Commit graph

7373 commits

Author SHA1 Message Date
Satish Balay
d071c6d341 petsc: configure works with python3 in current petsc@develop - and will work in future releases [3.11+] (#10380) 2019-01-26 16:28:20 +01:00
Matthias Diener
f299507fa9 diffutils: add version 3.7 (#10406) 2019-01-26 16:26:47 +01:00
Matthias Diener
2826d37a45 rust: add version 1.32.0 (#10407) 2019-01-26 16:26:16 +01:00
Ricardo Silva
3fc8203b93 bcftools: do not use bundled htslib (#10445)
* if the path to htslib is not specified the bundled one is built instead
* additionally this fixes the build with the intel compiler
2019-01-26 16:21:04 +01:00
Chuck Atkins
e867319ac3 perl-data-dumper: New package (#10425)
This package is added to satisfy a build time dependency for llvm-openmp
2019-01-26 16:16:03 +01:00
Chuck Atkins
76c757de22 libuv: Bump version to 1.25.0 (#10423) 2019-01-26 16:11:45 +01:00
Chuck Atkins
3266c69352 cmake: Use system libs by default (#10424)
This also fixes the libuv version dependency for 3.11+
2019-01-26 16:11:32 +01:00
wspear
68eb2a1418 Added the py-send2trash package as a pre-req for py-jupyterhub (#10441) 2019-01-26 16:10:02 +01:00
Piotr Luszczek
b94c8c2d53 magma: add version 2.5.0 (#10438) 2019-01-26 16:03:05 +01:00
Levi Baber
248452df4f capstone: new package (#10449) 2019-01-26 15:52:39 +01:00
sameershende
7d12ff6e16 Update ecp st tau pdt (#8192)
* Updated MPI and TAU versions in the TAU package
* Updated PDT versions
* Added support for Python (+python), default to `False`
* Cleaned up binutils, python, mpi usage.
* Updated binutils install to add additional header files to the include/extra directory.
* Resolving review problems with TAU and binutils packages.
  The binutils package was updated to include support for installing
  the ELF headers as a +headers variant.  The TAU package was updated
  to use all known Spack dependencies.
2019-01-23 20:40:58 -08:00
Justin Stanley
9252f7f957 trinotate: remove perl-dbd-mysql, move runtime files to HOME (#9850) 2019-01-22 14:26:31 -06:00
Justin Stanley
7baea68278 r-gamlss: new package (and data) at 5.1-2 (#10360)
* r-gamlss-data: new package at 5.1-0

* r-gamlss-dist: new package at 5.1-1

* r-gamlss: new package at 5.1-2

* r-gamlss: add mass, survival, nlme imports
2019-01-22 14:25:57 -06:00
Justin Stanley
bb942e1fc5 entrezdirect: new package (#10374) 2019-01-22 14:25:10 -06:00
Justin Stanley
4b7510ec38 py-whatshap: new package at 0.17 (#10377)
* py-whatshap: new package at 0.17

* py-whatshap: remove unused build_args
2019-01-22 14:24:45 -06:00
Justin Stanley
c1a1415e90 r-rrcov: new package at 1.4-7 (#10387) 2019-01-22 14:22:37 -06:00
Justin Stanley
e8014be017 r-robust: new package at 0.4-18 (#10391) 2019-01-22 14:22:24 -06:00
Justin Stanley
1bcc6e4d9c r-dynamictreecut: new package at 1.63-1 (#10388) 2019-01-22 14:22:09 -06:00
Peter Scheibel
c0972a3260
Exclude system mkl installs from numpy (#10383)
Fixes #10361
Fixes #6634

When mkl isnt in the spec, still write an explicit mkl entry to
prevent numpy from looking in system dirs and using a system install
of mkl. Do the same for openblas and atlas (although mkl was the only
system install reported to interfere with Spack's choice).
2019-01-22 12:18:54 -06:00
Justin Stanley
636d6007ba py-pyvcf: new package at 0.6.0 (#10375) 2019-01-22 17:11:19 +01:00
Justin Stanley
bb1f8b0e3e py-pyfaidx: new package at 0.5.5.2 (#10376) 2019-01-20 14:16:43 +01:00
Matthias Diener
ab00de9e81 cmake: add version 3.13.3 (#10397) 2019-01-20 14:14:37 +01:00
Jon Rood
e896ce7457 Update Nalu-Wind and dependencies (#10204)
* Updating nalu-wind, nalu, openfast, and tioga packages. Includes
  improved handling of +shared variant.
* Add fftw and catalyst support to nalu-wind.
* Restrict ParaView to use matplotlib versions before 3 (which
  require Python 3)
2019-01-18 18:43:59 -06:00
Owen Solberg
7a2315aa38 adding checksum for latest lmod release (#10381) 2019-01-18 08:49:26 +01:00
Hadrien G
3497098978 Update templight pseudo-release to remove need for patching (#10290)
* Update templight+LLVM combo

* Bring back old pseudo-release
2019-01-16 10:36:34 -06:00
Massimiliano Culpo
4bc3936004 Openblas: added version 0.3.5 (#10364) 2019-01-16 08:11:07 -06:00
sknigh
b31ecb0342 Added latest version of singularity 2.x (#10354) 2019-01-16 13:14:32 +01:00
George Hartzell
1f9fe02309 Add package for Hugo (static website generator) (#10358) 2019-01-16 13:11:15 +01:00
Tom Payerle
01bd67eb43 py-modred: New package (#10309)
* py-modred: New package

Parallelized python module for finding modal decompositions and
reduced order models.

* fix license
I think?

