Commit graph

11319 commits

Author SHA1 Message Date
Toyohisa Kameyama
0477f829a2
xabclib: added package at v1.03 (#16271) 2020-04-27 13:33:28 +02:00
asmaahassan90
35717b556b
spglib: added libs property (#16318) 2020-04-27 13:26:10 +02:00
Christoph Junghans
3ea21fef4b
votca-csg: Block gromacs@2020 and newer (#16315) 2020-04-27 04:57:26 -06:00
Toyohisa Kameyama
ca4de491ba
ppOpen-APPL/AMR-FDM: New package (#16199)
* ppOpen-APPL/AMR-FDM: New package

* separate build and install.

* Fix description.
2020-04-26 22:09:06 -05:00
Axel Huebl
4f3cc19ec7
qt: fix macOS w/ AppleClang (mesa libs) (#16302)
Building the `py-jupyter` stack on macOS with AppleClang breaks on
the `py-qtconsole` -> `py-qtconsole` -> `qt +opengl` package build
environment setup with:
```
 ==> Error: AttributeError: Query of package 'mesa' for 'libs' failed
 ...
 ==> Error: Failed to install qt due to ChildError: AttributeError: Query of package 'mesa' for 'libs' failed
```

This tries to add more library targets build by `mesa` to avoid this.
2020-04-26 17:07:13 -07:00
Axel Huebl
199ce66a3c
libpciaccess: mirror (#16312)
Support mirrors for libpciaccess downloads.
2020-04-26 17:06:37 -07:00
Axel Huebl
af7e323f67
libbsd: mirror (#16313)
Add a mirror for `libbsd` to improve fetch stability.
libbsd.freedesktop.org sometimes failes in my nightly CI/CD scripts.
2020-04-26 17:06:27 -07:00
Axel Huebl
e8efeda14a
py-profilehooks (new package) (#16305)
Adds the py-profilehooks package.
2020-04-26 17:08:21 -05:00
Axel Huebl
f202023876
py-blosc (new package) (#16307)
Add the py-blosc python package.
2020-04-26 11:46:40 -05:00
Axel Huebl
31e8d646af
py-h5py: master (new version) (#16306)
Add the `master` branch of h5py as a version.
2020-04-26 11:45:04 -05:00
Adam J. Stewart
63a0647282
PyTorch: disable XNNPACK build (#16304) 2020-04-26 11:29:52 -05:00
Axel Huebl
75042c381c
LLVM lldb 10.0: Python Link Dependency (#16299)
* LLVM: Python Dependency

Effort to expose the linked python library when building LLVM.
This might fix the forward propagation of libintl that comes
with the static python library build on darwin.

* LLDB Py: Remove Ignored Old Flags

Changed in LLVM 10.0+
2020-04-25 21:36:08 -07:00
Adam J. Stewart
4cd537f6c7
py-pyyaml: add new version and variant (#16301) 2020-04-25 15:43:14 -05:00
Adam J. Stewart
b5be99cdb7
libyaml: add new version (#16300) 2020-04-25 15:42:40 -05:00
Sajid Ali
9b0e4cd20b
ucx : add version, modify variants (#16252)
* fixes

* remove extra newline
2020-04-25 12:39:33 -05:00
Adam J. Stewart
9bd0b0fbe1
py-spacy: add new package (#16293) 2020-04-25 10:35:57 -05:00
Jonathon Anderson
b796d2736c
Version bump: jdk 14 (#15821) 2020-04-25 10:35:33 -05:00
Adam J. Stewart
5fce2ac96b
py-thinc: add new package (#16295) 2020-04-24 23:50:56 -05:00
Joseph Ciurej
914f380bb6
Improved the accuracy of the dependencies for the 'visit' package. (#16297)
Added a fix for the 'visit' package when building variant '@3%gcc'.
2020-04-24 21:25:48 -05:00
Adam J. Stewart
b5bf816577
py-preshed: add new package (#16292) 2020-04-24 21:24:33 -05:00
Adam J. Stewart
d0ccab7d17
py-srsly: add new package (#16294) 2020-04-24 20:01:22 -05:00
Adam J. Stewart
dbd0fe8190
py-wasabi: add new package (#16296) 2020-04-24 20:01:09 -05:00
Adam J. Stewart
7a2f47d181
py-plac: add new package (#16291) 2020-04-24 20:00:55 -05:00
Adam J. Stewart
510d8821e5
py-nltk: add new package (#16290) 2020-04-24 20:00:42 -05:00
Adam J. Stewart
0ee023d29f
py-murmurhash: add new package (#16289) 2020-04-24 20:00:28 -05:00
Adam J. Stewart
ab87617d55
py-cymem: add new package (#16288) 2020-04-24 20:00:15 -05:00
Adam J. Stewart
3153610bb8
py-catalogue: add new package (#16287) 2020-04-24 20:00:02 -05:00
Adam J. Stewart
441c16bafb
py-blis: add new package (#16286) 2020-04-24 19:59:48 -05:00
Adam J. Stewart
89914f521e
py-wheel: add new version (#16285) 2020-04-24 19:59:30 -05:00
Adam J. Stewart
0606091775
py-tqdm: add new version (#16284) 2020-04-24 19:59:15 -05:00
Toyohisa Kameyama
051d0d935a
Chainer: New Package. (#16251)
* Chainer: New Package.

* 1. Add maintainers.
2. fix dependency.
3. Add typing-extention@3.6.6 and fix version dependency.

* afixed dependency.

* remove python dependency for version 6.
2020-04-24 11:56:10 -05:00
Adam J. Stewart
433a0b243f
oneDNN: add new version (#16267) 2020-04-23 19:50:22 -05:00
Jeffrey Salmond
9b3a0355bb
add fontconfig as vim dependency (#16268) 2020-04-23 19:50:05 -05:00
Christoph Junghans
a844467c25
eospac: prefer 6.4.0 (#16266) 2020-04-23 15:53:51 -06:00
Mark W. Krentel
686f0e21de
libunwind: add 1.4.0 release and 1.5 stable branch (#16261) 2020-04-23 12:34:19 -05:00
Andrew Gaspar
2a3942fa4c
Rust 1.43.0 (#16260) 2020-04-23 12:33:02 -05:00
Andrew W Elble
d5d232e207
tensorflow: compile against spack-provided protobuf (#16258)
This allows horovod to be built with frameworks=pytorch,tensorflow.

I tracked down the crash I observed in #15719, where loading torch
before tensorflow would cause a crash in:

google::protobuf::internal::(anonymous
namespace)::InitSCC_DFS(google::protobuf::internal::SCCInfoBase*)

The solution is to make tensorflow compile against the protobuf
version Spack provides, instead of allowing it to use it's own.
It's likely we'll want to go after some of the others
that are listed in third_party/systemlibs/syslibs_configure.bzl
in the future.
2020-04-23 11:14:09 -05:00
jthies
ca67df6e3d
phist: don't apply patch to 1.9.0 (#16257) 2020-04-23 11:11:54 -05:00
darmac
6cad7a585d
Go: support for aarch64 (#16083) 2020-04-23 11:01:20 -05:00
darmac
df2cfd26cd
ambari: added package at v2.7.5 (#16149) 2020-04-23 12:43:12 +02:00
Michael Kuhn
b1133cb5db
py-setuptools: added v44.1.0 and v46.1.3 (#16171) 2020-04-23 10:09:09 +02:00
Michael Kuhn
f07cdd7f7a
openssl: added 1.1.1g (#16247) 2020-04-23 10:01:23 +02:00
darmac
807a08a69b
enca: added package at v1.19 (#16255) 2020-04-23 09:59:32 +02:00
Joseph Ciurej
044985af80
cryptopp : added 'shared' variant and sse detection (#16213) 2020-04-23 09:38:10 +02:00
darmac
7c0aee4127
cpp-httplib: added package at v0.5.9 (#16228) 2020-04-23 09:35:14 +02:00
darmac
04457fe031
Py coilmq (#16203)
* Add new package: py-coilmq

* remove FIXME comment

* fix depends_on
2020-04-22 23:13:44 -05:00
darmac
fb1498abac
Add new package: dnsmasq (#16253) 2020-04-22 23:13:04 -05:00
darmac
15882d7868
Add new package: py-django (#16234) 2020-04-22 23:09:06 -05:00
darmac
7299de74c6
Add new package py-sqlparse (#16231)
* Update var/spack/repos/builtin/packages/py-sqlparse/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Add new package py-sqlparse

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-22 20:40:25 -05:00
Axel Huebl
d0bff870a6
macOS+GCC: Conflicts CMake, libuv, CPython (#16249)
The major building blocks in many software stacks:
- CPython
- CMake (libuv)

do not build on macOS with GCC. The main problem is that some macOS
framework includes pull in objective-c code and that code does get
misinterpreted as (invalid) C by GCC by default.
2020-04-22 19:41:33 -05:00
Vicente Adolfo Bolea Sanchez
4166c97a82
vtk-m: update Vtk-m pkg to its latest version v1.5.1 (#16192)
Last month VTK-m releases its lastest version named `v1.5.1`. This new
release only contains bugfixes related to compiler error / warnings.

