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2020-04-02pmix: add option for toggling pmi backwards compatibility (#15838)Carson Woods1-0/+9
* Add option for toggling pmi backwards compatibility * Remove trailing whitespace
2020-04-02New Package: py-astropy-helpers (#15658)Jennifer Herting1-0/+21
* [py-astropy-helpers] created template * [py-astropy-helpers] - removed boilerplate - added homepage - added depends_on('py-astropy') * [py-astropy-helpers] Setuptools versioning * [py-astropy-helpers] cleaned up unused build_args method * [py-astropy-helpers] py-astropy is a runtime dependency * [py-astropy-helpers] requires python@3.6: * [py-astropy-helpers] cleaned up unnecessary older versions * [py-astropy-helpers] turns out py-astropy isn't actually a dependency
2020-04-02argobots: new version 1.0 (#15786)Shintaro Iwasaki1-0/+1
2020-04-02Updates versions of Intel packages (#15839)Robert Mijakovic8-0/+14
* update version: intel packages daal, ipp, mkl-dnn, mkl, mpi, parallel-studio, pin, tbb and makes url parameter consistent and always use single quote. * Fixes a typo with one of the sha256 checksum.. * Adds version entries for new versions of Intel packages. Co-authored-by: Robert Mijakovic <robert.mijakovic@lrz.de>
2020-04-02mpip: add demangling and setjmp variants (#15837)Carson Woods1-0/+14
* Add demangling to mpip * Add setjmp support to mpip * Flake8 fixes
2020-04-02intel-mkl-dnn: add 1.3Adam J. Stewart1-1/+2
2020-04-02go: Add 1.14.1 and 1.13.9Michael Kuhn1-3/+5
2020-04-02unqlite: Patching unqlite to be able to build a shared library (#15830)Matthieu Dorier2-0/+34
* Patching unqlite to be able to build a shared library * Correcting a whitespace for flake8 to pass * added comment about PR on unqlite * extra commit to force github to merge
2020-04-02c-blosc: Add variants to disable building tests and benchmarks (#15789)iarspider1-0/+7
* Add variants to disable building tests and benchmarks * Flake8 * Update package.py * Update package.py * Update package.py
2020-04-02ppOpen-APPL/BEM: added new package at v0.5.0 (#15819)Toyohisa Kameyama1-0/+79
2020-04-02py-pyfits: added new package at v3.5 (#15825)健美猞猁1-0/+19
2020-04-02py-ephem: added new package at v3.7.71 (#15438)健美猞猁1-0/+16
2020-04-02cmake: added v3.17.0 (#15822)Kelly (KT) Thompson1-0/+1
2020-04-02cryptsetup: added v2.2.2, v2.2.3 and v2.3.1 (#15823)Jonathon Anderson1-1/+4
Also confined the included patch to the earlier versions, as indicated.
2020-04-02qt: added v5.14.2 (#15824)Jonathon Anderson1-0/+1
2020-04-01package: update flit and py-pyelftools versions (#15817)Michael Bentley2-11/+16
* Update flit package to v2.1.0 and add dependencies * flit: comment out bash dependency The host system should have bash available and compiling bash through spack failed for me. I'm not sure if binutils and coreutils should be listed as dependencies as well. * Add new version of py-pyelftools * py-pyelftools: add py-setuptools as a build dependency * Address review comments
2020-04-01package: add variants to cgns (#15816)Carson Woods1-7/+25
* Add additional configuration options for cgns * Fix syntax errors * Further syntax fixes * Convert tabs to spaces Co-authored-by: Carson Woods <carwood@sandia.gov>
2020-04-01package: add static library build option for yaml-cpp (#15814)Carson Woods1-0/+4
* Add static build option * Fix flake8 errors and standardize spacing of build commands Co-authored-by: Carson Woods <carwood@sandia.gov>
2020-04-01New package:dhpmm-f (#15798)takanori-ihara1-0/+51
* New package:dhpmm-f * Remove unnecessary line
2020-04-01hdf5: prefer version 1.10 for now (#15810)Todd Gamblin1-1/+4
HDF5 1.12 broke backward compatibility, so we're preferring version 1.10 for now. Packages that need the new API should specify: depends_on("hdf5@1.12:") to be explicit. We can eventually change the preference, but at the moment most libraries have not udpated to use the new HDF5.
