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2019-11-20ampliconnoise: Change return type of function. (#13766)t-karatsu2-7/+72
* ampliconnoise: Change function type. * ampliconnoise: updated api call to setup run environment
2019-11-20find-circ: a new package. (#13767)健美猞猁1-0/+34
* find-circ: a new package. * flake8.
2019-11-20miranda: a new package. (#13768)健美猞猁1-0/+16
2019-11-20tensorflow-serving-client: add new package (#13771)Figroc Chen1-0/+19
2019-11-20bpp-suite: Clarify 'isinf' function's namespace. (#13777)t-karatsu2-0/+94
2019-11-20Fix for overlong shebang in valgrind (#13779)David Hows1-0/+8
Fix for some overlong shebangs in valgrind. Borrowed from verrou/package.py
2019-11-20py-numexpr3: fix version (#13781)noguchi-k1-1/+1
2019-11-20mpich: Add 3.3.2 (#13790)Ken Raffenetti1-0/+1
2019-11-20genrich: new package at 0.6 (#13791)Justin S1-0/+19
2019-11-20sentieon-genomics: add 201808.07 (#13794)Justin S1-0/+1
2019-11-20Add old version of py-gast (#13806)Adam J. Stewart1-1/+1
2019-11-20Add py-google-pasta package (#13807)Adam J. Stewart1-0/+18
2019-11-20Add new py-grpcio package (#13808)Adam J. Stewart1-0/+30
2019-11-20Add c-ares 1.15.0 (#13809)Adam J. Stewart1-2/+3
2019-11-20Add old versions and missing dependencies to py-protobuf (#13811)Adam J. Stewart1-4/+8
2019-11-20Add old version of jdk (#13805)Adam J. Stewart1-7/+14
* Add old version of jdk * setup_environment -> setup_build_environment
2019-11-20Added package for Clara command line parser (#13763)Brian Van Essen1-0/+40
* Added package for Clara command line parser
2019-11-20Features/expand microarch for aarch64 (#13780)t-karatsu4-0/+117
* Add process to determine aarch64 microarchitecture * add microarchitectures for thunderx2 and a64fx * Add optimize flags for gcc on aarch64 family processors thunderx2 and a64fx. * Add optimize flags for clang on aarch64 family processors thunderx2 and a64fx * Add testing for thunderx2 and a64fx microarchitectures
2019-11-19add MAX_CPU_COUNT variant to HPX package (#13769)albestro1-0/+10
* add MAX_CPU_COUNT variant to HPX package * compatibility with python2 * correct variant description Co-Authored-By: Mikael Simberg <mikael.simberg@iki.fi> * add maintainers list
2019-11-19zlib: use setup_build_environment for build env (#13786)George Hartzell1-3/+3
zlib was using the deprecated setup_environment call. Now it's using the current setup_build_environment. (noticed this in some `spack -d` output)
2019-11-18add more legion version and expose more flecsi options (#13741)ktsai72-24/+90
* add more legion version and expose more flecsi options * formatting * update version pointing to master to master * fix indentation * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py * use self.run_tests Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py * Update package.py * Update package.py * Update package.py
2019-11-18binary distribution: relocate text files properly in relative binaries (#13578)Greg Becker3-17/+37
* Make relative binaries relocate text files properly * rb strings aren't valid in python 2 * move perl to new interface for setup_environment family methods
2019-11-18py-rnacocktail: a new package. (#13761)健美猞猁1-0/+25
* py-rnacocktail: a new package. * flake8. * Add build-time dependencies.
2019-11-18fix libxml2 url (#13770)albestro1-1/+1
http to https
2019-11-18environment-modules: add version 4.4.0 (#13772)Xavier Delaruelle1-1/+9
2019-11-18py-xattr: fix a package that was pointing to a fork (#13685)Massimiliano Culpo1-5/+6
The package now points to the official github repository for master and to PyPI for release versions.
2019-11-17Update scalpel package.py (#13746)oracleLee1-1/+2
* Update package.py Update scalpel version 0.5.4 * Update package.py
2019-11-17update to add ascent 0.5.0 release (#13709)Cyrus Harrison6-85/+155
* fix metis src dl url * update ascent, vtk-h and vtk-m recipes * update conduit package * fix vtk-m shas * mfem conduit fix * use vtk-h develop * fix issue with stripped include paths in mfem * more metis fixes * simpler fix for mfem conduit include issue * finish mfem changes * pin to cmake 3.14, since we hit cuda issues with 3.15 * add rtd theme as dep for ascent * add vtk-h 0.5.0 release, update ascent to use it * add ascent 0.5.0 release * fix cmake pin to allow all vers of 3.14 * fix format string error in mfem pkg * review fixes for mfem pkg * review fixes for vtk-h and vtk-m packages * address review comments for ascent pkg * changing default off of develop broke downstream use * revert prefed
2019-11-17openPMD-api: 0.10.0 (#13750)Axel Huebl1-0/+1
Add latest release and first to be tagged by number in Spack, version 0.10.0.
