Commit graph

9439 commits

Author SHA1 Message Date
健美猫
05f51c46dd Bump gatk version to 4.0.4.0. (#7985)
* Bump gatk version to 4.0.4.0.

* Update.

* Fixed.

* Fixed.
2018-05-03 10:08:48 -05:00
健美猫
fb9898230e A new package: py-openslide-python. (#7907)
* A new package: py-openslide-python.

* Update.

* Remove py-pytorch package.

* Remove nektar package.

* Remove install_time_test_callbacks
2018-05-03 08:37:52 -05:00
Michael Kuhn
937ab7d5cc go: Update to 1.10.2 (#7982) 2018-05-03 12:14:52 +02:00
Elizabeth Fischer
cbd77e3a8d make symlinking python3->python optional (#7960)
* Make symlinking python3->python optional
* Added reference to PEP 394
2018-05-02 12:26:30 -07:00
Adam Moody
7909e15d83 mvapich2: add 2.3rc2 (#7976) 2018-05-02 14:23:32 -05:00
Elizabeth Fischer
f054fa2f43 sphinx: Updated to v1.7.4 (#7977)
* sphinx: Updated to v1.7.4

* Update package.py
2018-05-02 14:23:02 -05:00
Tim Law
73ded1a60c Added BookLeaf_Cpp and Typhon packages. (#7969) 2018-05-02 10:45:30 -05:00
Michael F. Herbst
f1ce2e3351 Add libcint version 3.0.12 (#7972) 2018-05-02 10:44:58 -05:00
Eric
fdc6ea0645 bedops: Create new package (#7956)
* bedops: Create new package

* fix install method
2018-05-02 08:14:00 -05:00
David Wootton
c23387e89b Fix Spectrum MPI package spec file for PGI compilers (#7964)
* Added magma package

* Incorporated Serban's change

* Remove deleted files

* argparse.py

* Sync forked Spack repo in github

* Use reported version of IBM XL Fortran compiler for compiler versions
>= 16.0.

Starting with the April 2018 release, the IBM XL C and Fortran
compilers report the same version, 16.0.  Consequently, there is
no need to downgrade the Fortran compiler version to match that
of the C compiler.

* Eliminate blank lines.

* Update the Spectrum MPI package.py file to specify the correct compilation
scripts for the PGI compilers.
2018-05-02 08:12:08 -05:00
Christoph Junghans
9d1456393f
openmc is not a proxy (#7968)
https://github.com/spack/spack/issues/7965#issuecomment-385953224
2018-05-02 06:48:16 -06:00
scheibelp
d17372290d
Fix initialization of defaults in yaml schema validation (#7959)
Fixes #7924

Spack's yaml schema validator was initializing all instances of
unspecified properties with the same object, so that updating the
property for one entry was updating it for others (e.g. updating
versions for one package would update it for other packages).

This updates the schema validator to instantiate defaults with
separate object instances and adds a test to confirm this behavior
(and also confirms #7924 without this change).
2018-05-01 17:23:27 -07:00
Adam Moody
29b47e0e01 mvapich2: add registration cache and file systems variants (#7948)
* mvapich2: add registration cache and file systems variants, avoid empty --with-pm= if no process manager is specified, add missing leading dash in --disable-silent-rules
2018-04-30 18:12:13 -07:00
Adam Moody
2db4beac12 mpifileutils: roll back to dtcmp v1.0.3, add option to build master branch (#7949)
* mpifileutils: roll back to dtcmp v1.0.3 due to API change, add option to build master branch

* add comment to explain why certain dtcmp is required, rename version for git branch

* dtcmp v1.0.2 is missing github tarball
2018-04-30 18:46:17 -05:00
Eric
7088e547a3 vt: Create new package (#7947) 2018-04-30 12:11:06 -05:00
健美猫
094eb5f9a8 Build shared libs for tinyxml. (#7914) 2018-04-30 10:03:24 -05:00
Kelly (KT) Thompson
d02b5b96d3 Patch eospac package to allow compilation with %clang. (#7928)
When building eospac with %clang, spack's Fortran compiler wrapper is called
'flang', which is rejected by the eospac build system..Allow compilation with
%clang by patching the eospac build system.

