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2017-12-14Skip collection of compilers which report an empty version (#6684)scheibelp2-19/+39
Fixes #6200 For compilers that successfully run a version detection script but don't actually return a version, Spack was keeping track of the empty version and then failing when attempting to construct a compiler spec. This skips any attempt to add a compiler entry when no version is reported (but logs when a compiler fails to report a version).
2017-12-14added breakdancer (#6319)Douglas Duckworth1-0/+47
2017-12-14fftw: added version 3.3.7 (#6678)Massimiliano Culpo1-0/+1
2017-12-14misc fixes, changed to EnvironmentModifications (issue #6501) (#6541)Mark Olesen1-11/+52
* Support pruning of vars with Env from_sourcing_file (issue #6501) - Blacklist string literals or regular expressions of environment variables that are to be removed from consideration as being affect by the sourcing of the file. Conversely, whitelist modifications that should not ignored. Whitelisted variables have priority over blacklisting. Eg, EnvironmentModifications.from_sourcing_file ( bashrc blacklist=['JUNK_ENV', 'OPTIONAL_.*'], whitelist=['OPTIONAL_REQUIRED.*'] ) This modification can be used to eliminate environment variables that are not generalized for modules (eg, user-specific variables). * BUG: module prepend-path in wrong order (fixes #6501) * STYLE: module variables in sorted order (issue #6501) - looks nicer and also helps when comparing the contents of different module files. * ENH: remove duplicates from env paths when creating modules (issue #6501) - this makes for a cleaner module environment and helps avoid some unnecessary changes to the environment that are only provoked by redundancies in the PATH. eg, before PATH=/usr/bin after PATH=/usr/bin:/usr/bin:/my/application/bin should only result in /my/application/bin being added to the PATH and not /usr/bin:/my/application/bin Activate via the 'clean' flag (default: False): EnvironmentModifications.from_sourcing_file(bashrc, clean=True,..
2017-12-14Add TIOGA package and optional dependency of Nalu on TIOGA (#6638)Jon Rood2-0/+64
2017-12-14libharu: Make dependencies on zlib and libpng explicit (#6682)Scott Wittenburg1-0/+13
2017-12-13relion: add version and cuda arch variant (#6317)Douglas Duckworth1-1/+20
Add preferred version 2.0.3. Added beta version. Added conflict with gcc versions >= 5 when building with cuda@8 (which is currently the only supported cuda version). Added cuda architecture variant. Added comment about current lack of cuda@9 support.
2017-12-13tasmanian: add new package (#6659)Denis Davydov1-0/+36
2017-12-13CUDA: 9.1 (#6663)Axel Huebl1-1/+4
Add the latest CUDA release, 9.1
2017-12-13py-pysam: adding old version 0.7.7 (#6675)peetsv1-0/+1
2017-12-13SPAdes: add version 3.11.1 (#6668)Eric1-0/+1
2017-12-13 picard: added version 2.13.2 (#6669)David Orman1-0/+1
2017-12-13Ignore log files that appear in root dir with "spack -d install ..." (#6670)Scott Wittenburg1-0/+2
2017-12-12new packages: biopieces and dependencies (#6478)Audrey Thoma47-13/+1784
This also adds the tcl, tk, and libx11 dependencies to ruby. All other changes are new packages.
2017-12-12laghos: inject CXX (#6664)Christoph Junghans1-0/+1
2017-12-12swfft: inject CC/CXX (#6666)Christoph Junghans1-0/+11
2017-12-12xsdk: update xsdk@develop to use sundials, plasma, magma (#6649)Satish Balay1-1/+6
Also update xsdk@0.3.0 to use a fixed version of magma
2017-12-11Add new package minisign (#6644)nshtg1-0/+36
A dead simple tool to sign files and verify signatures. See https://jedisct1.github.io/minisign
2017-12-11libsodium: Update to 1.0.15 (#6643)nshtg1-0/+1
2017-12-11git: Update to 2.15.1 (#6642)nshtg1-0/+5
2017-12-11openssl: Update to 1.0.2n (#6641)nshtg1-1/+2
From 07.12.2017, fixes CVE-2017-3737
2017-12-11Py h5py update (#6635)Brian Van Essen1-0/+2
2017-12-11add -d option for edit command (#6416)becker331-3/+21
* add -d option for edit command and improve suffix extrapolation from '.py' to use glob
2017-12-11intel-parallel-studio: restrict patch to versions > 2016 (#6523)健美猫1-4/+5
Fixes #6522 Patch psxevars.sh and psxevars.csh only when year > 2016. pxevars.csh does not exist for versions before 2017. psxevars.sh does not appear to require this patch for versions before 2017.
