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2020-02-27hpcviewer: add version 2020.02Mark W. Krentel1-0/+6
2020-02-27New package: XCFun (#15199)Roberto Di Remigio1-0/+37
2020-02-27Add new timeout fetch_optionMichael Kuhn2-4/+11
This allows packages to override the global connect_timeout.
2020-02-27Generalize curl_options into fetch_optionsMichael Kuhn1-17/+15
This allows us to support higher-level concepts such as 'cookie' and 'timeout' without users having to specify curl options.
2020-02-27release sz 2.1.8.3 (#15250)Sheng Di1-0/+1
2020-02-27new package: py-cnvkit and py-pomegranate (#15222)Glenn Johnson2-0/+51
The py-pomegranate package is a dependency of py-cnvkit
2020-02-27new package: py-pycifrw (#15224)Glenn Johnson1-0/+18
2020-02-27new package: py-pycosat (#15225)Glenn Johnson1-0/+20
2020-02-27New packages: py-pymc3 and py-arviz (#15226)Glenn Johnson2-0/+55
This PR adds py-pymc3 and py-arviz as a dependency.
2020-02-27Added go 1.14 (#15249)Paul1-0/+1
2020-02-27arpack-ng: ILP64 support (#15103)Kai Torben Ohlhus1-1/+5
Details about ILP64 support: `INTERFACE64=1` are described on the [ARPACK-NG GitHub website](https://github.com/opencollab/arpack-ng).
2020-02-26f77-zmq: add version 4.3.2 (#15204)Anthony Scemama1-1/+3
Version 4.3.1 only works with Python3. Version 4.3.2 also works with Python2. These constraints were not listed before and are added by this commit.
2020-02-26py-git-review: add version 1.28 (#15203)Andreas Baumbach1-0/+1
2020-02-26AWS ParallelCluster: add version 2.6.0 (#15240)Luca Carrogu1-1/+2
2020-02-26h5py: add version 2.10.0 (#15205)genric1-1/+3
Also add dependency on py-cached-property
2020-02-26SQLite shouldn't be enabled by default for TAU package (#15228)Kevin Huck1-1/+5
Also Adding conflict for SQLite and ADIOS2 for older TAU releases
2020-02-26Default to +termlib for ncurses for LLVM (#15039)Seth R. Johnson1-1/+1
LLVM is the only package that explicitly sets the "termlib" variant of ncurses and it specifies +termlib. ncurses defaults to ~termlib; if a package depends on LLVM and ncurses, there is a concretizer bug that incorrectly detects a constraint conflict (see #267). Setting +termlib as the default is a stopgap measure to avoid this conflict. If other packages were to explicitly request ~termlib in the future, the same issue would come up again (and could not be resolved by adjusting the default of "termlib"). Setting +termlib on ncurses moves some symbols into a separate "libtinfo". Not all packages may be able to detect libtinfo properly so may require an update; vim, samtools, and libedit have been updated to use ncurses+termlib (in the case of libedit, the only necessary action was to add a newer version where the build system was updated to check libtinfo).
2020-02-26Basis set exchange command-line tool (#15126)Anthony Scemama1-0/+33
* Flake8 OK * Update var/spack/repos/builtin/packages/py-basis-set-exchange/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-basis-set-exchange/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Added missing dependencies proposed by @adamjstewart * Without py-versioneer * Added py-versioneer * Python2 for bse * Python build error * Update var/spack/repos/builtin/packages/py-basis-set-exchange/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Removed py-versioneer, according to @adamjstewart Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-25qrupdate: ILP64 support (#15104)Kai Torben Ohlhus1-6/+20
- When compiling qrupdate with `FFLAGS=-fdefault-integer-8` it can be perfectly used for larger problem dimensions. - Improved the readability of the file with the added rules.
2020-02-24Adding ADIOS2 and SQLite3 output support to TAU. Also fixing MPI include ↵Kevin Huck1-3/+17
and library paths. (#15189) Setup package to use MPI the way Spack recommends, and remove extra iowrapper option from configure Making flake happy
2020-02-24Update of OpenFOAM package.py (#15190)OliverPerks1-2/+4
2020-02-24suite-sparse: add version 5.7.1 (#15195)Kai Torben Ohlhus1-0/+1
Release notes: https://github.com/DrTimothyAldenDavis/SuiteSparse/releases/tag/v5.7.1 Version 5.7.0 was an incomplete release.
