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2018-12-06tests: fully parametrize multimethod testTodd Gamblin1-37/+47
- all multimethod tests are now run for both `multimethod` and `multimethod-inheritor` - do this with a parameterized fixture (pkg_name) that runs the same tests on both
2018-12-06multimethod uses Spec() instead of parse_anonymous_spec()Todd Gamblin3-22/+12
- simplify logic in multimethod - remove the requirement of multimethod invocations to walk up the stack.
2018-12-06spec: refactor and clean up Spec initializationTodd Gamblin2-206/+248
- Since early Spack versions, the SpecParser has (weirdly) been responsible for initializing Spec fields. - This refactors initialization to take place in Spec.__init__, as it probably should have originally. - This makes the code easier to read, the parser easier to understand, and removes the use of __new__ in the parser to initialize the Spec. - This also makes it possible to make a completely empty Spec with `Spec()` -- this is an abstract Spec that will match anything.
2018-12-06remove spurious print in zlib patch methodTodd Gamblin1-4/+0
2018-12-06Added test for multimethod inheritanceGregory Becker3-0/+21
2018-12-06superlu-dist: update to version 6.1.0 (#10037)Satish Balay1-0/+1
2018-12-06Adding patch to remove unicode character from pyrope readme file (#9988)Jon Rood2-1/+18
* Adding new versions of py-rope.
2018-12-06Quantum ESPRESSO update - Nov 2018 (#9853)Nichols A. Romero1-23/+80
* Add mising QE releases. * Update QE dependencies and conflicts. * QE 6.3 install method requires a patch to work properly. * include QE git develop branch * QE HDF5 needs Fortran support. HDF5 versions prior to 1.8.16 leads to QE runtime errors. * Number of MKL related conflicts for QE. * Flake8 fixes for QE for hdf5 lines. * Pass in all compilers properly to QE configure * Fixed external BLAS/LAPACK linkage in QE. * Library search was problematic in QE. * Add section headings to QE package. * External FFTW compatible libraries properly detected in QE. * Flake8 fixes for QE * QE configure defaults to False for ELPA, thus Spack package should as well. * QE depends on FFTW3 provider instead of FFTW explictly. * Primary QE repo is gitlab.com, not github.com. Github mirror lags behind gitlab site. * Support both 6.3-backports branch and develop branch in QE. * QE patch needed for proper MKL detection. MKL_ROOT is detected and preferred, still falls back to finding first MKL installation in /opt/intel. * Use FFTW-API provider versioned interface for specify QE FFT dependency. * QE FFTW conflicts no longer need thanks to FFTW-API provider versioned interface. * Flake8 3.6.0 fix in support of https://github.com/spack/spack/pull/9853 * Fix QE conflict with ilp64 variant in support of https://github.com/spack/spack/pull/9853 * Remove custom url_for_version for QE package and use builtin url instead. In support of https://github.com/spack/spack/pull/9853 * Use FFTW builtin flags for QE instead of custom Python code. In support of https://github.com/spack/spack/pull/9853 * Fix typo in QE package comments. In support of https://github.com/spack/spack/pull/9853 * Future proof QE package patches in anticipation of QE >= 6.3.1. In support of https://github.com/spack/spack/pull/9853
2018-12-05DIAMOND: Add version 0.9.23 (#10030)Eric1-1/+2
2018-12-05Fix doxygen package (#10021)Jannek Squar1-2/+5
2018-12-05cloc: add version 1.80 (#10029)Matthias Diener1-0/+3
2018-12-05Rewrite Rust package (#9998)sknigh1-40/+26
2018-12-05openblas: add version 0.3.4 (#10016)Matthias Diener1-0/+1
2018-12-05pfunit: add mpi-test patch (#9387)Christoph Junghans2-0/+39
2018-12-05Hwloc and numactl updates (#9987)Jon Rood2-2/+11
* Adding version 2.0.12 of numactl. * Adding new versions of hwloc. * Adding NVML variant to hwloc. * Adding gl variant to hwloc. * Updating hwloc numactl dependency and gl dependency. * Using gl virtual package in hwloc.