2020-04-01Version bump for slurm package (#15790)Jonathon Anderson1-1/+3
2020-04-01openssl: add v1.1.1f (#15802)Christoph Junghans1-0/+1
2020-04-01amrex: New version 20.04 (#15808)Erik Schnetter1-0/+1
2020-04-01Added v3 of Laghos (#15806)Robert Pavel1-3/+13
* Added v3 of Laghos Added v3 of Laghos as per https://github.com/CEED/Laghos/blob/v3.0/README.md * Update var/spack/repos/builtin/packages/laghos/package.py Changed develop->master as per PR Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Made Metis Dependency Explicit Added explicit metis dependency * Folded @develop Laghos Deps in to @3.0: Theoretically there will be a difference between develop and 3.0: in the future but currently there is not Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-01OpenDX: add new package (#15737)Adam J. Stewart1-0/+20
2020-04-01Fixed Remaining Shared Objects in Static Lua (#15787)Robert Pavel1-26/+31
Fixed removal of remaining references and symlinks to so files when building lua with static libraries
2020-04-01Minor LLVM libomptarget fixes (#15788)Nichols A. Romero1-10/+3
* Add myself as a maintainer * This was a regression that occured in previous PR. Flang has been excised from LLVM for now until f18 is merged upstream. * Libraries only needed when a GPU backend is present.
2020-04-01Package/sfcgal fix typo (#15796)Sinan1-2/+2
* fix typo in dependency definition * remove arbitrary dependency constraint Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
2020-04-01Add libgit2 1.0.0 and 0.28.5 (#15801)Andrew Gaspar1-0/+4
2020-04-01Spelling fixes (#15805)Greg Sjaardema9-17/+17
* Spelling fixes * spelling fixes * spelling fixes * spelling fixes * spelling fix * spelling fix * spelling fix * spelling fixes * spelling fix
2020-04-01pybind11 2.5.0: Include Change (#13905)Axel Huebl1-3/+9
Add pybind11, version 2.5.0. This release adds improved include helpers.
2020-04-01new package: py-spatialite (#12597)Sinan1-0/+20
* new package: py-spatialite * make flake8 happy Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
2020-04-01slurm: new version, system configuration path (#15466)Dr. Christian Tacke1-0/+7
* Add version 18-08-9-1 * Add variant to allow setting the sysconfdir: See below About sysconfdir: slurm has a server and a client. To use the correct communication channel, the client needs to be able to read the correct config. This config is in PREFIX/etc. Let's assume one has the server part installed as a system package. This generally is a good idea, so that the server gets started during boot. This means, that the config is in /etc/slurm. If one now wants to use the client part (library!) via spack, one has a problem: spack's slurm looks in SPACK-PACKAGE-PREFIX/etc for the config. There needs to be a way to let the spack installed package use the system's config. So add a variant to override the path during build: sysconfdir=/etc/slurm. This is much like what happened in #15307 for munge.
2020-03-31Allow Spack Environments with '-h' in the name (#15429)Adam J. Stewart2-32/+63
If a user invoked "spack env activate example-henv", Spack would mistakenly interpret the "-h" from "example-henv" as the "-h" option. This commit allows users to create and activate environments with "-h" in the name. This issue existed for bash shell support as well as csh support, and this commit addresses both, along with some other unrelated csh support issues.