2019-11-16guile package: Handling the threads option. (#13730)Hector Martinez-Seara1-4/+17
* guile package: Handling the threads option. Currently guile by default tries to compile its thread variant. However, the threaded version can only be compiled if bdw-gc is compiled with some threads support. Currently, the default compilation of the bdw garbage collector is compiled without any thread support resulting in a compilation error. I have changed the the default guile compilation to the non-threaded version. I have also added the appropiated options for the bdw-gc compilation in case the user prefers the threaded variant. * guile package(flake8): fixed identation issues
2019-11-16revbayes: add new versions (#13760)Nick Booher1-2/+17
2019-11-15Fix for issue #13754 (#13755)Tim Fuller1-2/+3
* remove reference to `spack.store` in method definition Referencing `spack.store` in method definition will cache the `spack.config.config` singleton variable too early, before we have a chance to add command line and environment scopes.
2019-11-15Document use of the maintainers field (#12270)Adam J. Stewart2-1/+20
* Document use of the maintainers field * Use fake GitHub usernames * GitHub action is not automatic yet
2019-11-14Config option to allow gpg warning suppression (#13743)Greg Becker4-3/+17
Add a configuration option to suppress gpg warnings during binary package verification. This only suppresses warnings: a gpg failure will still fail the install. This allows users who have already explicitly trusted the gpg key they are using to avoid seeing repeated warnings that it is self-signed.
2019-11-14xsdk@0.5.0 (#13682)Satish Balay3-25/+86
Update: hypre@2.18.2 mfem@4.0.1-xsdk superlu-dist@6.1.1 trilinos@12.18.1 - dtk-3.1 petsc@3.12.1 dealii@9.1.1 pflotran@xsdk-0.5.0 alquimia@xsdk-0.5.0 sundials@5.0.0 plasma@19.8.1 magma@2.5.1 amrex@19.08 slepc@3.12.0 omega-h@9.29.0 strumpack@3.3.0 pumi@2.2.1 tasmanian@7.0 phist@1.8.0 New: ginkgo@1.1.0 py-libensemble@0.5.2 precice@1.6.1 butterflypack@1.1.0 Add variants: ginkgo libensemble precice butterflypack strumpack trilinos tasmanian: use ~openmp only on OSX precice: disable on OSX enable sundials+superlu-dist sundials+superlu-dist requires OpenMP 4.5+ (so enable only for gcc@6.1+) enable mfem+sundials enable sundials+petsc+superlu_dist remove hypre~internal-superlu petsc: build with +batch on cray precice: use ~petsc on cray libensemble: add as runtime dependency for PYTHONPATH
2019-11-14z3: bugfix about python dependency and fallthrough annotation. (#13713)t-karatsu3-2/+30
* z3: * Fixed python dependency to always be required. * bugfix about fallthrough annotation. * z3: Add patch for before ver.4.4.1. * Update var/spack/repos/builtin/packages/z3/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-14Mark conflicts between newer packages and Intel 14 compilers (#13729)Seth R. Johnson4-0/+11
* Mark compiler/version conflict for CMake Intel 14 lacks some C++11 features needed to compile new versions of cmake. ``` /tmp/s3j/spack-stage/spack-stage-cmake-3.15.5-46lgp4ybhopy2p4rr66rxnew5iaddvmg/spack-src/Source/ cm_static_string_view.hxx(28): error: expected an operator friend static_string_view operator"" _s(const char* data, size_t ^ ``` * Mark compiler/version conflict for icu4c With Intel 14.0.4 on Linux for icu4c 60.1 and higher: ``` locid.cpp(1156): error #1140: a using-declaration may not name a constructor or destructor using KeywordEnumeration::KeywordEnumeration; ``` * Mark compiler/version conflict for nasm Error installing `nasm@2.14.02%intel@14.0.4`: ``` In file included from nasmlib/crc64.c(35): ./include/nasmlib.h(116): error: expected a ";" fatal_func nasm_assert_failed(const char *, int, const char *); ``` * Mark compiler/version conflict for bison Installing `bison@3.4.2%intel@14.0.4`: ``` In file included from /tmp/s3j/spack-stage/spack-stage-bison-3.4.2- uzjszv4owvqsymjpxtxvvegfavc6k5my/spack-src/lib/quotearg.c(33): /tmp/s3j/spack-stage/spack-stage-bison-3.4.2-uzjszv4owvqsymjpxtxvvegfavc6k5my/spack-src/lib/ xalloc.h(51): warning #303: explicit type is missing ("int" assumed) extern _Noreturn void xalloc_die (void); ``` * Mark compiler/version conflict for icu4c With `icu4c@60.1%intel@16.0.4` and `icu4c@64.1%intel@16.0.4`: ``` In file included from ucurr.cpp(26): static_unicode_sets.h(130): error #913: invalid multibyte character sequence {POUND_SIGN, u'£'}, ^ ``` * Change conflict comments into messages
2019-11-14py-matplotlib only needs backports when ^python@:2 (#13712)George Hartzell3-3/+3
