call pkg_deps,$(pkgname)))))
 endif
 
+
+# Use this target to list common targets of this Makefile (in particular for
+# installation with `sage -i`.
+list:
+	@for pkg in $(SAGE_I_TARGETS) $(NORMAL_PACKAGES) $(PIP_PACKAGES) $(SCRIPT_PACKAGES); do\
+		echo $$pkg;\
+	done
+
+
 .PHONY: $(NORMAL_PACKAGES) $(addsuffix -clean,$(NORMAL_PACKAGES)) \
         $(PIP_PACKAGES) $(addsuffix -clean,$(PIP_PACKAGES)) \
-        $(SCRIPT_PACKAGES) $(addsuffix -clean,$(SCRIPT_PACKAGES))
+        $(SCRIPT_PACKAGES) $(addsuffix -clean,$(SCRIPT_PACKAGES)) \
+		list

build/make/deps

@@ -14,11 +14,18 @@ endif
 # We need to be able to override this to support ./sage -i -c PKG
 SAGE_SPKG = sage-spkg
 
+# List of targets that can be run using `sage -i` or `sage -f`
+# These should generally have an associated -clean target for `sage -f` to
+# work correctly
+SAGE_I_TARGETS = sagelib doc
+
 STARTED = $(SAGE_LOCAL)/etc/sage-started.txt
 
+
 # Tell make not to look for files with these names:
-.PHONY: all all-sage all-toolchain all-build start \
-	base toolchain toolchain-deps sagelib \
+.PHONY: all all-sage all-toolchain all-build all-sageruntime \
+	all-start build-start base toolchain toolchain-deps base-toolchain \
+	sagelib \
 	doc doc-html doc-html-jsmath doc-html-mathjax doc-pdf \
 	doc-clean doc-src-clean doc-output-clean \
 	clean sagelib-clean build-clean
@@ -27,24 +34,21 @@ STARTED = $(SAGE_LOCAL)/etc/sage-started.txt
 # Note that we put the "doc" target first in the rule below because
 # the doc build takes the most time and should be started as soon as
 # possible.
-all: all-toolchain
+all-start: toolchain-deps
 	$(MAKE) doc all-sage
 	$(MAKE) '$(STARTED)'
 
 # Build everything except the documentation
-all-build: all-toolchain
+all-build: toolchain-deps
 	$(MAKE) all-sage
 
 
-# Make the 3 preliminary build phases:
-# base, toolchain, 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.
-all-toolchain:
-	$(MAKE) base
+base-toolchain: base
 	env SAGE_BUILD_TOOLCHAIN=yes $(MAKE) toolchain
-	$(MAKE) toolchain-deps
 
 # All targets except for the base packages
 all-sage: \
@@ -76,18 +80,21 @@ toolchain-deps:
 	$(MAKE) $(inst_mpfr)
 	$(MAKE) $(inst_mpc)
 
+all-toolchain: base-toolchain
+	$(MAKE) toolchain-deps
+
 # Everything needed to start up Sage using "./sage".  Of course, not
 # every part of Sage will work.  It does not include Maxima for example.
 SAGERUNTIME = sagelib $(SCRIPTS) $(inst_ipython) $(inst_pexpect) \
 		$(inst_psutil) $(inst_future)
 
-sageruntime: all-toolchain
+all-sageruntime: toolchain-deps
 	$(MAKE) $(SAGERUNTIME)
 
 
 # Start Sage at least once to check that it works
 # (i.e. when we just installed Sage for the first time).
-start: all-build
+build-start: all-build
 	$(MAKE) '$(STARTED)'
 
 # We make this depend on all standard packages because running

build/pkgs/atlas/configuration.py

@@ -169,13 +169,8 @@ def close(self):
 
 conf['bits'] = platform.architecture()[0]
 
-if os.environ.get('SAGE64', 'no') == 'yes':
-    assert conf['bits'] == '64bit', 'SAGE64=yes on a 32-bit system!'
-    conf['64bit?'] = True
-else:
-    conf['64bit?'] = (conf['bits'] == '64bit')
-
-conf['32bit?'] = not conf['64bit?']
+conf['64bit?'] = (conf['bits'] == '64bit')
+conf['32bit?'] = (conf['bits'] != '64bit')
 
