Merge branch 'develop' into t/20559/interactivelpproblem__dictionarie…

…s__add_constraint___add_row_methods

README.md

@@ -3,7 +3,7 @@
 >   "Creating a Viable Open Source Alternative to
 >    Magma, Maple, Mathematica, and MATLAB"
 
->   Copyright (C) 2005-2014 The Sage Development Team
+>   Copyright (C) 2005-2016 The Sage Development Team
 
    http://www.sagemath.org
 
@@ -67,7 +67,7 @@ source. More detailed instructions, including how to build faster on
 multicore machines, are contained later in this README and in the  
 Installation Guide:  
 
-   http://www.sagemath.org/doc/installation
+   http://doc.sagemath.org/html/en/installation
 
 __1. Make sure you have the dependencies and 5 GB of free disk space.__
 
@@ -110,14 +110,19 @@ __3. cd into the Sage directory and type make:__
    should work fine on all fully supported platforms. If it does not, we  
    want to know!  
 
+   If you'd like to contribute to Sage, be sure to read the
+   Developer's Guide:
+
+   http://doc.sagemath.org/html/en/developer/index.html
+
 
 Environment Variables
 ---------------------
 
 There are a lot of environment variables which control the install  
 process of Sage, see:  
 
-   http://sagemath.org/doc/installation/source.html#environment-variables
+   http://doc.sagemath.org/html/en/installation/source.html#environment-variables
 