- Depends on CMake >= 3.12
- Set VTKm_NO_ASSERT=ON by default
- add maintainers

Signed-off-by: Vicente Adolfo Bolea Sanchez <vicente.bolea@kitware.com>
2020-04-22 18:54:55 -05:00
Mark W. Krentel
ec54f86c0b
gotcha: add version 1.0.3 (#16239) 2020-04-22 16:48:41 -05:00
Kelly (KT) Thompson
650745746a
Provide new version 0.6.10. (#16240) 2020-04-22 16:34:58 -05:00
Greg Becker
ec23e4ffe5
update compiler config with bootstrapped compiler when already installed (#16221)
Update compiler config with bootstrapped compiler when it was already installed and added config defaults to code so mutable_config test fixture works.
2020-04-22 14:26:29 -07:00
Adam J. Stewart
46e90692e8
PyTorch: add conflict for Apple Clang 11.0.3 (#16238)
* PyTorch: add conflict for Apple Clang 11.0.3

* Flake8 fix
2020-04-22 15:47:14 -05:00
Tim Haines
0d2ebbf996
hwloc: Add netloc variant (#16001)
hwloc depends on MPI when netloc is enabled. Note that OpenMPI depends on
netloc, so hwloc cannot use OpenMPI as the MPI provider when netloc is
enabled (this would result in a cyclic dependency).
2020-04-22 13:34:32 -07:00
darmac
b874b3e1fe
Add new package: isc-dhcp (#16230) 2020-04-22 11:23:40 -05:00
darmac
169b9bebd8
Add new package: kea (#16232) 2020-04-22 11:17:30 -05:00
darmac
769f350802
Add new package: py-asgiref (#16233) 2020-04-22 11:16:49 -05:00
Rao Garimella
d77576d85d
update Jali version and dependent MSTK version (#16236)
Co-authored-by: Rao Garimella <rao@abyzou.lanl.gov>
2020-04-22 11:12:28 -05:00
Cameron Smith
e7906d6507
kokkos: generate_makefile calls cmake (#16237) 2020-04-22 11:11:55 -05:00
Sajid Ali
5f285fdd05
fix code-signing on macOS (#15592)
* rebase

* move if statement location

* remove whitespace

* spec to self.spec

* switch statements as per review

* fix erronous indent

* add missing cmake arg

* minor placement fix for cmake args

* edit comment

* fix erronous return

* clarify conflicts with messages

* remove duplicate comment

* simplify logic

* macos wasn't a variant, fix that

* remove extra blank line

* address reviewer comments on spaces
2020-04-22 09:49:07 -05:00
darmac
2a5592f419
Add new package: py-pid (#16202)
* Add new package: py-pid

* fix depends_on
2020-04-22 09:47:45 -05:00
asmaahassan90
d65b809f9b
Add new versions to Avizo (#16204)
* Add new versions

add versions 2019.3 and 2019.4 and adjust the install stage accordingly

* one small fix

* fix lint

* re-ordering the versions
2020-04-22 09:44:03 -05:00
Joseph Ciurej
0419f2c6df
Updated 'qt' to support '@5.12.7', '+debug', and '+opengl' with older OpenGL versions. (#16220) 2020-04-22 09:29:40 -05:00
Kelly (KT) Thompson
9c2819bdb3
libsm: added libuuid as dependency (#16226)
While building _visit_, I ran into an undefined symbol at link time. I tracked
the missing dependency to _libsm_ needing to know about _libuuid_ at link time.
2020-04-22 14:53:01 +02:00
darmac
be0aed9d8a
libcgroup: added package at v0.41 (#16229) 2020-04-22 13:19:01 +02:00
Jeffrey Salmond
b065150354
metis: fix build when version > 5.0 (#16186) 2020-04-22 12:18:38 +02:00
Elizabeth Fischer
0b753b9a77
py-pyproj: added v2.6.0 (#16176)
Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
2020-04-22 11:50:36 +02:00
Servesh
3e9af610e7
source-highlight: fix detection of boost (#16102)
Co-Authored-By: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-04-22 11:43:02 +02:00
darmac
ab35780fae
buddy: added package at v2.4 (#16166) 2020-04-22 10:55:07 +02:00
darmac
4c9c6b2a68
linux-pam: added package at v1.3.1 (#16137)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-22 10:53:28 +02:00
darmac
1e243023d8
cmaq: added new package at v5.3.1 (#16224)
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-22 08:56:13 +02:00
jthies
ac228050ab
Phist int64 variant (#16209)
* phist: add int64 variant and resulting conflicts and dependencies

* phist: use Trilinos TPLs as soon as they are in the spec, not just if +trilinos isexplicitly set
and remove a redundant depends-statement

* phist: use int as gotype for Trilinos dependency if ~int64

* phist: new version 1.9.0

* phist: remove trailing whitespace

* phist: updated checksum (version tag was moved)
2020-04-21 23:10:11 -05:00
darmac
1289d3589a
Add new package: cmockery (#16225) 2020-04-21 23:01:49 -05:00
Axel Huebl
2f7e940872
Fix: Flex Reconfigure (#16194)
* Fix: Flex Reconfigure

Learn the `flex` package how to reconfigure itself when needed.
Fix #11551

Co-authored-by: Andrew W Elble <aweits@rit.edu>

* Autoreconf: only when actually desired

Co-authored-by: Andrew W Elble <aweits@rit.edu>
2020-04-21 22:36:02 -05:00
Andrew Gaspar
667fee0703
catch2 2.12.1 (#16211) 2020-04-21 16:52:50 -07:00
Joseph Ciurej
272c47207d
Updated the 'opengl' package to include all older versions of the library. (#16219) 2020-04-21 16:20:45 -05:00
Adam J. Stewart
54ca52943d
PyTorch: add 1.5.0 (#16212) 2020-04-21 16:20:11 -05:00
Michael Kuhn
f3aceddbfb
py-tap-py: Add 3.0 and 2.6.2 (#16169) 2020-04-21 16:09:14 -05:00
Gregor Daiß
745804582b
Add new package: sgpp (#15961)
* sgpp: Added recipe

* sgpp: Removed maintainer and updated patch

* sgpp: Added more conflicts

* sgpp: Added conflicts for older combigrid versions

* sgpp: Added one more maintainer

* sgpp: Add version 3.3.0 and sane defaults

* sgpp: Better description and c++11 conflicts

* sgpp: Updated maintainers

* sgpp: Fix flake8 errors

* sgpp: Fix dependencies and minor issues

- Added py-setuptools dependency
- Fixed zlib link dependency
- Added git url
- Using spec.satisfies where appropriate

* sgpp: Added testing to package

* sgpp: Remove simd variant and use spec instead

* sgpp: Remove java variant

* sgpp: Small bugfixes

* sgpp: Add datadriven patch and patch explanations
2020-04-21 16:03:46 -05:00
Glenn Johnson
74c159b883
New package: sumo (#16096)
* New package: sumo

This PR adds the sumo package, as well as the fox package as a
dependency. It also updates and adds some fixes for openscenegraph.

For fox, the patch is for the development version. That patch should not
be necessary in future versions as it has been applied upstream. The
stable version is 1.6.57 and is marked as preferred. This is the version
needed for sumo.

Added dependencies for openscenegraph as well as set constraints on qt
versions.

* Update var/spack/repos/builtin/packages/sumo/package.py

I had intended to set this version constraint but somehow did not.

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Add dependency types to sumo recipe

- googletest: 'test'
- swig: 'build'
- java: 'build', 'run'

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-21 13:27:34 -05:00
Adam J. Stewart
4f5bd044d6
py-torchvision: add new version (#16208) 2020-04-21 11:43:30 -05:00
Michael Kuhn
b9655636ce
gettext: Fix typo (#16206) 2020-04-21 08:48:48 -07:00
Andrew Gaspar
a41b9365a9
catch2: added v2.12 (#16207) 2020-04-21 17:15:59 +02:00
Michael Kuhn
cd5d477db9
qgis: Fix pkgconfig dependency (#16188) 2020-04-21 08:02:45 -05:00
Axel Huebl
6c8e15ee18
gettext: add missing iconv dependency (#16193)
`gettext` will pick up a random `iconv` dependency if not
specified, which crashes python and its own builds on macOS.
2020-04-20 21:47:04 -07:00
Christoph Junghans
ca86e56572
votca-*: remove rc versions (#16197) 2020-04-20 20:30:43 -06:00
darmac
e4805bb75f
Add new package: sse2neon (#16168) 2020-04-20 16:59:51 -05:00
Adam J. Stewart
45fee6edbd
Python: add latest Python 2 releases (#16191) 2020-04-20 16:57:08 -05:00
G-Ragghianti
5e69125e51
Implemented +shared and +static_tools variants (#16105) 2020-04-20 16:54:44 -05:00
Toyohisa Kameyama
c6ef9c2b87
Add ppOpen-APPL/FDM and ppOpen-APPL/FDM-AT. (#16116) 2020-04-20 16:36:36 -05:00
Toyohisa Kameyama
8e7f55e6d6
ppOpen-APPL/DEM-util: New package (#16120) 2020-04-20 16:29:06 -05:00
darmac
c2ca832883
Add new package: audacious (#16121) 2020-04-20 16:24:33 -05:00
darmac
e8a7e4f5ec
Add new package: bgpdump (#16122) 2020-04-20 16:23:47 -05:00
darmac
cf12541281
Add new package: byacc (#16123)
* Add new package: byacc

* refine byacc info
2020-04-20 16:22:37 -05:00
Amjad Kotobi
a70e76d043
Package Bonniepp adding sbin to PATH (#16124) 2020-04-20 16:19:55 -05:00
Michael Kuhn
8635c0d804
rocksdb: Add 6.7.3 (#16189)
This also adds a shared variant, so we can build both the static and
shared libraries at the same time. It also adds a pkg-config file.
2020-04-20 16:16:51 -05:00
Michael Kuhn
e3966d2791
pixman: Add 0.40.0 (#16190) 2020-04-20 16:16:39 -05:00
Amjad Kotobi
78f1940646
update package py-graphviz version (#16131) 2020-04-20 16:11:07 -05:00
Hadrien G
ac17d0783a
Add Acts v0.22 (#16141) 2020-04-20 16:08:44 -05:00
darmac
eb0d82a7e4
Add new package: codec2 (#16142) 2020-04-20 16:07:44 -05:00
darmac
126491288a
Add new package: libsamplerate (#16143) 2020-04-20 16:07:18 -05:00
darmac
cab1d06d6a
Add new package: collectd (#16144) 2020-04-20 16:06:31 -05:00
darmac
ed13319a4b
Add new Package: accumulo (#16148) 2020-04-20 15:59:16 -05:00
Justin S
73e0dd9f61
prism: new package at 4.5 (#16187) 2020-04-20 15:39:53 -05:00
Michael Kuhn
1f49fb8ceb
python: Add 3.7.7 (#16170) 2020-04-20 15:32:58 -05:00
Elizabeth Fischer
742a4b7e2a
proj (#16175)
Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
2020-04-20 15:21:36 -05:00
Elizabeth Fischer
3a9ce3ac4a
glib (#16179)
Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
2020-04-20 15:15:38 -05:00
Adam J. Stewart
0db2f00635
PyTorch: remove CUDA conflicts (#16136) 2020-04-20 14:57:56 -05:00
Todd Gamblin
de13ea2284
autotools: remove FORCE_UNSAFE_CONFIGURE from docs, commands, code (#16145)
Since #16132, we've consolidated the setting of FORCE_UNSAFE_CONFIGURE to
`autotools.py`, so we don't need to use it in packages like `coreutils`,
in our commands, or in our container recipes.

