* Switch from coveralls to codecov

- Add .codecov.yml, simplify .travis.yml
- Add codecov badge to README.md

* Add tests for spack graph.

* py-numpy: fix blas/lapack section title

* py-numpy: rework BLAS/LAPACK

including a workaround for MKL due to
limited config system of numpy

* Spec.satisfies accesses Spec.concrete as property

Fixes #2760

When copying a spec, _concrete is always set to False for each
dependency. "Spec.satisfies" was accessing the member "_concrete"
directly instead of using the property "concrete". This means that
if you copy a spec, the dependencies will be considered equal, but
did not necessarily satisfy one another. Spec.satisfies is a
prerequisite for a package to be considered an extension; as a
consequence, an extension with run-time dependencies that were also
extensions did not activate those extensions. This updates
Spec.satisfies to avoid checking the cached member "_concrete"
directly.

* Added test to check for activation of dependency extension

* Added test to check for transitive satisfiability between a spec and its copy

* Update libquo's homepage, url, and description.

Recently LANL moved to lanl (from losalamos).

* Fix formatting.

Conform to style guidelines.

* More style updates.

Doesn't appear to be necessary, but for good measure.

* oce: fix fetching

apparently the fetcher is confused when there is a mixture of 3-digits
versions and 2-digits versions, i.e. 0.18 and 0.17.2

* flake8

Not all compilers support AVX2 instructions, and the package’s test for this is much too simplistic.

* Updating udunits.

Udunits 2.2.21 is no longer on the unidata ftp site.
The latest is 2.2.23, adding that and it's md5sum.

* Updating udunits2 download URL.

The Unidata ftp site does not keep previous versions of udunits.
However all the tagged versions are in their github.com repository.
Updating the URL to use github.

* Updating udunits2 with a autoreconf def.

The udunits packages on github do not contain a configure script.
One has to run autoreconf to generate it, so adding that to
package file.

Also updated to the latest version and all md5 checksums.

- Allows hashes to be specified after other parts of the spec
- Does not allow other parts of the spec to be specified after the hash
- The hash must either end input or be followed by another separate spec
- The next spec cannot be an anonymous spec (it must start with a package name or a hash)

See #2769 (after it was merged) for further discussion of this interface addition. That discussion resulted in these requirements:

```
python                     # 1 spec
/abc123                    # 1 spec
python /abc123             # 1 spec
/456789                    # 1 spec
python /abc123 /456789     # 2 specs
python /456789 /abc123     # 2 specs
/abc123 /456789            # 2 specs
/456789 /abc123            # 2 specs
/456789 /abc123 python     # 3 specs
```

assuming `abc123` and `456789` are both hashes of different python specs.

* Add support for IBM threaded compilers, xl*_r

Added new compiler class, xl_r; added default flags to the compilers.yaml file.

* Add cppflags to the set of default flags to be added to the compilers stanza in compiler.yaml.

These flags are optional. Only defined flags will be listed in the compilers.yaml file.

* Fix scripting warnings revealed by flake8.

Updated __init__.py and xl_r.py to conform with flake8 rules.

* Add justification to the definition of the XL default compiler flags.

* PackageMeta: `run_before` is an alias of `precondition`, `run_after` an alias of `sanity_check`

* PackageMeta: removed `precondition` and `sanity_check`

* PackageMeta: decorators are now free-standing

* package: modified/added docstrings. Fixed the semantics of `on_package_attributes`.

* package: added unit test assertion as side effects of install

* build_systems: factored build-time test running into base class

* r: updated decorators in package.py

* docs: updated decorator names

* Add dependency on perl

The build process uses perl and also needs `Test::More`.

Some distros, e.g. CentOS, break the core Perl distribution
into separate packages, so it's possible to "have perl" but
not have all the bits one needs to build OpenSSL.

We'll just install one of ours, which comes with all of its
factory parts included.

* Remove uninformative comment

>  # Also requires make

doesn't really add any value...

* add static options for some libraries

* make requested changes: add comments and use configure_args

Take advantage of new configuration options in the @develop branch

Also, it seems the cmake_args API has changed in spack

* Add --without-x when building r~X

* Add latest version of R

* Run patch for latest version as well

* oce: force rpath on Sierra to avoid issues with load commands size

* trilinos: use rpath on Sierra to avoid load commands limit

* documentation: reworked packaging guide to add build-system phases

* documentation: improvements to AutotoolsPackage autodocs

* build_systems: updated autodocs

* run-tests: added a few information on how to run tests fixes #2606 fixes#2605

* documentation: fixed items brought up by @davydden

    * typos in docs
    * consistent use of 'build system' (i.e. removed 'build-system' from docs)
    * added a note on possible default implementations for build-time tests

* documentation: fixed items brought up by @citibeth

    * added note to explain the difference between build system and language used in a package
    * capitalized bullet items
    * added link to API docs

* documentation: fixed multiple cross-references after rebase

* documentation: fixed minor issues raised by @tgamblin

* documentation: added entry in table for the `PythonPackage` class

* docs: fixed issues brought up by @citybeth in the second review

* Fix configure's zlib version check

R wants a version of zlib that is 1.2.5 or newer.

The version checking code just does a lexicographic comparison
of the first 5 characters of the string, so it seesthat the latest
zlib version, 1.2.10, as 1.2.1 and fails.

This patch changes the comparison to use zlibs' hex ZLIB_VERNUM
so that it does not suffer from this problem.

A version of this patch is wending it's way through the R comunity
community and will/should be included in a future release.

I tested the patch with the current R, 3.3.1.

* Tighten zlib dependency version (>= 1.2.5)

* Convert patch to level=1 format.

* Simplify unit tests listed in Contribution Guide

* Use long name for option flags

* libevent: Properly declare OpenSSL dependency version bounds

* libevent: Handle ~openssl variant correctly

* libmonitor does not exist at
http://libmonitor.googlecode.com/svn/trunk/

Change location to HPCToolkit version at github. Specify the hash corresponding
to the 20130218 version.

* When xcb is version 1.11, patch the configure file so it doesn't trip on
pthread-stubs and xau.

* Add os.getcwd()/lib to LD_LIBRARY_PATH, instead of nuking
existing LD_LIBRARY_PATH.

* cfitsio: Allow building as shared libraries

- Allow building as shared libraries
- Also add optional bzip2 variant
- Also update to newest version

This requires the recent correction to “fix_darwin_install_name”.

* cfitsio: Simplify code, default to +shared

Previously, fix_darwin_install_name would only handle dependencies that have no path set, and it ignore dependencies that have the build directory as path baked in. Catch this, and replace it by the install directory.