Commit graph

10985 commits

Author SHA1 Message Date
Matthias Wolf
3c6d484150 enh: buildcache list should behave similar to find (#10052)
The current output of buildcache list is very verbose and I feel like
some details are getting lost. By making the output similar to find, I
think users will be able to get a better overview of what is stored in
the cache.
2019-01-11 13:57:10 -08:00
Dan Ibanez
f9967d2f6f Omega_h changed its URL (#10315)
From https://github.com/ibaned/omega_h
To https://github.com/SNLComputation/omega_h
2019-01-11 13:29:56 -06:00
Satish Balay
4cbeec07a0 omega-h: fix CMAKE_BUILD_TYPE: breaks with spack deafult 'RelWithDebInfo' (#10297) 2019-01-11 10:08:28 -08:00
Denis Davydov
f4bda74b30 dealii: fix concretization of xsdk package (#10288)
* dealii: fix concretization of xsdk package

* tests: add concretization tests for deal.II and xSDK, which are often broken due to limitations in the concretizer

* use pytest.mark.parametrize
2019-01-11 10:07:28 -08:00
Brian Van Essen
9102cd5790 Updating LBANN and related packages (#10305)
Updated LBANN, Hydrogen, and Aluminum to not require CUDA-aware MPI
even when using CUDA.  Fixed small bugs within both LBANN and Hydrogen
packages.  Added requirements for breathe and cereal to LBANN.
2019-01-10 17:10:11 -08:00
Mark W. Krentel
08c4b9d47a boost: fix the bjam build for Cray (#10295)
Fixes issues #9613 and #3209.

Remove the spack wrapper directories from PATH for the bootstrap step.
This was breaking the build for Cray (and other cross-compile) because
bjam was built for the BE and died on SIGILL on the FE.

This only affects building bjam.  The boost libraries are still built
the normal spack way with the spack wrappers.
2019-01-10 16:34:05 -08:00
Mark W. Krentel
7e8b17b177 hpctoolkit: variants to build for cray and blue gene (#10223)
Add variants 'cray' and 'bgq' to build for Cray and Blue Gene compute
nodes.  These systems need separate options to find the MPI compiler
for hpcprof-mpi.
2019-01-10 12:50:58 -08:00
Cody Balos
60a44d5155 sundials: add version 4.0.1 and remove 4.0.0-dev series (#10306)
The 4.0.1 release is the culmination of the SUNDIALS 4.0.0 preview releases,
i.e. the 4.0.0-dev versions. As such, the 4.0.0-dev releases are now
being removed.
2019-01-10 14:47:48 -06:00
Eric
b25f27d442 py-checkm-genome: Add version 1.0.13 (#10304)
* py-checkm-genome: Add version 1.0.13

* py-checkm-genome: Add missing py-backports-functools-lru-cache dependency

* py-checkm-genome: Fix missing whitespace
2019-01-10 12:28:07 -06:00
Jon Rood
12cf4eb734 Explicitly listing blas and lapack sections in site.cfg for numpy (#8708)
* Explicitly listing blas and lapack sections in site.cfg for numpy when using netlib-lapack so that scipy can find them as well.

* Reducing code to use a function call instead of copying and pasting.

* Fixing flake8 errors.

* Fixing python 3.6 error when site.cfg lists library_dirs multiple times.

* Formatting.

* Verifying blas and lapack are enabled before writing to site.cfg.

* Fixing flake8 errors.

* Fixing conflicts since this package file has been updated.

* Fixing flake8 stuff.

* Handling blas and lapack variants for netlib-lapack in site.cfg for py-numpy.

* Don't write netlib-lapack site.cfg file if no blas or lapack variants enabled in py-numpy.

* Removing redundant if statement.

* Fixing mistake in py-numpy site.cfg generation.

* Separating blas and lapack further in site.cfg for netlib-lapack in py-numpy.
2019-01-10 11:14:24 -06:00
Owen Solberg
586fe32166 update r-rcpp package with new versions (#10301) 2019-01-10 09:07:09 -06:00
Adam J. Stewart
72a41a4918 spack versions: only list safe versions (#10004)
* spack versions: only list safe versions
* Add unit tests for spack versions -s
2019-01-10 00:32:47 -08:00
Greg Becker
450b0e3059 Allow combinatorial projections in views (#9679)
Allow customizing views with Spec-formatted directory structure

Allow views to specify projections that are more complicated than
merging every package into a single shared prefix. This will allow
sites to configure a view for the way they want to present packages
to their users; for example this can be used to create a prefix for
each package but omit the DAG hash from the path.