- [x] Remove FORCE_UNSAFE_CONFIGURE from packages
- [x] Remove FORCE_UNSAFE_CONFIGURE from container recipes
- [x] Remove FORCE_UNSAFE_CONFIGURE from `spack ci` command
2020-04-20 08:32:03 -07:00
darmac
e9e2d1d3ca
Httpd: added package at v2.4.43 (#16152) 2020-04-20 09:32:39 +02:00
Glenn Johnson
dff5a4ba57
ngmerge: added package at v0.3 (#16160) 2020-04-20 09:26:22 +02:00
Adam J. Stewart
9a522505e4
Cython: add new version (#16159) 2020-04-19 19:30:21 -05:00
Adam J. Stewart
f9733058a4
NumPy: add new version (#16158) 2020-04-19 17:28:18 -05:00
Toyohisa Kameyama
f1d48a2a8e
FrontFlow/Red: New Package. (#15965)
* FrontFlow/Red: New Package.

* fix comment.
use libs.ld_flags.

* typo fix.

* typo fix.
2020-04-18 22:58:43 -05:00
Veselin Dobrev
d9992a778f
CEED v3.0 release (#15500)
* [mfem] A few updates: add 'strumpack' variant; add 'zlib'
       variant (same as 'gzstream'); fix optmization flag
       for v4.0.

* [mfem] flake8 fix

* [mfem] Add version 4.1

* [mfem] Add/tweak some 'conflicts' directives.

* [gslib] Add new release versions + 'develop' version.

* [petsc] Restrict hdf5 version to <= 1.10.99 since 1.12.0 fails

* [metis] Use the original metis url for v4.0.3.

* [conduit] Remove restrictions to the used hdf5 variant to allow
          building with other packages that use hdf5, e.g. petsc.

* [mfem] Few updates:
* Replace the 'gzstream' variant with 'zlib' variant.
* Do not add system library paths with -L flags.
* Allow '+pumi+shared' variant.
* Update the 'test_builds.sh' script.

* [occa] Add version 1.0.9.

* [mfem] Some OCCA and RAJA updates.

* [gslib] Fix the build for new versions of the library.

* [mfem] Add 'gslib' variant for GSLIB.

* [mfem] Add 'cuda' variant.

* [mfem] Add 'libceed' variant + a few more tweaks.

* [mfem] Add 'umpire' variant.

* [ceed] Add a draft for v3.0. Not tested. Just made sure that
       concretization works for 'ceed' and 'ceed+cuda'.

* [nek] Fix Nek5000/NekCEM

* [nek] Add Nek5000-v19 & polishing Nek packages

* [flake8] Fix flake8 failure

* petsc: use of HDF5 does not care about +hl+fortran

* [petsc] Temporarily allow any hypre version with petsc@develop.

[ceed] Remove the requirement for hypre@develop.

* [libceed] Do not explicitly set NVCCFLAGS for v0.5 and later.

* [laghos] Add version 3.0, pointing to dev branch for now.
         Do not set CXX at the make command line.
         Simplify the dependecy directives a little.

[ceed] Use laghos v3.0 for ceed v3.0.0.

* [laghos] Keep the injection of CXX in the makefile for laghos
         versions <= 2.0.

* [nekcem] Recovert hash-versions used by older versions of the
         'ceed' package.

* [occa] Disable hip autodetection because it fails on some machines.

* [laghos] Update v3.0 with the actual release source.

* [suite-sparse] Explicitly add the c11 flag to CFLAGS.

* Update package.py (#15749)

* [magma] Add forgotten specification of the 'cuda_arch' variant.

* [ceed] Use magma v2.5.3 for ceed v3.0.

* libceed-0.6

* mfem: depend on libceed 0.6:, not 0.6.0:

* [libceed] Add 'magma' variant -- enable MAGMA backend.

* [ceed] In v3.0, use '+magma' variant of libceed when cuda is enabled.

* Initial package for Remhos (needs to be updated with actual sha256

* Adding Remhos to CEED-3.0, for now @develop

* petsc: add 3.13.0 (using petsc-lite) and 3.12.5

* ceed: update to petsc@3.13.0:3.13.99

* Temporary fix

* [nekcem] Add hash-version for ceed v3.0.

* [nek5000] Simplify source urls.

* [nektools] Use the same sources and versions as in nek5000.

* [ceed] Update Nek-related package versions.

* libceed: add v0.6 portabilty fix

* libceed: better v0.6 portabilty fix

* Adding Remhos 1.0 release in CEED-3.0

* Updating hash for Remhos-1.0

* [petsc] Add cuda variant.

* [libceed] Flake8 fix.

* [petsc] Add cuda variant.

* [ceed] Fix the OCCA version to 1.0.9. Enable petsc+cuda when
       compiling ceed@3.0.0+cuda.

* nek5000: fix python 2.7+ syntax

* [laghos] Fix testing.

* [remhos] Fix testing.

* [remhos] For testing use the 'tests' target instead of 'test'.

* Add/update the maintainers for ceed, libceed, mfem, laghos, and remhos.

* [ceed] Remove unnecessary dependencies.

* libceed: activate AVX when supported

Co-authored-by: Thilina Rathnayake <thilinarmtb@gmail.com>
Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: Stan Tomov <tomov@eecs.utk.edu>
Co-authored-by: Tzanio <tzanio@llnl.gov>
2020-04-18 16:57:57 -07:00
Christoph Junghans
5d008dc37b
votca-*: add v1.6 (#16139) 2020-04-18 08:16:48 -07:00
Daryl W. Grunau
6cb11d489b
DDD bugfix (#16095)
* DDD: apply extended-prompt patch

* DDD: apply extended-prompt patch

* use the upstream patch

Co-authored-by: Daryl W. Grunau <dwg@lanl.gov>
2020-04-17 21:34:49 -05:00
Levi Baber
73d78ae176
py-cutadapt: add version 2.9 (#16135) 2020-04-17 18:35:33 -07:00
Adam J. Stewart
def1d5e637
MPFR: fix patch checksum, add dependencies (#15783)
* MPFR: fix patch checksum, add dependencies

* Update checksum again
2020-04-17 16:30:45 -05:00
Adam J. Stewart
28995b25bc
OpenMPI: add +cxx variant (#15477)
* OpenMPI: add +cxx variant

* C++ support will be removed in 5.0.X release
2020-04-17 16:29:50 -05:00
Adam J. Stewart
284e450c91
Language-specific PIC flags (#15474)
* Language-specific PIC flags

* Add tests for every compiler flag

* Fix bad rebase

* pic_flag -> cxx_pic_flag
2020-04-17 16:28:51 -05:00
Jordan Ogas
ad8977467b
charliecloud: fix url (#16133) 2020-04-17 13:51:18 -07:00
Nichols A. Romero
ebd86bd1eb
LLVM libomptarget fixes (#16104)
* Throw an error at spack install invocation instead of most of the way through the build process when cuda_arch is unspecified.

* Clean-up of CMake booleans. No actual change.

* Use CMake variables for hwloc and libelf installation directories and avoid injecting extra flags into CMAKE_CXX_FLAGS

* Conflict should only exist for +cuda variant.
2020-04-17 15:18:27 -05:00
Todd Gamblin
ac54b7d5c1 coreutils: add variant for g prefix
- [x] Add a `gprefix` variant to coreutils, so that the 'g' prefix on
  binaries is optional.
- [x] Make un-prefixed binaries the default again
2020-04-17 11:21:50 -07:00
Adam J. Stewart
85e089e3fa
NCCL: add new version (#16130) 2020-04-17 13:14:36 -05:00
Adam J. Stewart
435470a93b
oneDNN: add new version (#16129) 2020-04-17 13:14:22 -05:00
Andrew W Elble
985af94c45
singularity: new variants to enable non-suid and non-network builds (#16088)
Defaults are left as they are currently
2020-04-17 17:38:22 +02:00
ilbiondo
854a82bbec
New package: Biopandas python package (#16066)
* Biopandas python package

* Update var/spack/repos/builtin/packages/py-biopandas/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-biopandas/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* remove scipy dependency

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-17 09:50:33 -05:00
Stan Tomov
950180ab03
magma: added v2.5.3 (#16097)
Also updated maintainer list
2020-04-17 11:33:24 +02:00
Michael Kuhn
791e354b2a
py-gcovr: added new package at v4.2 (#16100) 2020-04-17 11:32:19 +02:00
darmac
4c81efcf0b
open-iscsi: added new package at v2.1.1 (#16113) 2020-04-17 11:11:19 +02:00
darmac
330454acb0
aespipe: added new package at v2.4f (#16114) 2020-04-17 11:05:48 +02:00
Kai Germaschewski
a8eef2f812
sz: run "make clean" after configure (#15759)
At least the v2.0.2.0 tar ball contains compiled object files etc, which
cause the build to fail on other architectures (ppc64le in particular), so
this patch adds a `make clean` after configuring first.
2020-04-17 10:59:42 +02:00
darmac
dd3378bda4
asdcplib: added new package at v2.10.35 (#16118) 2020-04-17 10:42:14 +02:00
Harmen Stoppels
81a154de4a
libtree: added v1.1.2 (#16119) 2020-04-17 10:30:05 +02:00
Axel Huebl
abbc47823d
SourceForge: Mirror Mixin (#16112)
* SourceForge: Mirror Mixin

Add a mixing class for direct `CNAME`s to sourceforge mirrors.
Since the main gateway servers are often down, this could reduce
timeouts and fetch errors for sourceforge.net hosted software.

* SourceForge: unspectacular mirror replacement

add mirrors to all sourceforge packages with trivial
download logic.

tested fetch of latest version of each of these packages
with various mirrors before committing.

* SourceForge: xz

the author homepage is chronocially overrun and this is the offical
upload with many mirrors.
2020-04-16 21:35:30 -07:00
Todd Gamblin
e476a9061b
bugfix: fix emacs support on macOS (#16110)
- fix missing self.spec
2020-04-16 17:40:37 -07:00
Axel Huebl
4d25632e59
macOS: Fix emacs Linking (#16106)
* macOS: Fix emacs Linking

Fix linking issue of emacs on macOS (clang and gcc).

