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Author SHA1 Message Date
Audrey Thoma
5f0e1514ac kentutils: new pacakge (#4831) 2017-07-20 13:16:32 -05:00
jiseung
16fbd0fc41 new package:SNAP (#4826) 2017-07-20 13:15:43 -05:00
becker33
f962aba6ce Allow packages to control handling of compiler flags (#4421) 
* Initial work on flag trapping using functions called <flag>_handler and default_flag_handler

* Update packages so they do not obliterate flags

* Added append to EnvironmentModifications class

* changed EnvironmentModifications to have append_flags method

* changed flag_val to be a tuple

* Increased test coverage

* added documentation of flag handling
 2017-07-19 20:12:00 -07:00
George Hartzell
acca75b368 Add info for zsh@5.3.1 (#4827) 2017-07-19 21:49:15 -05:00
Jim Galarowicz
a2d57f0550 Fix more flake issues caused by last changes. 2017-07-19 19:50:10 -05:00
pkondamudi
9df9a809a8 Add MPI support and tags to embs package (#4824) 2017-07-19 19:04:48 -05:00
pkondamudi
bdcd63ed70 Add tags to nekbone package (#4825) 2017-07-19 19:03:53 -05:00
Jim Galarowicz
8c82834ca2 Remove extra unnecessary routine to adjust build arguments. Fix if-else clause issue. 2017-07-19 18:52:30 -05:00
jiseung
9ae36849af new package: cns-nospec (#4806) 
* new package: cns-nospec

* made changes as suggested and added proxy-app tag

* updated edit()

* adjusted logic for '+debug'
 2017-07-19 17:05:19 -05:00
jiseung
301b457de3 new package: amr-exp-parabolic (#4821) 
* new package: amr-exp-parabolic

* removed boilerplate and added tag
 2017-07-19 17:04:53 -05:00
pkondamudi
1b0d2888bb Package/xsbench (#4822) 
* 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 and other minor changes.

* removed tags from description.
 2017-07-19 17:04:17 -05:00
Jim Galarowicz
eee748db33 Add dependencies for MPI to be passed to cbtf-krell, so it can build the MPI collectors requested by the builder of openspeedshop. 2017-07-19 11:38:30 -05:00
Jim Galarowicz
7a5e806b7a Fix new travis errors. 2017-07-19 08:58:19 -05:00
jiseung
60cffbb9d0 new package PENNANT added (#4708) 
* new package PENNANT

* made adjustments based on comments

* edited logic for mpi variant

* replaced with 'else'

* prefix.bin instead of 'bin'
 2017-07-19 08:50:53 -05:00
Akhil Reddy Patlolla
a6cac6ac99 Added Proxy App CoSP2 (#4726) 
*  Added Proxy App CoSP2

*  Updated the PATH

* Updated MPI Fix

*  Fixed Issues

*  Fixed Issues with compiler and Flake8

*  Enhanced block of code.

*  Intended
 2017-07-19 08:49:29 -05:00
Akhil Reddy Patlolla
7165129598 Added Proxy App CoHMM (#4727) 
*  Added Proxy App CoSP2

*  Added Proxy App CoHMM

*  Updated PATH cohmm

*  Chages Fixing Minor issues

* Minor Fix  git add cohmm/package.py

*  Updated

* Resolved TAG Conflict

*  Updated based on the codecov failure
 2017-07-19 08:48:41 -05:00
jiseung
e3e8893ed9 new package: CLAMR (#4728) 
* new package: CLAMR

* changed from bool variants to single value variants and corresponding logic in build_type and cmake_args

* lowercase variant values

* updated conditionals for variants

* adjusted url and docstring
 2017-07-19 08:48:03 -05:00
pkondamudi
45a7e8bb12 New Package: SimpleMOC (#4742) 
* New Package SimpleMOC

* addressed comments

* removed tags as per PR# 4749

* flake8 fix.

* travis fix.

* added proxy app tags to description.

* added mpi and openmpi depedency.

* removed openmpi depdedency.

* addressed comments.

* adding openmp flag conditionally.

* flake 8 fix for tabs.
 2017-07-19 08:46:42 -05:00
Jim Galarowicz
6646fe1b74 Add more refinements to the conversion from Package to CMakePackage. 2017-07-19 08:10:46 -05:00
Kshitij Mehta
6e2eb83943 codar-cheetah: URL fix (#4815) 2017-07-18 22:49:51 -05:00
Adam J. Stewart
5fc0243d35 Improve version detection of release versions (#4816) 2017-07-18 22:48:39 -05:00
jiseung
d1c199e15d new package: SMC (#4817) 
* new package: SMC

* removed template and added proxy-app tag

* added comp variant in edit()

* edited comp variant in edit()
 2017-07-18 22:48:21 -05:00
Jim Galarowicz
aed2119e5c Add more changes for PR 4765. 2017-07-18 20:15:52 -05:00
Gregory Lee
b411849200 Misc python updates (#4807) 
* updated py-pylint version

