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2019-11-20mirror bug fixes: symlinks, duplicate patch names, and exception handling ↵Paul Ferrell4-17/+24
(#13789) * Some packages (e.g. mpfr at the time of this patch) can have patches with the same name but different contents (which apply to different versions of the package). This appends part of the patch hash to the cache file name to avoid conflicts. * Some exceptions which occur during fetching are not a subclass of SpackError and therefore do not have a 'message' attribute. This updates the logic for mirroring a single spec (add_single_spec) to produce an appropriate error message in that case (where before it failed with an AttributeError) * In various circumstances, a mirror can contain the universal storage path but not a cosmetic symlink; in this case it would not generate a symlink. Now "spack mirror create" will create a symlink for any package that doesn't have one.
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.
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