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2018-10-17relicense: update COPYRIGHT, LICENSE-*, README, CONTRIBUTING, and NOTICETodd Gamblin7-536/+344
This updates Spack's top-level metadata files to reflect the new Apache-2.0 and MIT licenses.
2018-10-17relicense: add `spack license` commandTodd Gamblin3-0/+228
- `spack license list-files`: list all files that should have license headers - `spack license list-lgpl`: list files still under LGPL-2.1 - `spack license verify`: check that license headers are correct - Added `spack license verify` to style tests
2018-10-17relicense: add Apache2/MIT header to `spack create`Todd Gamblin1-4/+12
2018-10-17relicense: replace LGPL headers with Apache-2.0/MIT SPDX headersTodd Gamblin3359-76151/+13518
- remove the old LGPL license headers from all files in Spack - add SPDX headers to all files - core and most packages are (Apache-2.0 OR MIT) - a very small number of remaining packages are LGPL-2.1-only
2018-10-17relicense: remove LGPL-2.1-only farmhash packageTodd Gamblin2-64/+0
- we did not get consent for this package
2018-10-17relicense: remove significant contributions from peetsvTodd Gamblin17-711/+0
- This is bundled into one commit to make it easy to revert if we do get consent from peetsv's company to relicense these contributions. - Revert "dialign-tx adding patch for gcc@5.4.0 (#6413)" - This reverts commit 09eeb991a2ac0d749ffdbfe2f1cc415dd5d5dc85. - Remove the following LGPL-2.1 packages because we have not gotten consent to relicense them: - fast-gbs - igv - metasv - perl-xml-libxml - py-cnvkit - py-crossmap - py-pybedtools - py-pyfaidx - py-pyvcf - py-vmd-python - r-cghflasso - r-dismo - r-proc - r-spatial - r-utf8
2018-10-17omega-h: fix dependencies (#9552)Dan Ibanez1-11/+5
* omega-h: fix dependencies 1. Remove Gmodel altogether. Omega_h doesn't actually call Gmodel for anything, it was more or less just doing additional unit testing for Gmodel 2. Make Trilinos off by default. Most codes do not need the ParameterList interface, and Kokkos through Trilinos is not well explored in Spack 3. Use modern CMake style to choose the zlib dependency
2018-10-17omega-h: update to versions 9.19.0, 9.19.1 (#9548)Satish Balay1-0/+5
* omega-h: update to versions 9.19.0, 9.19.1 * omega-h: add build conflict for gcc-8
2018-10-17pflotran: switch to parallel build (#9554)Satish Balay1-1/+3
2018-10-17amrex: add version 18.10.1 (#9550)Satish Balay1-0/+1
2018-10-17gmodel: switch from .zip to .tar.gz to avoid unzip dependency (#9549)Satish Balay1-2/+2
2018-10-17Fixes to Omega_h C++ compiler flags (#9545)Dan Ibanez1-2/+2
* omega-h: fix CMake CXX flag options * omega-h: turn warnings off by default
2018-10-16docs: add note about compilers with modules (#9520)Mark W. Krentel1-0/+8
compilers.yaml can track a module that is needed for a compiler, but Spack does not fill this in automatically. This adds a note to the documentation informing the user how to do this.
2018-10-16stc and turbine: fix depends_on(type) (#9537)Justin M Wozniak2-6/+6
2018-10-16libsharp: new package (#9530)Jordan Moxon1-0/+61
2018-10-16py-setuptools: add version 40.4.3 (#9534)Leonhard Reichenbach1-0/+1
2018-10-15sspace-standard: use Getopt::Std instead of getopts.pl (#9516)snehring1-0/+3
getopts.pl is not listed as a Spack dependency of sspace-standard, so without this change, this package was only working on systems where getopts.pl was already installed.
2018-10-15update py-mock dependencies based on requirements.txt (#9496)Andreas Baumbach1-1/+5
2018-10-15pmix package: add new versions (#9532)Daniel Topa1-0/+6
2018-10-15cabana: initial commit (#9444)Christoph Junghans1-0/+55
* cabana: initial commit * Cabana: added v0.1.0-rc0
2018-10-15ssht: new package (#9518)Jordan Moxon1-0/+44
2018-10-15redundans: replace incorrect hard-coded path for sspace-standard (#9483)snehring1-0/+5
2018-10-15cmake: add version 3.12.3 (#9528)Matthias Diener1-0/+1
2018-10-15meson: explicitly add --libdir (#9504)Michael Kuhn1-0/+6
If we do not specify libdir explicitly, Meson chooses something like lib/x86_64-linux-gnu, which causes problems when trying to find libraries and pkg-config files.
2018-10-15sra-toolkit: new version and preserve symlinks (#9525)Ricardo Silva1-2/+3
Before this, the same files were copied 3 times
2018-10-15Build Nalu-Wind and Trilinos statically on Darwin (#9522)Jon Rood3-5/+22
* Added conflict in Trilinos for STK when building as shared on Darwin. * Created shared variant for Nalu and Nalu-Wind to automatically build Trilinos as static library on Darwin. * Moved ECP tags from Nalu to Nalu-Wind (the latter is the official ECP application).
