Merge tag '9.1.beta1' into t/29053/installation_manual__generate__apt…

…_get_install__and__yum_install__lines_from_build_pkgs_at___bootstrap_time

SageMath version 9.1.beta1, Release Date: 2020-01-21

.lgtm.yml

@@ -2,6 +2,10 @@ queries:
   - exclude: py/call/wrong-named-class-argument
   - exclude: py/call/wrong-number-class-arguments
   - exclude: py/unsafe-cyclic-import
+path_classifiers:
+  imports_only:
+    - "**/all.py"
+    - "**/*catalog*.py"
 extraction:
   python:
     python_setup:

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.1.beta0, Release Date: 2020-01-10
+SageMath version 9.1.beta1, Release Date: 2020-01-21

build/make/Makefile.in

@@ -35,6 +35,11 @@ PYTHON = python@SAGE_PYTHON_VERSION@
 MP_LIBRARY = @SAGE_MP_LIBRARY@
 BLAS = @SAGE_BLAS@
 
+# Because some .pc files are generated at configure time we can't write their
+# names explicitly the Makefile, so we use the wildcard function here at make
+# runtime
+PCFILES = $(subst $(SAGE_SRC),$(SAGE_LOCAL),$(wildcard $(SAGE_SRC)/lib/pkgconfig/*.pc))
+
 # Files to track installation of packages
 BUILT_PACKAGES = @SAGE_BUILT_PACKAGES@
 DUMMY_PACKAGES = @SAGE_DUMMY_PACKAGES@

build/make/deps

@@ -64,7 +64,7 @@ download-for-sdist:
 
 # TOOLCHAIN consists of dependencies determined by configure.
 # These are built after the "base" target but before anything else.
-toolchain: $(foreach pkgname,$(TOOLCHAIN),$(inst_$(pkgname)))
+toolchain: $(foreach pkgname,$(TOOLCHAIN),$(inst_$(pkgname))) $(PCFILES)
 
 # Build all packages that GCC links against serially, otherwise this
 # leads to race conditions where some library which is used by GCC gets
@@ -174,7 +174,8 @@ sagelib: \
 		$(inst_six) \
 		$(inst_symmetrica) \
 		$(inst_zn_poly) \
-		$(EXTCODE)
+		$(EXTCODE) \
+		$(PCFILES)
 	$(AM_V_at)if [ -z "$$SAGE_INSTALL_FETCH_ONLY" ]; then \
 		cd $(SAGE_SRC) && source bin/sage-env && \
 		sage-logger -p 'time $(MAKE) sage' '$(SAGE_LOGS)/sagelib-$(SAGE_VERSION).log'; \
@@ -197,6 +198,11 @@ $(SAGE_EXTCODE)/%: $(SAGE_SRC)/ext/%
 	@mkdir -p "$(@D)"
 	$(AM_V_at)cp $< $@
 
+# Install sage-specific generated .pc files
+$(SAGE_PKGCONFIG)/%.pc: $(SAGE_SRC)/lib/pkgconfig/%.pc
+	@mkdir -p "$(@D)"
+	$(AM_V_at)cp -P $< $@
+
 
 ###############################################################################
 # Building the documentation

build/make/install

@@ -17,6 +17,7 @@ fi
 
 export SAGE_SHARE="$SAGE_LOCAL/share"
 export SAGE_EXTCODE="$SAGE_SHARE/sage/ext"
+export SAGE_PKGCONFIG="$SAGE_LOCAL/lib/pkgconfig"
 export SAGE_LOGS="$SAGE_ROOT/logs/pkgs"
 export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed"
 . "$SAGE_SRC"/bin/sage-version.sh

build/pkgs/bzip2/spkg-configure.m4

@@ -1,5 +1,8 @@
 SAGE_SPKG_CONFIGURE([bzip2], [
-    AC_CHECK_HEADER(bzlib.h, [], [sage_spkg_install_bzip2=yes])
-    AC_SEARCH_LIBS([BZ2_bzCompress], [bz2], [], [sage_spkg_install_bzip2=yes])
-    AC_CHECK_PROG(bzip2, [break], [sage_spkg_install_bzip2=yes])
+    AC_CHECK_HEADER(bzlib.h, [
+      AC_SEARCH_LIBS([BZ2_bzCompress], [bz2], [
+        AC_PATH_PROG([bzip2_prog], [bzip2])
+	AS_IF([test x$bzip2_prog = x], [sage_spkg_install_bzip2=yes])
+      ], [sage_spkg_install_bzip2=yes])
+    ], [sage_spkg_install_bzip2=yes])
 ])

