Merge tag '8.8.rc1' into t/25097/public/normaliz-3.7.0-algebraic

SageMath version 8.8.rc1, Release Date: 2019-06-13

README.md

@@ -66,11 +66,13 @@ files installed
    has been shown that Sage can be successfully built against other
    SSL libraries, with some of its features disabled.
 
+
 1. Make sure you have the dependencies and 5 GB of free disk space
 
-   * __All Linux versions:__ gcc, make, m4, perl, ranlib, and tar (a
+   * __All Linux versions:__ gcc, make, m4, perl, ranlib, git, and tar (a
    matching set of gcc, gfortran and g++ will avoid the compilation
-   of Sage-specific compilers).
+   of Sage-specific compilers). It should also be possible to use clang/clang++,
+   however this is less well-tested.
 
    * __Fedora or RedHat systems:__ the perl-ExtUtils-MakeMaker package.
    (install these using your package manager)
@@ -85,10 +87,22 @@ files installed
        When using OS X Mountain Lion or earlier, you need to install the
        command line tools from Xcode: run Xcode; then from the File
        menu, choose "Preferences", then the "Downloads" tab, and then
-       "Install" the Command Line Tools.
+       "Install" the Command Line Tools. You might also have Homebrew or
+       a similar "Apple's missing package manager" system installed, with
+       and libraries such gfortran, gmp, etc installed. (However, this
+       is still experimental as of May 2019).
 
    * __Other platforms:__ See detailed instructions below.
 
+1. It might be desirable, it terms of faster building and better portability,
+   to install, as system packages, an ever increasing [list of Sage packages](https://trac.sagemath.org/ticket/27330)
+   which otherwise might have to be built. The following is a list of Sage packages
+   "replaceable" by system's packages as of Sage release 8.8:
+   `bzip2`, `curl`, `cmake`, `gcc/clang`, `gf2x`, `gfortran` (usually part of `gcc` installation),
+   `git`, `gmp`, `libffi`, `patch`, `pcre`, `perl_term_readline_gnu`, `xz/lzma`, `yasm`, `zeromq`,  `zlib`.
+   Details and names of system packages containing these are system-dependent.  E.g. on Debian
+   `bzip2` lives in `libbz2-dev`. More details on this are in Installation manual.
+
 1. Extract the tarball
 
        tar zxvf sage-*.tar.gz
@@ -113,9 +127,8 @@ Implementation
 --------------
 
 Sage has significant components written in the following languages:
-C/C++, Python, Cython, Lisp, and Fortran. Lisp (ECL), Python, and Cython
-are built as part of Sage and a GNU Fortran (gfortran) binary is
-included (OS X only), so you do not need them in order to build Sage.
+C/C++, Python, Cython, Lisp, Fortran, and a bit of Perl. Lisp (ECL), Python, and Cython
+are built as part of Sage.
 
 Docker Images
 -------------
@@ -133,14 +146,15 @@ More Detailed Instructions to Build from Source
 
    * __Linux:__ See quick instructions above.
 
-   * __OS X:__ Make sure you have Xcode version >= 2.4, i.e. `gcc -v` should
-   output build >= 5363. If you don't, go to https://developer.apple.com/
-   sign up, and download the free Xcode package. Only OS X >= 10.4 is
-   supported.
+   * __OS X:__ (a.k.a __MacOS__) Make sure you have a recent Xcode version.
+   If you don't, go to https://developer.apple.com/,
+   sign up, and download the free Xcode package. Usually, Xcode's command line
+   tools suffice to build Sage, although several times new releases of Xcode broke this.
+   Only OS X >= 10.4 is supported, and (as of May 2019) we only test Sage on OS X >= 10.6.
 
    * __Solaris and OpenSolaris:__ Building Sage on these platforms is more
    tricky than on Linux or OS X. For details on how to build Sage on
-   these platforms, see [our wiki](https://wiki.sagemath.org/solaris).
+   these platforms, see [our wiki](https://wiki.sagemath.org/solaris) (outdated as of May 2019).
 
