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2019-06-16Add py-cligj 0.5.0 (#11727)Adam J. Stewart1-1/+2
2019-06-16Add py-numpy 1.16.4 (#11726)Adam J. Stewart1-1/+2
2019-06-16Add libjpeg-turbo 2.0.2 (#11725)Adam J. Stewart1-1/+2
2019-06-16Update URL for older version of jackcess (#11724)Adam J. Stewart1-1/+2
2019-06-16Add HDF 4.2.14 (#11723)Adam J. Stewart1-3/+4
2019-06-16Add new package py-boto3 (#11722)Adam J. Stewart1-0/+25
2019-06-16Add new package py-s3transfer (#11721)Adam J. Stewart1-0/+22
2019-06-16Add new package py-botocore (#11720)Adam J. Stewart1-0/+30
2019-06-16Add new package py-jmespath (#11719)Adam J. Stewart1-0/+20
2019-06-16Add new package py-freezegun (#11718)Adam J. Stewart1-0/+25
2019-06-16Rename py-dateutil -> py-python-dateutil (#11717)Adam J. Stewart12-38/+54
2019-06-16Add py-aenum package (#11716)Adam J. Stewart1-0/+20
2019-06-15intel: add version 19.0.4 (#11741)Kevin Manalo3-0/+6
2019-06-15Updates to poppler to get pdf2svg working (#11681)Adam J. Stewart2-13/+28
2019-06-15Fix latest HPL for MKL use (#11712)Glenn Johnson1-0/+5
The 2.3 version of HPL needs LDFLAGS set for use of MKL libraries.
2019-06-15docs: fix config tutorial (#11715)Michael Kuhn1-30/+35
This fixes a few typos, adds a hint to `spack config blame` and brings the variant specification in line with other docs sections.
2019-06-15pybind11: v2.3.0 (#11713)Axel Huebl1-0/+2
Add the latest 2.3.0 release and me as package maintainer.
2019-06-15new package: mutationpp (#11705)brietzke1-0/+50
* new package: mutationpp * Update package.py * flake8: correct package.py for flake8-python-style * Update package.py * modifications as requested by reviewer for #11705
2019-06-15r3d: add version 2019-04-24 (#11710)Gabriel Rockefeller1-0/+1
2019-06-14montage: new package at 6.0 (#11696)Justin S1-0/+27
2019-06-14scons: add version 3.0.5 (#11709)Matthias Diener1-0/+1
2019-06-14dtk@develop now requires 'submodules=True' flag (#11694)Satish Balay1-0/+1
2019-06-14swift-t: New release packages for 1.4.3 (#11684)Justin M Wozniak4-8/+52
2019-06-13Ensure mock configuration directory is cleaned up on session exit. (#11700)Tamara Dahlgren1-1/+4
2019-06-13add charliecloud-0.9.10 (#11471)Jordan Ogas1-10/+19
* add charliecloud-0.9.10; remove obsolete version * revert older version changes; add version function * fix space issue * remove url declaration * revert url removal * remove self reference * fix url; removed preferred tag; use newer package url
2019-06-13Add tests for "spack location" command (#11661)Tamara Dahlgren2-0/+135
The "spack location" command was previously untested. This also adds a check to ensure that composite Stages can report whether they were expanded (this property was previously only recorded in Stage but not in CompositeStage).
2019-06-13Always treat DIYStage as expanded (#11663)Tamara Dahlgren2-2/+73
DIYStage, used to treat a user-managed directory as a staging area, should always be considered expanded (i.e. the source has been decompressed if it was stored in an archive). This also: * Adds checks to ensure that the path used to instantiate a DIYStage refers to an existing directory. * Adds tests to check the behavior of DIYStage (including behavior added here, but it was generally untested before).
2019-06-13intel-xed and hpcviewer: adapt to new resource placement (#11676)Mark W. Krentel2-5/+5
Change 'destination' to 'placement' in the use of resource() for intel-xed and hpcviewer. Recent commits (1842873f and eb584d89) changed the directory path for a resource and thus broke the build for these packages.
