Merge tag '9.5.beta0' into t/29847/install_sage_setup_with_pip__move_…

…sage_include_directories__cython_aliases_from_sage_env_to_sage_setup

SageMath version 9.5.beta0, Release Date: 2021-08-31

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.4.rc1", 
-    "version": "9.4.rc1", 
+    "title": "sagemath/sage: 9.5.beta0", 
+    "version": "9.5.beta0", 
     "upload_type": "software", 
-    "publication_date": "2021-08-08", 
+    "publication_date": "2021-08-31", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.4.rc1", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.5.beta0", 
             "relation": "isSupplementTo"
         }, 
         {

README.md

@@ -237,24 +237,16 @@ Guide](https://doc.sagemath.org/html/en/installation).
    (also for Red Hat, CentOS), and
    [slackware.txt](build/pkgs/_prereq/distros/slackware.txt).
 
-7. Optional, but highly recommended: Make sure your system has an SSL
-   library and its development files installed.
-
-   Like Python, on which it is based, Sage uses the OpenSSL library
-   for added performance if made available by the operating system. It
-   has been shown that Sage can be successfully built against other
-   SSL libraries, with some of its features disabled.
-
-8. Optional: It is recommended that you have both LaTeX and the
+7. Optional: It is recommended that you have both LaTeX and the
    ImageMagick tools (e.g. the "convert" command) installed since some
    plotting functionality benefits from it.
 
-9. Optionally, review the configuration options, which includes
+8. Optionally, review the configuration options, which includes
    many optional packages:
 
         $ ./configure --help
 
-10. Optional, but highly recommended: Set some environment variables to
+9. Optional, but highly recommended: Set some environment variables to
    customize the build.
 
    For example, the `MAKE` environment variable controls whether to
@@ -271,7 +263,7 @@ Guide](https://doc.sagemath.org/html/en/installation).
    building Sage, see [the installation
    guide](https://doc.sagemath.org/html/en/installation/source.html#environment-variables).
 
-11. Type `./configure`, followed by any options that you wish to use.
+10. Type `./configure`, followed by any options that you wish to use.
    For example, to build Sage with `gf2x` package supplied by Sage,
    use `./configure --with-system-gf2x=no`.
 
@@ -291,37 +283,37 @@ Guide](https://doc.sagemath.org/html/en/installation).
    available; only the most recent releases of your distribution will
    have all of these recommended packages.
 
-12. Optional: If you choose to install the additional system packages,
+11. Optional: If you choose to install the additional system packages,
    a re-run of `./configure` will test whether the versions installed
    are usable for Sage; if they are, this will reduce the compilation
    time and disk space needed by Sage. The usage of packages may be
    adjusted by `./configure` parameters (check again the output of
    `./configure --help`).
 
-13. Type `make`.  That's it! Everything is automatic and
+12. Type `make`.  That's it! Everything is automatic and
    non-interactive; but it will take a few hours (on a recent
    computer).
 
    The build should work fine on all fully supported platforms. If it
    does not, we want to know!
 
-14. Type `./sage` to try it out.
+13. Type `./sage` to try it out.
 
-15. Optional: Type `make ptestlong` to test all examples in the documentation
+14. Optional: Type `make ptestlong` to test all examples in the documentation
    (over 200,000 lines of input!) -- this takes from 10 minutes to
    several hours. Don't get too disturbed if there are 2 to 3 failures,
    but always feel free to email the section of `logs/ptestlong.log` that
    contains errors to the [sage-support mailing list](https://groups.google.com/group/sage-support).
    If there are numerous failures, there was a serious problem with your build.
 
-16. The HTML version of the [documentation](https://doc.sagemath.org/html/en/index.html)
+15. The HTML version of the [documentation](https://doc.sagemath.org/html/en/index.html)
    is built during the compilation process of Sage and resides in the directory
    `local/share/doc/sage/html/`.
 
-17. Optional: If you want to build the PDF version of the documentation,
+16. Optional: If you want to build the PDF version of the documentation,
     run `make doc-pdf` (this requires LaTeX to be installed).
 
