Merge branch 't/29233/bootstrap____make_distclean_broken' into t/2178…

…5/install_sage_src_ext__in_package_data_of_sage_package_by_setup_py__not_sage_local_share_sage_ext__by_build_make_makefile

Makefile

@@ -102,6 +102,7 @@ distclean: build-clean
 # source tarball
 bootstrap-clean:
 	rm -rf config configure build/make/Makefile-auto.in
+	rm -f src/doc/en/installation/*.txt
 
 # Remove absolutely everything which isn't part of the git repo
 maintainer-clean: distclean bootstrap-clean
@@ -193,7 +194,7 @@ ptestoptional: all
 ptestoptionallong: all
 	$(PTESTALL) --long --logfile=logs/ptestoptionallong.log
 
-configure: configure.ac src/bin/sage-version.sh m4/*.m4 build/pkgs/*/spkg-configure.m4
+configure: bootstrap src/doc/bootstrap configure.ac src/bin/sage-version.sh m4/*.m4 build/pkgs/*/spkg-configure.m4 build/pkgs/*.txt build/pkgs/*/distros/*.txt
 	./bootstrap -d
 
 install: all

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.1.beta4, Release Date: 2020-02-13
+SageMath version 9.1.beta5, Release Date: 2020-02-21

bootstrap

@@ -92,6 +92,7 @@ SAGE_SPKG_ENABLE([$pkgname], [$pkgtype])" ;;
     done
     echo "$spkg_configures" >> m4/sage_spkg_configures.m4
 
+    SAGE_ROOT="$SAGE_ROOT" src/doc/bootstrap && \
     install_config_rpath && \
     aclocal -I m4 && \
     automake --add-missing --copy build/make/Makefile-auto && \
@@ -154,7 +155,7 @@ save () {
     # Create configure tarball
     echo "Creating $NEWCONFBALL..."
     mkdir -p upstream
-    tar zcf "$NEWCONFBALL" configure config/* build/make/Makefile-auto.in
+    tar zcf "$NEWCONFBALL" configure config/* build/make/Makefile-auto.in src/doc/en/installation/*.txt
 
     # Update version
     echo "$NEWCONFVERSION" >$PKG/package-version.txt

build/bin/sage-print-system-package-command

@@ -0,0 +1,35 @@
+#!/usr/bin/env bash
+#
+system=$1
+command=$2
+if [ -z "$system" -o -z "$command" ]; then
+    echo >&2 "usage: $0 {debian|arch|conda|...} {install|remove|...} PACKAGES..."
+    exit 1
+fi
+shift 2
+system_packages="$*"
+if [ -z "$system_packages" ]; then
+    # No command needed to install nothing
+    exit 0
+fi
+shopt -s extglob
+case $system:$command in
+    debian*|ubuntu*)
+        echo "sudo apt-get $command $system_packages"
+        ;;
+    @(fedora*|redhat*|centos*):install)
+        echo "sudo yum install $system_packages"
+        ;;
+    arch*:install)
+        echo "sudo pacman -S $system_packages"
+        ;;
+    *conda*:install)
+        echo "conda install $system_packages"
+        ;;
+    homebrew*:install)
+        echo "brew install $system_packages"
+        ;;
+    *)
+        echo "# $command the following packages: $system_packages"
+        ;;
+esac

build/bin/sage-spkg

@@ -366,40 +366,17 @@ if [ $INFO -ne 0 -a "$USE_LOCAL_SCRIPTS" = yes ]; then
                 debian)
                     # Generic
                     echo "Debian/Ubuntu:"
-                    echo "  sudo apt-get install $system_packages"
-                    ;;
-                debian*|ubuntu*)
-                    # Specific distribution
-                    echo "$system:"
-                    echo "  sudo apt-get install $system_packages"
                     ;;
                 fedora)
                     # Generic
                     echo "Fedora/Redhat/CentOS:"
-                    echo "  sudo yum install $system_packages"
-                    ;;
-                fedora*|redhat*|centos*)
-                    # Specific distribution
-                    echo "$system:"
-                    echo "  sudo yum install $system_packages"
-                    ;;
-                arch*)
-                    echo "$system:"
-                    echo "  sudo pacman -S $system_packages"
-                    ;;
-                *conda*)
-                    echo "$system:"
-                    echo "  conda install $system_packages"
-                    ;;
-                homebrew*)
-                    echo "$system:"
-                    echo "  brew install $system_packages"
                     ;;
                 *)
                     echo "$system:"
-                    echo "  install the following packages: $system_packages"
                     ;;
             esac
+            echo -n "  "
+            sage-print-system-package-command $system install $system_packages
         fi
     done
     if [ -z "$system" ]; then