 
 Implementation
@@ -325,7 +330,7 @@ SAGE_ROOT                 Root directory (sage-x.y.z in Sage tarball)
 ```
 For more details, see:
 
-    http://sagemath.org/doc/developer/coding_basics.html#files-and-directory-structure
+    http://doc.sagemath.org/html/en/developer/coding_basics.html#files-and-directory-structure
 
 
 Relocation
@@ -343,7 +348,7 @@ Sage as root at least once prior to using the system-wide Sage as a
 normal user. See the Installation Guide for further information on  
 performing a system-wide installation:
 
-   http://www.sagemath.org/doc/installation/source.html#installation-in-a-multiuser-environment
+   http://doc.sagemath.org/html/en/installation/source.html#installation-in-a-multiuser-environment
 
 If you find anything that doesn't work correctly after you moved the  
 directory, please email the sage-support mailing list.  

VERSION.txt

@@ -1 +1 @@
-SageMath version 7.3.beta4, Release Date: 2016-06-12
+SageMath version 7.3.beta8, Release Date: 2016-07-14

build/bin/sage-download-file

@@ -24,5 +24,5 @@ except ImportError:
     sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
     import sage_bootstrap
 
-from sage_bootstrap.cmdline import SageDownloadFileApplication
-SageDownloadFileApplication().run()
+from sage_bootstrap.download.cmdline import run_safe
+run_safe()

build/bin/sage-package

@@ -38,5 +38,5 @@ except ImportError:
     sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
     import sage_bootstrap
 
-from sage_bootstrap.cmdline import SagePkgApplication
-SagePkgApplication().run()
+from sage_bootstrap.cmdline import run
+run()

build/bin/sage-spkg

@@ -520,32 +520,36 @@ fi
 ##################################################################
 
 if [ "$USE_LOCAL_SCRIPTS" = yes ]; then
+    # New-style package
     echo "Setting up build directory for $PKG_NAME"
     cp -Rp "$PKG_SCRIPTS" "$PKG_NAME"
     cd "$PKG_NAME" || exit $?
+
+    sage-uncompress-spkg -d src "$PKG_SRC"
+    if [ $? -ne 0 ]; then
+        echo >&2 "Error: failed to extract $PKG_SRC"
+        exit 1
+    fi
 else
+    # Old-style package (deprecated)
     echo "Extracting package $PKG_SRC"
     ls -l "$PKG_SRC"
-fi
 
-sage-uncompress-spkg -d src "$PKG_SRC"
-if [ $? -ne 0 ]; then
-    echo >&2 "Error: failed to extract $PKG_SRC"
-    exit 1
-fi
-
-if [ "$USE_LOCAL_SCRIPTS" = yes ]; then
-    echo "Finished set up"
-else
-    echo "Finished extraction"
+    sage-uncompress-spkg "$PKG_SRC"
+    if [ $? -ne 0 ]; then
+        echo >&2 "Error: failed to extract $PKG_SRC"
+        exit 1
+    fi
 
     cd "$PKG_NAME"
     if [ $? -ne 0 ]; then
-        echo >&2 "Error: after extracting, the directory $PKG_NAME does not exist"
+        echo >&2 "Error: after extracting, the directory '$PKG_NAME' does not exist"
         exit 1
     fi
 fi
 
+echo "Finished extraction"
+
 ##################################################################
 # The package has been extracted, prepare for installation
 ##################################################################

build/bin/sage-uncompress-spkg

@@ -31,6 +31,7 @@ from __future__ import print_function
 import argparse
 import copy
 import os
+import stat
 import sys
 import tarfile
 import zipfile
@@ -84,9 +85,14 @@ class SageTarFile(tarfile.TarFile):
     See http://trac.sagemath.org/ticket/20218#comment:16 for more background.
     """
 
-    def __init__(self, *args, **kwargs):
-        super(SageTarFile, self).__init__(*args, **kwargs)
+    def __new__(cls, *args, **kwargs):
+        # This is is that SageTarFile() is equivalent to TarFile.open() which
+        # is more flexible than the basic TarFile.__init__
+        inst = tarfile.TarFile.open(*args, **kwargs)
+        inst.__class__ = cls
+        return inst
 
+    def __init__(self, *args, **kwargs):
         # Unfortunately the only way to get the current umask is to set it
         # and then restore it
         self.umask = os.umask(0o777)
@@ -115,19 +121,19 @@ class SageTarFile(tarfile.TarFile):
     def chmod(self, tarinfo, target):
         tarinfo = copy.copy(tarinfo)
         tarinfo.mode &= ~self.umask
+        tarinfo.mode &= ~(stat.S_ISUID | stat.S_ISGID)
         return super(SageTarFile, self).chmod(tarinfo, target)
 
     def extractall(self, path='.', members=None):
         """
         Same as tarfile.TarFile.extractall but allows filenames for
         the members argument (like zipfile.ZipFile).
         """
-
         if members:
+            name_to_member = dict([member.name, member] for member in self.getmembers())
             members = [m if isinstance(m, tarfile.TarInfo)
-                         else self.getmember(m)
-                         for m in members]
-
+                       else name_to_member[m]
+                       for m in members]
         return super(SageTarFile, self).extractall(path=path, members=members)
 
     def extractbytes(self, member):
@@ -184,7 +190,7 @@ ARCHIVE_TYPES = [SageTarFile, SageZipFile]
 
 def main(argv=None):
     parser = argparse.ArgumentParser()
-    parser.add_argument('-d', dest='dir', nargs=1, metavar='DIR',
+    parser.add_argument('-d', dest='dir', metavar='DIR',
                         help='directory to extract archive contents into')
     parser.add_argument('pkg', nargs=1, metavar='PKG',
                         help='the archive to extract')
@@ -195,7 +201,7 @@ def main(argv=None):
     args = parser.parse_args(argv)
 
     filename = args.pkg[0]
-    dirname = args.dir[0]
+    dirname = args.dir
 
     for cls in ARCHIVE_TYPES:
         if cls.can_read(filename):
@@ -207,7 +213,7 @@ def main(argv=None):
 
     # For now ZipFile and TarFile both have default open modes that are
     # acceptable
-    archive = cls.open(filename)
+    archive = cls(filename)
 
     if args.file:
         contents = archive.extractbytes(args.file)
@@ -233,11 +239,23 @@ def main(argv=None):
 
         if len(top_levels) == 1:
             top_level = top_levels.pop()
-
-    archive.extractall(members=archive.names)
-
-    if top_level:
-        os.rename(top_level, dirname)
+        else:
+            os.makedirs(dirname)
+
+    prev_cwd = os.getcwd()
+
+    if dirname and not top_level:
+        # We want to extract content into dirname, but there is not
+        # a single top-level directory for the tarball, so we cd into
+        # the extraction target first
+        os.chdir(dirname)
+
+    try:
+        archive.extractall(members=archive.names)
+        if dirname and top_level:
+            os.rename(top_level, dirname)
+    finally:
+        os.chdir(prev_cwd)
 
     return 0
 

build/pkgs/atlas/spkg-install

@@ -143,6 +143,7 @@ if 'SAGE_ATLAS_LIB' in os.environ:
 
     paths = [ ATLAS_LIB, os.path.join(ATLAS_LIB, 'lib64'), os.path.join(ATLAS_LIB, 'lib') ]
     ATLAS_LIB = None
+    libraries = []
     for libs in libraries_sets:
         for path in paths:
             if is_atlas_lib_path(path, libs):
@@ -209,7 +210,7 @@ if 'SAGE_ATLAS_LIB' in os.environ:
     for lib in libraries + libraries_optional:
         symlinkOSlibrary(prefix+lib)
 
-    if 'atlas' in libs:
+    if 'atlas' in libraries:
         write_pc_file(['cblas', 'atlas'], 'cblas')
         write_pc_file(['f77blas', 'atlas'], 'blas')
         # The inclusion of cblas is not a mistake. ATLAS' lapack include

build/pkgs/boost/spkg-install

@@ -16,6 +16,12 @@ if [[ $? -ne 0 ]]; then
 fi
 
 echo "Building boost"
+# By default this is populated by a system value.
+# If the boost build system (b2, bjam and associated files under /usr/share/boost-build)
+# has been installed system wide it can cause interference.
+# The build will fail purely and simply without much of an explanation.
+# see http://trac.sagemath.org/ticket/20776 for details.
+export BOOST_BUILD_PATH="${SAGE_LOCAL}"/share/boost-build
 ./b2
 if [[ $? -ne 0 ]]; then
     echo >&2 "Failed to build boost."

build/pkgs/brial/checksums.ini

@@ -1,4 +1,4 @@
 tarball=brial-VERSION.tar.bz2
-sha1=8b30a7b331323eae094752dd7f88b398e6ed742a
-md5=66275eea0654cb1eb6438a6262140885
-cksum=2952216147
+sha1=12ef021fc1236e25ff0b46680720918489fb4931
+md5=f332eaa0378e9b630f958e4dcd4ea6e8
+cksum=2509320148

build/pkgs/brial/package-version.txt

@@ -1 +1 @@
-0.8.4.3
+0.8.5