My testing only covers %clang where flang is actually gfortran.  However, this
patch only registers 'flang' as a known Fortran compiler and does not set any
flags or options that are compiler specific.
.
2018-04-29 18:40:27 -06:00
Adam J. Stewart
c1febf8d9c Document how to run unit tests with print statements (#7860) 2018-04-28 17:59:33 +02:00
Christoph Junghans
810fe884d0 mfem: fix concretization (#7923)
* mfem: fix concretization

* Fix hypre deps again

* Update package.py
2018-04-28 07:16:43 -05:00
Chris Green
dec7a10249 Update with recent versions through 4.8.3 and add variants. (#7933)
Add configurable HTTP, Python and readline support.

Add previously missing dependencies.

Minor patch to improve Python support (see https://github.com/xrootd/xrootd/pull/695).
2018-04-27 10:11:33 -05:00
Levi Baber
dfc4a2aef1 bcftools: new version (#7930) 2018-04-26 22:48:01 -05:00
Sinan
581a240c86 add versions 3.4.3. and 3.5.0 (#7929) 2018-04-26 21:12:17 -05:00
Chris Green
6cc79f8142 Allow len(Version) to return number of split components. (#7918) 2018-04-26 15:38:43 -07:00
Levi Baber
310addea91 samtools: new version (#7921) 2018-04-26 17:17:00 -05:00
serbanmaerean
963c103a67 XL Fortran compiler >= 16.0 is synced with C compiler version (#7887)
* Use reported version of IBM XL Fortran compiler for compiler versions >= 16.0.

Starting with the April 2018 release, the IBM XL C and Fortran compilers report the same version, 16.0.  Consequently, there is no need to downgrade the Fortran compiler version to match that of the C compiler.
2018-04-26 14:50:14 -07:00
Sergey Kosukhin
0f35f00b6e Use GitLab's API endpoint for fetching a git snapshot. (#7881)
* Use GitLab's API endpoint for fetching a git snapshot.

* More GitLab packages use the API.

* find_list_url for GitLab's API URLs.

* Flake8

* Url for 'hacckernels'.

* Check GitLab API regexps before the non-API ones.
2018-04-26 16:40:11 -05:00
healther
8afdaa5805 add patch to get aspell to build on OSX (#7919) 2018-04-26 15:19:52 -05:00
健美猫
9dad069e89 config_args does NOT apply to CMakePackage. (#7917) 2018-04-26 13:03:45 -05:00
Simon Flood
6a99ca362f Add Trinity package (#7828)
* Add Trinity package

New package to install Trinity - another odd installer (assumes installation to /usr/local/bin and doesn't copy dot files hence deleting them)

* Update package.py

added dependencies from https://github.com/trinityrnaseq/trinityrnaseq/wiki/Installing-Trinity

* Update package.py

Copy tree to prefix.bin so that PATH can correctly be set for the Trinity command - can't split it off as it seems everything needs to stay together.

* Update package.py

Fixed over-length lines and space before comma
2018-04-26 09:11:58 -05:00
Sergey Kosukhin
fd85c1f0c0 Package 'gdbm': do not set CC. (#7912) 2018-04-26 08:44:17 -05:00
Geoffrey Oxberry
d54ceb6ce7 mfem: add valid range of hypre version numbers (#7903)
This commit fixes #7900.

In short: in the absence of constraints to the contrary, spack will
download the preferred version of a package, which is usually the most
recent non-develop version. On a clean spack installation without
hypre installed, `spack install mfem` will download hypre 2.14.0,
which is API-incompatible with mfem 3.3.2 (and earlier versions of
mfem), so spack will throw compiler errors re: the API mismatch.

This commit fixes that error by restricting mfem release versions
3.3.2 and earlier to hypre version 2.10.b to 2.13.999 (only 2.13.0
currently exists, but if it has a non-2.14.x maintenance release,
these versions of hypre should also be permitted).
2018-04-26 08:43:20 -05:00
Denis Davydov
2ec701d1dd adol-c: add boost optional dependency (#7905) 2018-04-26 08:42:03 -05:00
健美猫
3b82124d96 A new package: loki. (#7908)
* A new package: loki.