This includes a new YAML format file for specifying the simplified
prefix for a spec in a view. This configuration allows the use of
different prefix formats for different specs (i.e. specs depending
on MPI can include the MPI implementation in the prefix).
Documentation on usage of the view projection configuration is
included.

Depending on the projection configuration, paths are not guaranteed
to be unique and it may not be possible to add multiple installs of
a package to a view.
2019-01-09 17:39:35 -08:00
Greg Becker
f5bb93c75b tutorial basics section: fix gcc install version (#10298) 2019-01-09 17:37:37 -06:00
Satish Balay
8ca674a574 petsc: fix petsc+debug to not reset COPTFLAGS - i.e use configure defaults '-g' (#10296) 2019-01-09 17:36:28 -06:00
Daryl W. Grunau
d1bb9caba4 eospac version bump to 6.4.0beta.4 (#10294) 2019-01-09 15:57:05 -06:00
Mark W. Krentel
1b991f9385 elfutils: option to install elf.h header file (#10185)
* elfutils: option to install elf.h header file

Add variant 'elfh' (default False) to install the elf.h header file to
the include directory.  This provides access to a newer version of
elf.h and allows an elf application to build with the same elf.h that
libelf.so was built with.

Add version 0.175.

* Drop the variant 'elfh' and always install elf.h instead.
2019-01-09 14:40:15 -06:00
Eric
b4dc73bed4 py-pyyaml: Add version 3.13 (#10293) 2019-01-09 13:39:34 -06:00
Simon Flood
0b2314bbc4 R: add version 3.5.2 (#10292) 2019-01-09 12:19:58 -06:00
Andreas Baumbach
730c629b09 New package: git-fat-git (#10266)
* new package: git-fat

* backport of rsync -> older versions no longer available

Change-Id: I3a41f17df0f88ca11e08ea6fd2f2d381435e0f09

* fix legal stuff and use new git attribute

Change-Id: Ice156dfe8ad4137a861f7b2938ee92f4024142be

* use date as version number rather than hash

Change-Id: Ib537659e368f69124895306d6a6ac0c5e36061a7

* only use the date once

Change-Id: I2592fa28aaa53fed949ddc82959d712ff3f6f752
2019-01-09 09:07:12 -06:00
marvinbernhardt
7571787a3a gromacs: added simd and rdtscp variants + version 2019 (#9931) 2019-01-09 10:39:05 +01:00
Axel Huebl
efe3e905a3 OpenMPI: Add Development Version (#10257)
Add the development version of OpenMPI from the git repo
in `master`.
2019-01-08 20:48:55 -06:00
sknigh
e3a2c94d60 Updated fish to 3.0.0 (#10286) 2019-01-08 20:47:52 -06:00
Owen Solberg
c48b0a13b9 bug fix: copy permissions when staging (#10285)
Fixes #10284

#10152 replaced shutil.move with llnl's copy and copy_tree for
resources. This did not copy permissions so led to later failures
if an executable was copied (e.g. a configure script). This uses
install/install_tree instead, which preserve permissions.
2019-01-08 17:56:16 -08:00
Srinath Vadlamani
4fdd3b6794 Armcompiler (#9840)
* Initial compiler support

* added arm.py

* Changed licence to Arm suggested header

* Changed licence to the same as clang.py
Main author of file is Nick Forrington <Nick.Forrington@arm.com>
Minor changes by Srinath Vadlamani <srinath.vadlamani@arm.com>

* compilers: add arm compiler detection to Spack

- added arm.py with support for detecting `armclang` and `armflang`

Co-authored-by: Srinath Vadlamani <srinath.vadlamani@arm.com>

* Changed to using get get_compiler_version

* linking to general cc for arm compiler

* For arm compiler add CFLAGS to use compiler-rt rtlib.

* Escape for special characters in rexep

* Cleaned up for Flake8 to pass.