Applies the same work-around as conda-forge:
  b051f6c928/recipe/build.sh

Homebrew avoids this by linking against the system ncurses lib:
  https://github.com/Homebrew/homebrew-core/blob/master/Formula/emacs.rb

* ncurses: fix outdated variant comment

this comment was build on the assumption that gnutls
triggers a termlib dependency in emacs. that's not the
case, ncurses itself depends on termlib when build with
this feature.
2020-04-16 17:30:24 -07:00
Axel Huebl
ddb6e99a28 libpng: github download
libpng still has its sourceforge page but is actively been
developed on github.

since the sourceforge urls are too often down (as seen in
my nightly CI/CD tests), just switch the download source to
GitHub instead.
2020-04-16 17:27:50 -07:00
Axel Huebl
bacbaeb563
ncurses: forward termlib libs (#16101)
These libs need to be forwarded, as in ncurses `pkg-config` file.
2020-04-16 17:27:30 -05:00
Axel Huebl
bb2849002b
emacs: libxml2 deps (#16103)
emacs depends on libxml2.
2020-04-16 17:27:09 -05:00
Glenn Johnson
07a4ac67b8
Add ncurses+termlib dependency to mesa (#16038)
Mesa links against libtinfo so needs to depend on ncurses. It also needs
a little help finding the library directory so an LDFLAGS configure
option is added.
2020-04-16 13:25:28 -05:00
Amjad Kotobi
2e4e34e6cc
New version xrootd-4.11.3 (#16092) 2020-04-16 12:53:20 -05:00
Carlos Arango Gutierrez
5d7f4db9ad
singularity: updated maintainer list (#16093) 2020-04-16 18:43:38 +02:00
athanasio
f912cce7ee
openbabel: fix compilation errors (#16090)
- Disable maeparser as it is broken with CMake
- Added missing dependencies
2020-04-16 10:49:43 -05:00
Amjad Kotobi
e1777c5708
New package bonniepp added (#16091) 2020-04-16 10:49:30 -05:00
Harmen Stoppels
7dcc8a5463
Add new version 1.1.1 (#16087) 2020-04-16 09:50:48 -05:00
Antonio Arena
fd3cdffb40
New matlab versions (#16086) 2020-04-16 09:50:14 -05:00
Axel Huebl
125fc2e611
MPark.Variant: GCC 7.3.1 Conflict (#16081)
* MPark.Variant: GCC 7.3.1 Conflict

Due to an ICE in this specific patch-release of GCC, compile
errors in downstream packages should be avoided with a clean
conflict.

* Fix superfluous spaces

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Fix typo

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-16 09:48:19 -05:00
Tiziano Müller
7c5fc6acea
dbcsr: expose all options, check openblas feats (#16034)
* dbcsr: expose all options, check openblas feats

* dbcsr: use Ninja to build, ensure serialized tests

* dbcsr: add myself as maintainer
2020-04-16 09:47:31 -05:00
asmaahassan90
7ac6f7fed9
Add Cubist (#16069)
* Add Cubist

* enhance recipe

* Not using OS module anymore

* remove white space

* Fix build shell

* make Flake8 happy

* use bash shell for build

* Convert it To MakefilePackage as per peer-review
2020-04-16 08:24:35 -05:00
ilbiondo
b0ec2788ab
HAL: added new package at v2.1 (#16085)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-04-16 12:19:20 +02:00
darmac
04c6a781b6
Add new package: zookeeper-benchmark (#16067)
* Add new package: zookeeper-benchmark

* refine zookeeper version

* refine zookeeper version variant

* remove unused variant
2020-04-15 23:33:45 -05:00
darmac
f66bd41d9a
Neo4j (#16068)
* Update var/spack/repos/builtin/packages/neo4j/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Add new package: neo4j

* refine neo4j package

* fix flake8 warning

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-15 20:45:46 -05:00
Harsh Bhatia
29e2475a68
update: memsurfer with python3 (#15636)
* update: memsurfer with python3

* flake8 compliance

* Update var/spack/repos/builtin/packages/memsurfer/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/memsurfer/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/memsurfer/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* removed build_type preferences at adamjstewart's suggestion

* Added build/run dependency on python3.7

as suggested by adam stewart

* more flake8 horror!

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-15 20:11:48 -05:00
Rao Garimella
05afce85fa
Upgrade MSTK versions (#16079) 2020-04-15 18:13:47 -05:00
Carson Woods
a28c127043
netcdf-cxx4: bugfix (#16080)
* Add new variants

* Fix missing config_args variable
2020-04-15 18:05:42 -05:00
Axel Huebl
d9630b572a x.org packages: mirror mixin
overhaul all x.org packages to use available mirrors.
2020-04-15 14:44:13 -07:00
wspear
999c8e3a67
Added maintainers (#16078)
Co-authored-by: Wyatt Spear <wspear@cs.uoregon.edu>
2020-04-15 16:07:57 -05:00
ilbiondo
e41ac9af8a
Sonlib (#16060)
* sonLib package as required by the HAL toolkit

* cleanup

* Update var/spack/repos/builtin/packages/sonlib/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/sonlib/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-15 16:04:06 -05:00
Kelly (KT) Thompson
fef4e80a6d
New package: py-cmake-format (#16055)
* New package py-cmake-format

* wrap long lines

* Fix package description formatting.
2020-04-15 16:01:50 -05:00
Harmen Stoppels
f072d24c98
Bump version of libtree (#16051) 2020-04-15 15:57:21 -05:00
Axel Huebl
e1e804168a Tests: Mirror Mixin Classes 2020-04-15 11:44:14 -07:00
Axel Huebl
7e5257e44a x.org: mirror mixin
According to my nightly CI/CD tests, x.org is another large provider
of software in common build chains that is often down.

Added a hand-selected amount of mirrors that is well up-to-sync.
Tested with `util-macros` that has a quite "recent" patch release.

Other packages to follow in an individual PR.
2020-04-15 11:44:14 -07:00
Federico Ficarelli
94aa368af8
Fix grcp@1.27.0: (#16052)
Current default version was missing a dependency.
2020-04-15 11:32:08 -05:00
darmac
6eee7b6bb8
Add new package: mrbench (#16062) 2020-04-15 11:25:49 -05:00
darmac
c470a8da6a
Add new package: kinesis (#16063) 2020-04-15 11:25:21 -05:00
Robert Pavel
8935406756
Added Laghos v3 to Proxy Apps v3 (#16070)
Also fixed upper bound for v2 apps
2020-04-15 11:13:07 -05:00
Michael Kuhn
a157b479c8
julea: New package (#16071) 2020-04-15 11:12:28 -05:00
ilbiondo
4afdaa5f4b
IQ-TREE: added new package at v1.6.12 (#16064) 2020-04-15 16:37:25 +02:00
ilbiondo
666bc844be
Phylobayes MPI: added new package at v1.8b (#16065) 2020-04-15 13:26:37 +02:00
Massimiliano Culpo
ff0ec9cf61
openfoam: set run environment by sourcing bashrc (#15949) 2020-04-15 12:21:02 +02:00
ilbiondo
d41e366d0d
py-sonlib: added new package (#16058)
Co-Authored-By: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-04-15 10:35:01 +02:00
Dan Lipsa
fd2e6ee50f
Apply same patch to version 10. (#15963) 2020-04-14 22:30:45 -05:00
Adam J. Stewart
69f7bae8fe
libssh2: fix linking on macOS (#16012)
* libssh2: fix linking on macOS

* Fix libgit2 linkage to libssh2
2020-04-14 17:10:45 -05:00
Tyler Reddy
cba5f71eee
MAINT: Charliecloud OSX error (#16049)
* MAINT: Charliecloud OSX error

* raise an appropriate error when attempting to build
Charliecloud on Mac OSX, since it will otherwise fail
with a more confusing configure stage link check failure

* Update var/spack/repos/builtin/packages/charliecloud/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* MAINT: PR 16049 revision

* remove an unused import

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-14 15:55:10 -06:00
Sajid Ali
9a18f8b1d7
fix typo (#16043) 2020-04-14 16:44:09 -05:00
Andrew W Elble
a031bc3166
new package: py-torch-nvidia-apex (#16050) 2020-04-14 16:43:30 -05:00
Carson Woods
993491c83c
Add new variants (#16047) 2020-04-14 16:01:57 -05:00
Adam J. Stewart
293e4e80f1
py-memory-profiler: add new version (#16048) 2020-04-14 14:54:28 -05:00
Tiziano Müller
f917f7149e
cp2k: add version 7.1 (#16037)
* cp2k: add version 7.1

* cp2k: add option to use COSMA for CP2K 8+
2020-04-14 13:33:49 -05:00
Carson Woods
8edd352c22
tau: remove deprecated variants (#16041)
* Add more tau variants

* Add more tau variants

* Remove deprecated packages

* Fix flake8 issue
2020-04-14 13:33:33 -05:00
Andrew Gaspar
98cdd8777a
Add support for pre-release builds of Rust (beta, master, nightly) (#16042) 2020-04-14 12:53:42 -05:00
Adam J. Stewart
94272cc7aa
py-tokenizers: add 0.5.2 (#16039) 2020-04-14 12:41:33 -05:00
Harmen Stoppels
f393355781
libtree: new package at 1.0.3 (#16036)
* Add new package libtree

* Fix linter issues
2020-04-14 11:39:52 -05:00
Tom Payerle
e10c134745
pfft: fix to handle 'precision' variant in fftw (#16029)
* pfft: fix to handle 'precision' variant in fftw

pfft had been checking for +double, etc. in fftw spec, which no longer
are present (replaced by Multivalued variant precision).

* pfft: fix to handle 'precision' variant in fftw

pfft had been checking for +double, etc. in fftw spec, which no
longer are present (replaced by Multivalued variant precision).

(amended to use more idiomatic checks as suggested by @alalazo)
2020-04-14 11:14:20 -05:00
Justin S
71fb29fccf
muscle: add 3.8.31 (#15974)
* muscle: add 3.8.31

* muscle: use build_directory property

* muscle: add url_for_version, fix version comparison
2020-04-14 11:13:16 -05:00
Axel Huebl
5acea35e82
sourceware.org: mirror urls (#15992)
sourceware.org is often quite overrun and times out or results in
certificate errors.

