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2020-03-05Allow overrides for spack.config set() and override(). (#14432)Chris Green2-17/+141
Allows spack.config InternalConfigScope and Configuration.set() to handle keys with trailing ':' to indicate replacement vs merge behavior with respect to lower priority scopes. Lists may now be replaced rather than merged (this behavior was previously only available for dictionaries). This commit adds tests for the new behavior.
2020-03-05Recover coverage from subprocesses during unit tests (#15354)Tamara Dahlgren5-16/+16
* Recover coverage from subprocesses during unit tests
2020-03-05Add Checksum for 1.4.1.4 Release (#15363)Adam J. Stewart1-0/+4
* Add Checksum for 1.4.1.4 Release Add checksum for 1.4.1.4 release. Mark myself as maintainer. List develop version. * Update var/spack/repos/builtin/packages/libhio/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-03-05Python: add 3.8.2 (#15365)Adam J. Stewart1-0/+1
2020-03-05Update legion versions (#15364)Adam J. Stewart1-5/+3
2020-03-05unifyfs: add patch to fix #15292 (#15315)eugeneswalker2-1/+30
It was reported that UnifyFS had a bug with the --enable-mpi-mount config option, which corresponds to the auto-mount variant. This bug was fixed in the UnifyFS dev branch, however remains broken for the 0.9.0 version. This adds a patch to the unifyfs package to fix the auto-mount variant when installing with version 0.9.0. This also removes the openssl dependency as unifyfs does not directly depend on it. This was said to be a non-explicit dependency in #15258. However, if it is needed, it is likely a non-explicit dependency of one of unifyfs's dependencies and should be added there. Fixes: #15292
2020-03-05lammps: add most recent stable release (#15335)Adam J. Stewart1-1/+10
* lammps: add most recent stable release * Update var/spack/repos/builtin/packages/lammps/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-03-05Allow buildcaches keys to find public keys on the e4s mirror (#15361)Patrick Gartung1-3/+6
2020-03-05lastz: declare ch as type int (#15350)Adam J. Stewart3-72/+247
2020-03-05update maintainers for bmi, darshan, and margo (#15356)Adam J. Stewart4-1/+7
Signed-off-by: Phil Carns <carns@mcs.anl.gov>
2020-03-05New package: fd-find (#15344)Axel Huebl1-0/+21
* New package: fd-find Add package for fd-find: A simple, fast and user-friendly alternative to 'find'. * Update copyright date
2020-03-05New package: ripgrep (#15343)Axel Huebl1-0/+31
Add package for ripgrep: ripgrep is a line-oriented search tool that recursively searches your current directory for a regex pattern. ripgrep is similar to other popular search tools like The Silver Searcher, ack and grep.
2020-03-05New package: opensubdiv (#15310)Adam J. Stewart1-0/+85
* [opensubdiv] created stub for opensubdiv * [opensubdiv] added homepage and description * [opensubdiv] removed boilerplate * [opensubdiv] working on dependencies and variants * [opensubdiv] fixed syntax error * [opensubdiv] defined spec * [opensubdiv] added dev version * [opensubdiv] building on CudaPackage * [opensubdiv] always build with open gl and depends_on('gl') * [opensubdiv] applying cuda flags * [opensubdiv] worked on doc variant * [opensubdiv] added some x11 libraries * [opensubdiv] depends on glfw * [opensubdiv] locating glew * [opensubdiv] added openmp variant * [opensubdiv] flake8 fixing * [opensubdiv] fixed develop version name * [opensubdiv] fixed description to not need @
2020-03-05Correct pytest.raises matches to match (#15346)Massimiliano Culpo3-10/+10
2020-03-05Bugfix: resolve StopIteration message attribute failure (#15341)Massimiliano Culpo2-1/+22
Testing the install StopIteration exception resulted in an attribute error: AttributeError: 'StopIteration' object has no attribute 'message' This PR adds a unit test and resolves that error.
2020-03-04py-matplotlib: add 3.2.0 (#15349)Adam J. Stewart1-6/+6
2020-03-04xgboost: add version 0.90 (#15321)Peter Scheibel1-0/+2
2020-03-04New version of simplejson (#15325)Axel Huebl1-0/+1
2020-03-04ADIOS2: Cleanup, Development Branch Name (#15334)Adam J. Stewart1-4/+4
* ADIOS2: Version `master` Rename branch version to supported, real development branch `master`. The old name is legacy Spack when alternative development branch names were not yet supported. * ADIOS: Simplify via spec Variable use the already defined local variable `spec` to shorten lines
2020-03-04ADIOS2: Testing Depends on Python (#15336)Adam J. Stewart1-3/+9
Add the python dependency and CMake hints when build with tests. `spack install --tests=root adios2`
2020-03-04Add function replace_prefix_nullterm for use on mach-o rpaths. (#15347)Patrick Gartung1-4/+35
This recovers the old behavior of replace_prefix_bin that was modified to work with elf binaries by prefixing os.sep to new prefix until length is the same as old prefix.
2020-03-04Fixed the sha has for 1.3.3. (#15331)Adam J. Stewart1-1/+1
2020-03-04libfabric: default 1.8.1 (#15337)Adam J. Stewart1-2/+2
Since 1.9.0 is broken for Darwin, which impacts many developers, and the fix is still a RC, let's keep the previous release as default. This avoids distruption for OSX developers and CI.
