Commit graph

8408 commits

Author SHA1 Message Date
Adam J. Stewart
a9efae271b Add latest version of apr (#4931) 2017-07-31 19:35:48 +02:00
George Hartzell
c126c5553c zsh: add variant that skips tcsetpgrp test (#4923)
zsh's configure script fails if there's it tries to test for terminal
functionality if there's not a terminal (e.g. in a Jenkins build).

The configure script has a switch that asserts that tcsetpgrp works
and thereby avoids running that test.

This commit adds a variant that invokes that switch, defaulting to
True.
2017-07-31 11:17:04 -05:00
Axel Huebl
6d97397ab0 gBenchmark: v1.2.0 (#4935)
Adds a the latest version of gBenchmark, release 1.2.0.

This is the first gBenchmark version with proper
[CMake config package installs](https://github.com/google/benchmark/issues/363).
This is important for dependencies building against it, such as gRPC.
2017-07-31 10:06:17 -05:00
Robert Pavel
f7c24289e5 Initial Spackage for qmd-progress library (#4924)
* Initial Spackage for qmd-progress library

PROGRESS is a library is focused on the development of general solvers
that are commonly used in quantum chemistry packages.

* Removed LA-CC from description to fix formatting

* Added Additional Formatting Requests

Added requested formatting changes and also ensured that graphlib and
mpi are disabled if not enabled
2017-07-28 17:10:24 -05:00
sknigh
92ea7c4337 Fix for m4%clang (#4912)
* Fix for m4%clang

* Restricted condition to not subsitute rtlib on OSX
2017-07-28 11:32:53 -05:00
Jon Rood
c5d2206206 Adding QWT package. (#4911)
* Adding QWT package.

* Using builtin file filtering.

* Formatting.
2017-07-27 16:22:29 -05:00
Christoph Junghans
78d7587c93 bml: fix homepage (#4918) 2017-07-27 16:07:47 -05:00
Akhil Reddy Patlolla
6bdc373100 Added Proxy App tag (#4917)
* Added Proxy App tag

*  NO changes except proxy app tag
2017-07-27 15:56:59 -05:00
pkondamudi
ce601a9304 New Package: lcals (#4792)
* New Pacakge: lcals

* added logic for arch detection and compiler choice.

* fixes for comments.

* addressed comments.

* removed LCALS_ARCH and added flags though spack.

* addressed comments.

* flake 8 fix.

* reerted the changes along with comments.
2017-07-27 14:24:28 -05:00
Jim Galarowicz
99cac0bf94 Fix for Krell openspeedshop spack package bug. New multi-value variant for GUI build. (#4880)
* Update the krell institute products to use the latest features of spack for building on cluster platforms.

* Address travis error messages and resubmit the pull request.

* Update the contents of openspeedshop package.py so it passes the flake8 tests.

* Fix flake8 error-whitespack issue in mrnet package.py file.

* Add updates based on spack reviewer feedback.

* More fixes based on comments from reviewers.  Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH.

* More review related changes.  Update MPIOption.append lines and take out xercesc references.

* Create a base options function for common openspeedshop base cmake options to reduce redundencies.

* Add libxml2+python depends on to get around issues with the libxml2 package file.

* Using boost over 1.60.0 causes compile errors.  This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build.

* Fix bad syntax in specifying the boost version range.

* Update the version numbers for the krell institute components and tools: cbtf and openspeedshop.

* Do not build glib for qt3, it is not needed and causes build problems at this time anyway.

* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.

* Update the fix for qt3 build by setting LD_LIBRARY_PATH instead of checking for whether it is set or not per Adams comment that spack clears LD_LIBRARY_PATH.

* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.

* Trim comments to fit more concisely.

* Fix tabs versus spaces and swap if and else clause check from a negative to a positive check.

* Fix issues with the cbtf-argonavis build, update to use dyninst-9.3.2, fixes to openspeedshop package build.

* Fix issues with the cbtf-argonavis package.py files related to comments.

* Add changes for changing the krell packages from Package to CMakePackage.

* Add better changes for changing the krell packages from Package to CMakePackage.

* Add more modifications for changing the krell packages from Package to CMakePackage.

* Add additional modifications for changing the krell packages from Package to CMakePackage and fixing Travis erros

* Fix new travis errors.

* Fix new travis errors.

* Add more changes for PR 4765.

* Add more refinements to the conversion from Package to CMakePackage.

* Fix new travis errors.

* Add dependencies for MPI to be passed to cbtf-krell, so it can build the MPI collectors requested by the builder of openspeedshop.

* Remove extra unnecessary routine to adjust build arguments. Fix if-else clause issue.

* Fix more flake issues caused by last changes.

* Fix a bug where openspeedshop will not build when no mpi variants are specified.  Also switch to a multiple level variant for building the gui(s).  Use none, qt3, and qt4 as the variants with qt3 being the default.