2020-02-24update flecsi and legion package.py (#15159)ktsai72-19/+35
* update flecsi and legion package.py * comment out a conflict * update to use extend
2020-02-24add new package : agrep (#15165)darmac1-0/+23
* add new package : agrep * agrep: move binary to bin/
2020-02-24Added extra versions of OCaml (#15177)Anthony Scemama1-0/+11
* Aded extra versions for OCaml * Added maintainer
2020-02-24sz: update to version 2.1.8.1 (#15154)Robert Underwood1-12/+81
The newer versions of SZ now uses CMake to build.
2020-02-24Update py-bx-python package (#15175)Glenn Johnson2-4/+29
* Update py-bx-python package - add update to py-bx-python - switch to pypi downloads - set dependencies * Update var/spack/repos/builtin/packages/py-bx-python/package.py I had initially pulled version 0.8.6 and then updated that to 0.8.8 but missed the change in the python specs between those two versions. Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Fix version 0.7.4 - set dependency on python2 - add dependency on py-python-lzo - add py-python-lzo package - set py-numpy dependency to correspond to latest version that works with python2 * Add constraint for py-six dependency * Update var/spack/repos/builtin/packages/py-bx-python/package.py Ah, I had that `when` clause in and then took it out as it did not seem to be needed. I guess it is always better to be more explicit. Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Remove py-numpy constraint Let the concretizer catch the conflict with python2 and py-numpy versions. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-23Update py-rseqc package (#15176)Glenn Johnson1-4/+10
This PR depends on #15175 - add updated version - set depedencies
2020-02-23add new package : batctl (#15160)darmac1-0/+24
* add new package : batctl * batctl: move binary to bin/
2020-02-23add new package : bubblewrap (#15162)darmac1-0/+28
* add new package : bubblewrap * bubblewrap: remove some comment in package.py
2020-02-23py-setproctitle: Add new package (#15170)Michael Kuhn1-0/+18
2020-02-23Separate HepMC2 and HepMC3 build recipes; Python3 support for HepMC3 (#15147)iarspider1-6/+28
* Fixes & additional variant(s) for HepMC3 * Syntax * Restore recipe for HepMC2 * Remove FIXME * Update package.py * Apply suggestions from code review Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-23Fix silex build (#15172)Seth R. Johnson1-10/+18
* Mark silo+silex as requiring QT4 * Add missing readline dependency to silo * Fix silo QT4 usage and verify silex works on mac ``` -- darwin-mojave-x86_64 / clang@11.0.0-apple -------------------- 7gdcud4 silo@4.10.2+fortran~mpi patches=7b5a1dc2a0e358e667088d77e7caa780967fa8ea60be89c44986605df9990abe +pic+shared+silex pk3wbwd hdf5@1.10.6~cxx~debug~fortran+hl~mpi+pic+shared+szip~threadsafe slsy6ko libszip@2.1.1 xj36ejk zlib@1.2.11+optimize+pic+shared u4662xx libx11@1.6.4 3lpe6j3 qt@4.8.7~dbus~examples~framework freetype=none ~gtk~opengl patches=03f9893882c63a9a9617d9ecab9caf80661c96df13f596a9b24fc4579490144a,a4f37427b34d88df6a6adc16e1e6c805087d4f3a7c658e1797450b0912fcbf5d,f17e0b5fb1f43bccadf7298533eca57294f4acab11ed83b176c61c441f745c19 ~phonon+shared~sql~ssl~tools~webkit shdhdbh glib@2.56.3~libmount patches=c325997b72a205ad1638bb3e3ba0e5b73e3d32ce63b2d0d3282f3e3a2ff4663c tracing=none msyeqht gettext@0.20.1+bzip2+curses+git~libunistring+libxml2+tar+xz ysmjykg bzip2@1.0.8+shared w354vrb libxml2@2.9.9~python jg6ekuh libiconv@1.16 b7n722h xz@5.2.4 zbgxvxi ncurses@6.1~symlinks~termlib 2e6sifw tar@1.32 7yg7qah libffi@3.2.1 zg55iyu pcre@8.43~jit+multibyte+utf zqrlxlz perl@5.30.0+cpanm+shared+threads