build/bin/write-dockerfile.sh

@@ -132,6 +132,7 @@ cat <<EOF
 RUN mkdir -p /sage
 WORKDIR /sage
 ADD Makefile VERSION.txt README.md bootstrap configure.ac sage ./
+ADD src/doc/bootstrap src/doc/bootstrap
 ADD m4 ./m4
 ADD build ./build
 ADD src/bin/sage-version.sh src/bin/sage-version.sh

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=5331e588682dfea9308e8308e510d47429500e76
-md5=fe1a9a72f856549d946340703d20d791
-cksum=888161184
+sha1=c5ac16fd484b7d261fdd5f9ddc0ad144d212c074
+md5=6e01232385ed6a22fae6873990ca2b9a
+cksum=45471057

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-158b93057a44377a3dd8235795317aa0bd412ed9
+f363300209b159a65d9ceaf6b79bb684a9c71db1

build/pkgs/coxeter3/package-version.txt

@@ -1 +1 @@
-8ac9c71723c8ca57a836d6381aed125261e44e9e
+8ac9c71723c8ca57a836d6381aed125261e44e9e.p0

build/pkgs/coxeter3/patches/makefile.patch

@@ -9,7 +9,7 @@ diff -druN src/makefile src/makefile
 
  ifdef optimize
  	NDEBUG = true
-@@ -22,18 +23,74 @@
+@@ -22,18 +27,78 @@
  	cflags = $(pflags)
  endif
 
@@ -53,21 +53,25 @@ diff -druN src/makefile src/makefile
 +executable: $(objects)
 +	$(CXX) -o $(EXENAME)$(EXEEXT) $(objects)
 +
-+DATADIR="$$SAGE_LOCAL/coxeter/"
-+INCLUDEDIR="$$SAGE_LOCAL/include/coxeter/"
-+LIBRARYDIR="$$SAGE_LOCAL/$(LIBDIR)"
++BINDIR=$$SAGE_LOCAL/bin/
++DATADIR=$$SAGE_LOCAL/coxeter/
++INCLUDEDIR=$$SAGE_LOCAL/include/coxeter/
++LIBRARYDIR=$$SAGE_LOCAL/$(LIBDIR)
 +
 +install: coxeter executable
-+	cp $(EXENAME)$(EXEEXT) "$$SAGE_LOCAL/bin/"
-+	cp $(LIBRARY) $(LIBRARYDIR)
++	mkdir -p "$(DESTDIR)$(BINDIR)"
++	mkdir -p "$(DESTDIR)$(LIBRARYDIR)"
++	cp $(EXENAME)$(EXEEXT) "$(DESTDIR)$(BINDIR)"
++	cp $(LIBRARY) "$(DESTDIR)$(LIBRARYDIR)"
 +	if [ $(UNAME) = "CYGWIN" ]; then                 \
-+	    cp $(IMPLIB) "$$SAGE_LOCAL/lib/";  \
++	    mkdir -p "$(DESTDIR)$$SAGE_LOCAL/lib/";      \
++	    cp $(IMPLIB) "$(DESTDIR)$$SAGE_LOCAL/lib/";  \
 +	fi
 +
-+	mkdir -p $(DATADIR)
-+	cp -r coxeter_matrices headers messages $(DATADIR)
-+	mkdir -p $(INCLUDEDIR)
-+	cp -r *.h *.hpp $(INCLUDEDIR)
++	mkdir -p "$(DESTDIR)$(DATADIR)"
++	cp -r coxeter_matrices headers messages "$(DESTDIR)$(DATADIR)"
++	mkdir -p "$(DESTDIR)$(INCLUDEDIR)"
++	cp -r *.h *.hpp "$(DESTDIR)$(INCLUDEDIR)"
 +
 +check: coxeter executable
 +	$(EXENAME)$(EXEEXT) < test.input > test.output

build/pkgs/gfortran/set-library-path

@@ -0,0 +1 @@
+../gcc/set-library-path

build/pkgs/gfortran/spkg-build

@@ -1 +1,3 @@
+. ./set-library-path
+
 ./build-gcc --disable-bootstrap --enable-languages=fortran