* Add dependency on py-numpy

and remove commented out code
2019-01-15 16:42:20 -06:00
sknigh
eaa340eba7 Added hpl 2.3 (#10345)
* Added hpl 2.3

* Added requested build fixes, added step to copy HPL.dat in 2.3+
2019-01-15 16:41:33 -06:00
Adam J. Stewart
d7fb3fd88e
r requires cairo+pdf (#10350) 2019-01-15 09:58:53 -06:00
Owen Solberg
2585c04b50 explicitly depend_on cairo with X **and** pdf variants (#10351) 2019-01-15 09:58:39 -06:00
Elizabeth Fischer
0628ebefd8 Add useful comment explaining why this is not needed for Python3. (#10326) 2019-01-15 07:31:20 -08:00
Axel Huebl
89a493522c openPMD-api: Dependency Update (#10314)
openPMD-api now only supports Python 3, needs a newer CMake and
ADIOS1 and also learned to read & write JSON :-)
2019-01-15 09:28:13 -06:00
Neil Flood
49dedb2443 vigra: new package (#10337)
* vigra: new package

* Better constraints and types on some depends_on. Use site_packages_dir variable for Python install dir. Explicit switch-offs where available. Change some local variables to suit style checks.

* Take care of lines too long

* Explicit WITH_HDF5=ON
2019-01-14 20:39:34 -06:00
Andrew Gaspar
04d4b07636 Add span-lite version (#10347) 2019-01-14 18:22:29 -06:00
sknigh
a1994d883c Added latest rust releases and develop branch (#10341)
* Added latest rust releases and develop branch

* Fixed spacing
2019-01-14 17:22:38 -06:00
Levi Baber
d1b7e560bd namd: fixing to reflect renamed charmpp per #9216 (#10342) 2019-01-14 17:22:03 -06:00
sknigh
43e6114db7 Added latest version of libfabric (#10343) 2019-01-14 17:21:33 -06:00
Geoffrey Oxberry
baf595351e feature: py-invoke: new python package (#10225) 2019-01-14 17:13:17 -06:00
George Hartzell
7abc2fb26d bugfix/gdk-pixbuf (#10312)
* docbook processing works correctly for gdk-pixbuf

1. The various bits of documentation in gdk-pixbuf include hardcoded
   references to dtd's and stuff at their canonical, Internet,
   locations.  BUT, gdk-pixbuf runs xslt-proc with the `--nonet`
   option, which forbids it from using the network.  Sadness ensues.

   Traditionally folks use XML Catalogs to map these to local copies.
   Our docbook-xsl package wasn't setting the appropriate env var in
   its dependents environments to use our catalog.

   Now it does.  Less sadness ensues.

2. If we're going to use these things, we should depend on them.

* Add gdk-pixbuf's bin to build environment

The "post-install.sh" script uses gdk-pixbuf-query-loaders, which was
installed earlier.

If py-psyclone can set its own bin on its PATH, so can we...

* Make gdk-pixbuf use recognizable docbook location

Our docbook-xsl package assumes that the canonical location is
`http://cdn.docbook.org/release/xsl/current/manpages/docbook.xsl`, but
the gdk-pixbuf's meson build script uses
`http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl`.

This means that our XML Catalog doesn't fix the reference and sadness
happens.

Just patch the build that we see what we want to see, then we can make
it all go away.

* Add commentary re docbook patch

* Make catalog helper a property

Thanks @adamjstewart!

* Run tests if/when run_tests is true

Thanks @adamjstewart!

* Tune up dependencies

Thanks @adamjstewart!

* Wordsmit commentary
2019-01-13 14:40:20 -06:00
Cyrus Harrison
9350db5665 update alpine ascent and friends (#10320)
This adds a lot of fixes and updates for alpine ascent and its dependencies:

* add support for static (via ~shared) and use vtk-m 1.2
* update vtkh package to output cmake configure file and pinning it to vtkm 1.2
* make conduit respect ~python
* fix ascent python logic
* consistant cmake usage
* conditionally add tbb in ascent if vtkh
* enable openmp
* more robust handling of variants
* update ascent and conduit for static builds
* add optional support for mfem in ascent
* enable mfem conduit support for ascent
* add optional adios dep to conduit
* remove ver req from conduit
* ascent: remove confusing comment
* tweaks to conduit and ascent pkg recipes
* fix typo in conduit package
* pref conduit master
* changing mfem to depend on conduit@master to get updated relay
* restore use of conduit 0.3.1 or greater for mfem
* set master as preferred conduit version
* allow mfem to use conduit master
* adding rover package and editing ascent
* updating vtkm cmake dep
* guard ascent python support on +shared
* removing rover to simply ascent package
* add fortran variant to conduit, to allow us to turn off conduit support even when a fortran compiler is specified
* fix fortran compiler check so it can work on cray systems
* working towards cuda fix for vtkm lagrange filter
* update ascent package with more variants, and patch to avoid nvcc issue
* hdf5 flags fix for BGQ
* add post install test
* add testing to ascent
* add testing of the using-with-make example
* add ctest output on error for run_tests
2019-01-12 17:43:39 -08:00
Jiawei Zhuang
07d9d444ea Added osu-micro-benchmarks@5.5 (#10333) 2019-01-12 17:31:13 -08:00
George Hartzell
6c638600d7 Add libxslt v1.1.33 info (#10328) 2019-01-12 17:36:53 -06:00
Denis Davydov
09033e991e dealii: does not support sundials 4.x (#10324) 2019-01-12 15:28:57 -06:00
Neil Flood
04c1af0ee2 gdal: Add variant for GRIB driver (#10322) 2019-01-12 10:33:18 -06:00
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