    * __Windows:__ [Download and install VirtualBox](https://www.virtualbox.org/wiki/Downloads),
    and then download the [Sage virtual appliance](https://wiki.sagemath.org/SageAppliance).
@@ -256,17 +270,18 @@ someone there will have some helpful suggestions.
 Supported Compilers
 -------------------
 
-Sage includes a GCC (_GNU Compiler Collection_) package. In order to
-build Sage, you need a C compiler which can build GCC and its
-prerequisites. gcc version 4.0.1 or later should probably work. On
-Solaris or OpenSolaris, building with the Sun compiler should also work.
+Sage includes a GCC (_GNU Compiler Collection_) package. However,
+it almost always better to use C, C++ and Fortran compilers
+already available one the system. To force using  specific compilers,
+set environment variables `CC`, `CXX`, and `FC` (for C, C++, and Fortran compilers,
+respectively) to the desired values,
+and run `./configure`. E.g. `CC=clang CXX=clang++ FC=gfortran ./configure`
+will configure Sage to be built with Clang C/C++ compilers and Fortran
+compiler gfortran.
 
-The GCC package in Sage is not always installed. It is determined
-automatically whether it needs to be installed. You can override this
-by setting the environment variable `SAGE_INSTALL_GCC=yes` (to force
-installation of GCC) or `SAGE_INSTALL_GCC=no` (to disable installation of
-GCC). If you don't want to install GCC, you need to have recent
-versions of gcc, g++ and gfortran; moreover, the versions must be equal.
+It is determined automatically whether Sage's GCC package, or just its part containing
+Fortran compiler `gfortran` needs to be installed. This can be overwritten
+by running `./configure` with option `--without-system-gcc`.
 
 There are some known problems with old assemblers, in particular when
 building the ECM package. You should ensure that your assembler
@@ -291,7 +306,8 @@ SAGE_ROOT                 Root directory (sage-x.y.z in Sage tarball)
 │   ├── bin               Executables
 │   ├── include           C/C++ headers
 │   ├── lib               Shared libraries
-│   ├── share             Databases, architecture-independent data
+│   ├── share             Databases, architecture-independent data, docs
+│       └── doc           Viewable docs of Sage and of some components
 │   └── var
 │       ├── sage          List of installed packages
 │       └── tmp           Temporary files when building Sage
@@ -302,12 +318,14 @@ SAGE_ROOT                 Root directory (sage-x.y.z in Sage tarball)
 │       ├── atlas-3.10.1.p7.log
 │       …
 │       └── zn_poly-0.9.p11.log
+├── m4                    M4 macros for configure
+│   ├── *.m4
 ├── Makefile              Running "make" uses this file
 ├── README.md             This file
 ├── sage                  Script to start Sage
 ├── src                   All of Sage source (not third-party packages)
 │   ├── bin               Scripts that Sage uses internally
-│   ├── doc               Sage documentation
+│   ├── doc               Sage documentation sources
 │   └── sage              The Sage library source code
 ├── upstream              Source tarballs of packages
 │   ├── atlas-3.10.1.tar.bz2
@@ -356,8 +374,8 @@ in order to build `build/make/Makefile` since it's a prerequisite for most of
 Sage's make targets.
 
 The `configure` script itself, if it is not already built, can be generated by
-running the `bootstrap` script.  The top-level `Makefile` also takes care of
-this automatically.
+running the `bootstrap` script (the latter requires _GNU autotools_ being installed).
+The top-level `Makefile` also takes care of this automatically.
 