2020-03-31Extrae: update package shasum and binutils version (#15516)Phil Tooley1-2/+2
Co-authored-by: telemin <telemin@protonmail.ch>
2020-03-31packages.yaml: allow virtuals to specify buildable: false (#14934)Greg Becker9-153/+155
Currently, to force Spack to use an external MPI, you have to specify `buildable: False` for every MPI provider in Spack in your packages.yaml file. This is both tedious and fragile, as new MPI providers can be added and break your workflow when you do a git pull. This PR allows you to specify an entire virtual dependency as non-buildable, and specify particular implementations to be built: ``` packages: all: providers: mpi: [mpich] mpi: buildable: false paths: mpich@3.2 %gcc@7.3.0: /usr/packages/mpich-3.2-gcc-7.3.0 ``` will force all Spack builds to use the specified `mpich` install.
2020-03-31GMT: add 6.0.0 (#15785)Adam J. Stewart1-13/+75
2020-03-31autoconf-archive: add new package (#15782)Adam J. Stewart1-0/+14
2020-03-31JasPer: add 2.0.16 (#15781)Adam J. Stewart1-6/+4
2020-03-31Update link for codecov's browser extensions (#15779)Massimiliano Culpo1-2/+2
2020-03-31geant4: new version 10.6 plus simplifications (#15447)Ben Morgan17-194/+329
* geant4: new version 10.6 plus simplifications Add new 10.6.0 release, migrating download of source to use Geant4's public release repo on CERN GitLab. Change versioning scheme to use clearer and standard semantic scheme. Update geant4-data and g4XXX data packages with new versions. Migrate geant4-data as a BundlePackage of the g4XXX packages, installing links to each under a single directory under share for geant4-data. Ensure each g4XXX package exports the environment variable pointing to its location expected by Geant4. Remove "data" variant from Geant4 package and always use geant4-data. Simplify cxxstd variant transport to dependencies. * g4<DATA>: Use self to resolve correct prefix * geant4, data: Fix flake8 errors * g4photonevaporation: flake8 fix * geant4: vecgeom version depends_on Geant4 major.minor versions have specific dependencies on vecgeom versions. Add missing vecgeom version for geant4 10.5, and match version requirements for vecgeom in geant4 depends_on. * geant4: c++17 patch specific for 10.4.3 * geant4: simplify geant4-data setup * geant4: Use new define_from_variant function * geant4: fix flake8 errors
2020-03-30ppOpen-APPL/FVM: new package. (#15772)Toyohisa Kameyama1-0/+63
* ppOpen-APPL/FVM: new package. * copy_tree -> install_tree.
2020-03-30superlu-dist: add new version 6.3.0 (#15766)Satish Balay1-0/+1
2020-03-30helics: add new package (#15763)Ryan Mast1-0/+105
* helics: add new package * Remove FIXME boilerplate * Use open @master: verison range for git dependency and remove mpi fix branch version * Add blank line after spack import
2020-03-30Balay/petsc 3.13.0 (#15767)Satish Balay1-4/+15
* petsc: add 3.13.0 (using petsc-lite) and 3.12.5 * petsc@3.13.0: update hdf5 and superlu-dist dependencies * flake8 fix * fixes for comments Co-authored-by: Jed Brown <jed@jedbrown.org>
2020-03-30py-torch: make sure unit tests are registered (#15765)Adam J. Stewart1-3/+5
2020-03-30CUDA 10.1+ supports ICC 19.0 (#15764)Axel Huebl1-2/+2
Fix the CUDA-ICC conflict check. Simplify the XL 17 check.
2020-03-30py-horovod: fix compilation of ~cuda (#15719)Adam J. Stewart2-65/+127
* py-horovod: fix compilation of ~cuda * Rewrite py-horovod with only 3 variants * Add upstream patch to workaround compilation issue
2020-03-30py-onnx: depends on cmake >= 3.1 (#15762)Andrew W Elble1-0/+1
* py-onnx: depends on cmake >= 3.1 * Update var/spack/repos/builtin/packages/py-onnx/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-03-30Update git version to 2.26.0 (#15756)Amjad Kotobi1-0/+5
* Update git version to 2.26.0 * Fix1