build/pkgs/cbc/spkg-configure.m4

@@ -0,0 +1,6 @@
+SAGE_SPKG_CONFIGURE([cbc], [
+    SAGE_SPKG_DEPCHECK([atlas openblas zlib bzip2], [
+        dnl  checking with pkg-config
+        PKG_CHECK_MODULES([CBC], [cbc >= 2.9.4], [], [sage_spkg_install_cbc=yes])
+    ])
+])

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=fef64fcd9915ea4f881bc5cfeecb8b3864bc555f
-md5=0b23947f22228ef6d5d1143a906cd4a6
-cksum=844195685
+sha1=029fe778cefcb82231353c0dab72a75769ffdcf9
+md5=b4231b3e4ce67fc656ba9532b123485a
+cksum=3808756319

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-7140d0e7bb897e008d315fdcd371c11528aa70d3
+4fd5d56ecea2c81d58e9e43bd5f07b05e863bc7c

build/pkgs/cvxopt/spkg-install

@@ -18,7 +18,7 @@ pkg_libs() {
 # Note that *_INC_DIR variables have to be non-empty.
 # Compilers don't like "-I ".
 export CVXOPT_BLAS_LIB="$(pkg_libs blas)"
-export CVXOPT_BLAS_LIB_DIR="${SAGE_LOCAL}"
+export CVXOPT_BLAS_LIB_DIR="$(pkg-config --variable=libdir blas)"
 export CVXOPT_LAPACK_LIB="$(pkg_libs lapack)"
 
 export CVXOPT_SUITESPARSE_LIB_DIR="${SAGE_LOCAL}"
@@ -29,8 +29,8 @@ export CVXOPT_GLPK_LIB_DIR="${SAGE_LOCAL}"
 export CVXOPT_GLPK_INC_DIR="${SAGE_LOCAL}/include"
 
 export CVXOPT_BUILD_GSL=1
-export CVXOPT_GSL_LIB_DIR="${SAGE_LOCAL}"
-export CVXOPT_GSL_INC_DIR="${SAGE_LOCAL}/include"
+export CVXOPT_GSL_LIB_DIR="$(pkg-config --variable=libdir gsl)"
+export CVXOPT_GSL_INC_DIR="$(pkg-config --variable=includedir gsl)"
 
 sdh_pip_install .
 

build/pkgs/fplll/checksums.ini

@@ -1,4 +1,4 @@
 tarball=fplll-VERSION.tar.gz
-sha1=4144f5fa3d85132585b1b17aed18865c7a146611
-md5=bc3569303ce36d731d21b5419ec733ac
-cksum=1239204327
+sha1=67b70f4dcbb835025abce879b9acb4500e2f1d2c
+md5=e72082af9084c5b2d427977c9b79a602
+cksum=65319984

build/pkgs/fplll/package-version.txt

@@ -1 +1 @@
-5.2.1
+5.3.2

build/pkgs/fpylll/checksums.ini

@@ -1,4 +1,4 @@
 tarball=fpylll-VERSION.tar.gz
-sha1=2f8f83038f7015b2c55d0ec21448ffb27d1d233f
-md5=83f57447a1643d0b5087ee3944ca90a8
-cksum=2076741335
+sha1=2d35022ac75457606d7e5d3497f6d9dd75deb19c
+md5=1c0d100203cb340cb3160ab9692f9208
+cksum=1547949297

build/pkgs/fpylll/package-version.txt

@@ -1 +1 @@
-0.4.1dev
+0.5.1dev

build/pkgs/gcc/spkg-configure.m4

@@ -159,19 +159,19 @@ SAGE_SPKG_CONFIGURE_BASE([gcc], [
         cmd_AS=`command -v $AS`
 
