Co-authored-by: Elizabeth Fischer <rpf2116@columbia.edu>

- this shoudl have been moved when we moved pytest.ini to lib/spack/spack/test

* gitignore everything in /etc/spack except /etc/spack/defaults

* Don't ignore subsubdirectories of /etc/spack/defaults

* Porting: substitute nose with ytest

This huge commit substitutes nose with pytest as a testing system. Things done here:

* deleted external/nose as it is no longer used
* moved mock resources in their own directory 'test/mock/'
* ported two tests (cmd/find, build_system) to pytest native syntax as an example
* build_environment, log: used monkeypatch instead of try/catch
* moved global mocking of fetch_cache to an auto-used fixture
* moved global mocking from test/__init__.py to conftest.py
* made `spack test` a wrapper around pytest
* run-unit-tests: avoid running python 2.6 tests under coverage to speed them up
* use `pytest --cov` instead of coverage run to cut down testing time

* mock/packages_test: moved mock yaml configuration to files instead of leaving it in the code as string literals

* concretize.py: ported tests to native pytest, reverted multiprocessing in pytest.ini as it was creating the wrong report for coveralls

* conftest.py, fixtures: added docstrings

* concretize_preferences.py: uses fixtures instead of subclassing MockPackagesTest

* directory_layout.py: uses fixtures instead of subclassing MockPackagesTest

* install.py: uses fixtures instead of subclassing MockPackagesTest

* optional_deps.py: uses fixtures instead of subclassing MockPackagesTest

optional_deps.py: uses fixtures instead of subclassing MockPackagesTest

* packages.py: uses fixtures instead of subclassing MockPackagesTest

* provider_index.py: uses fixtures instead of subclassing MockPackagesTest

* spec_yaml.py: uses fixtures instead of subclassing MockPackagesTest

* multimethod.py: uses fixtures instead of subclassing MockPackagesTest

* install.py: now uses mock_archive_url

* git_fetch.py: uses fixtures instead of subclassing MockPackagesTest

* hg_fetch.py: uses fixtures instead of subclassing MockPackagesTest

* svn_fetch.py, mirror.py: uses fixtures instead of subclassing MockPackagesTest
repo.py: deleted

* test_compiler_cmd.py: uses fixtures instead of subclassing MockPackagesTest

* cmd/module.py, cmd/uninstall.py: uses fixtures instead of subclassing MockDatabase

* database.py: uses fixtures instead of subclassing MockDatabase, removed mock/database

* pytest: uncluttering fixture implementations

* database: changing the scope to 'module'

* config.py: uses fixtures instead of subclassing MockPackagesTest

* spec_dag.py, spec_semantics.py: uses fixtures instead of subclassing MockPackagesTest

* stage.py: uses fixtures instead of subclassing MockPackagesTest. Removed mock directory

* pytest: added docstrings to all the fixtures

* pytest: final cleanup

* build_system_guess.py: fixed naming and docstrings as suggested by @scheibelp

* spec_syntax.py: added expected failure on parsing multiple specs closes #1976

* Add pytest and pytest-cov to Spack externals.

* Make `spack flake8` ignore externals.

* run-unit-tests runs spack test and not pytest.

* Remove all the special stuff for `spack test`

- Remove `conftest.py` magic and all the special case stuff in `bin/spack`

- Spack commands can optionally take unknown arguments, if they want to
  handle them.

- `spack test` is now a command like the others.

- `spack test` now just delegates its arguments to `pytest`, but it does
  it by receiving unknown arguments and NOT taking an explicit
  help argument.

* Fix error in fixtures.

* Improve `spack test` command a bit.

- Now supports an approximation of the old simple interface
- Also supports full pytest options if you want them.

* Use external coverage instead of pytest-cov

* Make coverage use parallel-mode.

* change __init__.py docs to include pytest

* First version of Abinit package

* Ignore *.swp files

* Add libxc, etsf_io packages

* AtomPaw package

* Make Abinit depend on mpi@2: and external version of libxc, netcdf, hdf5, etsf_io

* etsf_io: install Fortran modules in prefix.include

* Remove etsf_io from abinit requirements

* Add libxc2.2.1 (required by Abinit and atompaw)

* Cleanup

* Run make check

* Cleanup

* Use ld_flags instead of hard-coded libs, fix pep8, add copyright

* Put scalapack before lapackblas

* Transferred pending changes from efischer/develop

* 1. Rewrite of "Getting Started": everything you need to set up Spack, even on old/ornery systems.  This is not a reference manual section; items covered here are covered more systematically elsewhere in the manual.  Some sections were moved here from elsewhere.