Since libffi, bzip2, elfutils, etc. are quite fundamental in
build chains, lets add some official mirrors.

libffi, bzip2, elfutils, lvm2, valgrind: add mirrors
2020-04-14 11:09:30 -05:00
Jordan Ogas
25e2548489
add charliecloud 0.15 (#16023) 2020-04-14 11:02:22 -05:00
Justin S
b131cc5ce0
py-vcf-kit: new package at 0.1.6 (#15976) 2020-04-14 15:51:52 +02:00
Antonio Arena
c6e257ae39
VMD: added new package at v1.9.3 (#16022) 2020-04-14 15:21:33 +02:00
darmac
5feed6bf6f
httpress: added new package at v1.1.0 (#15935) 2020-04-14 12:25:30 +02:00
Adam J. Stewart
723fd5a101
Rust: add missing dependencies (#16015)
* Rust: add missing dependencies

* 1.43.X won't support Python 3 either
2020-04-13 17:02:37 -05:00
Andrew W Elble
92edc68922
bazel: increase logging during build, set job limit (#16024)
To better help in troubleshooting build issues. Job limit might also
help with the memory limit issues we've been seeing.
2020-04-13 16:35:39 -05:00
Antonio Arena
0a6d9f4c55
Patch Mathematica (#16019)
* Patch Mathematica

Mathematica installer moves all files and directories from installation directory to a backup one. The problem is that it also moves .spack to this backup location. Once it's done it does not move .spack back where it was.

My patch creates a copy of .spack to /tmp then moves it back right before exiting the install call.

* Make lint happy

* Use Spack native copy()

As suggested in peer-review let's:
- Copy .spack to stage directory so I don't have to use random
- Use Spack native copy() to do these operations

* Use join_path to create paths

As per peer-review suggestion:
- Use join_path to create paths
- Use copy_tree since we're copying a directory that could have sub-directories
2020-04-13 13:22:29 -05:00
Kai Torben Ohlhus
0c28a271ae
suite-sparse: add version 5.7.2 (#16020)
Release notes: https://github.com/DrTimothyAldenDavis/SuiteSparse/releases/tag/v5.7.2
2020-04-13 11:03:30 -05:00
Jennifer Herting
0d364e71ec
New version: py-notebook@6.0.3 (#15975)
* Update package.py to include py-notebook 6.0.3 and sha

* Update package.py

* [py-notebook] updated py-tornado version requirements

* [py-notebook] reworked and reordered for readability

* [py-notebook] updated version requirement for py-jupyter-client

* [py-notebook] updated version requirements for py-jupyter-core

Co-authored-by: ehdeec <ehdeec@rit.edu>
2020-04-13 10:59:54 -05:00
Adam J. Stewart
b0a39bd905
py-sacremoses: add new version (#16018) 2020-04-12 23:03:19 -05:00
Dr. Christian Tacke
ab0101ec69
boost: Fix for Version Comparison on Newer Clang on Darwin (#16014)
Applying to boost @1.56.0:1.72.0 as that's the version
range, where this patch can be cleanly applied. I was not
able to test this myself, but got positive feedback.

See: https://github.com/boostorg/build/issues/440
See: https://github.com/macports/macports-ports/pull/6726
2020-04-12 22:26:57 -05:00
Glenn Johnson
9a0dd631d5
new package: BART (#16016)
* new package: BART

This PR adds the BART (Berkeley Advanced Reconstruction Toolset)
package.

Despite the presence of CMake files, this package builds with a
Makefile. It looks like the project is moving away from cmake. The patch
for MKL has been committed upstream so should only be necessary for this
version of BART.  The Makefile patch is meant for working with Spack and
would not be useful upstream. The bart scripts are still setup to use
bart with the subcommands being individual binaries. This patches those
to use the single binary with built-in subcommands and assumes that
spack is providing the TOOLBOX environment variable and setting PATH.

* Update var/spack/repos/builtin/packages/bart/package.py

Yes, '==' make more sense for a single string.

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* The python dependencies are run time only.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-12 19:41:37 -05:00
Jose E. Roman
a1fc761f18
New patch release SLEPc 3.13.1 (#16013)
* New patch release SLEPc 3.13.1

* Update var/spack/repos/builtin/packages/slepc/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-12 16:35:40 -05:00
Glenn Johnson
9209af950a
new package: py-youtube-dl + fixes for dependencies (#15978)
* new package: py-youtube-dl + fixes for dependencies

This PR adds the py-youtube-dl program. In addition, there are a couple
of dependency packages that needed to be updated.

* ffmpeg
This is needed by py-youtube-dl. However, the spack ffmpeg recipe does
not include a lot of options, specifically, a dependency on openssl for
working with the https protocol.

- Added updated version.
- Added variants for the different licensing options.
- Added "meta" variants for X and drawtext. These turn on/off several
  options.
- Set variants and dependencies for many options. The defaults are based
  on the configuration settings in ffmpeg.
- Set dependencies that were missing or that will likely get pulled in
  from the system.

* libxml2
The ffmpeg+libxml2 variant initially failed to build. The issue is that
libxml2 sets the headers property to

include_dir = self.spec.prefix.include.libxml2

The ffmpeg configure looks for prefix.include and fills in the rest.
This could probably be patched in ffmpeg but the headers property in the
libxml2 recipe is not consistent with the environment module or the
pkgconfig file, both of which set the headers path to prefix.include.
This PR sets the libxml2 headers property to

include_dir = self.spec.prefix.include

A spot check of a few libxml2 dependents did not rreveal any problems
with this change.

* Comment out libxml2 dependency in ffmpeg

The header property issue of the spack libxml2 package will need to be
resolved in another PR before libxml2 can be enabled in ffmpeg.
2020-04-12 13:50:49 -05:00
Adam J. Stewart
f14f97ea78
py-transformers: add new package (#16011) 2020-04-12 11:41:20 -05:00
Adam J. Stewart
17450e18e0
py-tokenizers: add new package (#16010) 2020-04-12 10:22:55 -05:00
Adam J. Stewart
e4aa10d0c9
py-sacremoses: add new package (#16009) 2020-04-12 09:17:03 -05:00
Adam J. Stewart
e1b308af58
py-setuptools-rust: add new package (#16008) 2020-04-12 09:16:49 -05:00
Carson Woods
97dcf7b8ee
tau: added new variants (#16005)
* Add more tau variants

* Add more tau variants
2020-04-11 19:44:26 -05:00
Andrew W Elble
a5f7cc887a
new package: openmm (#16002)
* new package: openmm

* dependency adjustments

* 1. modify dependencies
2. openmm dynamically compiles cuda kernels during runtime,
   attempt to set up an environment that will work.

* Update var/spack/repos/builtin/packages/openmm/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-11 16:29:56 -05:00
Jennifer Herting
91e22b8ae5
[py-jupyter-core] added version 4.6.3 (#15991)
* [py-jupyter-core] added version 4.6.3

* [py-jupyter-core] updated python version requirement
2020-04-10 15:59:00 -05:00
Christoph Junghans
78a9f73874
votca-tools: add mkl support (#15997)
* votca-tools: add mkl support

* Update package.py
2020-04-10 14:36:28 -05:00
Christoph Junghans
8e597e8a7a
votca-*: add v1.6_rc2 (#15999)
* votca-*: add v1.6_rc2

* votca-*: develop -> master
2020-04-10 14:36:09 -05:00
Paul
7b7458a0f4
Add Go versions 1.14.2 and 1.13.10 (#16000) 2020-04-10 14:35:51 -05:00
Christoph Junghans
c4360a918b
gromacs: install header files (#15996) 2020-04-10 13:36:26 -05:00
Tom Payerle
a29956d71e
gdal: Patch to support hdf linked against libtirpc (#15995)
If hdf was built with +libtirpc, we need to add -ltirpc to our link
flags.
2020-04-10 13:36:08 -05:00
Tom Payerle
343a499aa8
hdf: Add option to link against libtirpc package (#15993)
This adds a boolean 'libtirpc' variant to the hdf package.
Default is false, which will reproduce previous behavior (which
was to rely either on system xdr headers/library, or have hdf use
it's builtin xdr lib/headers (which are only for 32 bit))

If true, a dependency is added on 'libtirpc', and the LIBS and
CPPFLAGS are updated in the configure command to find the libtirpc
library and xdr.h header.

This is needed as RHEL8 (and presumably other distros have or will be)
removed xdr.h from glib-headers package,which was breaking the previous
behavior of using system xdr headers.
2020-04-10 13:23:05 -05:00
Andrew W Elble
c01a968ada
new package: py-torchsummary (#15990)
* new package: py-torchsummary

* add numpy
2020-04-10 13:13:51 -05:00
Andrew W Elble
42b63e6b7e
new package: py-torchaudio (#15989) 2020-04-10 10:53:12 -05:00
Andrew W Elble
aeb628ea74
opencv: assorted fixes (#15971)
* opencv: assorted fixes

1. depends on blas when +lapack
2. set cuda nvcc flags for cuda_arch
3. let cuda/contrib builds work
4. depends on hdf5 when cuda/contrib
5. depends on ant when +java
6. allow protobuf version to be different
7. let opencv recompile it's protoc files.

* ant is a build-time dependency

* register +cuda~contrib as impossible.
2020-04-10 09:49:32 -05:00
Andrew W Elble
3b3bd6e173
New package: tensorboardX (#15955)
* New package: tensorboardX

* prune back to just what's in setup.py for now
2020-04-10 09:37:18 -05:00
iarspider
77e144d6e5
Add new version of py-hypothesis (#15942)
* Add new version of py-hypothesis

* Update package.py

* Update package.py
2020-04-10 09:36:16 -05:00
Jacob Merson
d0fbe1add2
Update yaml-cpp package to enable for build of old api (#15983)
The old api is found in version 0.3.0 which uses a different release
name, so the url function was updated to properly find the older
releases. Also, this removes the boost constraint on the 0.3.0 version
which does not need it.
2020-04-10 09:35:36 -05:00
tilne
0d96e8a27d
update URL and sha256 for aws-parallelcluster 2.6.1 (#15980)
Signed-off-by: Tim Lane <tilne@amazon.com>
2020-04-09 22:00:03 -05:00
Justin S
2d220c8eb0
py-clint: new package at 0.5.1 (#15905)
* py-clint: new package at 0.5.1

* py-clint: update py-setuptools dep type
2020-04-09 17:12:17 -05:00
Michael Kuhn
35c4f614c4
meson: Add 0.54.0 (#15952)
* meson: Add 0.54.0

This change also improves the rpath patch we are using. Instead of never
removing the rpath, we now only keep it if running within Spack to
guarantee consistent behavior of Meson.