* libcompiler-rt should be part of the LDFLAGS not CFLAGS

* fixed m4 when using clang to used LDFLAGS.  Fixed comments for arm.py to display compiler --version output with # NOAQ for flakes pass.

* added arm compilers

* proper linked names
2019-01-08 16:31:25 -08:00
Owen Solberg
ee64db4764 r-ape: new versions (#10258)
* updated versions for r-ape

* added type=('build', 'run') to r dependency
2019-01-08 18:15:03 -06:00
Owen Solberg
aa20724519 r-cowplot: new versions, more specific dependencies (#10259)
* updated versions for r-cowplot

* depends_on: added type=('build', 'run') to r, and added r-scales
2019-01-08 18:14:50 -06:00
Owen Solberg
7a816b9a66 r-data-table: new versions (#10260)
* updated versions for r-data-table

* added type=('build', 'run') to r dependency
2019-01-08 18:14:34 -06:00
Owen Solberg
2bd054adff r-dbplyr: new versions (#10262)
* added new versions, and tightened up depends_on() specs

* added type=('build', 'run') to r dependency
2019-01-08 18:14:19 -06:00
thelfer
d3caad4cd7 New package: MGIS (#10273)
* add the tfel package

* fix the tfel package

* fix the tfel package

* fix the tfel package

* Taking Adam J. Steward' remarks into account

* fixes trailing white spaces

* Update description

* Update dependencies following @adamjstewart adices

* Style fixes

* Style fixes

* Add java optional support

* add the maintainers attribute (following @alalazo advice), disable interface not selected (following @adamjstewart advice)

* flake8 fixes

* Fix Cast3M and python-bindings support. Python detection is made compatible with cmake'FindPythonLibs module (at least how it is used in TFEL)

* Style fixes

* Style fixes

* Fix test on python version

* Follow @adamjstewart advices: code is much cleaner and readable

* Small fix

* Small fix

* Add comment

* Small fix in cmake option

* try again (trying to overcome Travis CI unstable build process)

* Add support for the MFrontGenericInterfaceSupport project (MGIS)

* Style fixes

* Package documentation update

* Package documentation update

* Fix a typo thanks to Andreas Baumbach review

* Follow Adam J. Stewart advices

* Fix type
2019-01-08 15:07:47 -06:00
Eric
45882e1b6f usearch: Make installed binary executable (#10269)
* usearch: Make binary executable

* usearch: remove join_path
2019-01-08 14:20:13 -06:00
sknigh
d9c8d2f27b Added bash 5.0 (#10282) 2019-01-08 13:20:30 -06:00
Owen Solberg
0e50ff7339 r-dt: new versions (#10261)
* updated release and checksums, also tightened depends_on()

* remove blank line at end of file

* removing new version 0.5
2019-01-08 13:06:36 -06:00
Owen Solberg
76dd4ca9ae updated versions (#10263) 2019-01-08 13:00:12 -06:00
Owen Solberg
5c4156cd39 updated versions and depends_on() (#10264) 2019-01-08 12:54:55 -06:00
dorier
0a60cae516 added openpa package (#10265) 2019-01-08 12:53:37 -06:00
Eric
6ce6c79beb libzip: Add zlib dependency (#10270)
* libzip: Add zlib dependency

* libzip: Add version limit
2019-01-08 12:49:03 -06:00
Andreas Baumbach
a33d167c72 new version 1.0.1 for py-html5lib (#10278)
Change-Id: I2837dc098fce142b152d2969687d1873e182bbc8
2019-01-08 12:43:33 -06:00
Ross Miller
2934eda311 Check for ARM compiler in addition to clang (#10280)
Add "-rtlib=compiler-rt" to CFLAGS when building with either Clang or
the ARM compiler.

Refs #10279
2019-01-08 12:41:05 -06:00
Eric
dabf4f17d3 salmon: Add version 0.12.0 (#10271) 2019-01-08 14:01:02 +01:00
Michael Kuhn
48db757be1 go: add 1.11.4 (#10272) 2019-01-08 13:57:25 +01:00
Andreas Baumbach
12b52baf7b new package: py-webencodings (#10277)
Change-Id: Icf20035367a34fa88acfef2d3fa3742c3f3901ac
2019-01-08 13:55:41 +01:00
Peter Josef Scheibel
9f79995718 For spec-file-based installs, store the initial spec read from the file as the abstract spec 2019-01-07 20:40:34 -08:00
George Hartzell
b984adb386 bowtie: new versions and %gcc@8.0.0: fix (#10232)
* bowtie: new versions and %gcc@8.0.0: fix

Bowtie development shifted from Sourceforge to GitHub.