2. Beginning to write three methods of application developer support.  Two methods were moved from elsewhere.

* Edits...

* Moved sections in preparation for additional text to be added from old efischer/docs branch.

* Moved 2 more sections.

* Avoid accid

* Applied proofreading edits from @adamjstewart

* Fixed non-standard section characters.

* Moved section on profiling to the developer's guide.

* Still working on Spack workflows...

* Finished draft of packaging_guide.rst

* Renamed sample projects.

* Updates to docstrings

* Added documentation to resolve #638 (content taken from #846)

* Added section on resolving inconsistent run dependencies.  Addresses #645

* Showed how to build Python extensions only compatible with certain versions of Python.

* Added examples of getting the right behavior from depends_on().  See #1035

* Added section on Intel compilers and their GCC masquerading feature.  Addresses #638, #1687.

* Fixed formatting

* Added fixes to filesystem views.  Added a caveats section to ``spack setup``.

* Updated section on Intel compiler configuration because compiler flags currently do not work (see #1687)

* Defined trusted downloads, and updated text based on them. (See #1696)

* Added workflow to deal with buggy upstream software.  See #1683

* Added proper separation between Spack Docs vs. Reference Manual

* Renamed spack_workflows to workflows.  Resolves a conflict with the .gitignore file.

* Removed repeated section.

* Created new "Vendor Specific Compiler Configuration" section and organized existing Intel section into it.  Added new PGI and NAG sections; but they need to be expanded  / rewritten based on the existing text plus research through Spack issues on GitHub.

* Fixed text on `spack load --dependencies` to conform to reality.  See #1662

* Added patching as option for upstream bugfixes.

* Added section on using licensed compilers.

* Added section on non-downloadable tarballs.

* Wrote sections on NAG and PGI.  Arranged compilers in alphabetical order.

* Fix indent.

* Fixed typos.

* Clarified dependency types.

* Applied edits from Adam J. Stewart.  Spellchecked workflows and getting_started.

* Removed spurious header

* Fixed Sphinx errors

* Fixed erroneous symbol in docstring.

* Fix many typos and formatting problems.

* Spacing changes

* Added section on fixing Git problems.  See #1779

* Fixed signature of install() method.

* Addressed system packages in greater detail.  See #1794 #1795

* Fixed typos

* Fixed quotes

* Duplicate section on Spack profiling removed from configuration.rst.  It had earlier been moved to developer_guide.rst, where it fits better.

* Minor edits

- Tweak supported platform language.
- Various small changes to the new getting started guide.

* Fixed bug with quotes.

- fix deptype support
- by default, graph command omits build depedencies
- update docs to use deptype args

Includes :
- treatment of a generic hierarchy (i.e. lapack + mpi + compiler)
- possibility to specify which compilers are to be considered Core
- correct treatment of the 'family' directive
- unit tests for most new features

- Spack will check if the index needs updating, and will only parse
  all package files if it does.

- Spack tries to parse as few package files as necessary.

- Default scope is versioned with spack and can be overridden by site
  or user config.

- Default scope provides sensible default concretization preferences
  for all of Spack.

- per-platform concretization scope can be added later (to force a
  particular MPI on, e.g., Cray systems)

I use a symlink to make it easy to swap out.

This reverts commit 79808da7.

- User and site config are now kept separately in memory.
- Merging is done on demand when client code requests the configuration.
- Allows user/site config to be updated independently of each other by commands.
- simplifies config logic (no more tracking merged files)

- specific module classes use __metaclass__ to register themselves.
- bugfixes in module writing.

- New spack.hooks package
  - contains modules with pre and post install hooks

- New dotkit hook module
  - generates/removes dotkits on install/uninstall

- New spack use, spack unuse commands
  - use same syntax as install/uninstall

- New setup-env.bash script
  - Sets up path, dotkit support

- new spack dotkit command
  - used by script to parse specs, generate
    specs of installed pckages for dotkit file names

- Allow version wildcards to match [_-.] instead of the exact separators
  the version was constructed with.
  - Handles the fact that boost versions are written both 1.55.0 and 1_55_0.

- Update spidering to handle parse errors and warn that Python < 2.7.3 has
  less robust HTML parsing abilities.