* py-matplotlib only needs backports when ^python@:2 This implements @scheibelp's suggestion in #13711. py-matplotlib should only depends_on py-backports-functools-lru-cache when it's using a python that actually *needs* it. See #13711 for details. * Don't depend_ons py-enum34 unless python@:3.3 * Tighten up enum34 dependency @adamjstewart cracked open the setup.py files and suggested a tighter dependency for py-enum34. 1.4 and 1.5 only require it for pythons before 3.4, 1.3 requires it unconditionally. So...., we'll do the same. * Remove conflict on python 3.4 from enum34 at @adamjstewart's request see PR notes
2019-11-14add boost dependency to stat package (#13735)Gregory Lee1-0/+2
2019-11-14update to v0.6.4 (#13737)xfzhao1-0/+3
2019-11-14Update DMTCP package to v2.6.0 (#13739)Emir İşman1-1/+2
2019-11-14Removed github repository and develop version from dataspaces package as it ↵Nicholas Sly1-2/+0
is no longer present/accessible. (#13740)
2019-11-14update vsearch (#13736)xfzhao1-0/+2
2019-11-14hwloc: added 'master' version pointing at the HEAD of the master branch (#13731)Massimiliano Culpo1-4/+6
2019-11-14new package Qscintilla (with python bindings via py-pyqt ) (#12793)Sinan3-3/+188
* qscintilla_with_python_bindings_disabled * pyqt5 with variant +qsci to compile qscintilla python bindings * fix a dyn linking issue for Qsci python module * fix a bug * fix bug: use sip provided by py-pyqt5 * fix typo * tidy up, make designer * tidy up * fix designer build issue, set env for designer plugin * tidy up * tidy up * minor improvements * improve style * build Qscintilla python bindings here * make qsci config option variant dependent * get rid of commented out code * improvements: add resource for qscintilla, improve config_args * flake8: spaces, blank lines etc * flake8: fix long lines * Update var/spack/repos/builtin/packages/py-pyqt4/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyqt4/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyqt4/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/qscintilla/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * dont install source tree under prefix * remove duplicate line * use os.path.join instead of + * separate build and run environment setups * flake8 * Update var/spack/repos/builtin/packages/py-pyqt5/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyqt5/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyqt5/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * fix rsrc path * use python_include_dir * use "with working_dir" * Update var/spack/repos/builtin/packages/py-pyqt4/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyqt5/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyqt5/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyqt5/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/qscintilla/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyqt4/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pyqt4/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * flake8
2019-11-14package/geopm: Added versions 1.0.0 and 1.1.0 (#13721)Matthias Maiterth1-17/+28
* package/geopm: Added versions 1.0.0 and 1.1.0 Added changes for 1.1.0 and 1.0.0 in this patch. Patch for 1.0.0 was previously not merged. variant for hwloc removed since that is not a dependency since 0.5.1 and variant('hwloc', when=:0.5.1 is not supported afaik. made depends_on versions more explicit. * package/geopm: removed 1.0.0 release candidates 1 and 2.
2019-11-14Adding final bug-releases for the gromacs-2016 and -2018 and Plumed (#13715)Hector Martinez-Seara2-3/+12
* Adding final bug-releases for the gromacs-2016 and -2018 * Added newer versions of plumed and libmatheval not a dependency >v2.5 * plumed package: chamge name git branch to master
2019-11-14Fix libbsd on Intel compilers (#13720)Seth R. Johnson2-0/+13
Libbsd assumes GCC-defined compiler macros: ``` In file included from nlist.c(44): local-elf.h(238): catastrophic error: #error directive: Unknown ELF machine type #error Unknown ELF machine type ^ ``` The `__amd64__` and `__x86_64__` macros should be equivalent, but the latter is defined by intel.
2019-11-13symlink relativization: determine target relative to the link directory (#13710)Peter Scheibel1-3/+3
when making a package relative, relocate links relative to link directory rather than the full link path (which includes the file name) because `os.path.relpath` expects a directory.
2019-11-13Added "file" package and added missing depenency to VIM (#13705)sknigh6-0/+63
* Added "file" package and added missing depenency to Vim * added which and grep * Added gzip * added missing dependency to gmake
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