2018-12-04biobloom: new package at 2.2.0 (#10014)Justin Stanley1-0/+27
2018-12-04sdsl-lite: new package at 2.1.1 (#10013)Justin Stanley1-0/+36
2018-12-04added bwa runtime dep (#10012)Miles Perry1-0/+1
2018-12-04ffmpeg: add version 4.1 (#10015)Matthias Diener1-1/+2
2018-12-04dealii: do not hardcode prefix.include for BLAS/LAPACK (#10008)Denis Davydov1-4/+5
* dealii: do not hardcode prefix.include for BLAS/LAPACK * dealii: rename lapack_blas -> lapack_blas_libs
2018-12-04Remove openmp version guard in vtkm and add precision options (#10005)HAOCHENG LIU1-8/+18
Clang 8.0 now supports openmp 4.5 and many commerical compilers also support openmp >= 4.0. This commit removes the openmp version guard and rely on CMake to throw errors out when openmp version requirement is not satisified. It also add options for precision control.
2018-12-04CGNS: Add option for 64-bit integers (#9990)Greg Sjaardema1-0/+5
* CGNS: Add option for 64-bit integers Added the `int64` variant which will build the library using 64-bit integers for certain values. This gives the capability to have models with more than 2 billion cells and/or nodes. Beginning with CGNS-3.1.0, two new typedef variables have been introduced to support 64-bit mode. The `cglong_t` typedef is always a 64-bit integer, and `cgsize_t` will be either a 32-bit or 64-bit integer depending on how the library was built. Many of the C functions in the MLL have been changed to to use `cgsize_t` instead of `int` in the arguments. These functions include any that may exceed the 2Gb limit of an` int`, e.g. zone dimensions, element data, boundary conditions, and connectivity. In Fortran, all integer data is taken to be `integer*4` for 32-bit and `integer*8` for 64-bit builds.
2018-12-04EXODUS: Update version and dependencies (#9971)Greg Sjaardema1-5/+3
* EXODUS: Update version and dependencies Allow pulling master version from git. Note that I hope to have better versioning "soon" Add requirement to use Netcdf-4.6.1 or later as those versions no longer require changing the `maxdims` or `maxvars` defines in the netcdf.h include file. With these versions, Exodus can use an unmodified NetCDF. These versions of NetCDF are also better than previous versions (code quality, performance, robustness). It is still possible to run exodusII with previous NetCDF versions, but I don't know how to specify that the dependency where maxdims/maxvars variants are only needed for versions prior to 4.6.0. I also removed the explicit dependency on HDF5 as that dependency should be applied through the NetCDF dependency. * Remove white-space on blank line
2018-12-04c-blosc: 1.15.0 (#10009)Axel Huebl1-7/+8
Add latest version of c-blosc.
2018-12-04Provide a new spackage for py-pint. (#9991)Kelly (KT) Thompson1-0/+20
* Provide a new spackage for py-pint. Pint is a Python package to define, operate and manipulate physical quantities: the product of a numerical value and a unit of measurement. It allows arithmetic operations between them and conversions from and to different units. https://pint.readthedocs.io/en/latest/ * Switch hash from md5 to sha256.
2018-12-04MATIO: New versions (#9993)Greg Sjaardema1-4/+16
Add several new versions so that current functionality can be accessed. Current version is now 1.5.13. Update `url`, `list_url`, and `list_depth` so spack can find available versions
2018-12-04Add tmux@2.8 (#10010)Oliver Breitwieser1-0/+1
2018-12-04PNETCDF: Update with current versions (#9982)Greg Sjaardema1-3/+6
* PNETCDF: Update with current versions Added latest versions. (1.10.0, 1.9.0, 1.8.1) * PNETCDF: Revert version change in url Reverted the change in the url variable version since not required.