un7wzvl python@3.7.4+bz2+ctypes+dbm~debug+libxml2+lzma~nis~optimizations patches=210df3f28cde02a8135b58cc4168e70ab91dbf9097359d05938f1e2843875e57 +pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tix~tkinter~ucs4+uuid+zlib l4gxq46 expat@2.2.9~libbsd 3t4dwsv gdbm@1.18.1 h2bjtz2 readline@8.0 ugvknwc openssl@1.1.1d+systemcerts hsmq6ou sqlite@3.30.1~column_metadata+fts~functions~rtree lpfob23 icu4c@65.1 cxxstd=11 lf66vbr inputproto@2.3.2 afovyhg libjpeg-turbo@2.0.3 5dgw556 libmng@2.0.3 build_type=RelWithDebInfo 3z4lw2w lcms@2.9 flleuyu libtiff@4.0.10 67tigfp libpng@1.6.37 ```
2020-02-22Automatically run LLDB codesign script on mac (#15169)Seth R. Johnson1-5/+12
Newer versions of LLVM provide a one-line command to set up LLDB code signing. Now the build will abort only if this command fails. https://lldb.llvm.org/resources/build.html#code-signing-on-macos
2020-02-22add new package : brltty (#15161)darmac1-0/+30
2020-02-22add new package : audit-userspace (#15163)darmac1-0/+25
2020-02-22add new package : apachetop (#15164)darmac1-0/+27
2020-02-22add new package : advancecomp (#15166)darmac1-0/+24
2020-02-22add new package : acpid (#15167)darmac1-0/+28
2020-02-22lighttpd : fix pcre depends (#15168)darmac1-0/+2
2020-02-21sundials: add version 5.1.0 and trilinos variant (#15155)Cody Balos1-5/+50
* sundials: add version 5.1.0 and trilinos variant * sundials: add version 5.1.0 and trilinos variant
2020-02-21Changes necessary to build lbann@develop (#15153)Robert Blake1-2/+3
* Necessary changes to get lbann develop to compile. * Reformatting for flake8 * More flake8 changes. * Removing redundant clara dependency.
2020-02-21shtools: New package (#15133)Erik Schnetter1-0/+47
* shtools: New package * shtools: Convert to MakefilePackage, use Spack's generic compiler flags * shtools: Make function location explicit
2020-02-21Add extra version of py-jsonschema (#14993)iarspider2-3/+34
* Add extra version of py-jsonschema * Update dependencies * Update dependencies + flake8 * Add py-pyrsistent package * Update package.py * Update var/spack/repos/builtin/packages/py-jsonschema/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py * Update package.py * Apply suggestions from code review Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Apply suggestions from code review Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-21amrex: New version 20.02 (#15132)Erik Schnetter1-0/+1
2020-02-21Updating raja versions. (#15148)Robert Blake1-0/+3
2020-02-21Add clang compiler (#15152)Tim Haines1-0/+2
2020-02-21QE+QMCPACK Converter Update February 2020 (#15135)Nichols A. Romero2-8/+14
* Add a variant to QE that suppresses upstream patching. Need in order to do ddependency patching. * QE variant fails to build often. Set default variant to False as a user friendly change. * QMCPACK converter patch collides with internal QE patches. Deactivate internal patches when performing dependency patching. * Clearer description of QE patch variant that is also flake8 compliant.
2020-02-21Disable qt3d when opengl is disabled (#15149)Seth R. Johnson1-4/+11
* Disable qt3d when opengl is disabled * Remove `-skip qtquick3d` unless QT 5.14 Found while checking build of qt 5.14.
2020-02-21Add extra version of py-sqlalchemy (#15109)iarspider1-0/+8
* Add extra version of py-sqlalchemy * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py * Apply suggestions from code review Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py * Update package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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