Source tarball:

http://sage.math.washington.edu/home/rlmill/release/sage-4.1.alpha3.tar

sage.math binary:

http://sage.math.washington.edu/home/rlmill/release/sage-4.1.alpha3-sage.math-only-x86_64-Linux.tar.gz

Upgrade URL:

http://sage.math.washington.edu/home/rlmill/release/sage-4.1.alpha3/

I decided to cut an alpha release before rc0, since I think I've got
upgrading working, and I'd like to test it in more places than
sage.math. On sage.math, upgrading from a vanilla 4.0.2 to 4.1.alpha3
should work, and long doctests pass just as much as on a vanilla
alpha3 build. To do this, I bumped version numbers on the following
spkg's (without commenting in SPKG.txt or checking anything in):

 - cvxopt
 - cython
 - docutils
 - dsage
 - gd
 - gdmodule
 - gnutls
 - jinja
 - matplotlib
 - moin
 - numpy
 - pexpect
 - polybori
 - pyprocessing
 - pycrypto
 - pygments
 - python_gnutls
 - r
 - scipy
 - scipy_sandbox
 - setuptools
 - sphinx
 - sqlalchemy
 - sympy
 - weave
 - zodb
 - networkx
 - mercurial

I also modified the Python spkg to copy site-packages to site-packages-
old, so people don't lose anything by upgrading.

The following scripts patches were applied, which were thought to be
in alpha2:

#4712   [with patch, positive review] Make the doctest timeouts in
Sage easily adjustable
#5350   [with patch, positive review] sage-clone should use hard links
for the build directory
#5481   [with patch, positive review] devel/doc/output/* should be
filtered from the list of files to doctest
#5902   [with patch, positive review] Try SAGE_ROOT as base of
argument to "sage -t"

A patch fixing the merge state for the following ticket was merged
(this being in a broken state explains the regression we noticed in
sha_tate):

#5080   [with new patch, with positive review] Bug in decomposing
modular symbol subspace

The following tickets were also merged:

#6446   [with patch, with positive review] memory issue from #6394
#6406   [with patch, with positive review] fixing p_primary_bound on
Tate-Shafarevich groups not to allow the reducible case

There is one known doctest issue:
sage -t -long devel/sage/sage/misc/darwin_utilities.pyx

which is being tracked at
#6448   darwin_utilities import issues

---------------------------------------------------------------

This is my current list for rc0, aside from getting someone to fix
#6448:

#5882   [with patch; needs final review] implement general package for
finitely generated not-necessarily free R-modules
#6429   [with patch; positive review] sagedoc: make search_src and
friends less OS dependent
#6258   [with patch, positive review] Improve accuracy of graph
eigenvalues
#6196   [with patch, positive review] mpmath support
#6276   [with patch; positive review] atlas-3.8.3.p2 dumps core on
Solaris 10 with gcc 4.4.0
#5517   [with patch; positive review] cvxopt-0.9.p7: build failure due
to missing perl modules
#5854   [with patch, positive review] Include Michael Stoll's
ratpoints in Sage
#5866   [with patch, positive review] Fix freetype build on systems
where make is not GNU make.
#5867   [with patch, positive review] Fix gd build on FreeBSD
#5868   [with patch, positive review] Fix libgcrypt shared library
name on FreeBSD
#5869   [with patch, positive review] Fix libgpg-error shared library
name on FreeBSD
#5870   [with patch, positive review] Detect blas and atlas libraries
for linbox on FreeBSD
#5872   [with patch, positive review] Explicitly pass -fPIC into ntl
shared object build.
#5874   [with patch, positive review] Fix readline build on FreeBSD
#5875   [with patch, positive review] Support tachyon on FreeBSD
#6281   [with patch; positive review] enable parallel make for rubiks
spkg
#6302   [with patch; positive review] make openopt an optional spkg
#6380   [with patch, positive review] Allow NTL to build on Solaris
with Sun or GNU linker


-- Robert L Miller
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