2018-12-04NETCDF: Add new versions and update url (#9970)Greg Sjaardema1-8/+14
* NETCDF: Add new versions and update url Added the 4.6.2 version which was recently released. Changed the url to point to the official Unidata site and added option to retrieve master version from git. * NETCDF: checksum and version updates Reverted back to use of previous URL. The `https://github.com/Unidata/netcdf-c/archive/v4.6.2.tar.gz` location is newer, but spack does not seem to be able to access all of the versions at that location -- only goes back to 4.5.0. Since several installations are still providing 4.4.0, thought it best to go back to previous url. However, it looks like the naming convention has changed since 4.6.2, so need to provide explicit url for 4.6.2. Probably best to go to a `url_for_version()` scheme if that naming convention stays in place?
2018-12-04boost: 1.68 also needs `boost_1.67.0_pgi.patch` (#9980)Bert Wesarg1-1/+1
Its in upstream with the upcoming 1.69 release though.
2018-12-04improved constraint conflict error message (#9975)Peter Scheibel1-2/+8
2018-12-04fix: adapt junit template to escape std{out,err} (#9935)Matthias Wolf1-4/+4
2018-12-04Disallow bcl2fastq2 on OS X (#9966)George Hartzell1-0/+3
* Disallow bcl2fastq2 on OS X [Illumina's computing requirements][reqs] claim support for RHEL/CentOS and go on to say: > May be possible to install and run on other 64-bit Linux distributions or Unix variants. The sufficient issue is its reliance of malloc.h. There may be more. [reqs]: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software/computing-requirements.html * Add an informative msg for the user
2018-12-04Expand dependency on qt to allow qt4 (#9964)Neil Flood1-1/+1
2018-12-04petsc: when petsc is built with fortran [default in spack] its best to use ↵Satish Balay1-1/+1
hdf5+fortran (#9986)
2018-12-04r-optparse: new package (#9967)Neil Flood2-0/+22
2018-12-04pgi: Add checksum for PGI 18.10 (#9985)Nick Forrington1-0/+1
2018-12-04cmake: add version 3.13.1 (#9983)Matthias Diener1-0/+1
2018-12-04abyss: new version (#9981)Levi Baber1-0/+1
2018-12-04Added missing libtool dependencies to libvterm and unibilium (#10007)sknigh2-0/+4
2018-12-03Download CMake sources from the Github releases (#10003)Robert Maynard1-8/+1
Now that CMake is providing CMake release artifacts on github, we should prefer those as they have better download speeds and uptime.
2018-12-03Phist 1.7.4 (#9996)jthies1-0/+13
* packages/phist: new version 1.7.4 with new variant 'host' to enable/disable host-specific optimizations.
2018-11-30Bump vtkm to version 1.3 and add new features (#9968)HAOCHENG LIU1-27/+83
This commit allows users to enable openmp, rendering, logging and mpi in vtkm. Meanwhile, it adds support for cuda architecture selection. [VTK-m 1.3 Release notes](https://gitlab.kitware.com/vtk/vtk-m/tags/v1.3.0)
2018-11-30hpctoolkit: overhaul to use spack dependencies (#9946)Mark W. Krentel2-48/+67
Overhaul hpctoolkit to AutotoolsPackage and to build its dependencies directly from spack instead of using hpctoolkit-externals. Remove hpctoolkit-externals since it's no longer needed.
2018-11-28New versions for a few python modules (#9969)jwallior7-4/+11
* 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
2018-11-28Add PLASMA version 18.11.0 and Lua variant (#9689)Piotr Luszczek1-1/+19
* Add PLASMA 18.11.1 with optional Lua and test for headers
2018-11-28Add f18 package (#9183)Ondřej Čertík1-0/+23
* Add f18 package * Fix flake8 errors * Install the f18 binary into prefix.bin by hand * Add spack-build into the path * Fix the license header
2018-11-28Injected flags have a consistent order (#9960)Massimiliano Culpo4-16/+30
Fixes #9908 Spack was assembling flags in a manner that could in different orderings for repeated concretizations of the same spec and config
2018-11-28glib: disable SELinux explicitly (#9956)Michael Kuhn1-0/+2
2018-11-27bcl2fastq2 package: recursively delete after copy (#9959)George Hartzell1-2/+2
Fixes #9944 73c978d replaced a move with a copy, which cased rmdir to fail (as it expects an empty directory). This switches to use `shutil.rmtree` instead.
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