         if ! (test "$CXX_as" = "" -o "$CXX_as" -ef "$cmd_AS"); then
-            SAGE_SHOULD_INSTALL_GCC([there is a mismatch of assemblers])
-            AC_MSG_NOTICE([  $CXX uses $CXX_as])
-            AC_MSG_NOTICE([  \$AS equal to $AS])
+            AC_MSG_NOTICE([       $CXX uses $CXX_as])
+            AC_MSG_NOTICE([       \$AS equal to $AS])
+            AC_MSG_ERROR([unset \$AS or set it to match your compiler's assembler])
         fi
     fi
     if test -n "$LD"; then
         CXX_ld=`$CXX -print-prog-name=ld 2>/dev/null`
         CXX_ld=`command -v $CXX_ld 2>/dev/null`
         cmd_LD=`command -v $LD`
         if ! (test "$CXX_ld" = "" -o "$CXX_ld" -ef "$cmd_LD"); then
-            SAGE_SHOULD_INSTALL_GCC([there is a mismatch of linkers])
-            AC_MSG_NOTICE([  $CXX uses $CXX_ld])
-            AC_MSG_NOTICE([  \$LD equal to $LD])
+            AC_MSG_NOTICE([       $CXX uses $CXX_ld])
+            AC_MSG_NOTICE([       \$LD equal to $LD])
+            AC_MSG_ERROR([unset \$LD or set it to match your compiler's linker])
         fi
     fi
 

build/pkgs/gfan/spkg-configure.m4

@@ -0,0 +1,14 @@
+SAGE_SPKG_CONFIGURE(
+    [gfan], [
+        AC_CACHE_CHECK([for gfan >= 0.6.2], [ac_cv_path_GFAN], [
+        AC_PATH_PROGS_FEATURE_CHECK([GFAN_VERSION], [gfan_version], [
+            gfan_version=`$ac_path_GFAN_VERSION | $SED -n '/^gfan/s/gfan//p'`
+            AS_IF([test -n "$gfan_version"], [
+                AX_COMPARE_VERSION([$gfan_version], [ge], [0.6.2], [
+                    ac_cv_path_GFAN_VERSION="$ac_path_GFAN_VERSION"
+                ])
+            ])
+        ])
+    ])
+    AS_IF([test -z "$ac_cv_path_GFAN_VERSION"], [sage_spkg_install_gfan=yes])
+])

build/pkgs/gsl/spkg-configure.m4

@@ -6,7 +6,7 @@ SAGE_SPKG_CONFIGURE([gsl], [
           AC_CONFIG_COMMANDS([GSLPCPROCESS], [
             $SED -e 's/\${GSL_CBLAS_LIB}\ //' \
                  -e 's/GSL_CBLAS_LIB.*/Requires: cblas/' $GSL_PC \
-                  > "$SAGE_LOCAL"/lib/pkgconfig/gsl.pc
+                  > "$SAGE_SRC"/lib/pkgconfig/gsl.pc
           ], [
             SED=$ac_cv_path_SED
             GSL_PC="$GSLPCDIR"/gsl.pc

build/pkgs/libatomic_ops/spkg-configure.m4

@@ -0,0 +1,6 @@
+SAGE_SPKG_CONFIGURE([libatomic_ops], [
+  PKG_CHECK_MODULES([LIBATOMIC_OPS],
+                    [atomic_ops >= 7.6.2],
+                    [],
+                    [sage_spkg_install_libatomic_ops=yes])
+])

build/pkgs/nauty/spkg-configure.m4

@@ -0,0 +1,19 @@
+AC_DEFUN([SAGE_TEST_NAUTY_PROGS], [
+    m4_foreach([nautyprog], [directg, gentourng, geng, genbg], [
+      AC_PATH_PROG([$2]nautyprog, [[$1]nautyprog])
+      AS_IF([test x$[$2]nautyprog = x], [sage_spkg_install_nauty=yes])
+    ])
+    AC_SUBST(SAGE_NAUTY_BINS_PREFIX, ['$1'])
+])
+SAGE_SPKG_CONFIGURE([nauty], [
+  AC_PATH_PROG([GENGCHECK],[geng])
+  AS_IF([test x$GENGCHECK = x], [
+    AC_PATH_PROG([GENGnautyCHECK],[nauty-geng])
+     AS_IF([test x$GENGnautyCHECK = x], [sage_spkg_install_nauty=yes],
+       [SAGE_TEST_NAUTY_PROGS(nauty-,nau)])
+    ], [SAGE_TEST_NAUTY_PROGS(,foo)])
+ ], [], [], [
+ AS_IF([test x$sage_spkg_install_nauty = xyes], [
+   AC_SUBST(SAGE_NAUTY_BINS_PREFIX, [''])
+ ])
+])

