- Ported old run-flake8-tests qa script to `spack flake8` command.
- New command does not modify files in the source tree
- Copies files to a temp stage modifies them there, and runs tests.
- Updated docs and `run-flake8-tests` script to call `spack flake8`.

- generalized and fixed to work with any key in YAML file
- simplified schema writing, as well
- add more unit tests for the config system
- Rename test/yaml.py to test/spack_yaml.py
  - Add test/yaml.pyc to ignored pyc files.

- Added new preferences to config.yaml:
  - source_cache
  - misc_cache
  - verify_ssl
  - checksum
  - dirty

- Moved temp finding logic to spack.stage
- Updated stage tests
- Added tests for new path substaitution of $user, $spack, $tempdir

- Added a schema for config.yaml
- Moved install tree configuration to config.yaml
- Moved etc/spack/install.yaml to etc/spack/defaults/config.yaml
- renamed install_area to "store", to use a term in common with guix/nix.
  - in `config.yaml` file, it's called the `install_tree` to be more
    intuitive to users.
  - `install_tree` might've worked in the code, but `install_tree` is
    already a global function in the spack namespace, from
    llnl.util.filesystem.

Merge #2030 added a cyclic dependency between the Cray platform needing
to read a `targets.yaml` config file and `config.py` needing to get the
platform names.

This commit removes the cyclic dependency in favor of the more general
config scheme. It also removes the now functionless `targets.yaml`
config file. This breaks 'frontend' targets on the Cray platform but
all architecture targets, including the frontend, that are provided by
CrayPE are added to the Platform anyway so users can be explicit about
the architecture targeted by the Cray compiler wrappers:

```
spack spec libelf arch=cray-CNL-frontend
```

becomes

```
spack spec libelf arch=cray-CNL-mc8         # on an XK7 or
spack spec libelf arch=cray-CNL-sandybridge # on an older XC30, etc..
```

The only way the 'frontend' target can be defined after this commit is
through target environment variables.

On MacOS, brew installs /usr/local/bin/python but the Python prefix is not /usr/local/bin
Use the python command sys.exec to get the correct directory, instead of the ad hoc self.prefix
previously used

This was a bear to debug; been driving me nuts since I started using spack.
Since spack passes PYTHONHOME down to package builds in the environment
it was passing PYTHONHOME of /usr/local/bin to the PETSc build that uses Python so
the PETSc Python ./configure errored immediately with

ImportError: No module named site

since python could find no python modules. Todd Gamblin pointed out that my first try to fix
this was wrong since it assumed the spack python was the same python used to run spack. Elizabeth Fischer
suggested how to get it to work also with python3

Funded-by: IDEAS
Project: IDEAS/xSDK
Time:  7 hours
Thanks-to: Todd Gamblin, Elizabeth Fischer

* module file support: major rework of docs

* module file support: fixed issues found by @adamjstewart

- list or enumeration should not be indented
- use console instead of bash or csh in things that are not scripts
- other typos

* module file support: fixed other issues found by @adamjstewart

- tables should not be indented
- substitute lines with pyobject to import an entire function
- get help output running commands
- typos

* module file support: fixes according to review comments

- @citibeth moved `spack module loads` after `spack load`
- @glennpj tried to clarify installation table + changes to language
- @tgamblin Removed top level section and moved the whole thing into the reference manual

* module file support: moved directive before spack module loads

- enable keyword works again
- test/modules.py : proper clean-up after tests

External packages do not have an spec.yaml file so don't check for it.
Without this change any time a package depends on an external package
when the new package is installed you will get the error

Install prefix exists but contains no spec.yaml

This problem has also haunted me since I started using Spack since PETSc
depends on Python and I used an external python but fortunately it
was relatively easy to debug once I could reproduce it at will.

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

Fixes #1845

This replaces a custom token-based substitution format with calls to
Spec.format in modules.py

This also resolves a couple issues:

- LmodModules set configuration globally instead of in its initializer
  which meant test-specific configuration was not applied
- Added support for setting hash_length=0 for LmodModules. This only
  affects the module filename and not the directory names for the
  hierarchy tokens in the path. This includes an additional unit test.

* Made some refactoring improvements to the 'visit' and 'vtk' packages.

* Added a small fix for the 'vtk' package when building with 'qt+webkit'.

Funded-by: IDEAS
Project: IDEAS/xSDK
Time:  2 hours

The breaks `spack create`.

Removed documentation on false paths as per #2083

* document recommended usage of system blas/lapack

* update doc

* minor

* reword

Add the latest release of libSplash, version 1.5.0.

* spack install : added --log-format option (incorporates test-install command)

fixes #1907

* qa : removed extra whitespace

* openmpi: require fortran for now

* mpich: requre fortran for now

* mvapich2: require fortran for now

* openmpi: flake8 fixes

* Update the krell institute products to use the latest features of spack for building on cluster platforms.

* Address travis error messages and resubmit the pull request.

* Update the contents of openspeedshop package.py so it passes the flake8 tests.

* Fix flake8 error-whitespack issue in mrnet package.py file.

* Add updates based on spack reviewer feedback.

* More fixes based on comments from reviewers.  Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH.

* More review related changes.  Update MPIOption.append lines and take out xercesc references.

* Create a base options function for common openspeedshop base cmake options to reduce redundencies.

* Add libxml2+python depends on to get around issues with the libxml2 package file.

* veclibfort: add new package

* veclibfort: add a small test

Add a package for ant, a java build tool.

Add a package that installed the pre-built maven distribution.

I've given up, for now, on building maven from source.  That processed
stumbled on two points before I gave up:

1. It downloaded several hundred .{pop,jar} files and I despaired of
   figuring out some way of mirroring and checksumming them; and

2. It exploded complaining about too many unacceptable license files,
   which seems odd in its own source tree.

Perhaps someone with more Java fu that I admit to can figure it out.
In the meantime, this is useful.