* meson: Make ninja a hard dependency
2020-04-09 17:11:52 -05:00
Jennifer Herting
e0e092050c
[py-pygdal] added version 3.0.4.6 (#15973) 2020-04-09 16:58:50 -05:00
noguchi-k
834a520af4
aperture-photometry: add new version (#15967) 2020-04-09 12:04:27 -05:00
Ryan Pepper
f683d714f8
Update doxygen package (#15969)
* Update doxygen package

* Add new version releases 1.8.16 and 1.8.17
* Add mscgen as an optional dependency.

* Update doxygen package.py

Fix typo in mscgen dependency specification

* Remove whitespace for flake8
2020-04-09 12:03:30 -05:00
George Hartzell
1b2638c9b1
primer3: move to github, add 2.5.0, fix 2.3.7 (#15958)
* primer3: move to github, add 2.5.0, fix 2.3.7

- The Primer3 project moved to GitHub.

  - update the URL
  - compare the tarballs 2.3.7 from Sourceforge and github, no
    significant differences (e.g. the Sourceforge tarball contained a
    couple of "tmp" files).
  - update the signature for the 2.3.7 tarball.

- @2.3.7 doesn't build with gcc@8.4.0, there's a dubious pointer/int
  comparison that causes an error.  It was fixed upstream in newer
  versions, apply simple patch to this version so that it continues to
  be build-able with newer compilers.  See:

  - https://github.com/primer3-org/primer3/issues/2
  - https://github.com/primer3-org/primer3/issues/3

- Add info for @2.5.0, which builds cleanly.

* Flake8 cleanup
2020-04-09 11:53:34 -05:00
Sergey Kosukhin
05a80523c8
NetCDF packages: switch to the official FTP server. (#15641) 2020-04-09 09:57:07 -05:00
Jennifer Herting
b75ba93589
New package: gtk-doc (#15768)
* [gtk-doc] created template

* [gtk-doc] using custom url to standardize on dotted version

* [gtk-doc] added description and homepage

* [gtk-doc] added dependencies and added pdf variant

* [gtk-doc] commented out pdf variant

* [gtk-doc] cleaned up leftover fixmes

* [gtk-doc] flake8

* [gtk-doc] readded url

* [gtk-doc] python packages are build and run dependencies
2020-04-09 09:56:33 -05:00
Massimiliano Culpo
e53a98cb4f
papi: check existence of a fortran compiler (#15968)
fixes #5029
2020-04-09 15:33:24 +02:00
vvolkl
5320268033
[podio] add recipe for podio (#15726) 2020-04-09 10:29:19 +01:00
Andrew W Elble
ee0cbd7a17
py-torch: Fix v1.4.0 by adding v1.4.1 (#15761)
* py-torch: Fix v1.4.0 by adding v1.4.1

version/tag hack so that 1.4.0 is still workable.
see pytorch/pytorch#35149

* delete/disable fbgemm support in 1.4.0

* moved conflict
2020-04-09 10:50:08 +02:00
darmac
6d8a59be5b
uchardet: added package at v0.6.0 (#15937) 2020-04-09 09:19:52 +02:00
G-Ragghianti
f9c833e078
Papi packge: refactored to inherit from AutotoolsPackage (#15962) 2020-04-09 09:13:35 +02:00
darmac
93a53f1faf
elasticsearch: change depends on from jdk to java (#15964) 2020-04-08 22:35:46 -05:00
Michael Kuhn
3c8bd21dae
glib: Add new stable versions (#15947)
Newer versions of glib require Meson, so this PR adds support for that
using a hybrid approach. glib@5.28: will be built using Meson, older
versions still make use of Autotools.
2020-04-08 22:32:08 -05:00
T.Tian
e96750472e
py-gpaw: Add libvdwxc as variant (#15948)
* Add libvdwxc as variant

* py-gpaw: add missing line for libvdwxc conditions
2020-04-08 22:22:19 -05:00
Aniruddha Marathe
9035dc6b3d
- Fixes build issues. (#15951)
- Updates Kripke URL to its Github repository.
- Adds previous Kripke versions.
- Adds 'caliper' variant.
2020-04-08 22:13:13 -05:00
Andrew W Elble
8abffd4189
py-tensorflow-estimator: fix build (#15953)
Change the build to work again, and be more in line with the other
tensorflow packages. Add version 2.1.
2020-04-08 22:10:37 -05:00
Paul Ferrell
d05f25a4d0
Fixed bad expand option for openjdk versions. (#15956)
The most recent change to the openjdk package set expand=False for all versions
of the package. This means only the unexpanded archive will be installed, which is not correct.
2020-04-08 22:07:00 -05:00
Justin S
4886a2d5ef
py-awesome-slugify: new package at 1.6.5 (#15907)
* py-awesome-slugify: new package at 1.6.5

* py-awesome-slugify: fix typo in version range

* py-awesome-slugify: update dependencies
2020-04-08 21:45:33 -05:00
Nichols A. Romero
bf4eec94ca
F18 update April 2020 (#15930)
* Update dependencies and support variant for Fortran Intermediate Representation.

* Add Cmake flags that toggle Fortran Intermediate Representation on/off. Exclude Flang tests for now.

* f18+fir variant needs next release of llvm or master.

* Only build tests if you are pass in --test to spack install
2020-04-08 20:32:56 -05:00
Andrew W Elble
c5b625ca90
New package: py-tensorboard (#15829)
* New package: py-tensorboard

* some basic dependencies based on requirements.txt
remove the older version that doesn't build

* requested changes

* add additional dependencies

* more dependency changes
2020-04-08 12:46:36 -05:00
Andrew W Elble
c6c53df916
py-onnx: only use py-typing if python < 3.5 (#15931)
* py-onnx: only use py-typing if python < 3.5

avoids a 'Callable has no attribute __abc_registry' error. See
onnx/onnx#2199 and python/typing#573

* add version 1.6.0 while we're here.
2020-04-08 12:46:16 -05:00
iarspider
8ed8bb0a76
MariaDB: added v10.4.12 (#15943) 2020-04-08 14:34:56 +02:00
iarspider
fcf0c6cb68
pytest: added v4.6.9 (#15944) 2020-04-08 14:34:09 +02:00
darmac
62cc8158de
http-parser: added package at v2.9.4 (#15936) 2020-04-08 09:04:01 +02:00
Xavier Delaruelle
4031e9a2a7
environment-modules: add version 4.5.0 (#15938)
Add new version 4.5.0 and update quarantine variable list to also
include LD_PRELOAD in addition to LD_LIBRARY_PATH (to avoid side-effect
when the first depends on the latter).
2020-04-08 09:01:22 +02:00
George Hartzell
66cec5a151
Update hugo version and add extended variant (#15933)
- Add info for version 0.68.3
- Add variant to package that enables the "extended" features.  It
  works with both of the existing versions (not sure how far back it
  goes, but confirmed that it's valid fro 0.53).

Tested on OS X with go@1.14.1.
2020-04-07 22:27:23 -05:00
darmac
e16593e551
Add new package: open-isns (#15914)
* Add new package: open-isns

* refine args
2020-04-07 22:27:04 -05:00
Justin S
998dc7a121
py-cyvcf2: new package at 0.11.7 (#15908)
* py-cyvcf2: new package at 0.11.7

* py-cyvcf2: update dependencies
2020-04-07 20:41:18 -05:00
Justin S
7927394fb3
py-yahmm: new package at 1.1.3 (#15909)
* py-yahmm: new package at 1.1.3

* py-yahmm: update dependencies
2020-04-07 20:41:01 -05:00
Justin S
233fc5ff23
py-unidecode: new package at 1.1.1 (#15906)
* py-unidecode: new package at 1.1.1

* py-unidecode: update py-setuptools dep type

* py-unidecode: add python version
2020-04-07 20:40:33 -05:00
Justin S
9b33788573
py-utils: new package at 1.0.1 (#15904)
* py-utils: new package at 1.0.1

* py-utils: update py-setuptools dep type

* py-utils: fix dependency condition
2020-04-07 20:39:39 -05:00
Justin S
cc4bf086b9
py-args: new package at 0.1.0 (#15903)
* py-args: new package at 0.1.0

* py-args: update dependencies
2020-04-07 20:39:03 -05:00
Massimiliano Culpo
fb0bcf4127
openfoam: modified flex to be a build + link dependency (#15917)
fixes #15863

Since openfoam-org needs FlexInclude.h "flex" needs to
be also a link dependency.
2020-04-07 17:04:54 -05:00
ktsai7
0ac77b815f
update gasnet spackage cmake args (#15920)
* update gasnet spackage cmake args

* fix style errors

* trailing whitespace
2020-04-07 17:03:32 -05:00
Benjamin Tovar
0074995ecf
updates CCTools to version 7.1.2 (#15923) 2020-04-07 17:03:18 -05:00
Nichols A. Romero
46bcbac719
Make use of Spack's builtin CUDA build system. (#15924) 2020-04-07 17:02:38 -05:00
Robert Pavel
36f7def307
Addded Draco@7.5.0:7.6.0 (#15926)
Updated version hashes for draco spackage to specify 7.5 and 7.6
2020-04-07 17:01:06 -05:00
George Hartzell
153c888432
Fix lua build, missing deref of self for spec (#15927)
Looks like something changed and a case was missed.

Function doesn't have a spec arg, need to dereference it off of
self.