-18. Optional: You might install optional packages of interest to you: type
+17. Optional: You might install optional packages of interest to you: type
    `./sage --optional` to get a list.
 
 Troubleshooting

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.4.rc1, Release Date: 2021-08-08
+SageMath version 9.5.beta0, Release Date: 2021-08-31

build/pkgs/_prereq/distros/freebsd.txt

@@ -16,4 +16,4 @@ gmake
 automake
 bash
 dash
-python	# python metaport for bootstrapping the build
+python # python metaport for bootstrapping the build

build/pkgs/_prereq/distros/opensuse.txt

@@ -23,3 +23,6 @@ gcc-c++
 ca-certificates
 # gunzip needed for ppl spkg
 gzip
+# Trac #32368
+findutils
+diffutils

build/pkgs/arb/spkg-configure.m4

@@ -9,7 +9,7 @@ SAGE_SPKG_CONFIGURE([arb], [
         AC_CHECK_HEADER(arb.h, [
         dnl below function added in version 2.16 of arb
             AC_CHECK_LIB([arb], [acb_mat_eig_simple], [],
-	      [dnl in Debian the name of dylib is different.
+              [dnl in Debian the name of dylib is different.
                AC_CHECK_LIB([flint-arb], [acb_mat_eig_simple],
                 [SAGE_ARB_LIBRARY="flint-arb"], [sage_spkg_install_arb=yes])])
         ], [sage_spkg_install_arb=yes])

build/pkgs/brial/spkg-configure.m4

@@ -15,7 +15,7 @@ SAGE_SPKG_CONFIGURE([brial], [
         USING_NAMESPACE_PBORI
         USING_NAMESPACE_PBORIGB
 
-	class MyConstant : public BooleConstant{
+        class MyConstant : public BooleConstant{
           public: void negate() { this->m_value = !this->m_value; }
         };
       ],[
@@ -35,56 +35,58 @@ SAGE_SPKG_CONFIGURE([brial], [
       dnl for which the version is verifiable by the following code.
       AC_MSG_CHECKING([version not equal to 1.2.5])
       AC_RUN_IFELSE([
-          AC_LANG_PROGRAM(
+        AC_LANG_PROGRAM(
           [[#include <polybori.h>
             #include <polybori/config.h>
           ]], [[
              if (VERSION=="1.2.5") return 0;
              else return 1;
-          ]])
-	  ], [
-          AC_MSG_RESULT([found a possibly buggy 1.2.5. Rejecting])
-	  sage_spkg_install_brial=yes
-	  ], [
-          AC_MSG_RESULT([yes])
-          sage_spkg_install_brial=no
-      ], [AC_MSG_RESULT([cross compiling. Assume yes])
-          sage_spkg_install_brial=no])
+        ]])
+      ], [
+        AC_MSG_RESULT([found a possibly buggy 1.2.5. Rejecting])
+        sage_spkg_install_brial=yes
+      ], [
+        AC_MSG_RESULT([yes])
+        sage_spkg_install_brial=no
+      ], [
+        AC_MSG_RESULT([cross compiling. Assume yes])
+        sage_spkg_install_brial=no
+      ])
     ],
     [
       AC_MSG_RESULT([no])
       sage_spkg_install_brial=yes
     ],
     [
-     AC_MSG_CHECKING([if we can link against brial libraries])
-     AC_LINK_IFELSE([
-       AC_LANG_PROGRAM([
-         #include <polybori.h>
-         #include <polybori/groebner/groebner_alg.h>
-         USING_NAMESPACE_PBORI
-         USING_NAMESPACE_PBORIGB
+      AC_MSG_CHECKING([if we can link against brial libraries])
+      AC_LINK_IFELSE([
+        AC_LANG_PROGRAM([
+          #include <polybori.h>
+          #include <polybori/groebner/groebner_alg.h>
+          USING_NAMESPACE_PBORI
+          USING_NAMESPACE_PBORIGB
 
