* nyancat: adding the most important piece of software ever written

* nyancat: some formatting updates

* nyancat: flake8 error fix

* Also add missing zlib dependency

* LIBXSMM 1.10

* Accurately replaced MD5 with SHA256 sums (libxsmm).

Needed to compile with gcc@8 and recent versions of glibc.

glib should not use the globally installed gtk-doc. Otherwise, gtk-doc
can fail with Python errors such as `ImportError: No module named site`.

This is due to the fact that Spack sets `PYTHONHOME`, which can confuse
the global Python installation that is used by gtk-doc.

* r-combinat: new package at 0.0-8

* r-combinat: add list_url

* Add pic variant to cflags in boost.

* Improve description in pic variant of boost, see spack#9750.

* trinotate: fix perl location

* trinotate: not where that is

* trinotate: glob

* trinotate: needs perl-dbd-sqlite

* intel-parallel-studio: add missing updates

* add 2018.4

* use AutotoolsPackage so config.guess get updated by autoreconf step, fix build problem on ppc spack#9673

* same error, same fix under ppc arch

* erne: new package starting at 2.1.1

* erne: remove unused configure args

* erne: remove unused prefix arg

* erne: add explicit mpi disable

- Add 1.85
- OPENSSL_PREFIX has to be set in the environment, otherwise Spack's
  openssl will not be found

Required for [email protected] compatibility.

…9647)

Libunwind releases are few and far between, so we need access to
recent snapshots from the git repository.

Pass cflags to configure so that make will respect the value from the
spack install line.

Pass cflags to configure so that configure gets the values from the
spack install line.

Disable -Werror so that we don't fail the build over a stray warning.

* mark: Create new package.

* mark: change description.

* mark: change description.

* mark: Delete set_up environment.

* mark: replace join_path(prefix.bin, mark) with prefix.bin.mark

…#8986)

* zoltan: only add gussed MPI libs if no MPI wrappers are used

- if MPI-wrappers are used for compilation, we can assume that
  linking works without manually specifying MPI libs
  (guessing may result in wrong libs, cf. spack#8979)
- thus, only guess the NPI libs and add them explicitly if no
  MPI-wrappers are used
- use llnl.util.filesystem.find_libraries instead of a locally
  defined routine to guess the MPI libs if needed
  (cf. spack#8979)

* zoltan: rely on MPI-wrappers to know the required MPI libs

* GDL: python integration fixes

* renamed python-related variants to follow the convention
* building the Python module requires patches currently targetting 0.9.8 othwerwise asking for the Python module *only* builds the Pyhton module
* building the python module also requires patching the vendored (with the GDL) antlr to be built as a shared library

* Typo

Co-Authored-By: rmsds <[email protected]>

* Rename embed-python variant to embed_python

* SEACAS: Add preliminary support for seacas package

* Eliminate leftover from package I copied from.

* And remove another stray line

Sorry, thought I had checked this better...

* SEACAS: Shorten long lines; fixup indentation

* SEACAS: Remove unused os import

* Add PLASMA version 18.11.0 and Lua variant (spack#9689)

* Add PLASMA 18.11.1 with optional Lua and test for headers

* New versions for a few python modules (spack#9969)

* py-jupyter-console: Add version 5.2.0

* py-jupyter-core: add version 4.4.0

* py-lxml: add version 4.2.5

* py-zmq: add version 17.1.2

* py-terminado: add version 0.8.1

* py-pexpect: add version 4.6.0

* py-pytables: add version 3.4.4

* SEACAS: Default to mpi on

* SEACAS: Modify to reduce variants

Instead of using an `allpkgs` or explicitly specifying each individual subset,
changed to minimize variants:
 * By default, the exodus and IOSS libraries are built and a few
   executables directly related to the IOSS library.
 * variant `common` defaults to True and builds the "common" seacas
   applications.  This is based on my definition, so there may be
   could be some discussion on what belongs here.
 * variant `legacy` defaults to True and builds the remainder of the
   seacas applications.  These are still used, but mainly in more
   esoteric areas.  Might be better to default to False, but I wanted
   default to just build everything which is what other SEACAS builds
   always do...

Removed the `kokkos` variants for now as I need to do some more
thinking on how best to support this.  Not often used currently,
so shouldn't be an issue.

Cleaned up other issues raised by Adam and found by me.

* SEACAS: Address flake8 issues

* SEACAS: Clean up variant package logic

Fixed package variant logic.
Consolidated some other variant handling logic
Other minor refactors for hopefully better readability

* SEACAS: Fix flake8 error

Missing whitespace around operator fixed.

- previous removal of FOAM_EXT_LIBBIN (ThirdParty) from the environment
  during the build could lead to the system scotch library being found
  instead of the spack installation.

  Avoid this largely cosmetic change to the setting in favour of
  improved build robustness. These modifications will be largely
  superfluous in the 1812 release anyhow.

- Split the patching algorithm into 'regular' and '@:1806' since the
  next versions of openfoam will again need fewer patches.

- Add hook into foamCreateManpage to be used where available

* Add patch to fix windows.h include in freetype

* Fix patch

* Update Spack's Bash completion script

* spack mirror create options changed

This reverts commit 90b34c9.

* Added rocksdb package

* Fixes based on @tristan0x and @pramodk comments

* Cleanup

* A couple minor fixes based on @adamjstewart 's advice

* Fixed flake8 errors

* Add spack package for saga-gis

* Adjusted license header

* Adjust saga-gis package, added fixme comments

* Removed version constraint

* Fixed fixme comment

* Add thread count variant

Atlas automatically configures itself and optimizes to run with a fixed number of threads. This can be overridden during compile by setting a flag and atlas will tune itself to use the specified number, rather than all system CPUs. 

Default value is the existing logic, autoconfigure.

* Fix Linting

* Another lint for longline

spack#9933)

When this variant is set, it requires boost to be built with the +pic variant.

* clp: add build_directory, remove old hack

* clp: use spack-build for building

Also unpin the version from the arrow package.

Conflicts:
	lib/spack/spack/cmd/env.py
	lib/spack/spack/environment.py
	lib/spack/spack/schema/config.py
	lib/spack/spack/test/conftest.py
	lib/spack/spack/test/environment_modifications.py
	lib/spack/spack/util/environment.py
	var/spack/repos/builtin/packages/sqlite/package.py