2019-06-12added jpeg,png,ffmpeg variants to lammps (#10404)marvinbernhardt1-0/+16
2019-06-12Update remaining packages to use Stage.source_path (#11662)Tamara Dahlgren11-30/+46
#11528 updated Stage to always store a Package's source in a fixed directory accessible via `Stage.source_path` This left behind a number of packages which were expecting to access the source code via `Stage.path`. This Updates those packages to use `Stage.source_path` instead. This also updates the name of the fixed directory: The original name of the fixed directory was "src", so if an expanded archive created a "src" directory, then users inspecting the directory structure could see paths like "src/src" (which wasn't wrong but could be confusing). Therefore this also updates the name of the fixed directory to "spack-src".
2019-06-12Make "spack compiler find" check PATH by default (#11683)Massimiliano Culpo5-21/+60
Fixes #11678 `spack compiler find` was not searching `PATH` when provided with no arguments. ea7910a updated the API for the search function and the command logic did not update how it called this function. This also adds a test to ensure that `spack compiler find` will collect compilers from `PATH`.
2019-06-12warpx: only allow master branch, and fix build on darwin (#11667)Dave1-3/+24
* warpx: only allow master branch, and fix build on darwin * warpx: Added CXXFLAGS=-std=c++11 for clang * warpx: further clean up of openmp and c++11 flags * warpx: Get around the problem with resources The update uses placement instead of destination
2019-06-12Fixed Flecsi Backend Dependencies (#11679)Robert Pavel1-14/+28
Fixed logic behind flecsi backends to not require legion for an mpi build and to better support required combinations. Also made graphviz support and tutorial building optional
2019-06-11Add additional common C++ and Fortran header file extensions (#11600)Adam J. Stewart1-1/+8
* Add additional common C++ and Fortran header file extensions * Add .hxx extension * Add .txx and .tcc extensions * Add .icc extension
2019-06-11new python package/py-typesentry (#11657)Sinan1-0/+20
* new python package/py-typesentry * add proper version
2019-06-11Add support for using python3 in new verison of VTK. (#11673)Dan Lipsa1-3/+12
* Add support for python3 in new versions of VTK.
2019-06-11Add extra logic for C std flags on PGI, XL, and Cray (#11635)Chuck Atkins3-7/+57
2019-06-11Paraview: Add motionfx Intel workaround (#11608)psakievich2-0/+11
* Paraview/VTK: Fix failure on intel builds Paraview@5.6.0 fails to build with intel compilers on certain platforms. Error messages have been traced to the optional MotionFX lib. (see https://discourse.paraview.org/t/error-build-5-6-0-rc1/572) Turning off motionfx allows for succesful builds on these platforms.
2019-06-10Fix recursive module find for upstream dependencies (#11304)Peter Scheibel4-64/+223
"spack module tcl find -r <spec>" (and equivalents for other module systems) was failing when a dependency was installed in an upstream Spack instance. This updates the module index to handle locating module files for upstream Spack installations (encapsulating the logic in a new class called UpstreamModuleIndex); the updated index handles the case where a Spack installation has multiple upstream instances. Note that if a module is not available locally but we are using the local package, then we shouldn't use a module (i.e. if the package is also installed upstream, and there is a module file for it, Spack should not use that module). Likewise, if we are instance X using upstreams Y and Z like X->Y->Z, and if we are using a package from instance Y, then we should only use a module from instance Y. This commit includes tests to check that this is handled properly.