* Add fix for spack issue #4843, where LTDL include files were not found.

* Add the build_type variant back into the openspeedshop package file.
2017-07-27 11:06:44 -05:00
pkondamudi
31a329d237 New Package: RSbench (#4752)
* New Package: RSbench

* minor change

* removed tags as per PR# 4749

* addressed comments and added gcc compiler.

* added proxy app tags to description.

* removed setting CC to pgicc through spec.

* removed compiler as depedency

* removed pgi variant.

* flake 8 fix.

* added mpi depedency with pgi compiler

* added  pgi compiler

* removed PGI compiler as depedency.

* added tags and addressed other code formattings.

* added tags and addressed other code formattings.

* addressed comments.
2017-07-27 10:59:30 -05:00
Denis Davydov
ddc1dcd084 openblas: add 0.2.20 (#4915) 2017-07-27 08:51:39 -05:00
Audrey Thoma
70a089287e snptest: new package (#4900)
* snptest: new package

* fixed version things

* fixed install phase
2017-07-26 17:44:15 -05:00
Adam J. Stewart
b33f92da34 Improve version detection for URLs with dynamic after version (#4902) 2017-07-26 17:43:54 -05:00
Robert Pavel
6e99e2c58e Updated Namespace of BML Repository (#4910) 2017-07-26 17:42:26 -05:00
pkondamudi
4ab12fb503 added MPI dependency to Nekbone package (#4903)
* removed the tags as per comment in PR# 4749

* addressed above comments

* changed fortran compiler.

* added proxy application tags.

* added tags by removing them from description.

* addressed comments

* used join_path instead of path concat.

* removed the tags as per comment in PR# 4749

* addressed above comments

* changed fortran compiler.

* added proxy application tags.

* added tags by removing them from description.

* addressed comments

* used join_path instead of path concat.

* added tags.

* changes to use MPI as depedency.

* removed MPI as variant.

* changed pointer to filtered makenek file.

* flake 8 fix.
2017-07-26 14:27:29 -05:00
Audrey Thoma
b62f0962b0 shortstack: new package (#4905) 2017-07-26 10:14:55 -05:00
Adam J. Stewart
07aec4366f Add universal build_type variant to CMakePackage (#4797)
* Add universal build_type variant to CMakePackage
* Override build_type in some packages with different possible values
* Remove reference to no longer existent debug variant
* Update CBTF packages with new build_type variant
* Keep note on build size of LLVM
2017-07-25 16:34:43 -07:00
Sam Bateman
4b996e9f49 tmux should not set PKG_CONFIG_PATH (#4901)
* fixes #967

* Version bump to 0.9.1

- Bugfixes for spack find
- 0.9.1 can read specs from current develop.

* Don't assume spack is in the path when building docs.

* Remove PKG_CONFIG_PATH from tmux configure

* Change tmux to AutotoolsPackage

* Correct link to libtinfo in tmux
2017-07-25 17:08:34 -05:00
becker33
30f6d2ab90 fix callpath bug (#4659)
* fix callpath bug I found while testing env/cc

* fix hanging indent for flake
2017-07-25 13:51:56 -07:00
Audrey Thoma
6693dc1092 transdecoder: new package (#4895)
* transdecoder: new package

* fixed package structure
2017-07-25 15:51:14 -05:00
Audrey Thoma
402233ecc8 transposome: new package (#4896) 2017-07-25 15:50:42 -05:00
Audrey Thoma
668233a819 trimgalore: new package (#4899) 2017-07-25 15:50:23 -05:00
Gregory Lee
42717bd8e8 fix config.guess patch for ppc64le (#4858)
* fix config.guess patch for ppc64le

* explicit patch for config.guess not required
2017-07-25 13:44:51 -07:00
Audrey Thoma
71991cd9c9 cleaveland4: new package (#4894)
* cleaveland4: new package

* fixing return line in viennarna url_for_version
2017-07-25 13:18:34 -05:00
Audrey Thoma
20ab66a2e9 tabix: new package (#4886)
* tabix: new package

* fixed docs location
2017-07-25 13:02:08 -05:00
Audrey Thoma
5184dda309 sumaclust: new package (#4884)
* sumaclust: new package

* tweaking url and make specs
2017-07-25 08:04:25 -05:00
Jimmy Tang
1d1a0e3d63 Update zstd version (#4873)
* Update zstd version

* Change order of versions

* Use MakefilePackage
2017-07-25 07:55:02 -05:00
Jimmy Tang
2b792f943f Rename the gpu variant to cuda, this is to be consistent with other (#4890)
packages.
2017-07-25 07:53:33 -05:00
Denis Davydov
b0b86e5ffe fix GobjectIntrospection on Darwin (#4872)
* fix GobjectIntrospection on Darwin