 To summarize, running a command like `make python2` at the top-level of the
 source tree goes something like this:
@@ -377,14 +395,15 @@ source tree goes something like this:
 Relocation
 ----------
 
-You *should* be able to move the `sage-x.y.z/` directory anywhere you
-want. If you copy the sage script or make a symbolic link to it, you
+It used to be possible to move the `sage-x.y.z/` directory anywhere you
+want, however, this is no longer supported.
+If you copy the sage script or make a symbolic link to it, you
 should modify the script to reflect this (as instructed at the top of
-the script). It is best if the path to Sage does not have any spaces in
-it.
+the script). It is important that the path to Sage does not have any spaces
+and non-ASCII characters in it.
 
-For a system-wide installation, as root you can move the `sage-x.y.z/`
-directory to a system-wide directory. Afterwards, you need to start up
+For a system-wide installation, you have to build Sage as a "normal" user
+and then as root you can change permissions. Afterwards, you need to start up
 Sage as root at least once prior to using the system-wide Sage as a
 normal user. See the [Installation Guide](https://doc.sagemath.org/html/en/installation/source.html#installation-in-a-multiuser-environment)
 for further information.

VERSION.txt

@@ -1 +1 @@
-SageMath version 8.8.beta6, Release Date: 2019-05-22
+SageMath version 8.8.rc1, Release Date: 2019-06-13

build/pkgs/arb/spkg-install

@@ -4,8 +4,8 @@ cd src
 # be removed in arb >= 2.8 when it is released
 export EXTRA_SHARED_FLAGS=$LDFLAGS
 
-./configure --disable-static --prefix="$SAGE_LOCAL" $SAGE_CONFIGURE_GMP \
-            --with-flint="$SAGE_LOCAL" --with-mpfr="$SAGE_LOCAL" || \
+./configure --disable-static --prefix="$SAGE_LOCAL" --with-flint="$SAGE_LOCAL" \
+    $SAGE_CONFIGURE_GMP $SAGE_CONFIGURE_MPFR || \
     sdh_die "Error configuring arb."
 
 sdh_make verbose

build/pkgs/barvinok/spkg-install

@@ -3,9 +3,12 @@ cd src
 if [ -n "$SAGE_GMP_PREFIX" ]; then
    GMP_CONFIGURE="--with-gmp-prefix=$SAGE_GMP_PREFIX"
 fi
+if [ -n "$SAGE_NTL_PREFIX" ]; then
+   NTL_CONFIGURE="--with-ntl-prefix=$SAGE_NTL_PREFIX"
+fi
 
 sdh_configure $GMP_CONFIGURE \
-              --with-ntl-prefix=${SAGE_LOCAL} \
+              $NTL_CONFIGURE \
               --with-isl=system               \
               --with-polylib=system           \
               --enable-shared-barvinok

build/pkgs/brial/checksums.ini

@@ -1,4 +1,4 @@
 tarball=brial-VERSION.tar.bz2
-sha1=60b5300cd11560681a1bf471d3c46a223f4d8273
-md5=6034158eb164786cde8399fa73fbab3a
-cksum=3355513438
+sha1=5795c0d73b63e9daa5318b0f22514b7797c59823
+md5=fddbc0cebfbac161de110acf30a6b89d
+cksum=2578889224

build/pkgs/brial/package-version.txt

@@ -1 +1 @@
-1.2.4
+1.2.5

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=c91befc71803600bcfcfa5637b8330f65dcf594c
-md5=eee7fd54b6aa2131981ab46442fe09a0
-cksum=2162906054
+sha1=9655d2f1711ae231ce14a8ce519d9a2af0fb1dc4
+md5=28acd9297494c8171c44584c18efbd20
+cksum=1129046285

