* 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

- Tell make about the source code path
- Install actual header files, not a wrapper with wrong paths
- Add a patch to prevent compiler warnings
- Improve description

* Fix detection of redhat enterprise compute node

* Add comma

* Remove space

* Add new version of libfabric that builds on macOS

See https://github.com/ofiwg/libfabric/issues/5339
Fixes https://github.com/spack/spack/issues/15244

Also reduced copy-paste of URLs with `url_for_version`.

* Address reviewer feedback

Signed-off-by: Howard Pritchard <howardp@lanl.gov>

* Fixups for jupyter

This PR fixes a few things for some jupyter related packages.

py-ipython:
- make the python depends_on statements reflect needs of different
  versions
- remove an unneeded conflicts directive

py-ipywidgets:
- add new version
- set version constraints for py-widgetsnbextension

py-jupyter-console
- add new version
- set python dependencies for versions as needed
- set version constraint for py-ipython
- set version constraints for py-prompt-toolkit

py-pyqt5
- build with py-sip

py-qtconsole
- add dependency on py-pyqt5

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

Tweak version ranges.

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

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

Tweak version range.

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

* Make py-pyqt5 a run dependency

Also, make formatting more consistent.

* Fix site_packages_dir

Change reference of site_packages_dir to self.site_packages_dir. Oddly,
this did not show up as a problem until I regenerated the module.

* Restore py-pyqt5 to previous state

* Explicitly set path to site_packages_dir

This change prevents an error when regenerating the py-pyqt5 module
file.

* Fix flake8 errors

* Make sure prefix is in join_path

* Fix flake8 errors

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

* Fixed url for SLEPc package

* Fixed homepage url for SLEPc package

* New package: py-librosa

This PR adds the py-librosa package, along with new dependency packages
and some updates of existing dependency packages.

- new package: py-audioread
- new package: py-resampy
- new package: py-soundfile
- update package: py-numba
- update package: py-llvmlite

py-numba:
- add updated version
- adjust constraints

py-llvmlite:
- add updated version
- adjust constraints
- fix version specifications for llvm
- add environment function to set PIC

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

Ah, yes, I see that `setuptools` is listed in the `install_requires` array. I missed that before.

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

* Fix dependency

- Add dependency of py-soundfile depends on libsndfile
- Add new libsndfile package

* Add py-pytest-runner build dep

* Make numpy a variant for py-soundfile

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

When building gcc7 and gcc8 on RHEL6 with Spack and installing it as
a spack-available compiler, OpenBLAS will fail to compile because GCC
generates newer instructions than rhel6's `as` assembler knows about
(e.g. "vpermpd").

Building gcc8 with binutils succeeds, and it generates a GCC that can
then successfully build OpenBLAS. This is also expected to work for
gcc7 on RHEL6.

* Added version 0.12.0 to fix issue #15218

* Added dependencies specs with compatible versions

* Switched py-scipy dependency to variant (default F)

* Removed variant py-scipy and didn't add py-dask

* Fixed typo: missing '

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

Fixing typos from version ranges in dependencies.

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

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

Removed repeating dependency option.

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

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

Limited version of py-numpy dependency to <2.0.

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

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Adding an option to build the C api for Umpire.

This is useful if you need to link to a C code and you're using
a compiler suite that doesn't support fortran.

* Also updating the versions while I'm here.

* Adding conflict: Fortran requires C.

To ease transition and confusion, default to C-bindings being
present.  This shouldn't hurt anyone who is upgrading an existing
installation.