build/pkgs/numpy/lapack_conf.py

@@ -8,6 +8,11 @@
 conf_file.write('library_dirs = '+ os.environ['SAGE_LOCAL']+ '/lib\n')
 conf_file.write('include_dirs = '+ os.environ['SAGE_LOCAL']+ '/include\n')
 
+conf_file.write('[DEFAULT]\n')
+conf_file.write('library_dirs = '+ os.environ['SAGE_LOCAL']+ '/lib\n')
+conf_file.write('include_dirs = '+ os.environ['SAGE_LOCAL']+ '/include\n')
+
+
 pc_blas   = pkgconfig.parse('cblas blas')
 pc_lapack = pkgconfig.parse('lapack')
 

build/pkgs/openblas/spkg-configure.m4

@@ -2,9 +2,9 @@ SAGE_SPKG_CONFIGURE([openblas], [
   PKG_CHECK_MODULES([OPENBLAS], [openblas >= 0.2.20], [
     PKG_CHECK_VAR([OPENBLASPCDIR], [openblas], [pcfiledir], [
        AC_CONFIG_LINKS([
-         $SAGE_LOCAL/lib/pkgconfig/blas.pc:$OPENBLASPCDIR/openblas.pc
-         $SAGE_LOCAL/lib/pkgconfig/cblas.pc:$OPENBLASPCDIR/openblas.pc
-         $SAGE_LOCAL/lib/pkgconfig/lapack.pc:$OPENBLASPCDIR/openblas.pc])
+         $SAGE_SRC/lib/pkgconfig/blas.pc:$OPENBLASPCDIR/openblas.pc
+         $SAGE_SRC/lib/pkgconfig/cblas.pc:$OPENBLASPCDIR/openblas.pc
+         $SAGE_SRC/lib/pkgconfig/lapack.pc:$OPENBLASPCDIR/openblas.pc])
        ], [
        AC_MSG_WARN([Unable to locate the directory of openblas.pc. This should not happen!])
        sage_spkg_install_openblas=yes

build/pkgs/pillow/patches/setup.py.patch

@@ -10,13 +10,15 @@ index 15d81e4..5893d3d 100755
  import warnings
  from distutils import ccompiler, sysconfig
  from distutils.command.build_ext import build_ext
-@@ -311,6 +312,9 @@ class pil_build_ext(build_ext):
+@@ -311,6 +312,11 @@ class pil_build_ext(build_ext):
              # darwin ports installation directories
              _add_directory(library_dirs, "/opt/local/lib")
              _add_directory(include_dirs, "/opt/local/include")
++            # Check variable introduced in #27631.
 +            sysroot = sysconfig.get_config_var('Py_MACOS_SYSROOT')
-+            _add_directory(library_dirs, sysroot+"/usr/lib")
-+            _add_directory(include_dirs, sysroot+"/usr/include")
++            if sysroot is not None:
++                _add_directory(library_dirs, sysroot+"/usr/lib")
++                _add_directory(include_dirs, sysroot+"/usr/include")
 
              # if Homebrew is installed, use its lib and include directories
              try:

build/pkgs/pillow/spkg-install

@@ -6,10 +6,18 @@ rm -rf \
    "$SAGE_LOCAL"/lib/python*/site-packages/PIL-*.egg* \
    "$SAGE_LOCAL"/lib/python*/site-packages/Pillow-*.egg*
 
