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

…nature__determinant_and_bounded_scale_of_a_jordan_block_

Conflicts:
	src/sage/quadratic_forms/genera/genus.py

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,3 @@
+Unfortunately we are not accepting issues on GitHub yet. To report an issue,
+please head over to https://trac.sagemath.org, log in with your GitHub account,
+and create a ticket there :)

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,8 @@
+Thanks for contributing to Sage! Unfortunately we are not accepting pull
+requests on GitHub yet. To propose a change to Sage, please log in with your
+GitHub account at https://trac.sagemath.org, create a ticket, and push your
+changes to that ticket as explained in our
+[Developer's Guide](https://doc.sagemath.org/html/en/developer/manual_git.html).
+
+Please make sure to also have a look at our
+[Code Style Conventions](https://doc.sagemath.org/html/en/developer/coding_basics.html).

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.3.beta1, Release Date: 2018-05-14
+SageMath version 8.3.beta6, Release Date: 2018-06-17

build/bin/sage-spkg

@@ -167,11 +167,13 @@ if [ -z "$SAGE_BUILD_DIR" ]; then
     export SAGE_BUILD_DIR="$SAGE_LOCAL/var/tmp/sage/build"
 fi
 
-mkdir -p "$SAGE_SPKG_INST"
-if [ $? -ne 0 ]; then
-    error_msg "Error creating directory $SAGE_SPKG_INST"
-    exit 1
-fi
+for dir in "$SAGE_SPKG_INST" "$SAGE_SPKG_SCRIPTS"; do
+    mkdir -p "$dir"
+    if [ $? -ne 0 ]; then
+        error_msg "Error creating directory $dir"
+        exit 1
+    fi
+done
 
 
 # Remove '.' from PYTHONPATH, which may also come from SAGE_PATH, to avoid
@@ -660,7 +662,7 @@ cd ..
 # passed in as an absolute path.
 write_script_wrapper() {
     local script="$1"
-    local pkgdir="$(dirname "$script")"
+    local script_dir="$2"
 
     trap "echo >&2 Error: Unexpected error writing wrapper script for $script; exit \$_" ERR
 
@@ -676,7 +678,7 @@ write_script_wrapper() {
 
 export SAGE_ROOT="$SAGE_ROOT"
 export SAGE_SRC="$SAGE_SRC"
-export SAGE_PKG_DIR="$pkgdir"
+export SAGE_PKG_DIR="$script_dir"
 
 export PKG_NAME="$PKG_NAME"
 export PKG_BASE="$PKG_BASE"
@@ -714,8 +716,22 @@ __EOF__
 }
 
 
-for script in build install check postinst; do
+WRAPPED_SCRIPTS="build install check postinst legacy-uninstall prerm postrm"
+INSTALLED_SCRIPTS="prerm postrm"
+
+
+for script in $WRAPPED_SCRIPTS; do
+    # 'Installed' scripts are not run immediately out of the package build
+    # directory, and may be run later, so set their root directory to
+    # $SAGE_ROOT
+    if echo "$INSTALLED_SCRIPTS" | grep -w "$script" > /dev/null; then
+        script_dir="$SAGE_ROOT"
+    else
+        script_dir="$(pwd)"
+    fi
+
     script="spkg-$script"
+
     if [ -f "$script" ]; then
         if [ "$USE_LOCAL_SCRIPTS" = "yes" ]; then
             if [ -x "$script" ]; then
@@ -731,7 +747,7 @@ for script in build install check postinst; do
                 fi
             fi
 
-            write_script_wrapper $(pwd)/"$script"
+            write_script_wrapper "$(pwd)/$script" "$script_dir"
         else
             if [ ! -x "$script" ]; then
                 echo >&2 "WARNING: $script is not executable, making it executable"
@@ -787,12 +803,6 @@ echo "C compiler version:"
 $CC -v
 echo "****************************************************"
 
-##################################################################
-# Remove install markers for any other versions of this spkg.
-##################################################################
-
-rm -f "$SAGE_SPKG_INST/$PKG_BASE-"*
-
 ##################################################################
 # Poison the proxy variable to forbid downloads in spkg-install
 ##################################################################
@@ -858,6 +868,10 @@ else
     fi
 fi
 