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-320
+324

build/pkgs/cryptominisat/spkg-install

@@ -5,11 +5,6 @@ then
    EXTRA_OPTS="-DFORCE_PYTHON2='ON'"
 fi
 
-cmake -DCMAKE_INSTALL_PREFIX="${SAGE_LOCAL}" \
-      -DZLIB_ROOT="${SAGE_LOCAL}" \
-      -DUSE_GAUSS='ON' \
-      $EXTRA_OPTS \
-      . || sdh_die 'Error configuring cryptominisat'
-
+sdh_cmake -DUSE_GAUSS='ON' $EXTRA_OPTS
 sdh_make VERBOSE=ON
 sdh_make_install VERBOSE=ON

build/pkgs/deformation/spkg-install

@@ -3,7 +3,7 @@ cd src
 # Note: Not actually an autoconf-generated configure; doesn't support
 # all standard flags, so we can't use sdh_configure
 ./configure --prefix="$SAGE_LOCAL" --disable-static \
-            $SAGE_CONFIGURE_GMP --with-mpfr="$SAGE_LOCAL" \
+            $SAGE_CONFIGURE_GMP $SAGE_CONFIGURE_MPFR \
             --with-flint="$SAGE_LOCAL" || \
             sdh_die "Failed to configure deformation"
 sdh_make

build/pkgs/eclib/spkg-install

@@ -28,7 +28,7 @@ rm -rf "$SAGE_LOCAL"/include/eclib/
 cd src/
 
 
-sdh_configure --with-ntl="$SAGE_LOCAL" \
+sdh_configure $SAGE_CONFIGURE_NTL \
               --with-pari="$SAGE_LOCAL" \
               --with-flint="$SAGE_LOCAL" \
               --with-boost="no" \

build/pkgs/flint/spkg-install

@@ -17,8 +17,8 @@ echo "Configuring FLINT."
     --disable-static \
     --prefix="$SAGE_LOCAL" \
     $SAGE_CONFIGURE_GMP \
-    --with-mpfr="$SAGE_LOCAL" \
-    --with-ntl="$SAGE_LOCAL" \
+    $SAGE_CONFIGURE_MPFR \
+    --with-ntl="$SAGE_NTL_PREFIX" \
     $FLINT_CONFIGURE || sdh_die "Error: Failed to configure FLINT."
 
 sdh_make verbose

build/pkgs/gap_packages/spkg-install

@@ -27,6 +27,7 @@ sdh_install \
     liering-* \
     loops-* \
     MapClass-* \
+    PackageManager-* \
     polymaking-* \
     qpa-* \
     quagroup \

build/pkgs/gcc/build-gcc

@@ -61,7 +61,7 @@ fi
 ../src/configure \
     --prefix="$SAGE_LOCAL" \
     --with-local-prefix="$SAGE_LOCAL" \
-    $SAGE_CONFIGURE_GMP --with-mpfr="$SAGE_LOCAL" --with-mpc="$SAGE_LOCAL" \
+    $SAGE_CONFIGURE_GMP $SAGE_CONFIGURE_MPFR $SAGE_CONFIGURE_MPC \
     --with-system-zlib \
     --disable-multilib \
     --disable-nls \

build/pkgs/gdb/spkg-install

@@ -4,8 +4,8 @@ cd src
 export LDFLAGS="${LDFLAGS} -L${SAGE_LOCAL}/lib -ltinfo"
 
 sdh_configure \
-    --with-mpc="$SAGE_LOCAL" \
-    --with-mpfr="$SAGE_LOCAL" \
+    $SAGE_CONFIGURE_MPC \
+    $SAGE_CONFIGURE_MPFR \
     $SAGE_CONFIGURE_GMP
 sdh_make
 sdh_make_install

build/pkgs/gmpy2/checksums.ini

@@ -1,4 +1,4 @@
 tarball=gmpy2-VERSION.tar.gz
-sha1=e9fce01adf59ca47d8b7720e2d3a35c059a4dff2
-md5=d24f45b47928a43fc91fd9de39c66bec
-cksum=2865956140
+sha1=b78f6e6d06d6406f7896e71ff7dca4c43c7368f1
+md5=500cbece0fedbd13598b1ddc52c893c7
+cksum=3080201027

build/pkgs/gmpy2/package-version.txt

@@ -1 +1 @@
-2.1.0a4.p1
+2.1.0b1