* atlas: fix lapack stage path

* atlas: add a few links to other package managers

The advanced [Uninstalling Packages](spack.readthedocs.io/en/latest/tutorial_sc16_spack_basics.html#uninstalling-packages) via hash has a couple missing `.. code-block:: console` directives ;)

I have no idea what branch to direct this to though...

* likwid: add todo

* liwkid: add a note on hwloc dependency

Rename developer version, add new version, and make patch version
specific.

* clang: do xcode mockup iff requested by a package

* add a note

* add pkg to setup_custom_environment() and decide whether or not to use mockup XCode there based on the package

Main page states [3.3.1 is latest stable](http://eigen.tuxfamily.org/index.php?title=Main_Page).

Source project page states [6.0.4 is latest stable](http://scotch.gforge.inria.fr/)

Supports installing both a "known version" of PETSc/PFlotran that works and
the develop/master branches of both packages

Funded-by: IDEAS
Project: IDEAS/xSDK
Time: 4 hour

* update flux dependencies and package

* refinements from @adamjstewart

* fix flux document generation

The docbook-xsl package has been added, and correctly configures catalog
files to generate documentation correctly with asciidoc.

* astyle: do not set user/group when installing on macOS

* astyle: add new version

otherwise petsc may pickup libX11 on login nodes during config/build,
but libX11 may not be available on computation nodes.

* Make targets an attribute of compilers, similar to OS. Allows users to use `spack compiler find` to add compilers for the same platform/os but different targets when spack is installed on a file system mounted on machines with different targets.

* Changed get_compilers() method to treat old compilers with no target as target='any'

* flake8 changes

* Address change requests for comments/code clarity

* Added package 'uuid'.

* Added package 'cmor'.

* Updated 'cmor' and 'uuid': docstring formatting.

* Add support for parsing R-XML URL versions.

* Better url-parse debug output.

- just print the debug stuff all the time.

* fix R-XML versions.

* Update emacs: current release, use our x11 bits

Add checksum for 25.1 release.

Rework the X support:

- use Spack's X11 bits
- add ability to specify an X toolkit (gtk or athena, default is gtk).
- change toolkit names to align with Emacs' configure usage.

* PEP8 cleanups.

* glib dependency should not be type=build

I'd like to blame that on a typo, but it's a few too many characters
for that to be viable.  I'm not sure what I was thinking.

* Pass X variant down: emacs->pango->cairo

* X variants default to False, warn on bad toolkit

Change the X variants for emacs, pango and cairo to default to False.

Check that the toolkit is a valid choice and give a reasonable error if
not.

* Fix flake8 issue, reword warning text

* gtkplus needs to use +X variant for pango to work

In order for a useful variant of pango to be built into the spec I
needed to make the dependency on gtkplus explicitly specify it's X
variant.  The X variant is the default, but that wasn't enough to make
it happy.  Since it's happiness is the most imporant thing in the
world, this change! :)

* fix for  bluegene-q platform

* change powerpc to ppc64

* change CNK to cnk

Fixes #2306

Any dependency explicitly mentioned in a spec string ended up with the
build and link deptypes unconditionally. This fixes dependency
resolution to ensure that packages which are mentioned in the spec
string have their deptypes determined by the dependency information
in the package.py files. For example if a package has cmake as a build
dependency, and cmake is mentioned as a dependency in the spec string
for the package, then it ends up with just the build deptype.

Packages built targeting a backend may depend on packages like cmake
which can be built against the frontend. With this commit, any build
dependency or child of a build dependency will target the frontend by
default. In compiler concretization when packages copy compilers from
nearby packages, build dependencies use compiler information from
other build dependencies, and link dependencies avoid using compiler
information from build dependencies.

* Add version/digest for emacs 25.1

* Put newest version at top of list

yaml-cpp has a boost dependency, and according to [yaml-cpp
page](https://github.com/jbeder/yaml-cpp):
    yaml-cpp 0.5.3 has been released! This is a bug fix release. It also
    will be the last release that uses Boost; futures releases will require
    C++11 instead.

See #2059 for background.

I'm unable to install `lmod` because lua-luafilesystem fails.

The luarocks install bits attempt to do a shallow clone of the luafilesystem
sources and the default git on my CentOS 7 test box (`git version 1.8.3.1`)
fails.

This adds a build dependency that ensures that a relatively modern git is
available.

* Update texlive digest value

While the discussion in #2494 progresses, this changes fixes the digest
values so that builds succeeed.

* Add warning that texlive is not repeatably installable

Funded-by: IDEAS
Project: IDEAS/xSDK
Time: 1 hour

Funded-by: IDEAS
Project: IDEAS/xSDK
Time: 1 hour

* Update OpenMPI to the AutotoolsPackage

* Add Java support to OpenMPI

* Fix missing commas

* Be more specific about what versions support what flags

* Revert description for thread_multiple variant

* py-rtree: Added package

* py-rtree = RTree (spatial indexing) data structure for Python
* libspatialindex = Underlying C library wrapped by py-rtree

* Flake8 and Copyright issues.

* Fix Python syntax error.

* Fixed dependency type error.

* Added new version, based on updates requested in upstream PR

* 1. Change cmake to build dependency.
2. Updated to CMakePackage