Builds on OS X.
2020-04-07 17:00:53 -05:00
Satish Balay
45fe9add2e
update versions: petsc4py@3.13.0 and slepc4py@3.13.0 (#15928) 2020-04-07 17:00:34 -05:00
Hadrien G
b405278c43
[acts-core] Add version 0.21 (#15922)
* Add ACTS v0.21

* Update var/spack/repos/builtin/packages/acts-core/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-07 17:00:01 -05:00
Carson Woods
fc19f7de6c
ucx: add additional variants (#15925)
* Add more variants to ucx

* Fix flake8 issue
2020-04-07 15:18:40 -05:00
Jose E. Roman
fb841877c5
slepc 3.13 develop updates (#15897)
* slepc: updates for @devel

-  +arpack now works with int64
-  +blopex add conflict with int64
-  switch to using --with-arpack-lib [from --with-arpack-lib] with current slepc
-  use updated blopex with current slepc

* slepc: conflict with blopex should be in all versions

* slepc: add new downloads

* slepc: add whitespace around operator

Co-authored-by: Satish Balay <balay@mcs.anl.gov>
2020-04-07 15:13:32 -05:00
Andrew W Elble
dd463272e6
New package(s): py-pydeps and py-stdlib-list (#15828)
* New package(s): py-pydeps and py-stdlib-list

* requested changes

* Update var/spack/repos/builtin/packages/py-stdlib-list/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-07 13:59:24 -05:00
darmac
cb9c86e526
Add new package: shark (#15913) 2020-04-07 11:57:21 -05:00
Mark Olesen
8b275080ea
update OpenFOAM patch versions (#15916)
Co-authored-by: Mark Olesen <Mark.Olesen@esi-group.com>
2020-04-07 11:57:07 -05:00
Massimiliano Culpo
2dece3aee8
cryptsetup: restrict the version of automake if @2.2.1 (#15918)
* cryptsetup: restrict the version of automake if @2.2.1

fixes #15706

* Update var/spack/repos/builtin/packages/cryptsetup/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-07 11:56:54 -05:00
Themos Tsikas
375e1c62c7
NAG Compiler 7.0 (Build 7014) download checksum (#15899)
* NAG Compiler 7.0 (Build 7009) download checksum

* NAG Compiler 7.0 (Build 7014) download checksum
2020-04-07 11:38:11 -05:00
Jennifer Herting
e34ea80d52
New package: boinc-client (#15770)
* [boinc-client] Created template

* [boinc-client] removed non-client version

* [boinc-client] added description and homepage

* [boinc-client] specifically specify this as a client release

* [boinc-client] added dependencies

* [boinc-client] added variant: manager

* [boinc-client] added graphics variant

* [boinc-client] added dependency version specificity

* [boinc-client] systemd install path fix

* [boinc-client] added sqlite dependency

* [boinc-client] flake8

* [boinc-client] cleaned up left over fixme
2020-04-07 11:21:49 -05:00
Massimiliano Culpo
f83d46bb79
intel: fixed version number (update4 is 18.0.5) (#15915)
fixes #15811

See https://software.intel.com/en-us/articles/intel-compiler-and-composer-update-version-numbers-to-compiler-version-number-mapping
2020-04-07 15:47:22 +02:00
Toyohisa Kameyama
ae94c52f1c
ppOpen-APPL/FEM: New package. (#15911)
* ppOpen-APPL/FEM: New package.

* typo fix.
Update patch.
2020-04-07 08:43:46 -05:00
Adam J. Stewart
783793426d
Package rename: DNNL -> oneDNN (#15910) 2020-04-06 19:27:34 -05:00
Matthias Diener
e7a529322f
fish: add version 3.1.0 and switch to cmake (#15812)
Versions < 3 do not support building with CMake.
2020-04-06 19:25:39 -05:00
Diego Magdaleno
2542d80e10
Update nano and fix coreutils on Darwin (#15883)
* Fixed building coreutils on Darwin

* Bump nano version to 4.9

* Coreutils: Add program prefix g so we don't conflict with Apple utilities

* Fix intendation

* Make format more spack like

* Removed unnecesary changes

* Merge branch 'develop' of github.com:DiegoMagdaleno/spack into develop

Fix linking libgit2 on Darwin

* Revert "Merge pull request #3 from spack/develop"

This reverts commit 58dbbdb82bfa4aa689758971eb423ae2b9d2c293, reversing
changes made to dd7a413f4870fc2778f801c882a50cfade18fe97.

* Revert "Revert "Merge pull request #3 from spack/develop""

This reverts commit f956aa7b135c39ea0eb4ba6b9329714067098a7c.

* Revert "Merge branch 'develop' of github.com:DiegoMagdaleno/spack into develop"

This reverts commit 50321f798674ec30d5c62fe696b4f8bccef6ab3d.
2020-04-06 19:23:05 -05:00
Andrew W Elble
6ad0ca27c2
new package: nccl-tests (#15890)
* new package: nccl-tests

* fix dependency types
2020-04-06 19:21:36 -05:00
Andrew W Elble
26a754c023
new package: py-tensorboard-plugin-wit (#15898)
* new package: py-tensorboard-plugin-wit

dependency for py-tensorboard >= 2.2.0

* incorporate feedback
2020-04-06 19:21:16 -05:00
Carson Woods
379319ee2d
pdt: add PIC support as variant (#15851)
* Add fPIC support as variant

* Fix variant to use compiler agnostic fPIC option
2020-04-06 16:20:21 -05:00
Andrew W Elble
9d906658b3
nccl: supports infiniband/RoCE since 2.3.5-5 (#15889)
loads libibverbs via dlopen(), add dependency on rdma-core
2020-04-06 16:19:55 -05:00
Andrew W Elble
ebd0b14ad1
new package: py-google-auth-oauthlib (#15900) 2020-04-06 16:10:43 -05:00
Adam J. Stewart
18a9a265fd
py-smart-open: fix url/checksum, add deps (#15892) 2020-04-06 11:16:20 -05:00
Dr. Christian Tacke
b1bea70df1
nanomsg: add new Package (#15894) 2020-04-06 11:15:57 -05:00
François Trahay
55d15fc07e
new packages: libbacktrace, libpfm, numap, numamma (#15868)
* new packages: libbacktrace, libpfm, numap, numamma

* numap: use the existing libpfm4 package

* formatting
2020-04-06 08:01:58 -05:00
Christoph Junghans
268c2a19da
boost: boost-python in 1.72.0 broken with cxxstd=98 (#15885)
* boost: boost-python in 1.72.0 broken with cxxstd=98

* py-espressopp: depend on boost with cxxstd=11
2020-04-05 18:42:27 -05:00
Adam J. Stewart
1249d73630
py-spatialist: add maintainer and new version, fix url and deps (#15878) 2020-04-05 17:31:09 -05:00
Adam J. Stewart
a08d5fed0a
py-flake8-polyfill: fix url and deps (#15872) 2020-04-05 15:45:29 -05:00
Adam J. Stewart
2a074ce445
py-gensim: fix url and deps, add maintainer (#15870) 2020-04-05 15:45:17 -05:00
Adam J. Stewart
638e6d0f9e
py-humanfriendly: add new version, fix url and deps (#15873) 2020-04-05 15:45:04 -05:00
Adam J. Stewart
e359bb91e9
py-pep8-naming: add new version, fix url and deps (#15874) 2020-04-05 15:44:50 -05:00
Adam J. Stewart
4dc034a8e5
py-progressbar2: add new version, fix url (#15875) 2020-04-05 15:44:36 -05:00
Adam J. Stewart
f5fde735b6
py-python-utils: add new version, fix url and deps (#15876) 2020-04-05 15:44:23 -05:00
Adam J. Stewart
d87f44e987
py-scoop: fix url and deps (#15877) 2020-04-05 15:44:10 -05:00
Adam J. Stewart
cf68193ebe
py-tblib: add new version, fix url and deps (#15879) 2020-04-05 15:43:20 -05:00
Adam J. Stewart
a3b9dbcbfb
package urls: pypi.org -> pypi.io (#15880) 2020-04-05 15:43:09 -05:00
Adam J. Stewart
68b4beb725
py-sphinx: add 3.0.0 (#15881) 2020-04-05 15:42:57 -05:00
Adam J. Stewart
05532f9e27
py-ecdsa: add new version, fix download url (#15871) 2020-04-05 15:42:44 -05:00
健美猞猁
34627fcbe5
py-pywcs: a new package. (#15826)
* py-pywcs: a new package.

* Fix a flake8 issue.

* Add missing dependencies.

* run -> build.

* Add version specifications.
2020-04-05 11:21:54 -05:00
François Trahay
c99a88128a
Version bump: eztrace-1.1-10 (#15866)
* version bump: eztrace-1.1-10

* 'trahay' is the maintainer for package 'eztrace'
2020-04-05 09:39:57 -05:00
Christoph Junghans
b4271d1a26
py-espressopp: pin py-numpy to py2 version (#15865) 2020-04-04 13:00:04 -05:00
darmac
7f8102d6d0
openjdk: support aarch64 platform (#15840) 2020-04-04 11:35:46 -05:00
Adam J. Stewart
9b9b46c0a9
Package rename: intel-mkl-dnn -> dnnl (#15852) 2020-04-04 11:35:23 -05:00
Nichols A. Romero
4ee9fd46bc
LLVM support for mlir (#15859) 2020-04-04 11:12:21 -05:00
Simon Pintarelli
4bb1392d7d
SIRIUS add version 6.5.1 and 6.5.2 (#15860) 2020-04-04 11:11:17 -05:00
健美猞猁
a7f418e0b2
Check if CPU family is x86_64. (#15862)
* Check if CPU family is x86_64.