-     class MyConstant : public BooleConstant{
-           public: void negate() { this->m_value = !this->m_value; }
-         };
-       ],[
-         BoolePolyRing r = BoolePolyRing(2, COrderEnums::dlex);
-         ReductionStrategy rs = ReductionStrategy(r);
-         rs.llReduceAll(); // uses groebner lib
-         if (2 != r.nVariables()) { return 1; }
-         if (r.constant(true) == r.constant(false)) { return 2; }
-         MyConstant f = MyConstant();
-         f.negate(); // ensures v1.1.0+ if m_value isn't const
-         if (!f.isOne()) { return 3; }
-         return 0;
-       ])
-       ],[
-         AC_MSG_RESULT([yes])
-         sage_spkg_install_brial=yes
-       ],[
-         AC_MSG_RESULT([no])
-         sage_spkg_install_brial=no
-       ])
+          class MyConstant : public BooleConstant{
+            public: void negate() { this->m_value = !this->m_value; }
+          };
+        ],[
+          BoolePolyRing r = BoolePolyRing(2, COrderEnums::dlex);
+          ReductionStrategy rs = ReductionStrategy(r);
+          rs.llReduceAll(); // uses groebner lib
+          if (2 != r.nVariables()) { return 1; }
+          if (r.constant(true) == r.constant(false)) { return 2; }
+          MyConstant f = MyConstant();
+          f.negate(); // ensures v1.1.0+ if m_value isn't const
+          if (!f.isOne()) { return 3; }
+          return 0;
+        ])
+      ],[
+        AC_MSG_RESULT([yes])
+        sage_spkg_install_brial=yes
+      ],[
+        AC_MSG_RESULT([no])
+        sage_spkg_install_brial=no
+      ])
     ])
     LIBS=$SAVED_LIBS
     AC_LANG_POP

build/pkgs/bzip2/spkg-configure.m4

@@ -2,7 +2,7 @@ SAGE_SPKG_CONFIGURE([bzip2], [
     AC_CHECK_HEADER(bzlib.h, [
       AC_SEARCH_LIBS([BZ2_bzCompress], [bz2], [
         AC_PATH_PROG([bzip2_prog], [bzip2])
-	AS_IF([test x$bzip2_prog = x], [sage_spkg_install_bzip2=yes])
+        AS_IF([test x$bzip2_prog = x], [sage_spkg_install_bzip2=yes])
       ], [sage_spkg_install_bzip2=yes])
     ], [sage_spkg_install_bzip2=yes])
 ])

build/pkgs/cmake/spkg-configure.m4

@@ -1,6 +1,6 @@
 SAGE_SPKG_CONFIGURE(
     [cmake], [
-	AC_CACHE_CHECK([for cmake >= 3.4], [ac_cv_path_CMAKE], [
+        AC_CACHE_CHECK([for cmake >= 3.4], [ac_cv_path_CMAKE], [
         AC_PATH_PROGS_FEATURE_CHECK([CMAKE], [cmake], [
             cmake_version=`$ac_path_CMAKE --version 2>&1 \
                 | $SED -n -e 's/cmake version *\([[0-9]]*\.[[0-9]]*\.[[0-9]]*\)/\1/p'`

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=d0bd7eea48134f0698b2fa53a51ab07fc6ec488d
-md5=1417fa63769b87988e6d4e3d1a8c7580
-cksum=4077581907
+sha1=2d40d7b88d0e3b7b559c40e4b0bc593982fb7b55
+md5=9839944672f62c22accb4d06ac370444
+cksum=2416630844

