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2ed914aa1bfe65fe798583c3149f2a58ec267843
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Author SHA1 Message Date
stefanosoffia
2ed914aa1b Flex v2.6.4 conflicts with gcc@7.2.0 (#6819) 2018-01-03 09:46:57 -06:00
Douglas Duckworth
d466d8f3d3 singularity - added master branch (#6631) 
* singularity - added master branch as this has latest fixes - 2.4 does not compile on centos 6 without use of this branch

* renamed to develop

* added master branch properly
 2018-01-02 21:47:21 -06:00
Axel Huebl
5d2f752c1b New Package: py-adios (#5686) 
The ADIOS1 numpy bindings depend on an installed, fully loaded
ADIOS C library + its config tools to build properly.
 2018-01-02 21:37:59 -06:00
Brian Van Essen
3c63710532 Intel mkl dnn (#6268) 
* Added a package for the MDAnalysis toolkit.

* Added a package for the Intel MKL-DNN project.

* Fixed flake8 errors.

* Fixed Flake8
 2018-01-02 21:27:34 -06:00
Michael Kuhn
01bec7976b Fix HTML detection (#6394) 
Some servers report a content-type header instead of Content-Type.
 2018-01-02 21:21:36 -06:00
Eric
d2c3b3884b rsem: update version 1.3.0 md5sum (#6650) 2018-01-02 21:15:40 -06:00
Michael Kuron
2c5c7a37cb atom-dft: new package plus dependencies (#6653) 
* atom-dft: new package plus dependencies

* Indentation fix

* Use the compiler wrappers

* Pass variables instead of using FileFilter
 2018-01-02 20:32:37 -06:00
Jimmy Tang
ea6b6ef1ff Install all the cli tools from all the sub-directories (#6705) 
* Install all the cli tools from all the sub-directories

* Satisfy pep8
 2018-01-02 20:14:39 -06:00
Feiyi Wang
8ed1c84539 py-lrudict: a LRU-based cache dictionary (#6734) 
* add py-lrudict

* style fix

* style fix: add blank lines
 2018-01-02 20:10:49 -06:00
Feiyi Wang
8221265c3c py-scandir: a better directory iterator, backport to 2.7 (#6739) 2018-01-02 20:08:58 -06:00
Levi Baber
59cd2db8f3 gatk: boilerplate cleanup (#6744) 2018-01-02 20:05:04 -06:00
Denis Davydov
4b5fe75bc3 add OctavePackage (#6746) 
* add OctavePackage

1. remove import CudaPackage which is not needed anymore
2. mention CudaPackage and OctavePackage in packaging guide
3. adjust OctavePackageTemplate
4. add clue file for Octave build
5. sanity check on self.prefix

* use setup_environment
 2018-01-02 20:03:27 -06:00
Feiyi Wang
fd6b9ac3af py-xattr: a python interface to access extended file attribute (#6747) 
* py-xattr: a python interface to access extended file attribute

* py-xattr: style fix
 2018-01-02 20:02:03 -06:00
Brian Van Essen
a92268d62a Lbann update (#6751) 
* Added a package for the MDAnalysis toolkit.

* Updated the LBANN recipe to use the revised cmake environment being
rolled out.

* Flake8 errors
 2018-01-02 20:01:23 -06:00
Denis Davydov
3d257e8280 likwid: add stable 4.3.0 (#6761) 2018-01-02 19:59:14 -06:00
Denis Davydov
cc74da5aab mesa: disable binutils on macOS (#6763) 2018-01-02 19:58:38 -06:00
Levi Baber
353870fe50 jags: lapack fix (#6764) 
* jags: fixing openblas thows a lapack error when compiling. atlas works. other lapack providers may work. also adding tags

* changing blas/lapack reference

* removing openblas conflict

* jags: whitespace cleanup for flake8
 2018-01-02 19:57:54 -06:00
Milton Woods
6922ea5889 Esmf fixes for Cray, OSX and mpich (#6768) 
* esmf: put .mod files in the spack compiler search path

* esmf: allow building with Cray mpi

* esmf: create run-path dependent libraries on osx

* esmf: link fortran interface libraries when building with mpich
 2018-01-02 19:43:55 -06:00
Jon Rood
e1e24ff80e Adding option to build Nalu with Hypre support. (#6782) 2018-01-02 19:42:47 -06:00
peetsv
fef93d2221 perl-xml-libxml: adding perl module (#6783) 
* perl-xml-libxml: adding perl module

* line length change
 2018-01-02 19:42:09 -06:00
Sinan
7f319b9f84 create perl-file-which package (#6800) 
* create perl-file-which package