2017-12-11Simplified "Environment-Modules" section in getting started guide. (#6410)Massimiliano Culpo1-58/+21
Fixes #2440 The "Getting started" guide should be short and sweet. This commit simplifies the "Environment-Modules" section pruning: - outdated / wrong suggestions as noted in #2440 - uncommon setups that are better treated in a reference guide
2017-12-11bazel: include SPACK_DEBUG_LOG_ID in environment (#6562)Johann Klähn2-2/+12
Fixes #6521. Bazel's build system filters environment variables, including those set by Spack for use by its compiler wrapper. This updates the patch to include the SPACK_DEBUG_LOG_ID variable added in #5837.
2017-12-10disable plasma in xsdk 0.3.0 (#6621)Satish Balay1-1/+0
2017-12-10Fix reference to self.versions in neovim package (#6639)Adam J. Stewart1-1/+1
2017-12-08updates to conduit and ascent packages (new PR) (#6584)Cyrus Harrison3-30/+76
* optional path to use spacks py-site-pkgs, install host-cfg for provenance * add more comments and address review requests * only use st-pkgs-dir when +python * ascent does not need doxygen * capture mpiexec if it exists * added missing import * flake8 fix * default adios variant to False * ascent develop now reqs conduit master * optional path to use spacks py-site-pkgs, install host-cfg for provenance * add more comments and address review requests * only use st-pkgs-dir when +python * ascent does not need doxygen * capture mpiexec if it exists * added missing import * flake8 fix * default adios variant to False * ascent develop now reqs conduit master * conduit: use hdf5 1.8 for wider output compat
2017-12-08Relax restriction on lua version. (#5886)Chris Green1-1/+1
2017-12-08Add NekCEM package to spack (#6509)Thilina Rathnayake1-0/+90
2017-12-08Update the Nekbone package (#6508)Thilina Rathnayake1-21/+36
2017-12-08add restriction to py-setuptools dependency on py-flake8 (#6589)healther1-1/+1
2017-12-08Perl-statistics-descriptive: Create new package (#6588)Eric1-0/+34
2017-12-08Fix AstroPy: Missing Markupsafe (#6630)Axel Huebl1-0/+1
`py-markupsafe` was missing during `spack install` as a build error.
2017-12-08Add: Py-Plotly (#6628)Axel Huebl4-0/+42
* Add: Py-Plotly The requirements of py-plotlit are rather strict fixed to specific versions, so I did not add an "upper versions" `:` to the constrains. See https://github.com/plotly/plotly.py/blob/master/requirements.txt * Py-Requests, Py-Six, Py-Pytz: Older Versions Add two older versions of requests, pytz and six for plotly.
2017-12-08Fix in download url for package libaio (#6616)Paschalis Korosoglou1-1/+1
2017-12-08Update zsh to 5.4.2 (#6609)nshtg1-1/+2
2017-12-08r-tidycensus: Create new package. (#6595)lingnanyuan1-0/+53
2017-12-08r-rgdal: Create new package. (#6593)lingnanyuan1-0/+47
2017-12-08r-tigris: Create new package. (#6591)lingnanyuan1-0/+48
2017-12-08Update openSSL to 1.0.2m/1.1.0g (#6596)nshtg1-2/+4
2017-12-08Update openSSH to 7.6p1 (#6598)nshtg1-1/+2
2017-12-08Update tmux to 2.6 (#6597)nshtg1-1/+2
2017-12-08Updated hash for v1.0 tag of Laghos (#6626)Tzanio Kolev1-1/+1
2017-12-08Package 'openjpeg': set INSTALL_NAME_DIR on MacOS for old versions. (#6603)Sergey Kosukhin2-0/+18
2017-12-08r-rhtslib: added build dependency on autoconf (#6627)Paschalis Korosoglou1-0/+1
2017-12-08py-cogent: Create new package (#6624)Eric1-0/+37
2017-12-08dealii: update boost dependency (#6586)Denis Davydov2-22/+57
(i) blacklst 1.65.0 due to issues on Ubuntu with gcc 5.4.0 (ii) add a patch for 1.65.1 to fix serialization (iii) simplify boost's depends_on()
2017-12-08py-htseq: Create new package. (#6623)lingnanyuan1-0/+42
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