* Flake8.
2018-04-26 08:37:03 -05:00
Massimiliano Culpo
50122a585a
Added the latest versions of a few packages (#7910)
* automake: added version 1.16.1

* lmod: added version 7.7.29

* git: added version 2.17.0

* tmux: added version 2.7

* scala: added version 2.12.5, fixed typo in version 2.10.6

* Added spark@2.3.0, hadoop@3.1.0, jdk@8u172-b11

* picard: added version 2.18.3

* tar: added version 1.30
2018-04-26 14:46:45 +02:00
健美猫
e2092896b9 A new package: openslide. (#7906) 2018-04-26 07:17:15 +02:00
Bruno Turcksin
de9894a063 Add boost 1.67.0 (#7889)
* Add boost 1.67.0

* Remove boost 1.67.0 release candidate and the associated patch
2018-04-25 21:00:22 -05:00
mcneish1
94afb2430c Additional r packages (#7892)
* Add r-bbmisc

* Add r-dicekriging

* Add r-lhs

* Add r-mco

* Add r-misc3d

* Add r-mlr

* Remove boilerplate from r-mlr package

* Add r-mlrMBO

* Add r-parallelmap

* Add r-paramhelpers

* Add r-plot3d

* Add r-rgenoud

* Add r-smoof

* Add r-rinside 0.2.14

* Fix flake8 issues

* Add specific required versions

* Add more up-to-date versions of r-{mco, mlr, mlrMBO, smoof}
2018-04-25 20:59:46 -05:00
Robert Pavel
28901c8104 Added OpenMP Variant for Kokkos (#7902)
Added OpenMP variant for kokkos that can be disabled to build and test
on platforms where OpenMP is not available or desired. Also updated
version list
2018-04-25 10:50:58 -05:00
Levi Baber
a4e786a415 openmpi: libfabric support, ucx cleanup (#7842)
* openmpi: libfabric support, ucx cleanup

* openmpi: remove unnecessary parentheses
2018-04-25 10:37:48 -05:00
Levi Baber
7120e59c6a Libfabric: updating fabrics & adding deps (#7838)
* libfabric: mxm deprecated, adding mlx aka ucx

* libfabric: adding dependencies that we have in spack
2018-04-25 10:35:36 -05:00
Levi Baber
14e0307f04 ucx: needs numactl and rdma-core (#7836) 2018-04-25 10:34:55 -05:00
Levi Baber
a7ecb0364a psm: new package (#7834)
* psm: new package

* psm: setting latest stable to preferred
2018-04-25 10:34:31 -05:00
Levi Baber
0b284b45db rdma-core: new package (#7835)
* rdma-core: new package

* rdma-core: change to platform conflict
2018-04-25 10:33:30 -05:00
Levi Baber
a21571e737 libnl: new package (#7833)
* libnl: new package

* libnl: change platform constraint to a conflict
2018-04-25 10:33:01 -05:00
Sajid Ali
24f15a5f4b Added checksums for newer versions of numpy (#7853)
*  Committer: sajid <sajid@xrmlite.phys.northwestern.edu>

	modified:   var/spack/repos/builtin/packages/py-numpy/package.py

* Corrected typo

* removing whitespace

* remove whitespace

* remove whitespace, if not will do this in vim
2018-04-25 10:30:25 -05:00
Eric
4fdd24effa py-testinfra: Create new package (#7883)
* py-testinfra: Create new package

* py-testinfra: flake8 fixes

* py-testinfra: fix pytest version dependency

* py-testinfra: fix py-importlib version dependency
2018-04-25 10:29:45 -05:00
Levi Baber
0d5dd96762 fabtests: new package (#7837)
* fabtests: new package

* fabtests: fix hashes for github archive behavior & add libfabric dep

* fabtests: both versions confirmed working

* fabtests: use developer provided archive
2018-04-25 10:29:29 -05:00
健美猫
48a3cc67fc Add a new package: gloo. (#7894)
* Add a new package: gloo.

* Remove dependencies.
2018-04-25 10:05:16 -05:00
健美猫
fca267468e Add a new package: cpuinfo. (#7895) 2018-04-25 10:04:45 -05:00
健美猫
7095d4f414 Add a new package: fp16. (#7896) 2018-04-25 07:30:07 -05:00