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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`
2020-03-04Fixed 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.
2020-03-04precice: 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
2020-03-03intel-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
2020-03-02openblas: 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'.
2020-03-02lastz: set compile commands for each compiler (#15284)noguchi-k1-0/+4
2020-03-01Update tcsh package (#15283)Glenn Johnson1-4/+5
This PR adds some fixes for the tcsh package. - Adds new version - adds list_url so fetching works for current and old tarballs - sets ncurses dependency explicitly to `ncurses+termlib` If `+termlib` is not set then it will link against the system libtinfo.
2020-03-01lastz: cast from char to signed char (#15263)noguchi-k2-0/+73
2020-03-01Quantum-Espresso: qe-6.5 fails to detect MKL for FFT (#15276)TZ1-4/+15
* Quantum-Espresso: qe-6.5 fails to detect MKL for FFT qe-6.5 fails to detect MKL for FFT if BLAS_LIBS is set due to an unfortunate upsteam change in their autoconf/configure: - qe-6.5/install/m4/x_ac_qe_blas.m4 only sets 'have_blas' but no 'have_mkl' if BLAS_LIBS is set (which seems to be o.k.) - however, qe-6.5/install/m4/x_ac_qe_fft.m4 in 6.5 unfortunately relies on x_ac_qe_blas.m4 to detect MKL and set 'have_mkl' - qe-5.4 up to 6.4.1 had a different logic and worked fine with BLAS_LIBS being set However, MKL is correctly picked up by qe-6.5 for BLAS and FFT if MKLROOT is set (which SPACK does automatically for ^intel-mkl). Thus, do not set BLAS_LIBS when compiling qe-6.5 with intel-mkl. * replace all '^intel-mkl' by '^mkl' to match other packages which also provide MKL e.g. intel-parallel-studio+mkl as mentioned by @adamjstewart in #15276
2020-02-29Update kallisto (with hackery on std_cmake_args) (#15278)George Hartzell1-0/+29
* Filter problematic flag from std_cmake_args Including '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' in the cmake args causes bits of cmake's output to end up in the autoconf-generated configure script. See https://github.com/spack/spack/issues/15274 and * Don't build in parallel (sigh) * Constrain hackery for newer versions... ... to newer versions.
2020-02-29QGIS: fix typos (#15279)Sinan1-3/+4
* fix typos * minor improvement * add version 3.4.15
2020-02-29New package: QGIS (#12388)Sinan1-0/+214
* [WIP] new package: qgis * add maintainer * further improvements * reflect improvements to qscintilla installation paths * comment out qtkeychain dependency as the package is created * uncomment qtkeychaing dependency, since this package is now created * a comment on webkit * specify versions of dependencies, add variant * fix variant description * fix proj dependency logic * adjust conflicts and dependencies so that one can compile qgis@2 with qt4, python2.7 * minor improvement * fix some build errors, improve dependency specs * qsci python bindings will be build by py-pyqt * cmake variable QSCINTILLA_LIBRARY should point to library itself not the parent folder * turn grass off explicitly, fix typo, turn qspatialite off explicitly * fix typo * specify more cmake options that doesn"t seem to be set properly, and use spack provided pkg-config * fix libzip * fix build issue with sqlite variant, add runtime dependencies * add more runtime python package dependencies * reflect variant name change in sqlite * add maintainer, correct typo * add TODO's * add more versions * improve style * add latest versions * netcdf -> netcdf-c * add variants as shown in cmake config * add conflict: v3.8.1 won't build if qt@5.13: * change preferred version to latest long term release, 3.10.3 * add a zillion of build options * improve style * add descriptions for variants * remove and already implemented compilation tip * add "when" statements for optional dependencies * make flake8 happy * Update var/spack/repos/builtin/packages/qgis/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/qgis/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/qgis/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/qgis/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/qgis/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * convert conflicts to depends_on * undo str conversion for path objects * fix flake8 E131 * fix flake8 E128, E124 * improve style Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-29hpctoolkit: add version 2020.03.01 (#15277)Mark W. Krentel1-10/+14
Add version 2020.03.01, deprecate Blue Gene to 2019.12.28 and earlier, tighten a few dependencies.
2020-02-29Add kraken2 (#15053)Richard Berg1-0/+35
2020-02-29Caliper depends on python3. (#15260)Robert Blake1-1/+3
* Caliper depends on python3. The package needs to be told where to find it. * More flake8 formatting edits. * Change explicit python3 to spec['python'].command.path Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Removing defunct import for flake8 * Flake8 trailing whitespace warning. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-29opam: added versions up to v2.0.6 (#15178)Anthony Scemama1-2/+24
2020-02-29HPX: added v1.4.1 and "stable" branch (#15198)rtohid1-0/+3
2020-02-29MRCPP: New package. (#15201)Roberto Di Remigio1-0/+46
2020-02-29libhio: specify use of external json (#15209)plamborn1-0/+2
libhio has been building it's own json. With this change, libhio will rely on the json installed by spack.
2020-02-29Set http:// in homepage for a few packages (#15275)Glenn Johnson4-5/+5
This PR adds 'http://' to the homepage setting of a few packages that do not have it set. Not having that set can cause problems with some wiki apps when embedding the homepage value into markdown syntax. - bowtie2 - exuberant-ctags - perl-want - samtools
2020-02-28Update tree for v1.8.0 (#15272)George Hartzell1-0/+5
- add version info for v1.8.0 - v1.8.0 adds a new source file, `file.c`, which need to be included in our hardcoded list of objects to link. I discovered this while demonstrating "how easy it is to add a new package to Spack", only to scratch my head when it failed `spack install` but worked when I ran `make` in the stage dir. Finally looked at tree/package.py and it All Became Clear. Perhaps someone should rewrite this to use MakefilePackage, but the Makefile starts off with a bunch of twisty turny "uncomment these lines to run on this platform", so it might not be worth it.
2020-02-28Added package py-versioneer (#15130)Anthony Scemama1-0/+21
* Added package py-versioneer * Update python version * Added python2 to versioneer * Added python2 to versioneer * Update var/spack/repos/builtin/packages/py-versioneer/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Cleaning comments * Removed temporarily @warner as a maintainer, waiting for answer * Removed line Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-28Add version info for the-silver-searcher@2.2.0 (#15270)George Hartzell1-0/+1
2020-02-28OpenMPI nolegacylaunchers: avoid a fork bomb (#15268)Rémi Lacroix1-3/+3
Due to the use of backquotes, the replacement script for mpirun/mpiexec commands would recursively call itself, effectively causing a fork bomb.
2020-02-28gromacs: add v2019.6 (#15267)Christoph Junghans1-1/+2
* gromacs: add v2019.6 * Update var/spack/repos/builtin/packages/gromacs/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-28Fix expect on linux (#15230) (#15269)iarspider1-4/+5
* Fix expect on linux * Flake8
2020-02-28ssht: Correct recipe (#15217)Erik Schnetter2-4/+38
- Tell make about the source code path - Install actual header files, not a wrapper with wrong paths - Add a patch to prevent compiler warnings - Improve description
2020-02-28Add new version of libfabric that builds on macOS (#15254)Seth R. Johnson1-16/+17
* Add new version of libfabric that builds on macOS See https://github.com/ofiwg/libfabric/issues/5339 Fixes https://github.com/spack/spack/issues/15244 Also reduced copy-paste of URLs with `url_for_version`. * Address reviewer feedback
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