+# We are now ready to install the new package files into $SAGE_LOCAL, so first
+# uninstall the previous version of this package, if any
+sage-spkg-uninstall "$PKG_BASE"
+
 # All spkgs should eventually support this, but fall back on old behavior in
 # case DESTDIR=$SAGE_DESTDIR installation was not used
 echo "Copying package files from temporary location $SAGE_DESTDIR to $SAGE_LOCAL"
@@ -873,7 +887,7 @@ if [ -d "$SAGE_DESTDIR" ]; then
     # Generate installed file manifest
     FILE_LIST=""
     FIRST=1
-    IFS=$'\n'
+    old_IFS="$IFS"; IFS=$'\n'
     for filename in $(find "$PREFIX" -type f -o -type l | sort); do
         filename="${filename#$PREFIX}"
         if [ $FIRST -eq 1 ]; then
@@ -888,26 +902,53 @@ if [ -d "$SAGE_DESTDIR" ]; then
         fi
         $SAGE_SUDO mv "$PREFIX$filename" "${SAGE_LOCAL%/}/$filename"
         if [ $? -ne 0 ]; then
-            error_msg "Error moving files for $PKG_BASE."
+            error_msg "Error moving files for $PKG_NAME."
             exit 1
         fi
     done
+    IFS="$old_IFS"
 
     # Remove the $SAGE_DESTDIR entirely once all files have been moved to their
     # final location.
     rm -rf "$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
 
+
+# Some spkg scripts, if they exist, should also be installed to
+# $SAGE_SPKG_SCRIPTS; they are not included in the package's manifest, but are
+# removed by sage-spkg-uninstall
+INSTALLED_SCRIPTS_DEST="$SAGE_SPKG_SCRIPTS/$PKG_BASE"
+for script in $INSTALLED_SCRIPTS; do
+    script="spkg-$script"
+
+    if [ -f "$script" ]; then
+        mkdir -p "$INSTALLED_SCRIPTS_DEST"
+        if [ $? -ne 0 ]; then
+            error_msg "Error creating the spkg scripts directory $INSTALLED_SCRIPTS_DEST."
+            exit 1
+        fi
+
+        cp -a "$script" "$INSTALLED_SCRIPTS_DEST"
+        if [ $? -ne 0 ]; then
+            error_msg "Error copying the $script script to $INSTALLED_SCRIPTS_DEST."
+            exit 1
+        fi
+    fi
+done
+
+
 # Run the post-install script, if any
 if [ -f spkg-postinst ]; then
+    echo "Running post-install script for $PKG_NAME."
     time $SAGE_SUDO ./spkg-postinst
     if [ $? -ne 0 ]; then
-        error_msg "Error running the postinst script for $PKG_BASE."
+        error_msg "Error running the postinst script for $PKG_NAME."
         exit 1
     fi
 fi

build/bin/sage-spkg-uninstall

@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+
+# usage: sage-spkg-uninstall [-h] PKG [SAGE_LOCAL]
+#
+# Uninstall a Sage spkg installed in SAGE_LOCAL by removing all files
+# associated with that package.
+#
+# positional arguments:
+#   PKG         the name of the package to uninstall
+#   FILE        the path to SAGE_LOCAL (default: value of the $SAGE_LOCAL
+#               environment variable if set; exits otherwise)
+#
+# optional arguments:
+#   -h, --help  show this help message and exit
+
+
+try:
+    import sage_bootstrap
+except ImportError:
+    import os, sys
+    sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
+    import sage_bootstrap
+
+from sage_bootstrap.uninstall import run
+run()

build/make/Makefile.in

@@ -63,7 +63,6 @@ OPTIONAL_INSTALLED_PACKAGE_INSTS = \
 
 # All packages which should be downloaded
 SDIST_PACKAGES = @SAGE_SDIST_PACKAGES@
-SDIST_PACKAGE_INSTS = $(foreach pkgname,$(SDIST_PACKAGES),$(inst_$(pkgname)))
 