2018-10-15py-scikit-learn: added version 0.20.0 (#9526)Leonhard Reichenbach1-0/+1
2018-10-12Swift/T Release 1.3 (#4641)Justin M Wozniak4-10/+42
New release of Swift/T along with turbine, adlbx, and exmcutils dependencies. Update URLs for archive downloads.
2018-10-12py-spyder: update dependencies and fix build (#9207)Andreas Baumbach1-4/+13
* Remove py-setuptools dependency from py-spyder (fixes #9205) * Add constraint on transitive qt dependency to build with webkit extension (required for this package) * Update pycodestyle dependency constraints * reordered dependencies (py-zmq, py-chardet) to confirm to the ordering in setup.py
2018-10-12buildcache install: generate modules (#9509)Peter Scheibel1-0/+1
Spack packages installed using spack buildcache were not running post-install hooks, which create module files and manage licenses (if necessary). This was already occurring for Spack packages installed with spack install --use-cache
2018-10-12Added py-pandas@0.23.4 and py-bottleneck@1.2.1 (#9515)Leonhard Reichenbach2-0/+2
2018-10-12Update scorep and friends (#9495)Michael Kuhn5-9/+29
- cube: Add 4.4.2, add conflicts for ~gui, build 4.4 from cubegui tar - cubelib: Add 4.4.2 - cubew: Add 4.4.1 - opari2: Add 2.0.4 - scorep: Add 4.1
2018-10-12superlu-dist: fix v5.3.0 buid - its attempting to build internal blas (#9517)Satish Balay1-0/+1
https://github.com/spack/spack/issues/9514
2018-10-12vtk: Added mpi variant (#9494)Lars Bilke1-0/+9
2018-10-12codes, dia, nest: fix pkg-config dependency (#9498)Michael Kuhn3-3/+3
pkgconfig is the virtual provider, pkg-config is a specific implementation.
2018-10-12at-spi2-atk: add missing pkgconfig dependency (#9503)Michael Kuhn1-0/+1
2018-10-12dbus: add missing pkgconfig dependency (#9497)Michael Kuhn1-0/+1
2018-10-12Ease nlohmann-json conflict with gcc 4.8 (#9506)sknigh1-2/+4
2018-10-12libepoxy: fix build (#9508)Michael Kuhn1-0/+7
- Add missing pkgconfig dependency - Explicitly disable egl
2018-10-12dealii: add 9.0.1 and update to sha256 (#9511)Denis Davydov1-9/+10
2018-10-11permissions: add permission configuration to packages.yaml (#8773)Greg Becker10-9/+338
Spack can now be configured to assign permissions to the files installed by a package. In the `packages.yaml` file under `permissions`, the attributes `read`, `write`, and `group` control the package permissions. These attributes can be set per-package, or for all packages under `all`. If permissions are set under `all` and for a specific package, the package-specific settings take precedence. The `read` and `write` attributes take one of `user`, `group`, and `world`. packages: all: permissions: write: group group: spack my_app: permissions: read: group group: my_team
2018-10-11amrex: add in new version for xsdk [18.09.1, 18.10] (#9501)Satish Balay1-0/+2
2018-10-11updated tasmanian package with v6.0, improved depend_on and conflicts ↵Miroslav Stoyanov1-15/+36
information (#9438)
2018-10-11superlu-dist: switch to sha256sum (#9499)Satish Balay1-9/+9
replace 5.1.1 with 5.1.2 as 5.1.1 does not build for me. [and 5.1.3 is preferable in this 5.1 series anyway]
2018-10-11Update superlu-dist package.py to support latest release v6.0.0 (#9445)Gustavo Chávez1-73/+32
* superlu-dist: Update package.py for superlu-dist v6.0.0 using CMake * superlu_dist: Update the header of package.py * Specify lapack_blas and DCMAKE_INSTALL_LIBDIR disable support for superlu-dist before v5
2018-10-11trilinos: disable superlu-dist by default (#9492)Denis Davydov1-1/+1
current stable releases of PETSc and Trilinos have non-overlapping requirements on Superlu-dist. For now turn it off by default in Trilinos, which requires older versions.
2018-10-11go: Add 1.11.1 (#9493)Michael Kuhn1-0/+1
2018-10-10Make CDash reporting easier to use (#9357)Zack Galbreath2-2/+16
* Better default CLI arguments for CDash reporting --log-format=cdash is now implied if you specify the --cdash-upload-url option to spack install. We also now default to writing CTest XML files to cdash_report/ when using the CDash reporter if no --log-file argument was specified. * Improved documentation on how to use the CDash reporter
2018-10-10ncdu: add new versions (#9477)Robert Blake1-0/+2
2018-10-10Magma: add version 2.4.0 (#9478)Piotr Luszczek1-2/+3
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