* Properly ignore flake8 F811 redefinition errors
* Add unit tests for flake8 command
* Allow spack flake8 to work on systems with older git
* Skip flake8 unit tests for Python 2.6 and 3.3

* legion: add mpi inoperability

* legion: make +mpi the default

* legion: add shared variant

* Added magma package

* Incorporated Serban's change

* globalarrays: add global arrays package to Spack.

* globalarray: remove extreaneous comment from package file

- make the name more generic for posterity.

* Added a package for the MDAnalysis toolkit.

* Added the hash for the 1.0 release of caffe and put in a conflict
statemet indicating that protobuf requires a c++11 compiler.

* Changed minimum version number.

* Tweaked the minimum version number.

* Fixed flake8 error.

* Use six.moves.input instead of raw_input

* Remove comment mentioning raw_input

* new Intel libs do not require license to install

* updated Intel library package URLs

* disable license_required for new Intel libraries

* grib-api: add version 1.21.0

* libemos: add version 4.4.7 and allow choice of eccodes or grib-api

* magics: add version 2.32.0

* libemos: add description for eccodes variant

* eccodes: new package for encoding and decoding meteorological data

* eccodes: remove line breaks from package docstring

* eccodes: simplify names of variants

* eccodes: give a description for each variant

* eccodes: use succinct code for cmake_args

* eccodes: found extra dependency for python variant

* eccodes: add URL for a list of available releases

* treats correctly a change from `explicit=False` to `explicit=True` in an external package DB entry.
* added unit tests
* fixed issues raised by @tgamblin . In particular the PR is no more hash-changing for packages that are not external.
* added a test to check correctness of a spec/yaml round-trip for things that involve an external
* Don't find external module path at each step of concretization
    * it's not necessary.. The paths are retrieved at the end of concretizaion
* Don't find replacements for external packages.
* Test root of the DAG if external
    * No reason not to test if the root of the DAG is external when external
packages are now first class citizens!
* Create `external` property for Spec (for external_path and external_module)
* Allow users to specify external package paths relative to spack
    * Canonicalize external package paths so that users may specify their
locations relative to spack's directory.
* Update tests to use new external_path and external properly.
* skip license hooks on external

* Hack to fix python dependency ranges

* Flake8

* intel-mpi: add new package

* fix hashes

* fix typo

* flake8

* add install

* blank line

* error

* add bin64

* fix MPI wrappers in intel-parallel-studio

* add missing I_MPI_FC

* use shorter hashes

- py-setuptools is required by py-yt for importing yt in jupyter notebooks.
- add two dependencies needed for python 2.7
- add the py-subprocess32 package

- add setuptools dependencies to packages that need it.
- remove setuptools from packages that do not need it.

- Spack doesn't need eggs -- it manages its own directories

- Simplify install layout and reduce sys.path searches by installing all
  packages flat (eggs are deprecated for wheels, and this is also what
  wheels do).

- We now supply the --single-version-externally-managed argument to
  `setup.py install` for setuptools packages and setuptools.

- modify packages to only use setuptools args if setuptools is an
  immediate dependency

- Remove setuptools from packages that do not need it.

  - Some packages use setuptools *only* when certain args (likeb
    'develop' or 'bdist') are supplied to setup.py, and they specifically
    do not use setuptools for installation.

  - Spack never calls setup.py this way, so just removing the setuptools
    dependency works for these packages.

* fetch git submodules recursively

This is useful if the submodules have submodules themselves. On
the other hand doing a recursive update doesn't hurt if there
is only one level.

* fetch submodules with depth=1 as well (fix #2190)

* use git submodule with depth only for git>=1.8.4

Update tests to use codecov for multiple python versions.

- Spack install would previously fail if it could not load a package for
  the thing being uninstalled.

- This reworks uninstall to handle cases where the package is no longer
  known, e.g.:
    a) the package has been renamed or is no longer in Spack
    b) the repository the package came from is no longer registered in
       repos.yaml

* Convert LLVM to CMakePackage, update cmake dependency version

* Remove unused import

- gcc on macOS says it's version 4.2.1, but it's really clang, and it's
  actually the *same* clang as the system clang.

- It also doesn't respond with a full path when called with
  --print-file-name=libstdc++.dylib, which is expected from gcc in abi.py.
  Instead, it gives a relative path and _gcc_compiler_compare doesn't
  understand what to do with it.  This results in errors like:

  ```
  lib/spack/spack/abi.py, line 71, in _gcc_get_libstdcxx_version
      libpath = os.readlink(output.strip())
  OSError: [Errno 2] No such file or directory: 'libstdc++.dylib'
  ```

- This commit does two things:

  1. Ignore any gcc that's actually clang in abi.py.  We can probably do
     better than this, but it's not clear there is a need to, since we
     should handle the compiler as clang, not gcc.

  2. Don't auto-detect any "gcc" that is actually clang anymore.  Ignore
     it and expect people to use clang (which is the default macOS
     compiler anyway).

Users can still add fake gccs to their compilers.yaml if they want, but
it's discouraged.

* Checksum code wasn't opening binary files as binary.

- Fixes Python 3 issue where files are opened as unicode text by default,
  and decoding fails for binary blobs.

* Simplify fetch test parametrization.

* - add tests for URL fetching and checksumming.
- fix coverage on interface functions in FetchStrategy superclass
- add some extra crypto tests.

* Fix HPL build, convert to MakefilePackage

* Flake8 fix

* Fix: spec -> self.spec

* Properly query for system libraries

* Update Intel-MKL as well

* Recurse in system libs, fix MKL path, fixes lapack_libs

* Fix for llvm 4.0.0 on centos

This addresses https://github.com/LLNL/spack/issues/3791

* Only enable this option if on linux

* Change condition to satisfy standard

* Added a package for the MDAnalysis toolkit.

* Added has for Keras version 2.0.3

Since scorep does not support all use cases yet, vampirtrace is still
useful in some circumstances.