 SCRIPTS = @SAGE_SCRIPTS@
 
@@ -145,7 +144,7 @@ pkg_deps = \
 # <pkgname>: $(INST)/<pkgname>-<pkgvers>
 #
 # <pkgname>-clean:
-#     rm -rf $(INST)/<pkgname>-<pkgvers>
+#     sage-spkg-uninstall <pkgname> '$(SAGE_LOCAL)'
 #
 # For example, for python2 this will expand to:
 #
@@ -155,7 +154,7 @@ pkg_deps = \
 # python2: $(INST)/python2-2.7.14
 #
 # python2-clean:
-#     rm -rf $(INST)/python2-2.7.14
+#     sage-spkg-uninstall python2 '$(SAGE_LOCAL)'
 #
 # Note: In these rules the $(INST)/<pkgname>-<pkgvers> target is used
 # explicitly, rather than expanding the $(inst_<pkgname>) variable, since
@@ -174,6 +173,7 @@ $$(INST)/$(1)-$(2): $(3)
 $(1): $$(INST)/$(1)-$(2)
 
 $(1)-clean:
+	sage-spkg-uninstall $(1) '$$(SAGE_LOCAL)'
 	rm -rf $$(INST)/$(1)-$(2)
 
 endef

build/make/deps

@@ -60,9 +60,9 @@ all-sage: \
 
 # Download all packages which should be inside an sdist tarball (the -B
 # option to make forces all targets to be built unconditionally)
-download-for-sdist: base
+download-for-sdist:
 	env SAGE_INSTALL_FETCH_ONLY=yes $(MAKE) -B SAGERUNTIME= \
-		$(SDIST_PACKAGE_INSTS)
+		$(SDIST_PACKAGES)
 
 # TOOLCHAIN consists of dependencies determined by configure.
 # These are built after the "base" target but before anything else.

build/make/install

@@ -19,7 +19,8 @@ export SAGE_SHARE="$SAGE_LOCAL/share"
 export SAGE_EXTCODE="$SAGE_SHARE/sage/ext"
 export SAGE_LOGS="$SAGE_ROOT/logs/pkgs"
 export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed"
-export SAGE_VERSION=`cat $SAGE_ROOT/VERSION.txt | sed 's+.*\ \(.*\),.*+\1+'`
+. "$SAGE_SRC"/bin/sage-version.sh
+export SAGE_VERSION
 
 if [ -z "${SAGE_ORIG_PATH_SET}" ]; then
     SAGE_ORIG_PATH=$PATH && export SAGE_ORIG_PATH

build/pkgs/atlas/patches/atlas-config

@@ -22,7 +22,7 @@ def pid_exists(pid):
         return False
     try:
         os.kill(pid, 0)
-    except OSError, e:
+    except OSError as e:
         return e.errno == errno.EPERM
     else:
         return True
@@ -39,11 +39,11 @@ def unthrottle_posix(pid):
             f.write('performance')
 
     def signal_handler(signum, frame):
-        print 'Signal hanadler called with signal', signum
+        print('Signal handler called with signal', signum)
         for cpu, governor in zip(cpus, scaling_governor):
             with open(cpu, 'w') as f:
                 f.write(governor)
-        print 'Reverted throttling to the previous behaviour.'
+        print('Reverted throttling to the previous behaviour.')
         sys.exit(0)
 
     signal.signal(signal.SIGPIPE, signal_handler)
@@ -63,7 +63,8 @@ def unthrottle(pid):
     if os.name == 'posix':
         unthrottle_posix(pid)
     else:
-        print 'I don\'t know how to unthrottle your system ('+platform.system()+')'
+        print('I don\'t know how to unthrottle your system (' +
+              platform.system() + ')')
         sys.exit(3)
 