+if [ "$UNAME" = "Darwin" ] ; then
+    # #29019
+    # https://github.com/python-pillow/Pillow/issues/3438#issuecomment-555019284
+    # https://apple.stackexchange.com/questions/372032/usr-include-missing-on-macos-catalina-with-xcode-11/372600#372600
+    export CPATH="$CPATH:`xcrun --show-sdk-path`/usr/include"
+fi
+
 # Note: Avoid shared libraries inside egg files, Trac #19467
 sage-python23 setup.py \
        --no-user-cfg \
        build_ext \
+       --debug \
        --disable-jpeg \
        install \
        --single-version-externally-managed \

build/pkgs/r/spkg-install

@@ -160,12 +160,6 @@ if [ $? -ne 0 ]; then
     exit 1
 fi
 
-# Remove old install
-rm -rf "$SAGE_LOCAL"/lib/r
-rm -rf "$SAGE_LOCAL"/lib/R
-rm -rf "$SAGE_LOCAL"/lib/R.old
-rm -rf "$SAGE_LOCAL"/lib/libRblas.* "$SAGE_LOCAL"/lib/libRlapack.* "$SAGE_LOCAL"/lib/libR.*
-
 # Install new version
 $MAKE install
 if [ $? -ne 0 ]; then

build/pkgs/r/spkg-legacy-uninstall

@@ -0,0 +1,6 @@
+# Remove old install
+rm -rf "$SAGE_LOCAL"/lib/r
+rm -rf "$SAGE_LOCAL"/lib/R
+rm -rf "$SAGE_LOCAL"/lib/R.old
+rm -rf "$SAGE_LOCAL"/lib/libRblas.* "$SAGE_LOCAL"/lib/libRlapack.* "$SAGE_LOCAL"/lib/libR.*
+rm -f "$SAGE_LOCAL"/bin/R*

build/pkgs/sage_numerical_backends_gurobi/checksums.ini

@@ -1,4 +1,4 @@
 tarball=sage_numerical_backends_gurobi-VERSION.tar.gz
-sha1=1a3ea79350cb6bffaff0c785bdb310f4c21475f4
-md5=31e4da1d0538422c370a0149b4da809d
-cksum=2128488628
+sha1=64253f735ee6779b6ded809643b455061a105dc4
+md5=3df7d18fe53af89e0a796974a2d788b5
+cksum=3824076545

build/pkgs/sage_numerical_backends_gurobi/package-version.txt

@@ -1 +1 @@
-9.0b12
+9.0.0

build/sage_bootstrap/app.py

@@ -4,29 +4,26 @@
 """
 
 
-#*****************************************************************************
+# ****************************************************************************
 #       Copyright (C) 2016 Volker Braun <[email protected]>
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
 # the Free Software Foundation, either version 2 of the License, or
 # (at your option) any later version.
-#                  http://www.gnu.org/licenses/
-#*****************************************************************************
+#                  https://www.gnu.org/licenses/
+# ****************************************************************************
 
 import os
-import sys
 import logging
 log = logging.getLogger()
 
-from sage_bootstrap.env import SAGE_DISTFILES
 from sage_bootstrap.package import Package
 from sage_bootstrap.tarball import Tarball
 from sage_bootstrap.updater import ChecksumUpdater, PackageUpdater
 from sage_bootstrap.creator import PackageCreator
 
 
-
 class Application(object):
 
     def config(self):

build/sage_bootstrap/cksum.py

@@ -4,8 +4,6 @@
 This is a weak checksum, only included for legacy reasons.
 """
 
-import sys
-
 # Fun table, e.g. http://www.nco.ncep.noaa.gov/pmb/codes/nwprod/util/sorc/wgrib2.cd/grib2/wgrib2/crc32.c
 
 crctab = [

build/sage_bootstrap/cmdline.py

@@ -6,18 +6,16 @@
 is also exposed as "sage --package".
 """
 
-
-#*****************************************************************************
+# ****************************************************************************
 #       Copyright (C) 2016 Volker Braun <[email protected]>
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
 # the Free Software Foundation, either version 2 of the License, or
 # (at your option) any later version.
-#                  http://www.gnu.org/licenses/
-#*****************************************************************************
+#                  https://www.gnu.org/licenses/
+# ****************************************************************************
 
-import os
 import sys
 import logging
 log = logging.getLogger()