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2019-01-24fix issue where docker images were being pushed without login (#10379)Omar Padron1-3/+1
2019-01-23Update ecp st tau pdt (#8192)sameershende2-34/+135
* Updated MPI and TAU versions in the TAU package * Updated PDT versions * Added support for Python (+python), default to `False` * Cleaned up binutils, python, mpi usage. * Updated binutils install to add additional header files to the include/extra directory. * Resolving review problems with TAU and binutils packages. The binutils package was updated to include support for installing the ELF headers as a +headers variant. The TAU package was updated to use all known Spack dependencies.
2019-01-22trinotate: remove perl-dbd-mysql, move runtime files to HOME (#9850)Justin Stanley1-1/+8
2019-01-22r-gamlss: new package (and data) at 5.1-2 (#10360)Justin Stanley3-0/+61
* r-gamlss-data: new package at 5.1-0 * r-gamlss-dist: new package at 5.1-1 * r-gamlss: new package at 5.1-2 * r-gamlss: add mass, survival, nlme imports
2019-01-22entrezdirect: new package (#10374)Justin Stanley1-0/+30
2019-01-22py-whatshap: new package at 0.17 (#10377)Justin Stanley1-0/+31
* py-whatshap: new package at 0.17 * py-whatshap: remove unused build_args
2019-01-22r-rrcov: new package at 1.4-7 (#10387)Justin Stanley1-0/+25
2019-01-22r-robust: new package at 0.4-18 (#10391)Justin Stanley1-0/+23
2019-01-22r-dynamictreecut: new package at 1.63-1 (#10388)Justin Stanley1-0/+19
2019-01-22Exclude system mkl installs from numpy (#10383)Peter Scheibel1-4/+28
Fixes #10361 Fixes #6634 When mkl isnt in the spec, still write an explicit mkl entry to prevent numpy from looking in system dirs and using a system install of mkl. Do the same for openblas and atlas (although mkl was the only system install reported to interfere with Spack's choice).
2019-01-22py-pyvcf: new package at 0.6.0 (#10375)Justin Stanley1-0/+17
2019-01-21Typo fixes in .flake8 comments (#10399)Adam J. Stewart2-11/+19
2019-01-20py-pyfaidx: new package at 0.5.5.2 (#10376)Justin Stanley1-0/+17
2019-01-20cmake: add version 3.13.3 (#10397)Matthias Diener1-0/+1
2019-01-18Update Nalu-Wind and dependencies (#10204)Jon Rood7-44/+131
* Updating nalu-wind, nalu, openfast, and tioga packages. Includes improved handling of +shared variant. * Add fftw and catalyst support to nalu-wind. * Restrict ParaView to use matplotlib versions before 3 (which require Python 3)
2019-01-18adding checksum for latest lmod release (#10381)Owen Solberg1-0/+1
2019-01-16Update templight pseudo-release to remove need for patching (#10290)Hadrien G1-2/+16
* Update templight+LLVM combo * Bring back old pseudo-release
2019-01-16Openblas: added version 0.3.5 (#10364)Massimiliano Culpo1-0/+1
2019-01-16Added latest version of singularity 2.x (#10354)sknigh1-0/+1
2019-01-16Add package for Hugo (static website generator) (#10358)George Hartzell1-0/+26
2019-01-15py-modred: New package (#10309)Tom Payerle2-0/+38
* py-modred: New package Parallelized python module for finding modal decompositions and reduced order models. * fix license I think? * Add dependency on py-numpy and remove commented out code
2019-01-15Added hpl 2.3 (#10345)sknigh1-3/+31
* Added hpl 2.3 * Added requested build fixes, added step to copy HPL.dat in 2.3+
2019-01-15r requires cairo+pdf (#10350)Adam J. Stewart1-1/+1
2019-01-15explicitly depend_on cairo with X **and** pdf variants (#10351)Owen Solberg1-0/+1
2019-01-15Add useful comment explaining why this is not needed for Python3. (#10326)Elizabeth Fischer1-0/+1
2019-01-15openPMD-api: Dependency Update (#10314)Axel Huebl1-14/+19
openPMD-api now only supports Python 3, needs a newer CMake and ADIOS1 and also learned to read & write JSON :-)
2019-01-14vigra: new package (#10337)Neil Flood1-0/+91
* vigra: new package * Better constraints and types on some depends_on. Use site_packages_dir variable for Python install dir. Explicit switch-offs where available. Change some local variables to suit style checks. * Take care of lines too long * Explicit WITH_HDF5=ON
2019-01-14Add span-lite version (#10347)Andrew Gaspar1-0/+1
2019-01-14 Added latest rust releases and develop branch (#10341)sknigh1-0/+3
* Added latest rust releases and develop branch * Fixed spacing
2019-01-14namd: fixing to reflect renamed charmpp per #9216 (#10342)Levi Baber1-1/+1
2019-01-14Added latest version of libfabric (#10343)sknigh1-0/+1
2019-01-14feature: py-invoke: new python package (#10225)Geoffrey Oxberry1-0/+18
2019-01-14tutorial: update tutorial materials for ECP19Todd Gamblin1-14/+12
2019-01-13version bump: v0.12.1Gregory Becker1-1/+1
2019-01-13bugfix/gdk-pixbuf (#10312)George Hartzell3-2/+36
