Spack's fflags are meant for both f77 and fc. Therefore, they must
be passed as FFLAGS and FCFLAGS to the configure scripts of
Autotools-based packages.

* added UQTk package

* Add missing expat dependency to uqtk

Increase the connect timeout for elfutils to 60 sec.  Elfutils (and
bzip2) tar files are on sourceware.org which is often slow to respond.

and found when using the RelWithDebInfo build type.  Change protobuf
to only support Release and Debug build types.

cherry-picking global ordinal type variant from https://github.com/spack/spack/pull/14215

 and setting dealii to GO int, to make it compile again (#15288)

Co-authored-by: Andrey Prokopenko <andrey.prok@gmail.com>

* @develop needs the full git repo to use "git describe"
  properly

* If not specifying the cxxstd variant, let cmake use its
  default

* Improve fmt dependencies: fairlogger < 1.6.2 does not
  work with fmt >= 6.

* Small other stuff

* Created stub

* added description and homepage

* added dependencies

* removed extra boilerplae

* switched to the pkgconfig provider

Suite-sparse 5.7.0 and 5.7.1 need separate make and make install run to be able to compile, too

Just `depend_on('ncurses')`, pkgconfig seems to cause the right thing
to happen if the package is built +termlib or ~termlib (tested both
ways on a CentOS 7 system).

Additional details in: https://github.com/spack/spack/issues/15281

Tested by building all of the releases of tmux on a CentOS 7 box.

"container" is partly a misnomer, as it's realy
the extended allocators part of container.

But every part calls it container, so we do too.

The distributed build PR (#13100) -- did not check the install status of dependencies when using the `--only package` option so would refuse to install a package with the claim that it had uninstalled dependencies whether that was the case or not.

- [x] add install status checks for the `--only package` case.
- [x] add initial set of tests

[OpenBLAS 0.3.9](https://github.com/xianyi/OpenBLAS/releases/tag/v0.3.9) was released.

* add preliminary afqmc support in qmcpack

* afqmc updates

* fix spack typos

* edit AFQMC to only allow up 3.7 or above

* added NCCL library support for AFQMC build

* add CMAKE args for BUILD_AFQMC_WITH_NCCL

* update for just AFQMC support. No AFQMC+GPU support

* remove nccl for afqmc

* flake8 whitespace fix

* Update flag_handler for 'netcdf-fortran'.

* Refactoring.

* Enable old versions of netcdf-fortran for NAG.

* Disable parallel 'make check' for versions before 4.5.0.

* Fix shared libraries built with NAG instead of conflicting it.

* Add 'skosukhin' as a maintainer of 'netcdf-fortran'.

This PR adds some fixes for the tcsh package.

- Adds new version
- adds list_url so fetching works for current and old tarballs
- sets ncurses dependency explicitly to `ncurses+termlib`

If `+termlib` is not set then it will link against the system libtinfo.

* Quantum-Espresso: qe-6.5 fails to detect MKL for FFT

qe-6.5 fails to detect MKL for FFT if BLAS_LIBS is set due to
an unfortunate upsteam change in their autoconf/configure:
- qe-6.5/install/m4/x_ac_qe_blas.m4 only sets 'have_blas'
  but no 'have_mkl' if BLAS_LIBS is set (which seems to be o.k.)
- however, qe-6.5/install/m4/x_ac_qe_fft.m4 in 6.5 unfortunately
  relies on x_ac_qe_blas.m4 to detect MKL and set 'have_mkl'
- qe-5.4 up to 6.4.1 had a different logic and worked fine with
  BLAS_LIBS being set
However, MKL is correctly picked up by qe-6.5 for BLAS and FFT if
MKLROOT is set (which SPACK does automatically for ^intel-mkl).
Thus, do not set BLAS_LIBS when compiling qe-6.5 with intel-mkl.

* replace all '^intel-mkl' by '^mkl' to match other packages which also provide MKL

e.g. intel-parallel-studio+mkl as mentioned by @adamjstewart in #15276

* Filter problematic flag from std_cmake_args

Including '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' in the cmake args causes
bits of cmake's output to end up in the autoconf-generated configure
script.  See https://github.com/spack/spack/issues/15274 and

* Don't build in parallel (sigh)

* Constrain hackery for newer versions...

... to newer versions.

* fix typos

* minor improvement

* add version 3.4.15

* [WIP] new package: qgis

* add maintainer

* further improvements

* reflect improvements to qscintilla installation paths

* comment out qtkeychain dependency as the package is created

* uncomment qtkeychaing dependency, since this package is now created

* a comment on webkit

* specify versions of dependencies, add variant

* fix variant description

* fix proj dependency logic

* adjust conflicts and dependencies so that one can compile qgis@2 with qt4, python2.7

* minor improvement

* fix some build errors, improve dependency specs

* qsci python bindings will be build by py-pyqt

* cmake variable QSCINTILLA_LIBRARY should point to library itself not the parent folder

* turn grass off explicitly, fix typo, turn qspatialite off explicitly

* fix typo

* specify more cmake options that doesn"t seem to be set properly, and use spack provided pkg-config

* fix libzip

* fix build issue with sqlite variant, add runtime dependencies

* add more runtime python package dependencies

* reflect variant name change in sqlite

* add maintainer, correct typo

* add TODO's

* add more versions

* improve style

* add latest versions

* netcdf -> netcdf-c

* add variants as shown in cmake config

* add conflict: v3.8.1 won't build if qt@5.13:

* change preferred version to latest long term release, 3.10.3

* add a zillion of build options

* improve style

* add descriptions for variants

* remove and already implemented compilation tip

* add "when" statements for optional dependencies

* make flake8 happy

* Update var/spack/repos/builtin/packages/qgis/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/qgis/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/qgis/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/qgis/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/qgis/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* convert conflicts to depends_on

* undo str conversion for path objects

* fix flake8 E131

* fix flake8 E128, E124

* improve style

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Add version 2020.03.01, deprecate Blue Gene to 2019.12.28 and earlier,
tighten a few dependencies.

* Caliper depends on python3.

The package needs to be told where to find it.

* More flake8 formatting edits.

* Change explicit python3 to spec['python'].command.path

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Removing defunct import for flake8

* Flake8 trailing whitespace warning.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

libhio has been building it's own json.  With this change, libhio will rely on the json installed by spack.

This PR adds 'http://' to the homepage setting of a few packages that do
not have it set. Not having that set can cause problems with some wiki
apps when embedding the homepage value into markdown syntax.

- bowtie2
- exuberant-ctags
- perl-want
- samtools

- add version info for v1.8.0

- v1.8.0 adds a new source file, `file.c`, which need to be included
  in our hardcoded list of objects to link.

  I discovered this while demonstrating "how easy it is to add a new
  package to Spack", only to scratch my head when it failed `spack
  install` but worked when I ran `make` in the stage dir.  Finally
  looked at tree/package.py and it All Became Clear.

  Perhaps someone should rewrite this to use MakefilePackage, but the
  Makefile starts off with a bunch of twisty turny "uncomment these
  lines to run on this platform", so it might not be worth it.

* Added package py-versioneer

* Update python version

* Added python2 to versioneer

* Added python2 to versioneer

* Update var/spack/repos/builtin/packages/py-versioneer/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Cleaning comments

* Removed temporarily @warner as a maintainer, waiting for answer

* Removed line

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Due to the use of backquotes, the replacement script for mpirun/mpiexec commands would recursively call itself, effectively causing a fork bomb.

* gromacs: add v2019.6

* Update var/spack/repos/builtin/packages/gromacs/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Fix expect on linux

* Flake8