2019-06-10Add latest releases for pFUnit (#11642)Daniel Topa1-1/+9
* Add latest releases for pFUnit - 3.2.10, 3.3.0, 3.3.1, 3.3.2, 3.3.3 - 3.2.9 now with sha256 - 4.0.0 is added, but commented out (build fails, see errors) Verification builds Darwin x86_64: dantopa@cn100:pr-pfunit-darwin-general.spack $ spack find pfunit ==> 5 installed packages -- linux-centos7-x86_64 / gcc@4.8.5 ----------------------------- pfunit@3.2.9 pfunit@3.2.10 pfunit@3.3.0 pfunit@3.3.1 pfunit@3.3.2 pfunit@3.3.3 Darwin Power9: -- linux-rhel7-ppc64le / gcc@4.8.5 ------------------------------ pfunit@3.2.9 pfunit@3.2.10 pfunit@3.3.0 pfunit@3.3.1 pfunit@3.3.2 pfunit@3.3.3 Darwin ARM: dantopa@cn805:pr-pfunit-darwin-arm.spack $ spack find pfunit ==> 5 installed packages -- linux-rhel7-aarch64 / gcc@4.8.5 ------------------------------ pfunit@3.2.9 pfunit@3.2.10 pfunit@3.3.0 pfunit@3.3.1 pfunit@3.3.2 pfunit@3.3.3 2019-05-05 Signed-off-by: Daniel Topa <dantopa@lanl.gov> * answer @citibeth comments Signed-off-by: Daniel Topa <dantopa@lanl.gov> * shortened offending comment to comply with flake8; suppressed error message on entry for v4.0.0 Signed-off-by: Daniel Topa <dantopa@lanl.gov> * removed tailing space qt 20:55 Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2019-06-10ninja{-fortran}: make pkgs nonvirtual (fix #11628) (#11629)Geoffrey Oxberry3-6/+0
2019-06-10ParaView and Catalyst use python3. (#11485)Dan Lipsa2-13/+65
Use python3 for latest paraview and catalyst versions.
2019-06-10CD: Package Index (#11665)Axel Huebl5-0/+53
Build the docker image for the new package index REST API on each merge/push to develop and master.
2019-06-10Remove gnutls dependency and disable openssl when appropriate (#11646)Chuck Atkins1-4/+9
2019-06-10Define LDFLAGS when using fujitsu compiler (#11669)t-karatsu1-0/+3
2019-06-08dateutils: new package (#11623)Quinn1-0/+19
* Adding the dateutils package * Removing superfluous dependencies
2019-06-08tests: restore `spack spec mpileaks` in test output for Python 2 (#11664)Todd Gamblin1-5/+3
- also remove coverage calls of these commands - we JUST want coverage to tell us what is in the test suite.
2019-06-08concretization: don't apply build-dep constraints for installed packages ↵Peter Scheibel3-5/+85
(#11594) Spack currently tries to unify everything in the DAG, but this is too strict for build dependencies, where it is fine to build a dependency with a tool that conflicts with a version fo that tool for a dependent's build. To enable a workaround for conflicts among build dependencies, so that users can install in multiple steps to avoid these conflicts, make the following changes: * Dont apply package dependency constraints for build deps of installed packages * Avoid applying constraints for installed packages vs. concrete packages * Mark all dependencies of installed packages as visited in normalization method * don't remove dependency links for concrete specs in flat_dependencies Also add tests: * Update test to ensure that link dependencies of installed packages have constraints applied * Add test to check for proper handling of transitive dependencies (which is currently not the case)
2019-06-08fix qt build on gcc8.3 (#11633)Omar Padron3-7/+476
* fix qt build on gcc8.3 * source patches from upstream * remove old code adding the same patch
2019-06-08Add ADIOS2 option to Trilinos (#11609)Francois Budin1-1/+7
ADIOS2 is the latest implementation of the ADaptable Input Output System, ADIOS. This brand new architecture was designed to continue supporting the performance legacy of ADIOS, and extend its current capabilities to address current and future input/output (IO) challenges in the scientific data lifecycle through effective research and development (R&D) activities. ADIOS2 was recently added as a Third Party Library of Trilinos when it was integrated to IOSS, a library inside the SEACAS package.