[cctbxbb] Updated base dependencies (not Boost)

[Billy Poon]

Hi all,

I have a set of new dependencies for base running on a CentOS 6.7 machine.
The tests for PHENIX pass, but I'm still testing the GUI. It looks like
most of the DIALS tests pass, but there are some that fail due to an
updated Python Imaging Library. Testing will take a while longer, but I
attached the modified install_base_packages.py and package_defs.py scripts
for anyone who wants to try it out. Just use these in place of the ones in
cctbx_project/libtbx/auto_build. I'll also clean up the scripts (e.g.
remove cruft from the migration to wxPython 3.0.2, refactor some functions)
once testing is complete.

Aaron and I will be setting up "clean" virtual machine images for CentOS 5,
6, and 7, and Ubuntu 12.04, and 14.04, and eventually Windows 10 and maybe
OS X (only Server can be virtualized) for testing the installers. The goal
is to simulate what a user would get from a fresh install of an OS and test
that our installers work correctly. And after each test, we can revert the
virtual machine to an earlier snapshotted state. This should help in
debugging some of the recent installation issues.

Since our installers include the GUI, the Linux images will have their
respective desktop GUIs installed (desktop version instead of server
version). We thought about going with minimal server installs, but there
are external dependencies, namely X11/Xorg, that we expect the users to
have, and installing the desktop GUI would be the easiest way to satisfy
any external dependency.

Some highlights from the updates,
1) Python Imaging Library has not been updated since 2009. There is an
active fork called Pillow that seems to be mostly backwards compatible. I
have noticed one change in the API (replace PIL.Image.fromstring with
PIL.Image.frombytes), but more testing is needed.
2) The updated version of ReportLab depends on Pillow.
3) GTK2 was not updated to GTK3 since it seems like wxPython only added
support for GTK3 in 3.0.2. GTK2 is updated to the latest version.
Dependencies for GTK2 (cairo, pango, etc.) are updated. An additional
package, HarfBuzz, is needed.
4) libPNG was updated only to 1.5.x, not 1.6.x, because 1.6.x has some
stricter checks on the image. Warnings are raised in the GUI. Eventually,
this can be upgraded to 1.6.x, but I would need to reprocess all of the PNG
icons to remove the offending bits.
5) libFFI was added for the updated version of glib.

The updated dependencies have been built on CentOS 5, 6, and 7, and OS X
10.10, but not all the tests have been run yet. The 32-bit version of
CentOS 5 is going to require some more work before the updated packages
will compile.

Let me know if there are any questions or suggestions. Thanks!

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org
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