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-952f7f9006c84ef54ce7b5aa8e908cc5ea9379bf
+18383a70c541a8c8a7ee764b564d68b413d21e41

build/pkgs/cython/checksums.ini

@@ -1,5 +1,5 @@
 tarball=Cython-VERSION.tar.gz
-sha1=3aafce4489a7bc7a48c843cdfb8dac4677fdac50
-md5=12c5e45af71dcc6dff28cdcbcbef6f39
-cksum=3658613797
+sha1=21187175b7da94020e662c04f805d580f1071880
+md5=81aff945f5bfdfb86e7a5d24f5467668
+cksum=2423037501
 upstream_url=https://pypi.io/packages/source/C/Cython/Cython-VERSION.tar.gz

build/pkgs/cython/package-version.txt

@@ -1 +1 @@
-0.29.21
+0.29.24

build/pkgs/flint/spkg-configure.m4

@@ -15,8 +15,8 @@ SAGE_SPKG_CONFIGURE([flint], [
                                      [return 0;]
                                   [#endif]])],
                  [AC_MSG_RESULT([GC not enabled. Good.])],
-		        [AC_MSG_RESULT([GC enabled. Incompatible with Sage.])
-		         sage_spkg_install_flint=yes],
+                        [AC_MSG_RESULT([GC enabled. Incompatible with Sage.])
+                         sage_spkg_install_flint=yes],
                  [AC_MSG_RESULT(["cross compiling. assuming GC is not enabled"])])
             ], [sage_spkg_install_flint=yes])
           ], [sage_spkg_install_flint=yes])

build/pkgs/gcc/spkg-configure.m4

@@ -53,11 +53,11 @@ AC_DEFUN([SAGE_CHECK_BROKEN_GCC], [
 
 
 SAGE_SPKG_CONFIGURE_BASE([gcc], [
-	AC_REQUIRE([AC_PROG_CC])
-	AC_REQUIRE([AC_PROG_CPP])
-	AC_REQUIRE([AC_PROG_CXX])
-	AC_REQUIRE([AC_PROG_OBJC])
-	AC_REQUIRE([AC_PROG_OBJCXX])
+        AC_REQUIRE([AC_PROG_CC])
+        AC_REQUIRE([AC_PROG_CPP])
+        AC_REQUIRE([AC_PROG_CXX])
+        AC_REQUIRE([AC_PROG_OBJC])
+        AC_REQUIRE([AC_PROG_OBJCXX])
 
     if test -f "$SAGE_LOCAL/bin/gcc"; then
         # Special value for SAGE_INSTALL_GCC if GCC is already installed

build/pkgs/gfortran/spkg-configure.m4

@@ -52,7 +52,7 @@ SAGE_SPKG_CONFIGURE([gfortran], [
     # compiler.
     AC_REQUIRE([SAGE_SAVE_FCFLAGS])
     AC_FC_FREEFORM([SAGE_HAVE_FC_FREEFORM=yes], [
-	AC_MSG_NOTICE([Your Fortran compiler does not accept free-format source code])
+        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_HAVE_FC_FREEFORM=no])

build/pkgs/git/spkg-configure.m4

@@ -1,10 +1,10 @@
 SAGE_SPKG_CONFIGURE([git], [
     # Check whether git works by executing "git --version"
-	AC_CACHE_CHECK([for git], [ac_cv_path_GIT], [
-		AC_PATH_PROGS_FEATURE_CHECK([GIT], [git],
-		[${ac_path_GIT} --version >/dev/null 2>/dev/null &&
+        AC_CACHE_CHECK([for git], [ac_cv_path_GIT], [
+                AC_PATH_PROGS_FEATURE_CHECK([GIT], [git],
+                [${ac_path_GIT} --version >/dev/null 2>/dev/null &&
                       ac_cv_path_GIT=${ac_path_GIT} &&
                       ac_path_GIT_found=:
                 ],
-		[sage_spkg_install_git=yes; ac_cv_path_GIT=no])])
+                [sage_spkg_install_git=yes; ac_cv_path_GIT=no])])
 ])

build/pkgs/gmp/spkg-configure.m4

@@ -3,6 +3,6 @@ SAGE_SPKG_CONFIGURE([gmp], [
     if test x"$with_mp" = xgmp -o x"$_sage_spkg_install_gmp" = xyes; then
         if test x"$SAGE_MP_LIBRARY" = xgmp; then
             sage_spkg_install_gmp=yes
-	fi
+        fi
     fi
 ])