build/pkgs/gfortran/spkg-configure.m4

@@ -6,11 +6,15 @@ SAGE_SPKG_CONFIGURE([gfortran], [
     # This helps verify the compiler works too, so if some idiot sets FC to
     # /usr/bin/ls, we will at least know it's not a working Fortran
     # compiler.
-    AC_FC_FREEFORM([], [
+    AC_FC_FREEFORM([SAGE_HAVE_FC_FREEFORM=yes], [
 	AC_MSG_NOTICE([Your Fortran compiler does not accept free-format source code])
         AC_MSG_NOTICE([which means the compiler is either seriously broken, or])
         AC_MSG_NOTICE([is too old to build Sage.])
-        sage_spkg_install_gfortran=yes])
+        SAGE_HAVE_FC_FREEFORM=no])
+
+    AS_VAR_IF(SAGE_HAVE_FC_FREEFORM, [no], [
+        AS_VAR_SET(sage_spkg_install_gfortran, [yes])
+    ])
 
     # Special case: If we are already installing gcc then don't install
     # gfortran since it's included

build/pkgs/gfortran/spkg-install

@@ -1,9 +1,16 @@
 # Exit on error
 set -e
 
+# To work around #26996: Set a symlink so that writes into lib64/ end up in lib/
+(mkdir -p "$SAGE_DESTDIR_LOCAL" && cd "$SAGE_DESTDIR_LOCAL" && ln -sf lib lib64)
+. ./set-library-path
+
 cd gcc-build
 sdh_make_install
 
 # The spkg still installs a minimal C compiler that needs to be removed
 # so it doesn't conflict with the configured C compiler.
 rm "$SAGE_DESTDIR_LOCAL"/bin/gcc "$SAGE_DESTDIR_LOCAL"/bin/cpp
+
+# To work around #26996: Remove the symlink set, or we get "cp: cannot overwrite directory"
+rm -f "$SAGE_DESTDIR_LOCAL/lib64"

build/pkgs/gfortran/spkg-postinst

@@ -0,0 +1,20 @@
+# -*- mode: shell-script -*-
+
+# #27907: Symlink crt1.o and friends where gfortran can find it.
+if [ -n "$SAGE_CRTI_DIR" ]; then
+   INSTALLED_SCRIPTS_DEST="$SAGE_SPKG_SCRIPTS/$PKG_BASE"
+   LIBGCC=$(dirname -- $("$SAGE_LOCAL"/bin/gfortran -print-libgcc-file-name))
+   if [ -z "$LIBGCC" -o ! -d "$LIBGCC" ]; then
+       echo >&2 "Warning: Unable to locate LIBGCC directory, so cannot install crt symlinks"
+       exit
+   fi
+   echo "Installing symlinks to crt files."
+   echo "# Remove symlinks created by spkg-postinst" >> "$INSTALLED_SCRIPTS_DEST"/spkg-postrm
+   for f in "$SAGE_CRTI_DIR"/*crt?.o; do
+       if [ -r $f -a ! -r "$LIBGCC"/$f ]; then
+          ln -s $f "$LIBGCC"/
+          fb=`basename $f`
+          echo "rm -f \"$LIBGCC\"/$fb" >> "$INSTALLED_SCRIPTS_DEST"/spkg-postrm
+       fi
+   done
+fi

build/pkgs/gfortran/spkg-postrm

@@ -0,0 +1,3 @@
+# -*- mode: shell-script -*-
+
+## spkg-postinst adds commands to the bottom of the generated version of this file.

src/bin/sage-version.sh

@@ -1,5 +1,5 @@
 # Sage version information for shell scripts
 # This file is auto-generated by the sage-update-version script, do not edit!
-SAGE_VERSION='9.1.beta4'
-SAGE_RELEASE_DATE='2020-02-13'
-SAGE_VERSION_BANNER='SageMath version 9.1.beta4, Release Date: 2020-02-13'
+SAGE_VERSION='9.1.beta5'
+SAGE_RELEASE_DATE='2020-02-21'
+SAGE_VERSION_BANNER='SageMath version 9.1.beta5, Release Date: 2020-02-21'

src/doc/.gitignore

@@ -3,3 +3,4 @@
 /en/reference/sage
 /en/reference/sagenb
 /output
+/en/installation/*.txt