* setuptools required at runtime for pkg_resources

* fixed url for updated pylint
 2017-07-18 19:37:40 -05:00
Adam J. Stewart
2bd8d7a36a Always install xproto in serial (#4809) 2017-07-18 19:37:12 -05:00
Audrey Thoma
e2485efb94 poamsa: new package (#4808) 
* poamsa: new package

* fixed version specs
 2017-07-18 19:36:48 -05:00
jiseung
78c11320d6 new package to be added: NuT (#4760) 
* new package to be added: NuT

* removed cmake_args() and made other changes as suggested

* Added setup_environment()

* PEP8 compliant

* edited version name, build_targets, and files/directories to install

* corrected executable directory

* compiler dependencies based on version
 2017-07-18 16:37:47 -05:00
Audrey Thoma
748221840a price: new package (#4810) 2017-07-18 16:35:33 -05:00
Audrey Thoma
3e72263d79 New package busco (#4678) 
* busco: new package

* busco: fixing fussy paths

* removing paths, probably was a problem with our module setup

* fixed dep type
 2017-07-18 13:49:18 -05:00
Jon Rood
904f6f0572 Adding a bit more Mellanox MXM capability to OpenMPI. (#4762) 2017-07-18 13:45:43 -05:00
Audrey Thoma
0e28afef1e raxml: new package (#4777) 
* raxml: new package

* changed compiler variable

* removing if statement regarding intel compiler
 2017-07-18 13:43:42 -05:00
homerdin
68a8f63569 Package/minimd (#4788) 
* New Package: miniMD

* Minor Changes

* Corrected Dependency

* Renamed Executable

* Change to use build directory directly
 2017-07-18 13:42:57 -05:00
pkondamudi
e291f59ea3 New Package: OpenMC (#4790) 
* New Package: OpenMC

* comments addressed.

* comments addressed.

* changed 'os.makedirs' to 'mkdirp'

* flake 8 fix.
 2017-07-18 13:42:11 -05:00
becker33
d2a63d55fa Open ended variants (#4746) 
* Change directives to allow open-ended variants more easily

* make None default to open-ended
 2017-07-18 10:03:15 -07:00
Adam J. Stewart
1215c3b20c Change path to CMakeLists.txt to be relative to root, not pwd (#4420) 
* Change path to CMakeLists.txt to be relative to root, not pwd

* Changes requested during code review

* Revert back to old naming of root_cmakelists_dir
* Make relative directory more clear in docs

* Revert change causing build_type AttributeError

* Fix forgotten abs_path var

* Update CLHEP with new relative path

* Update more packages with new root_cmakelists_dir syntax
 2017-07-18 09:58:19 -07:00
Massimiliano Culpo
5a1ee22575 package: removed default no-op patch (#4103) 
* package: removed default no-op patch fixes #4085

* do_patch: handles NoSuchMethodError nicely
 2017-07-18 09:53:35 -07:00
健美猫
6b2d75a0a6 Repalce ftp:// with http:// for gdbm, mesa-glu and udunits2. (#4798) 2017-07-18 11:22:14 -05:00
Jim Galarowicz
65802c59fa Fix new travis errors. 2017-07-18 10:35:31 -05:00
George Hartzell
c597bdb284 somatic-sniper depends_in('curses') (#4796) 
somatic-sniper installs its own copy of samtools, which needs curses.
I'm not sure why I didn't stumble on this in my dev environment, but I
just stumbled over it in a standalone build.
 2017-07-18 09:40:41 -05:00
Jim Galarowicz
b819a9e70e Fix new travis errors. 2017-07-18 08:34:25 -05:00
健美猫
870062076f Add version 3.4.1 for r. (#4799) 2017-07-18 13:04:49 +02:00
Audrey Thoma
07d82422b8 pcma: new package (#4793) 2017-07-18 11:13:17 +02:00
Adam Fidel
da61455cc3 New Package: tig (#4794) 2017-07-18 11:10:39 +02:00
Jim Galarowicz
811557ed36 Add additional modifications for changing the krell packages from Package to CMakePackage and fixing Travis erros 2017-07-17 21:19:06 -05:00
Jim Galarowicz
6b694aecde Add more modifications for changing the krell packages from Package to CMakePackage. 2017-07-17 16:05:23 -05:00
homerdin
7c1ce6e206 Package/minixyce (#4789) 
* New Package: miniXyce

* Removed Tag
 2017-07-17 15:50:31 -05:00
Audrey Thoma
9872fe980b partitionfidner: new package (#4791) 2017-07-17 15:49:26 -05:00
Massimiliano Culpo
6dcbc30a2c qhull: fix to work around a known issue of the library with intel compiler (#4648) 2017-07-17 14:39:09 -05:00
Jim Galarowicz
eb45879c0e Add better changes for changing the krell packages from Package to CMakePackage. 2017-07-17 12:20:38 -05:00
Audrey Thoma
2bf140601b bsseeker2: new package (#4770) 2017-07-17 19:02:17 +02:00