- removes two files from root of repository
- `spack test` still works fine to run tests

* A new package: perl-compress-raw-zlib.

* A new package: perl-compress-raw-bzip2.

* A new perl package: perl-io-compress.

* flake8.

* Add zlib and bzip2 dependency.

- This complies with the unix directory hierarchy standard (which Spack
  attempts to follow)
- Also unclutters the repo root directory.

- make list test use SpackCommand
- convert to pytest
- add a test for HTML output

- I keep typing this based on `spack test -h` and `spack test -H`
- This finally makes my fingers happy

* petsc: remove dependency on boost - its required only as a dependency on trilinos

Also set COPTFLAGS='' etc - this way CFLAGS is the primary way optimization flags are set by spack

* petsc: update pkgs with petsc~boost dependency

* fix flake8

* boost is optional for trilinos - so adjust petsc dependency on boost [via trilinos] accordingly

* do not add boost dependency on petsc [due to trilinos requirement]. Trilinos adds this dependency anyway.

plasma@develop has another flag 'DHAVE_MKL' that needs to be disabled [for non-mkl build]

add dependency on gcc-6.0

add in new dependency on readline

plasma: requires both LIBS in make.inc and command line?

If cmd line is missing -some internal values from plasma makefile gets used - causing link errors [on Mac]

tools/lua-5.3.4/src/Makefile:   $(MAKE) $(ALL) SYSCFLAGS="-DLUA_USE_LINUX" SYSLIBS="-Wl,-E -lreadline"

if make.inc is missing - I get:

/usr/bin/ld: cannot find -lmkl_intel_lp64
/usr/bin/ld: cannot find -lmkl_sequential
/usr/bin/ld: cannot find -lmkl_core
collect2: error: ld returned 1 exit status

Also add a new dependency -ldl

m4 exited immediately (causing the nettle build to fail).

```
(alice)[11:09:46]spack>>/Users/hartzell/tmp/spack-mac/spack/opt/spack/darwin-highsierra-x86_64/clang-9.1.0-apple/m4-1.4.18-caxsf7l5yd7qbq2bown6bzi5el3ltfwf/bin/m4
Abort trap: 6
(alice)[11:10:18]spack>>fg
```

Tracked down a fix via the Homebrew recipe.  I'll send a note to the
`bug-m4@gnu.org` list to ensure that upstream knows about it.

* Fix gcc@5.5.0 on OS X 10.13.5

gcc@5.5.0 failed to build on my OS X 10.13.5 box.

I found/modified a patch in the MacPorts world that traced back to
Homebrewy, https://trac.macports.org/ticket/56502#no1

The issue has also been reported to gcc,
https://gcc.gnu.org/bugzilla/show_bug.cgi?id=83531

I eventually discovered a nearly identical version of the patch at
Homebrew.

https://github.com/Homebrew/formula-patches/blob/master/gcc%405/10.13_headers.patch

gcc builds with this and I can compile many things, but e.g. curl and
cmake both fail.  As @davydden and others observed in #1847, it seems
to be an apple thing.

* Fix mistaken change to patch when clause (added :)

I mistakenly deleted a colon from the
'darwin/gcc-7.1.0-headerpad.patch'.

cd /tmp/balay/spack-stage/spack-stage-joxtpr/omega_h-9.13.4/spack-build/src && /home/balay/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1.0-7ws4tgx4z3o
ru5g5skjrxs5sobpeiyef/bin/mpic++   -Domega_h_EXPORTS -I/home/balay/spack/var/spack/stage/omega-h-9.13.4-th4b67fz5es6cbgcar742jxamjt3tqjb/omega_h-9.13.4/src -I/tmp/bala
y/spack-stage/spack-stage-joxtpr/omega_h-9.13.4/spack-build/src -I/home/balay/spack/var/spack/stage/omega-h-9.13.4-th4b67fz5es6cbgcar742jxamjt3tqjb/omega_h-9.13.4/tpl
-I/home/balay/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb/include  -O2 -g -DNDEBUG -fPIC   -o CMakeFiles/omega_h.di
r/Omega_h_map.cpp.o -c /home/balay/spack/var/spack/stage/omega-h-9.13.4-th4b67fz5es6cbgcar742jxamjt3tqjb/omega_h-9.13.4/src/Omega_h_map.cpp
In file included from /usr/include/c++/5/chrono:35:0,
                 from /home/balay/spack/var/spack/stage/omega-h-9.13.4-th4b67fz5es6cbgcar742jxamjt3tqjb/omega_h-9.13.4/src/Omega_h_timer.hpp:4,
                 from /home/balay/spack/var/spack/stage/omega-h-9.13.4-th4b67fz5es6cbgcar742jxamjt3tqjb/omega_h-9.13.4/src/Omega_h_timer.cpp:1:
/usr/include/c++/5/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support must be enabled with the -std=c++11 or -std=gnu++11 compiler options.
 #error This file requires compiler and library support \
  ^

* Add the grass74 GIS system.

* Correct flake8 errors

* Made requested changes

* added correct types to python

* ncbi-magicblast: new package

* updated package.py

* updated ncbi-magicblast

To benefit from updates to config.guess for newer architectures.

More info: https://github.com/spack/spack/issues/2063

* Added minuit package

* Removed default method and template

* Different URLs for old versions

* Patches for versions down to 1.5.0

* Reverted ROOT package changes

* Removed print statement

* Added checksums for older versions

* Consistent version names

* elpa: add 2018.05.001.rc1 and 2017.11.001

* elpa: shift preferred

- All now have both 'ecp' and 'ecp-apps' tags.
- ECP ST projects will eventually also have ecp and ecp-software tags.

* Add latest release 3.0.2
https://www.open-mpi.org/software/ompi/v3.0/:x



Signed-off-by: Daniel Topa <dantopa@lanl.gov>

* Add in library version in comment

- pytest was not reporing the correct version from pytest.__version__.
  It reported 'unknown'

- this fixes issues on some systems where system-installed pytest plugins
  would try to use the version and convert it to an int

* New package xxhash.

* Change requested by @adamjstewart.

update the dependencies of openPMD-api