29446: improve handling of SAGE_ROOT to avoid symbolic links

With this change, SAGE_ROOT will always be the physical path, even if
the current directory when compiling Sage is a symbolic link
(non-physical path) to Sage's root directory.

In particular, this fixes a test failure in src/sage/env.py when Sage
was built from the symbolic/non-physical path.

build/pkgs/sage_conf/src/sage_conf.py.in

@@ -11,7 +11,7 @@ SAGE_NAUTY_BINS_PREFIX = "@SAGE_NAUTY_BINS_PREFIX@"
 # The following must not be used during build to determine source or installation
 # location of sagelib.  See comments in SAGE_ROOT/src/Makefile.in
 SAGE_LOCAL = "@prefix@"
-SAGE_ROOT = "@abs_top_srcdir@"
+SAGE_ROOT = "@SAGE_ROOT@"
 
 # Entry point 'sage-config'.  It does not depend on any packages.
 

configure.ac

@@ -62,6 +62,7 @@ AC_CONFIG_MACRO_DIR([m4])
 
 # Assume current directory is SAGE_ROOT.
 SAGE_ROOT=`pwd -P`
+AC_SUBST(SAGE_ROOT)
 
 SAGE_LOCAL="$prefix"
 # The following line is necessary because the code below

src/bin/sage-env-config.in

@@ -31,7 +31,7 @@ export SAGE_ENV_CONFIG_SOURCED=1
 export SAGE_LOCAL="@prefix@"
 
 # SAGE_ROOT is the location of the Sage source/build tree.
-export SAGE_ROOT="@abs_top_srcdir@"
+export SAGE_ROOT="@SAGE_ROOT@"
 
 #######################################
 # Compilers set at configuration time

src/sage/env.py

@@ -6,7 +6,8 @@
 - \R. Andrew Ohana (2012): Initial version.
 
 Verify that importing ``sage.all`` works in Sage's Python without any ``SAGE_``
-environment variables, and has the same ``SAGE_ROOT`` and ``SAGE_LOCAL``::
+environment variables, and has the same ``SAGE_ROOT`` and ``SAGE_LOCAL``
+(see also :trac:`29446`)::
 
     sage: env = {k:v for (k,v) in os.environ.items() if not k.startswith("SAGE_")}
     sage: from subprocess import check_output