build/pkgs/gp2c/spkg-configure.m4

@@ -55,7 +55,8 @@ SAGE_SPKG_CONFIGURE([gp2c], [
       # Gentoo:     $gp_prefix/share/pari/pari.cfg
       # Arch/Conda: $gp_prefix/lib/pari/pari.cfg
       # Fedora:     $gp_prefix/share/doc/pari/pari.cfg
-      m4_foreach([pari_cfg_path], [share/pari,lib/pari,share/doc/pari], [
+      # Fedora from 2.13.2-2: $gp_prefix/lib64/pari/pari.cfg
+      m4_foreach([pari_cfg_path], [share/pari,lib64/pari,lib/pari,share/doc/pari], [
         AS_IF([test -f "${gp_prefix}/pari_cfg_path/pari.cfg"], [
           libpari_pari_cfg="${gp_prefix}/pari_cfg_path/pari.cfg"
           AC_MSG_NOTICE([found a pari.cfg at $libpari_pari_cfg])
@@ -76,7 +77,7 @@ SAGE_SPKG_CONFIGURE([gp2c], [
 
       # If we can't find pari.cfg, gp2c isn't going to work.
       AS_IF([test -z "$libpari_pari_cfg"], [
-        AC_MSG_ERROR([using system pari and unable to locate pari.cfg])
+        AC_MSG_WARN([using system pari and unable to locate pari.cfg; building the optional pacakge gp2c will not work])
       ])
     ], [
       # Not using the system pari

build/pkgs/iml/spkg-configure.m4

@@ -1,16 +1,14 @@
 SAGE_SPKG_CONFIGURE([iml], [
-    dnl m4_pushdef([SAGE_IML_MINVER],["1.0.4"]) 1.0.5 seems OK too
-    SAGE_SPKG_DEPCHECK([gmp mpir openblas], [
-	AC_CHECK_HEADER([iml.h], [
-          AC_SEARCH_LIBS([nonsingSolvLlhsMM], [iml], [], 
-                [sage_spkg_install_iml=yes])
-          ], [
-          sage_spkg_install_iml=yes
-        ], [
-        #ifdef HAVE_GMP_H
-        #include <gmp.h>
-        #endif
-        ])
+  SAGE_SPKG_DEPCHECK([gmp mpir openblas], [
+    AC_CHECK_HEADER([iml.h], [
+      AC_SEARCH_LIBS([nonsingSolvLlhsMM], [iml], [],
+                     [sage_spkg_install_iml=yes])
+    ], [
+      sage_spkg_install_iml=yes
+    ], [
+      #ifdef HAVE_GMP_H
+      #include <gmp.h>
+      #endif
     ])
-    dnl m4_popdef([SAGE_IML_MINVER])
+  ])
 ])

build/pkgs/ninja_build/spkg-configure.m4

@@ -1,6 +1,6 @@
 SAGE_SPKG_CONFIGURE(
     [ninja_build], [
-	AC_CACHE_CHECK([for ninja >= 1.7.2], [ac_cv_path_NINJA], [
+        AC_CACHE_CHECK([for ninja >= 1.7.2], [ac_cv_path_NINJA], [
         AC_PATH_PROGS_FEATURE_CHECK([NINJA], [ninja], [
             ninja_version=`$ac_path_NINJA --version 2>&1 \
                 | $SED -n -e 's/\([[0-9]]*\.[[0-9]]*\.[[0-9]]*\).*/\1/p'`

build/pkgs/openssl/checksums.ini

@@ -1,5 +1,5 @@
 tarball=openssl-VERSION.tar.gz
-sha1=fbcb255c1bf11928f4bd52b8cf68ab8341238d4f
-md5=26581d6856356698414d71f50ece668d
-cksum=1374793308
+sha1=261ea1ad4bbf7738622bea5caa97da0283fc3166
+md5=53807796206619b62037a178846ebe7e
+cksum=980103943
 upstream_url=https://www.openssl.org/source/openssl-VERSION.tar.gz