This commit adds several versions from GitHub, using the archive
tarballs.  Note that the URL for 1.2.2 tarball is actually an '_p1'
tag....

It leaves the old 1.2 release download info in place.

Versions 1.2.0 and newer come from GitHub (I'm unsure if the 1.2 and
1.2.0 are equivalent).

Include a fix that enables %gcc@8.0.0: from:

  https://github.com/BenLangmead/bowtie/issues/87

But, v1.2.2 has trouble with "newer" gcc's, so it only adds v1.2.2 for
%gcc@6.0.0:.

Feel free to tighten this.  I know that:

- 1.2 -> 1.2.2 work with %gcc@5.5.0;
- 1.2 -> 1.2.1.1 work with %gcc@8.2.0; and
- 1.2.2 fails with %gcc@8.2.0

* Tighten to `conflicts('%gcc@8:', when='@1.2.2')`

* Point 1.2.2 and 1.2.2_p1 at the 1.2.2_p1 tarball
2019-01-07 11:30:59 -06:00
Chad Wood
3b59f70751 doxygen: URL and version hashes updated to project's GitHub home (#10250)
* Update package.py

Doxygen has migrated from a private SVN to GitHub. This PR updates the URLs and adds versioned commit hashes from GitHub. It also includes version 1.8.15 as the latest option.

* Update package.py
2019-01-07 10:38:32 +01:00
Massimiliano Culpo
c4521535e7 Multi-valued variants: better support for combinations (#9481)
This enforces conventions that allow for correct handling of
multi-valued variants where specifying no value is an option,
and adds convenience functionality for specifying multi-valued
variants with conflicting sets of values. This also adds a notion
of "feature values" for variants, which are those that are understood
by the build system (e.g. those that would appear as configure
options). In more detail:

* Add documentation on variants to the packaging guide
* Forbid usage of '' or None as a possible variant value, in
  particular as a default. To indicate choosing no value, the user
  must explicitly define an option like 'none'. Without this,
  multi-valued variants with default set to None were not parsable
  from the command line (Fixes #6314)
* Add "disjoint_sets" function to support the declaration of
  multi-valued variants with conflicting sets of options. For example
  a variant "foo" with possible values "a", "b", and "c" where "c"
  is exclusive of the other values ("foo=a,b" and "foo=c" are
  valid but "foo=a,c" is not).
* Add "any_combination_of" function to support the declaration of
  multi-valued variants where it is valid to choose none of the
  values. This automatically defines "none" as an option (exclusive
  with all other choices); this value does not appear when iterating
  over the variant's values, for example in "with_or_without" (which
  constructs autotools option strings from variant values).
* The "disjoint_sets" and "any_combination_of" methods return an
  object which tracks the possible values. It is also possible to
  indicate that some of these values do not correspond to options
  understood by the package's build system, such that methods like
  "with_or_without" will not define options for those values (this
  occurs automatically for "none")
* Add documentation for usage of new functions for specifying
  multi-valued variants
2019-01-04 19:02:34 -08:00
Michael Kuhn
051057caa3 mvapich2: add missing zlib dependency (#10254) 2019-01-04 20:52:00 -06:00
Elizabeth Fischer
f7b78412b1 Added package osmctools (#10249)
* Added package osmctools

* Simplified

Removed functions that did the same as existing defaults

* flake8
2019-01-04 20:51:44 -06:00
Peter Josef Scheibel
64deda1b0c Add tests for expanding/non-expanding resources 2019-01-04 17:04:28 -08:00
Michael Kuhn
41ef02ee10 stage: fix resources being deleted from local cache (#10152)
Non-expanded resources were being deleted from the cache on account
of two behaviors:

* ResourceStage was moving files rather than copying them, and uses
  "os.path.realpath" to resolve symlinks
* CacheFetchStrategy creates a symlink to a cached resource rather
  than copying it

This alters the first behavior: ResourceStage now copies the file
rather than moving it.
2019-01-04 17:04:28 -08:00