 
@@ -81,29 +82,30 @@ def is_throttled():
     if os.name == 'posix':
         return is_throttled_posix()
     else:
-        print 'I don\'t know how to unthrottle your system ('+platform.system()+')'
+        print('I don\'t know how to unthrottle your system (' +
+              platform.system() + ')')
         sys.exit(3)
 
 
 def check_root():
     if os.name == 'posix':
         if os.getuid() == 0:
             return
-        print '\nError: You need to be root to (un)throttle the CPU.\n'
+        print('\nError: You need to be root to (un)throttle the CPU.\n')
         sys.exit(1)
     else:
-        print 'I don\'t know how to probe administrator rights on your system ('+platform.system()+')'
+        print('I don\'t know how to probe administrator rights on your system ('+platform.system()+')')
         sys.exit(3)
 
 
 def check_nonroot():
     if os.name == 'posix':
         if os.getuid() > 0:
             return
-        print '\nError: You are crazy to run this as root, exiting.\n'
+        print('\nError: You are crazy to run this as root, exiting.\n')
         sys.exit(2)
     else:
-        print 'I don\'t know how to probe administrator rights on your system ('+platform.system()+')'
+        print('I don\'t know how to probe administrator rights on your system ('+platform.system()+')')
         sys.exit(3)
 
 
@@ -123,14 +125,14 @@ atexit.register(wait_for_command)
 def unthrottle_self():
     if os.name == 'posix':
         global command
-        print 'Running sudo atlas-config --unthrottle to turn CPU throttling off.'
+        print('Running sudo atlas-config --unthrottle to turn CPU throttling off.')
         command = subprocess.Popen(['sudo', os.path.abspath( __file__ ),
                                     '--unthrottle', str(os.getpid())])
     else:
-        print 'I don\'t know how to unthrottle your system ('+platform.system()+')'
+        print('I don\'t know how to unthrottle your system ('+platform.system()+')')
         sys.exit(2)
 
-    print 'Waiting for CPU throttling to be turned off...'
+    print('Waiting for CPU throttling to be turned off...')
     while is_throttled():
         time.sleep(1)
 
@@ -147,35 +149,28 @@ if __name__ == '__main__':
     unthrottle_self()
     print
     if os.environ.get('SAGE_FAT_BINARY', 'no') == 'yes':
-        print 'Building ATLAS with SAGE_FAT_BINARY (generic archdefs).'
-    elif os.environ.has_key('SAGE_ATLAS_ARCH'):
-        print 'Building ATLAS with SAGE_ATLAS_ARCH =', os.environ['SAGE_ATLAS_ARCH']
+        print('Building ATLAS with SAGE_FAT_BINARY (generic archdefs).')
+    elif 'SAGE_ATLAS_ARCH' in os.environ:
+        print('Building ATLAS with SAGE_ATLAS_ARCH =', os.environ['SAGE_ATLAS_ARCH'])
     else:
-        print 'Building ATLAS without specifying architecture.'
-    print 'This may take many hours during which you should leave the computer otherwise'
-    print 'idle to obtain accurate timings.'
+        print('Building ATLAS without specifying architecture.')
+    print('This may take many hours during which you should leave the computer otherwise')
+    print('idle to obtain accurate timings.')
     if args.archdef:
         os.environ['SAGE_ATLAS_SAVE_ARCHDEF'] = os.getcwd()
-        print 'The resulting <archdef>.tar.bz2 will be saved in '+os.getcwd()
-    print
-    print 'You have 5 seconds to interrupt...'
+        print('The resulting <archdef>.tar.bz2 will be saved in ' + os.getcwd())
+    print()
+    print('You have 5 seconds to interrupt...')
     time.sleep(1)
-    print 'You have 4 seconds to interrupt...'
+    print('You have 4 seconds to interrupt...')
     time.sleep(1)
-    print 'You have 3 seconds to interrupt...'
+    print('You have 3 seconds to interrupt...')
     time.sleep(1)
-    print 'You have 2 seconds to interrupt...'
+    print('You have 2 seconds to interrupt...')
     time.sleep(1)
-    print 'You have 1 second to interrupt...'
+    print('You have 1 second to interrupt...')
     time.sleep(1)
 
     sys.stdout.flush()
     sys.stderr.flush()
     os.system('sage -f atlas')
-
-
-
-
-
-
-

build/pkgs/brial/dependencies

@@ -1,4 +1,4 @@
-boost_cropped m4ri libpng pkgconf $(PYTHON) | pip
+boost_cropped m4ri libpng $(PYTHON) | pip pkgconf
 
 ----------
 All lines of this file are ignored except the first.