* trivial edits for package.py so

trivial edits for package.py so that flake8 will not complain
 2018-01-02 19:36:59 -06:00
stefanosoffia
2aaba189ed Updated 'nginx' from v1.12.0 to v1.13.8. (#6810) 
This fixes build issues with most recent gcc versions.
See issue #6252.
 2018-01-02 19:29:47 -06:00
Eric
958abe5b29 py-pyani: Create new package (#6811) 2018-01-02 19:27:42 -06:00
Eric
7db7b5b596 MinCED: Create new package (#6815) 2018-01-02 19:25:08 -06:00
Levi Baber
08ea9808c6 adding specific version url for augustus 3.3 due to old folder structure (#6813) 2018-01-02 19:24:28 -06:00
Jon Rood
285538a78d Tioga package: Explicitly list MPI compilers for Cmake (#6741) 2018-01-02 13:14:22 -08:00
Jon Rood
2812644ed7 paraview package: Explicitly specify MPI compilers in Cmake (#6738) 2018-01-02 13:06:25 -08:00
Milton Woods
5dd5dc01c2 new package: Pfunit: unit testing framework for Fortran (#6795) 2018-01-02 12:18:08 -08:00
Eric
e483f9297a new package: DIAMOND (#6793) 2018-01-02 12:03:45 -08:00
Eric
8271f0e271 new package: tantan (#6792) 2018-01-02 12:00:13 -08:00
Adam J. Stewart
b10098dc53 Cython only needed for develop version of mpi4py (#6780) 2018-01-02 11:34:24 -08:00
Adam J. Stewart
464ca87879 Add more unit tests for spack clean command (#6777) 2018-01-02 11:31:38 -08:00
Eric
9ac9017589 new package: py-rseqc (#6773) 2018-01-02 11:10:55 -08:00
Eric
e8b1e79fbf package py-biopython: remove py-mx dependency (#6772) 2018-01-02 10:59:21 -08:00
Eric
caa39d08d4 package r-rcurl: boilerplate cleanup (#6771) 2018-01-02 10:58:03 -08:00
Eric
c3b003e698 bamtools: Add version 2.5.1 (#6770) 2018-01-02 10:55:07 -08:00
Adam J. Stewart
05ce8407af Add unit tests for spack help command (#6779) 
* Add unit tests for spack help command
* Work around issue with using `spack help` twice in tests
 2017-12-30 22:55:49 -08:00
Adam J. Stewart
088c193a78 Update to the latest version of argparse (#6786) 
* Update to the latest version of argparse

* Re-add colified logic
 2017-12-30 16:08:35 -08:00
Adam J. Stewart
010334bf22 Update to distro 1.0.4 (#6788) 
* Update to the latest version of distro

* Update distro to 1.0.4
 2017-12-30 15:44:19 -08:00
Axel Huebl
da93c9b870 Add: lines-are-beautiful (#6784) 
Adds the C++ File API library "lines-are-beautiful" for the
reMarkable e-ink tablet.
 2017-12-30 12:29:27 -08:00
Nichols A. Romero
24743b7e5a QMCPACK package: update blas/lapack detection (#6753) 
* Fix detection of blas and lapack: provide libraries/includes as
  arguments to CMake rather than using CMake's auto-detection.
  This includes a patch to QMCPACK's CMake files to refer to
  Spack-built blas/lapack implementations. This also includes
  special-case logic for the intel-mkl implementation of blas/lapack

* Break up unit tests and short tests. Only hard failure if the unit
  tests fail, if short tests fail issue a warning only.

* Add QMCPACK 3.3.0, get rid of 3.0.0
 2017-12-22 16:47:49 -08:00
Adam J. Stewart
0c1f4a7997 Add more unit tests for spack list command (#6750) 2017-12-22 10:29:20 -08:00
Massimiliano Culpo
d3913709bb spack mirror remove: fix no-update error (#6559) 
Fixes #4573 

"spack mirror remove" was not actually removing mirrors from the
configuration.
 2017-12-22 10:28:23 -08:00
Denis Davydov
f764ac4573 dealii: support 64bit BLAS (#6758) 2017-12-22 15:55:04 +01:00
Andrey Prokopenko
937f68c359 clang,flang: update CC, CXX environment in installation module (#6737) 2017-12-22 07:32:10 +01:00
peetsv
d1786779c4 gmap-gsnap: adding version 2014_12_28 (#6720) 2017-12-22 06:56:58 +01:00
Adam J. Stewart
1ce0c1b556 Fix python3 compatibility bug in spack edit command (#6748) 
In Python 2, filter() returns a list, but in Python 3, filter()
returns an iterator, and iterators have no length.
 2017-12-21 17:45:15 -08:00
becker33
feb4f1b387 separate stdout and stderr for module loading (#6713) 2017-12-21 16:27:52 -08:00
Levi Baber
f2e061debf Feature/fasttree (#6227) 
* fasttree: new package

* fasttree: better version handling

* fixing line length for flake8
 2017-12-20 19:10:24 -08:00
Patrick Gartung
e5d6f28b4e binary caching: handle files misidentified as needing relocation (#6679) 
* Only specify a file as needing relocation if it contains the spack
  root as a text string (this constraint also applies to binaries)
* Don't fail if there is an error retrieving RPATH information from a
  binary (even if it is specified as requiring relocation)
 2017-12-20 18:21:41 -08:00