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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>
2020-02-20Add decentralized-internet package (#15129)Andrew Kamal1-0/+14
* Create package.py * Update package.py * Update package.py * Update package.py * Update package.py * Update var/spack/repos/builtin/packages/decentralized-internet/package.py Commit suggestion Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-20Package hashing: fix detection of directives (#14763)Peter Scheibel1-0/+27
The hashing logic looks for function calls that are Spack directives. It expects that when a Spack directive is used that it is referenced directly by name, and that the directive function is not itself retrieved by calling another function. When the hashing logic encountered a function call where the function was determined dynamically, it would fail (attempting to access a name attribute that does not happen to exist in this case). This updates the hashing logic to filter out function calls where the function is determined dynamically when looking for uses of Spack directives.
2020-02-20libf77zmq (#15125)Anthony Scemama1-0/+38
* libf77zmq * Cleaning mkdirp * Removed install function * Renamed to f77-zmq * Fixed Flake8 * Fixed Flake8
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