* minor
2017-07-24 19:51:17 -05:00
Audrey Thoma
4237e5fffd stacks: new package (#4875) 2017-07-24 19:50:40 -05:00
Stas Sergienko
07e60bc26b added new version of jdk 8u141-b15 (#4876) 2017-07-24 19:50:16 -05:00
Audrey Thoma
d2f08c95d9 swarm: new package (#4885) 2017-07-24 19:49:59 -05:00
Audrey Thoma
8038945145 structure: new package (#4879)
* structure: new pacakge

* fixing package structure (not a pun)
2017-07-24 18:02:20 -05:00
Audrey Thoma
0c96c330ec subread: new package (#4882) 2017-07-24 18:01:56 -05:00
Stas Sergienko
9aa3749787 added new version of cdo (#4877) 2017-07-24 15:50:44 -05:00
Audrey Thoma
bd0699b026 stringtie: new package (#4878) 2017-07-24 15:50:32 -05:00
Adam J. Stewart
250ee413e9 Change Version formatting properties and functions to return Version objects (#4834)
* Change version.up_to() to return Version() object
* Add unit tests for Version.up_to()
* Fix packages that expected up_to() to return a string
* Ensure that up_to() preserves separator characters
* Use version indexing instead of up_to
* Make all Version formatting properties return Version objects
* Update docs
* Tests need to test string representation
2017-07-24 13:02:13 -07:00
Jimmy Tang
df2fc25ddf Add a py-theano version from git repo (#4871) 2017-07-24 08:56:54 -05:00
健美猫
8a06e3d867 Add cuda variant for mvapich2. (#4800)
* Add cuda variant for mvapich2.

* Disable cuda for mvapich2 by default.
2017-07-23 12:18:05 -05:00
Stephen McDowell
1cdb3c61ca fix sphinx dependencies, add v1.6.3 (#4870) 2017-07-23 09:44:12 -05:00
Milton Woods
4044e9f918 Perl - allow package activation without PERL5LIB variable (#4540)
* perl: prepend default perl @INC path to support package activation

* perl: remove stray comma from list of configure arguments

* perl: final comma in configure arguments makes adding arguments safer

This reverts commit fdc10cd611f525ebc31ca1953e048095b1c75350.

* perl: add comment about modified @INC (thanks to George Hartzell)

* perl: use self.prefix.lib and self.prefix.bin for clarity

* perl: convert tabs added by editor to spaces for flake8

* perl: use new path syntax: prefix.lib.perl5

* perl: avoid line break before binary operator

* perl: use compact spack syntax for perl executable
2017-07-23 09:41:45 -05:00
Axel Huebl
62b4087c09 gBenchmark: Development Package (#4847)
* gBenchmark: Development Package

Add the development version (master branch) of `gBenchmark`

* gBenchmark: Remove Duplicate

Remove duplicate `gbenchmark` library
and keep its patch to remove the shipped
-Werror
2017-07-23 09:35:16 -05:00
Todd Gamblin
f159246d1d Make testing spack commands simpler (#4868)
Adds SpackCommand class allowing Spack commands to be easily in Python

Example usage:

    from spack.main import SpackCommand
    info = SpackCommand('info')
    out, err = info('mpich')
    print(info.returncode)

This allows easier testing of Spack commands.

Also:
* Simplify command tests
* Simplify mocking in command tests.
* Simplify module command test
* Simplify python command test
* Simplify uninstall command test
* Simplify url command test
* SpackCommand uses more compatible output redirection
2017-07-22 21:27:54 -07:00
Kshitij Mehta
c07d93a3e5 Savanna (#4856)
Installing the stable version 0.5 through the checksummed tar.gz does not fetch the git submodule in the package.
The submodule appears as an empty directory.

Thus, clone the commit tagged as v0.5 using git to get around this issue

* savanna: modified adios dependency spec
* Replaced adios+staging with adios+flexpath+dataspaces
* savanna: Enabling fortran support in adios by default
* savanna: reverting to variant 'staging' for enabling all staging transports
2017-07-21 23:47:13 -07:00
Audrey Thoma
aa96e1671b sparta: new package (#4867)
* sparta: new package

* fixing homepage
2017-07-21 21:40:31 -05:00
jiseung
e191ead9ac new package: miniGMG (#4849)
* new package: miniGMG

* changed based on comments

* removed cuda version
2017-07-21 20:52:09 -05:00
Audrey Thoma
cd9742a30b revbayes: trying this again (#4861) 2017-07-21 20:51:39 -05:00
Audrey Thoma
b56add1517 sortmerna: new package (#4866) 2017-07-21 20:51:03 -05:00
Gregory Lee
644f5b3229 added new pruners-ninja version (#4859) 2017-07-21 17:57:12 -05:00