* Remove the leading space.
2020-04-04 11:10:48 -05:00
Jennifer Herting
0891c5d854
New package: py-gluoncv (#15856)
* [py-gluoncv] created template

* [py-gluoncv] added description and homepage

* [py-gluoncv] added dependencies

* [py-gluoncv] unicode in readme is causing build to fail

* [py-gluoncv] cleaned up fixmes

* [py-gluoncv] removed unnecessary python dependency listing

* [py-gluoncv] added cython
2020-04-03 15:49:21 -05:00
G-Ragghianti
bf8fea1d53
Added support for new config process for papi@6:+lmsensors (#15858)
* Added support for new configuration process of lmsensors component for papi@6:

* Removed extraneous blank lines
2020-04-03 15:48:44 -05:00
Matthieu Dorier
4173c27868
unqlite: restricted patch to version 1.1.9 (#15857)
* restricted unqlite patch to version 1.1.9

* putting back the URL of the PR corresponding to the patch
2020-04-03 15:48:29 -05:00
Jennifer Herting
0a9d4f6720
New package: py-portalocker (#15854)
* [py-portalocker] Create template

* [py-portalocker] added homepage and description

* [py-portalocker] specified dependencies

* [py-portalocker] cleaned up fixmes

* [py-portalocker] removed unnecessary python dependency listing
2020-04-03 13:58:02 -05:00
G-Ragghianti
5e5b68c063
Papi package: updating with new bugfix version and variant (#15849)
* Added new variant "sde" to papi

* Updated papi with new version and new variant "sde"
2020-04-03 11:39:29 -05:00
Frédéric Simonis
be57c0f6e7
precice: Add version 2.0.2 (#15846) 2020-04-03 11:33:47 -05:00
Jennifer Herting
1461332e97
New package: libnotify (#15769)
* [libnotify] created template

* [libnotify] added homepage and description

* [libnotify] added dependencies

* [libnotify] patch location to docbook

* [libnotify] more dependency work

* [libnotify] reorder dependencies

* [libnotify] added variant docbook

* [libnotify] more accurate dependency version

* [libnotify] xsltproc still needed

* [libnotify] created test variant

* [libnotify] added gtkdoc varient

* [libnotify] cleaned up leftover fixme

* [libnotify] flake8

* [libnotify] test variant became self.run_tests

* [libnotify] pkgconfig is build dependency

* [libnotify] commented out broken variants

* [libnotify] flake8
2020-04-03 11:07:25 -05:00
健美猞猁
c0d2f70d02
py-stsci-distutils: new package at v0.3.8 (#15845) 2020-04-03 11:12:59 +02:00
Toyohisa Kameyama
87444aef7e
ppOpen-APPL/BEM-AT: added new package at v0.1.0 (#15841) 2020-04-03 11:11:46 +02:00
健美猞猁
e227a684b9
py-d2to1: added v0.2.12 (#15844) 2020-04-03 10:29:25 +02:00
Carson Woods
1662c3581b
pmix: add option for toggling pmi backwards compatibility (#15838)
* Add option for toggling pmi backwards compatibility

* Remove trailing whitespace
2020-04-02 21:09:33 -05:00
Jennifer Herting
1d14f74d19
New Package: py-astropy-helpers (#15658)
* [py-astropy-helpers] created template

* [py-astropy-helpers] - removed boilerplate - added homepage - added depends_on('py-astropy')

* [py-astropy-helpers] Setuptools versioning

* [py-astropy-helpers] cleaned up unused build_args method

* [py-astropy-helpers] py-astropy is a runtime dependency

* [py-astropy-helpers] requires python@3.6:

* [py-astropy-helpers] cleaned up unnecessary older versions

* [py-astropy-helpers] turns out py-astropy isn't actually a dependency
2020-04-02 20:11:48 -05:00
Shintaro Iwasaki
73ac853c3d
argobots: new version 1.0 (#15786) 2020-04-02 20:11:06 -05:00
Robert Mijakovic
37e9e450c9
Updates versions of Intel packages (#15839)
* update version: intel packages daal, ipp, mkl-dnn, mkl, mpi, parallel-studio, pin, tbb and makes url parameter consistent and always use single quote.

* Fixes a typo with one of the sha256 checksum..

* Adds version entries for new versions of Intel packages.

Co-authored-by: Robert Mijakovic <robert.mijakovic@lrz.de>
2020-04-02 19:39:44 -05:00
Carson Woods
0083c87c26
mpip: add demangling and setjmp variants (#15837)
* Add demangling to mpip

* Add setjmp support to mpip

* Flake8 fixes
2020-04-02 19:37:35 -05:00
Adam J. Stewart
4d2de863ef intel-mkl-dnn: add 1.3 2020-04-02 15:20:18 -07:00
Michael Kuhn
06ebb94f37 go: Add 1.14.1 and 1.13.9 2020-04-02 15:17:00 -07:00
Matthieu Dorier
8b52f9f37d
unqlite: Patching unqlite to be able to build a shared library (#15830)
* Patching unqlite to be able to build a shared library

* Correcting a whitespace for flake8 to pass

* added comment about PR on unqlite

* extra commit to force github to merge
2020-04-02 17:15:45 -05:00
iarspider
144557e945
c-blosc: Add variants to disable building tests and benchmarks (#15789)
* Add variants to disable building tests and benchmarks

* Flake8

* Update package.py

* Update package.py

* Update package.py
2020-04-02 08:52:37 -05:00
Toyohisa Kameyama
1f6f395337
ppOpen-APPL/BEM: added new package at v0.5.0 (#15819) 2020-04-02 12:08:09 +02:00
健美猞猁
d2b6ef98f1
py-pyfits: added new package at v3.5 (#15825) 2020-04-02 12:07:22 +02:00
健美猞猁
d921974db1
py-ephem: added new package at v3.7.71 (#15438) 2020-04-02 11:13:17 +02:00
Kelly (KT) Thompson
8078089914
cmake: added v3.17.0 (#15822) 2020-04-02 11:06:21 +02:00
Jonathon Anderson
7d44a0090d
cryptsetup: added v2.2.2, v2.2.3 and v2.3.1 (#15823)
Also confined the included patch to the earlier versions, as
indicated.
2020-04-02 10:55:20 +02:00
Jonathon Anderson
60f29a9f80
qt: added v5.14.2 (#15824) 2020-04-02 10:54:05 +02:00
Michael Bentley
c3c057f2b3
package: update flit and py-pyelftools versions (#15817)
* Update flit package to v2.1.0 and add dependencies

* flit: comment out bash dependency

The host system should have bash available and compiling bash through
spack failed for me.  I'm not sure if binutils and coreutils should
be listed as dependencies as well.

* Add new version of py-pyelftools

* py-pyelftools: add py-setuptools as a build dependency

* Address review comments
2020-04-01 22:05:58 -05:00
Carson Woods
bb0c79b504
package: add variants to cgns (#15816)
* Add additional configuration options for cgns

* Fix syntax errors

* Further syntax fixes

* Convert tabs to spaces

Co-authored-by: Carson Woods <carwood@sandia.gov>
2020-04-01 20:39:57 -05:00
Carson Woods
9b1820c2de
package: add static library build option for yaml-cpp (#15814)
* Add static build option

* Fix flake8 errors and standardize spacing of build commands

Co-authored-by: Carson Woods <carwood@sandia.gov>
2020-04-01 20:39:04 -05:00
takanori-ihara
814996eebc
New package:dhpmm-f (#15798)
* New package:dhpmm-f

* Remove unnecessary line
2020-04-01 20:38:09 -05:00
Todd Gamblin
5a814ad0c5
hdf5: prefer version 1.10 for now (#15810)
HDF5 1.12 broke backward compatibility, so we're preferring version 1.10
for now.  Packages that need the new API should specify:

    depends_on("hdf5@1.12:")

to be explicit. We can eventually change the preference, but at the
moment most libraries have not udpated to use the new HDF5.
2020-04-01 20:36:04 -05:00
Jonathon Anderson
e260eb4775
Version bump for slurm package (#15790) 2020-04-01 16:51:59 -05:00
Christoph Junghans
37c0039eb9
openssl: add v1.1.1f (#15802) 2020-04-01 13:57:19 -06:00
Erik Schnetter
8552efe54f
amrex: New version 20.04 (#15808) 2020-04-01 13:41:23 -05:00
Robert Pavel
47f135534c
Added v3 of Laghos (#15806)
* Added v3 of Laghos

Added v3 of Laghos as per
https://github.com/CEED/Laghos/blob/v3.0/README.md

* Update var/spack/repos/builtin/packages/laghos/package.py

Changed develop->master as per PR

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Made Metis Dependency Explicit

Added explicit metis dependency

* Folded @develop Laghos Deps in to @3.0:

Theoretically there will be a difference between develop and 3.0: in the
future but currently there is not

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-01 13:32:15 -05:00
Adam J. Stewart
64b14b64c0
OpenDX: add new package (#15737) 2020-04-01 13:30:03 -05:00
Robert Pavel
6ad717cc9d
Fixed Remaining Shared Objects in Static Lua (#15787)
Fixed removal of remaining references and symlinks to so files when
building lua with static libraries
2020-04-01 12:31:01 -05:00
Nichols A. Romero
917c0a0efd
Minor LLVM libomptarget fixes (#15788)
* Add myself as a maintainer

* This was a regression that occured in previous PR. Flang has been excised from LLVM for now until f18 is merged upstream.

* Libraries only needed when a GPU backend is present.
2020-04-01 12:28:36 -05:00
Sinan
67fbf257f0
Package/sfcgal fix typo (#15796)
* fix typo in dependency definition

* remove arbitrary dependency constraint

Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
2020-04-01 12:05:53 -05:00
Andrew Gaspar
58cb2e5092
Add libgit2 1.0.0 and 0.28.5 (#15801) 2020-04-01 12:02:55 -05:00
Axel Huebl
c430ad91c3
pybind11 2.5.0: Include Change (#13905)
Add pybind11, version 2.5.0.
This release adds improved include helpers.
2020-04-01 08:58:09 -07:00
Sinan
49aa28790c
new package: py-spatialite (#12597)
* new package: py-spatialite

* make flake8 happy

Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
2020-04-01 08:09:39 -05:00
Dr. Christian Tacke
97cfef320c
slurm: new version, system configuration path (#15466)
* Add version 18-08-9-1
* Add variant to allow setting the sysconfdir: See below

About sysconfdir:

slurm has a server and a client.
To use the correct communication channel, the client needs
to be able to read the correct config.  This config is in
PREFIX/etc.

Let's assume one has the server part installed as a system
package.  This generally is a good idea, so that the server
gets started during boot.  This means, that the config is
in /etc/slurm.

If one now wants to use the client part (library!) via
spack, one has a problem: spack's slurm looks in
SPACK-PACKAGE-PREFIX/etc for the config.

There needs to be a way to let the spack installed package
use the system's config.

So add a variant to override the path during build:
sysconfdir=/etc/slurm.

This is much like what happened in #15307 for munge.
2020-04-01 08:07:41 -05:00