 
 ######################################################################

build/pkgs/autotools/type

@@ -1 +1 @@
-optional
+experimental

build/pkgs/bleach/SPKG.txt

@@ -0,0 +1,17 @@
+= bleach =
+
+== Description ==
+
+An easy safelist-based HTML-sanitizing tool.
+
+== License ==
+
+Apache License v2
+
+== Upstream Contact ==
+
+Home Page: https://github.com/mozilla/bleach
+
+== Dependencies ==
+
+Python, html5lib, six

build/pkgs/bleach/checksums.ini

@@ -0,0 +1,4 @@
+tarball=bleach-VERSION.tar.gz
+sha1=ed09e5428b8a47d57e232457ad944119ce9cba06
+md5=47fb1e6a6fd82ca84c0e9fd1023321e6
+cksum=1206011431

build/pkgs/bleach/dependencies

@@ -0,0 +1,5 @@
+$(PYTHON) | setuptools pip
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.

build/pkgs/bleach/package-version.txt

@@ -0,0 +1 @@
+2.1.3

build/pkgs/bleach/spkg-install

@@ -0,0 +1 @@
+cd src && sdh_pip_install .

build/pkgs/bleach/type

@@ -0,0 +1 @@
+standard

build/pkgs/bzip2/spkg-install

@@ -1,14 +1,3 @@
-if [ "x$CFLAG64" = x ]; then
-    CFLAG64=-m64
-fi
-
-if [ "x$SAGE64" = xyes ]; then
-    echo "Building a 64-bit version of bzip2"
-    CFLAGS="$CFLAG64 $CFLAGS"
-fi
-
-export CFLAGS="-O2 -g $CFLAGS"
-
 cd src/src
 
 # Autotoolify bzip2

build/pkgs/cddlib/spkg-install

@@ -1,16 +1,3 @@
-# Normally for a 64-bit build, the -m64 option is added to
-# gcc, but other compilers will not accept that, so
-# allow it to be configured as something different if need
-# be.
-
-if [ -z $CFLAG64 ] ; then
-    CFLAG64=-m64
-fi
-
-if [ "x$SAGE64" = xyes ]; then
-    echo "64 bit build of cddlib"
-    CFLAGS="$CFLAGS $CFLAG64"; export CFLAGS
-fi
 export CPPFLAGS="-I$SAGE_LOCAL/include $CPPFLAGS"
 
 cd src

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=da31bee34bb5f75c85af4af3479783c061a357a2
-md5=310a850d0a886892a777570bca9333f9
-cksum=3849795753
+sha1=12c986c0c792c32279e4e7948e69feba57b51f92
+md5=83a4497b5cce2f0a3a17746f9a6e9528
+cksum=2212091534

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-256
+263

build/pkgs/cryptominisat/type

@@ -1 +1 @@
-optional
+experimental

build/pkgs/cvxopt/spkg-check

@@ -6,26 +6,6 @@ fi
 
 CUR=`pwd`
 
-# Let the user set an environment variable CFLAG64 to
-# indicate the C compiler flag for 64-bit builds. By
-# default this will be -m64. IBM's compiler on AIX
-# and HP's on HP-UX do NOT use -m64.
-
-if [ -z "$CFLAG64" ] ; then
-    CFLAG64=-m64
-fi
-
-# There is no C++ code in cvxopt, so no need to do likewise
-# with CXXFLAG64.
-
-if [ "x$SAGE64" = xyes ]; then
-    echo "Testing a 64-bit version of the cvxopt"
-    CFLAGS="$CFLAGS $CFLAG64"
-    CPPFLAGS="$CPPFLAGS $CFLAG64" ; export CPPFLAGS
-    LDFLAGS="$LDFLAGS $CFLAG64" ; export LDFLAGS
-    CC="$CC $CFLAG64" ; export CC
-fi
-
 if [ "x$SAGE_DEBUG" = xyes ] ; then
     CFLAGS="$CFLAGS -g -O0" # No optimisation, aids debugging.
 else

build/pkgs/cvxopt/spkg-install

@@ -6,21 +6,6 @@ fi
 
 cd src
 
-# Normally for a 64-bit build the -m64 option is added to
-# gcc, but other compilers will not accept that, so
-# allow it to be configured as something different if need
-# be.
-
-if [ -z $CFLAG64 ] ; then
-   CFLAG64=-m64
-fi
-
-if [ "x$SAGE64" = xyes ]; then
-   echo "Building a 64 bit version of cvxopt"
-   CFLAGS="$CFLAGS $CFLAG64"; export CFLAGS
-   CC="$CC $CFLAG64" ; export CC
-fi
-
 # Ensure FreeBSD build finds new, local math.h and complex.h
 if [ "$UNAME" = FreeBSD ]; then
     export CPPFLAGS="$CPPFLAGS -I$SAGE_LOCAL/include"