* docbook processing works correctly for gdk-pixbuf 1. The various bits of documentation in gdk-pixbuf include hardcoded references to dtd's and stuff at their canonical, Internet, locations. BUT, gdk-pixbuf runs xslt-proc with the `--nonet` option, which forbids it from using the network. Sadness ensues. Traditionally folks use XML Catalogs to map these to local copies. Our docbook-xsl package wasn't setting the appropriate env var in its dependents environments to use our catalog. Now it does. Less sadness ensues. 2. If we're going to use these things, we should depend on them. * Add gdk-pixbuf's bin to build environment The "post-install.sh" script uses gdk-pixbuf-query-loaders, which was installed earlier. If py-psyclone can set its own bin on its PATH, so can we... * Make gdk-pixbuf use recognizable docbook location Our docbook-xsl package assumes that the canonical location is `http://cdn.docbook.org/release/xsl/current/manpages/docbook.xsl`, but the gdk-pixbuf's meson build script uses `http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl`. This means that our XML Catalog doesn't fix the reference and sadness happens. Just patch the build that we see what we want to see, then we can make it all go away. * Add commentary re docbook patch * Make catalog helper a property Thanks @adamjstewart! * Run tests if/when run_tests is true Thanks @adamjstewart! * Tune up dependencies Thanks @adamjstewart! * Wordsmit commentary
2019-01-12update alpine ascent and friends (#10320)Cyrus Harrison6-70/+465
This adds a lot of fixes and updates for alpine ascent and its dependencies: * add support for static (via ~shared) and use vtk-m 1.2 * update vtkh package to output cmake configure file and pinning it to vtkm 1.2 * make conduit respect ~python * fix ascent python logic * consistant cmake usage * conditionally add tbb in ascent if vtkh * enable openmp * more robust handling of variants * update ascent and conduit for static builds * add optional support for mfem in ascent * enable mfem conduit support for ascent * add optional adios dep to conduit * remove ver req from conduit * ascent: remove confusing comment * tweaks to conduit and ascent pkg recipes * fix typo in conduit package * pref conduit master * changing mfem to depend on conduit@master to get updated relay * restore use of conduit 0.3.1 or greater for mfem * set master as preferred conduit version * allow mfem to use conduit master * adding rover package and editing ascent * updating vtkm cmake dep * guard ascent python support on +shared * removing rover to simply ascent package * add fortran variant to conduit, to allow us to turn off conduit support even when a fortran compiler is specified * fix fortran compiler check so it can work on cray systems * working towards cuda fix for vtkm lagrange filter * update ascent package with more variants, and patch to avoid nvcc issue * hdf5 flags fix for BGQ * add post install test * add testing to ascent * add testing of the using-with-make example * add ctest output on error for run_tests
2019-01-12cc: clean up cray compilers, fix issues with case-insensitive filesystems ↵Adam J. Stewart9-9/+6
(#10323) * Remove Cray CC compilers causing problems on case-insensitive filesystems * cray -> cce * Ensure that compiler-specific directory comes first in build-env * Point to compiler-specific symlinks
2019-01-12Added osu-micro-benchmarks@5.5 (#10333)Jiawei Zhuang1-0/+1
2019-01-12fix typo in docker test script (#10334)Omar Padron1-1/+1
2019-01-12Add libxslt v1.1.33 info (#10328)George Hartzell1-0/+1
2019-01-12dealii: does not support sundials 4.x (#10324)Denis Davydov1-1/+1
2019-01-12gdal: Add variant for GRIB driver (#10322)Neil Flood1-1/+6
2019-01-12fix archlinux docker build (#10289)Omar Padron2-8/+7
2019-01-11Binary caching bugfix: symlink relocation (#10073)Greg Becker3-9/+131
Binary caches of packages with absolute symlinks had broken symlinks. As a stopgap measure, #9747 addressed this by replacing symlinks with copies of files when creating binary cached packages. This reverts #9747 and instead, either relative-izes the symlink or rewrites the target. If the binary cache is created using '--rel' (as in "spack buildcache create --rel...") then absolute symlinks will be replaced with relative symlinks (in addition to making RPATHs relative as before); otherwise they are rewritten (when the binary cache is unpacked and installed).
2019-01-11enh: `buildcache list` should behave similar to `find` (#10052)Matthias Wolf1-15/+10
The current output of buildcache list is very verbose and I feel like some details are getting lost. By making the output similar to find, I think users will be able to get a better overview of what is stored in the cache.
2019-01-11Omega_h changed its URL (#10315)Dan Ibanez1-3/+3
From https://github.com/ibaned/omega_h To https://github.com/SNLComputation/omega_h
2019-01-11omega-h: fix CMAKE_BUILD_TYPE: breaks with spack deafult 'RelWithDebInfo' ↵Satish Balay1-0/+2
(#10297)
2019-01-11dealii: fix concretization of xsdk package (#10288)Denis Davydov2-2/+13
* dealii: fix concretization of xsdk package * tests: add concretization tests for deal.II and xSDK, which are often broken due to limitations in the concretizer * use pytest.mark.parametrize
2019-01-10Updating LBANN and related packages (#10305)Brian Van Essen3-11/+13
Updated LBANN, Hydrogen, and Aluminum to not require CUDA-aware MPI even when using CUDA. Fixed small bugs within both LBANN and Hydrogen packages. Added requirements for breathe and cereal to LBANN.
2019-01-10boost: fix the bjam build for Cray (#10295)Mark W. Krentel2-0/+36
Fixes issues #9613 and #3209. Remove the spack wrapper directories from PATH for the bootstrap step. This was breaking the build for Cray (and other cross-compile) because bjam was built for the BE and died on SIGILL on the FE. This only affects building bjam. The boost libraries are still built the normal spack way with the spack wrappers.
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