src/doc/bootstrap

@@ -0,0 +1,51 @@
+#!/usr/bin/env bash
+
+########################################################################
+# Regenerate auto-generated files, using information in SAGE_ROOT/build/
+#
+# This script is run by SAGE_ROOT/bootstrap as part of the bootstrapping phase
+# (before configure, before creating source distributions).
+########################################################################
+
+set -e
+
+if [ -z "$SAGE_ROOT" ]; then
+    echo Please run the top-level bootstrap script of the Sage distribution.
+    exit 1
+fi
+
+cd "$SAGE_ROOT"
+
+PROMPT='    $ '
+STRIP_COMMENTS="sed s/#.*//;"
+OUTPUT_DIR="src/doc/en/installation"
+mkdir -p "$OUTPUT_DIR"
+
+shopt -s extglob
+
+for SYSTEM in debian fedora; do
+    SYSTEM_PACKAGES=$(echo $(${STRIP_COMMENTS} build/pkgs/$SYSTEM.txt))
+    for PKG_SCRIPTS in build/pkgs/*; do
+        if [ -d $PKG_SCRIPTS ]; then
+            PKG_BASE=$(basename $PKG_SCRIPTS)
+            SYSTEM_PACKAGES_FILE=$PKG_SCRIPTS/distros/$SYSTEM.txt
+            PKG_TYPE=$(cat $PKG_SCRIPTS/type)
+            if [ -f $SYSTEM_PACKAGES_FILE -a -f $PKG_SCRIPTS/spkg-configure.m4 ]; then
+               PKG_SYSTEM_PACKAGES=$(echo $(${STRIP_COMMENTS} $SYSTEM_PACKAGES_FILE))
+               if [ -n "PKG_SYSTEM_PACKAGES" ]; then
+                   case "$PKG_TYPE" in
+                       standard)
+                           SYSTEM_PACKAGES+=" $PKG_SYSTEM_PACKAGES"
+                           ;;
+                       *)
+                           OPTIONAL_SYSTEM_PACKAGES+=" $PKG_SYSTEM_PACKAGES"
+                           ;;
+                   esac
+               fi
+            fi
+        fi
+    done
+    echo >&2 $0:$LINENO: installing "$OUTPUT_DIR"/$SYSTEM.txt and "$OUTPUT_DIR"/$SYSTEM-optional.txt
+    echo "$PROMPT$(sage-print-system-package-command $SYSTEM install $(echo $(echo $SYSTEM_PACKAGES | xargs -n 1 echo | sort)))" > "$OUTPUT_DIR"/$SYSTEM.txt
+    echo "$PROMPT$(sage-print-system-package-command $SYSTEM install $(echo $(echo $OPTIONAL_SYSTEM_PACKAGES | xargs -n 1 echo | sort)))" > "$OUTPUT_DIR"/$SYSTEM-optional.txt
+done

src/doc/en/reference/conf_sub.py

@@ -39,14 +39,14 @@
 title = title.replace(u'`', u'$')
 
 # General information about the project.
-project = u'Sage Reference Manual: ' + title
+project = u'Sage {} Reference Manual: '.format(release) + title
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-html_title = u'Sage Reference Manual v' + release + ': ' + title
+html_title = project
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
-html_short_title = title
+html_short_title = project
 
 # HTML theme (e.g., 'default', 'sphinxdoc').  The pages for the
 # reference manual use a custom theme, a slight variant on the 'sage'

src/doc/en/thematic_tutorials/geometry/polyhedra_quickref.rst

@@ -158,6 +158,7 @@ List of Polyhedron methods
     :meth:`~sage.geometry.polyhedron.base.Polyhedron_base.boundary_complex` | returns the boundary complex of simplicial compact polyhedron
     :meth:`~sage.geometry.polyhedron.base.Polyhedron_base.center` | returns the average of the vertices of the polyhedron
     :meth:`~sage.geometry.polyhedron.base.Polyhedron_base.representative_point` | returns the sum of the center and the rays
+    :meth:`~sage.geometry.polyhedron.base.Polyhedron_base.a_maximal_chain` | returns a maximal chain of faces
     :meth:`~sage.geometry.polyhedron.base.Polyhedron_base.face_fan` | returns the fan spanned by the faces of the polyhedron
     :meth:`~sage.geometry.polyhedron.base.Polyhedron_base.face_generator` | a generator over the faces
     :meth:`~sage.geometry.polyhedron.base.Polyhedron_base.faces` | the list of faces