2020-03-04Remove DB conversion of old index.yaml (#15298)Peter Scheibel1-84/+45
Removed the code that was converting the old index.yaml format into index.json. Since the change happened in #2189 it should be considered safe to drop this (untested) code.
2020-03-04use os.sep instead of null byte to pad replacement paths in binaries (#15338)Patrick Gartung1-1/+2
* use os.sep instead of null byte to pad replacement paths in binaries * Prefix the pading os.sep's
2020-03-04precice: Add version 2.0.1 (#15318)Adam J. Stewart1-0/+1
2020-03-04pgi-19.10 update version (#15330)Adam J. Stewart1-0/+1
2020-03-04gcc: Add 8.4.0 (#15323)Adam J. Stewart1-0/+1
2020-03-04Add extra version of py-contextlib2 (#15322)Adam J. Stewart1-0/+1
2020-03-04suite-sparse: fix installation for v5.X (#15326)Adam J. Stewart1-1/+2
fixes #15184 GraphBLAS depends on m4 according to CMake error message Do not use INSTALL= when compiling the library
2020-03-04ecp-proxy-apps: version bump (#14680)Christoph Junghans1-21/+14
2020-03-03Fix FCFLAGS handling for Autotools packages (#14788)Sergey Kosukhin2-1/+7
Spack's fflags are meant for both f77 and fc. Therefore, they must be passed as FFLAGS and FCFLAGS to the configure scripts of Autotools-based packages.
2020-03-03intel-xed does not support python>3.7 (#15308)sknigh1-1/+2
2020-03-03Added UQTk package (#14801)sknigh1-0/+20
* added UQTk package * Add missing expat dependency to uqtk
2020-03-03elfutils: increase connect timeout (#15262)Mark W. Krentel1-9/+12
Increase the connect timeout for elfutils to 60 sec. Elfutils (and bzip2) tar files are on sourceware.org which is often slow to respond.
2020-03-03Protobuf's cmake environment does not properly handle being exported (#15293)Brian Van Essen1-0/+3
and found when using the RelWithDebInfo build type. Change protobuf to only support Release and Debug build types.
2020-03-03cherry-picking global ordinal type variant from ↵Mathias Anselmann2-2/+12
https://github.com/spack/spack/pull/14215 and setting dealii to GO int, to make it compile again (#15288) Co-authored-by: Andrey Prokopenko <andrey.prok@gmail.com>
2020-03-03fairlogger: add version, other improvements (#15300)Dr. Christian Tacke1-6/+11
* @develop needs the full git repo to use "git describe" properly * If not specifying the cxxstd variant, let cmake use its default * Improve fmt dependencies: fairlogger < 1.6.2 does not work with fmt >= 6. * Small other stuff
2020-03-03Update package.py (#15299)Patrick Schratz1-0/+1
2020-03-03Created package glfw (#15296)Jennifer Herting1-0/+39
* Created stub * added description and homepage * added dependencies * removed extra boilerplae * switched to the pkgconfig provider
2020-03-03OpenMPI: patch for NAG. (#15301)Sergey Kosukhin5-0/+195
2020-03-03Suite sparse compilation fix for 5.7.0 and 5.7.1 (#15289)Mathias Anselmann1-2/+1
Suite-sparse 5.7.0 and 5.7.1 need separate make and make install run to be able to compile, too
2020-03-03Tmux should look for tinfo in -ltinfo (#15282)George Hartzell1-8/+2
Just `depend_on('ncurses')`, pkgconfig seems to cause the right thing to happen if the package is built +termlib or ~termlib (tested both ways on a CentOS 7 system). Additional details in: https://github.com/spack/spack/issues/15281 Tested by building all of the releases of tmux on a CentOS 7 box.
2020-03-02boost: Add "container" library (#14878)Dr. Christian Tacke1-1/+8
"container" is partly a misnomer, as it's realy the extended allocators part of container. But every part calls it container, so we do too.
2020-03-02amrex: New version 20.03 (#15294)Erik Schnetter1-0/+1
2020-03-02bugfix: ensure proper dependency handling for package-only installs (#15197)Tamara Dahlgren3-17/+149
The distributed build PR (#13100) -- did not check the install status of dependencies when using the `--only package` option so would refuse to install a package with the claim that it had uninstalled dependencies whether that was the case or not. - [x] add install status checks for the `--only package` case. - [x] add initial set of tests
2020-03-02openblas: Add version 0.3.9. (#15287)Kai Torben Ohlhus1-0/+1
[OpenBLAS 0.3.9](https://github.com/xianyi/OpenBLAS/releases/tag/v0.3.9) was released.
2020-03-02Qmcpack: new variant +afqmc (#14882)Cody Melton1-0/+13
* add preliminary afqmc support in qmcpack * afqmc updates * fix spack typos * edit AFQMC to only allow up 3.7 or above * added NCCL library support for AFQMC build * add CMAKE args for BUILD_AFQMC_WITH_NCCL * update for just AFQMC support. No AFQMC+GPU support * remove nccl for afqmc * flake8 whitespace fix
2020-03-02stat: new version 4.0.2 (#15290)Gregory Lee1-0/+2
2020-03-02Update flag_handler for 'netcdf-fortran'. (#14789)Sergey Kosukhin7-42/+612
* Update flag_handler for 'netcdf-fortran'. * Refactoring. * Enable old versions of netcdf-fortran for NAG. * Disable parallel 'make check' for versions before 4.5.0. * Fix shared libraries built with NAG instead of conflicting it. * Add 'skosukhin' as a maintainer of 'netcdf-fortran'.
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