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Author SHA1 Message Date
Harsh Bhatia
cb20f0152c
pygpu: fix linking with gpuarray (#17033) 
* add build_ext_args to link pygpu with gpuarray
* libgpuarray: add version 0.7.6
 2020-06-12 12:20:57 -07:00
Harmen Stoppels
804b6f2483
libtree package: add version 1.2.0, 1.1.4, and 1.1.3 (#17035) 2020-06-12 11:39:40 -07:00
Matthias Diener
c4756159f3
New package: clinfo (#17042) 2020-06-12 11:37:34 -07:00
Axel Huebl
42e6cb769e
Geant4 +Python: fix module load (#17046) 
Adding `extends('python')` makes sure that a

```
spack load -r geant4 +python
python -c "import Geant4"
```

find the module.
 2020-06-12 11:28:05 -07:00
Axel Huebl
34fb4b30dc
libffi 3.3: float128 ppc patch (#17043) 
Apply a patch to fix builds on Power7 and 8, wrongly requesting
float128 support.

Upstream patch: libffi/libffi#561
 2020-06-12 11:25:06 -07:00
Adam J. Stewart
4e39dc7174 readline: fix linking to ncurses 2020-06-12 11:05:28 -07:00
Robert Blake
50aba2729b
New package: antimony (#17061) 2020-06-12 10:42:59 -07:00
Brian Van Essen
dcd22517c7
hydrogen: add version 1.3.4 (#17066) 2020-06-12 09:53:50 -07:00
Tom Payerle
e1e455ef3f
magics: add version 4.2.4 (#17054) 
* Add version 4.2.4
* Update checksum for 4.1.0
* Version @4: requires python and py-jinja2 to build
 2020-06-12 09:53:08 -07:00
Michael Kuhn
f2ae9ffdf5 gcc: Add 7.5.0 2020-06-12 09:37:53 -07:00
Sinan
b50b930d6a
New package: py-uncertainties (#16997) 2020-06-11 08:26:43 -07:00
codeandkey
9820a23abd py-gpy: new package at 1.9.9 2020-06-11 08:25:14 -07:00
Justin S
19dba603ad
py-paramz: new package at 0.9.5 (#17026) 2020-06-10 18:57:08 -07:00
Axel Huebl
2827dca905
ADIOS 2.6.0: New Options (#17025) 
Control new options/dependencies in ADIOS2 to avoid pick-up of system
packages.
 2020-06-10 10:19:41 -04:00
Toyohisa Kameyama
f6020d259a
adios2: fix to build on Fujitsu MPI and Fujitsu compiler (#17034) 2020-06-10 14:53:09 +02:00
asmaahassan90
0de12be52a
add gaussian-view (#16890) 2020-06-09 16:58:34 -07:00
Rob Latham
31791f269b
teach spack how to build pmix from git (#16973) 
* teach spack how to build pmix from git

* add variant for new REST feature

* reorder package to match guidance
 2020-06-09 16:16:38 -05:00
Robert Blake
872ab21103
Add new package: wcs (#16958) 
* Adding a package for wcs.

* Turning on sbml for wcs.

* The cpp flag needs to be available for wcs.

* Wcs needs SBML to properly define the namespace.

* Flake8 fixes.

* Fixing the help string with the description.

* Changing cpp to use the new variant syntax.

* Fixing flake8 errors.

* Forgot to delete one last fixme comment.

* Spack "develop" needs to link to repo "devel"

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Robert Blake <rob.c.blake.3@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
 2020-06-09 16:13:54 -05:00
Joseph Ciurej
806a19c6b6
libffi: add patch for building with clang on power (#16855) 
* libffi: add patch for building with '%clang target=power*'

* libffi: fix version of clang/power patch
 2020-06-09 13:52:01 -07:00
darmac
8b1ffebe00 Add new package: py-workload-automation 2020-06-09 12:02:49 -07:00
victorusu
a52945613d
New package: py-pygelf (#17004) 2020-06-09 11:54:59 -07:00
Rob Latham
07e97e3ebc
jansson: add versions 2.10 to 2.13.1 (#17011) 2020-06-09 11:53:20 -07:00
Jen Herting
11b5fa7170
[util-linux] disabling systemd (#17008) 
If systemd support is enabled, install will attempt to modify files in
system systemd directories.
 2020-06-09 17:23:29 +02:00
Nathan
f70b72edc5
Set the BOOST_ROOT environment variable when library is loaded (#16818) 
* Adding BOOST_ROOT env variable

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
 2020-06-09 08:01:55 -05:00
Massimiliano Culpo
2e20ee8ea2
suite-sparse: build libraries without running demos (#17007) 
fixes #16638
 2020-06-09 06:54:50 +02:00
oracleLee
9cda38c03d
Update miniconda3@4.8.2 (#17003) 
* Update package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py
 2020-06-08 22:48:59 -05:00
Adam J. Stewart
bcf8ebff4f
Cray: fix Blue Waters support and user-built MPIs on Cray (#16593) 
* Cray: fix Blue Waters support

* pkg-config env vars needed on Blue Waters

* cray platform: fix support for user-build MPI on cray machines

* reintroduce cray environment cleaning behind cnl version guard

* cray platform: fix support for user-build MPI on cray machines

Co-authored-by: Gregory <becker33@llnl.gov>
 2020-06-08 16:44:07 -07:00
Ryan Mast
6f9bfec32e
HELICS: add version 2.5.1 (#17014) 2020-06-08 14:37:49 -07:00
darmac
4d064fd56c
rt-tests: fix build error (#16998) 
This is a makefile package and needs to invoke make.
 2020-06-08 10:51:59 -07:00
darmac
f8b5e413b4
Add new package: py-devlib (#16982) 
* Add new package: py-devlib

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* add depends

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
 2020-06-08 08:33:40 -05:00
vvolkl
8995b3ad3a
Add Package HSF-CMakeTools (#16951) 
* [hsf-cmaketools] add package

* fix formatting

* Apply suggestions from code review

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* [hsf-cmaketools] remove cmake_prefix_path which is set already by spack

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
 2020-06-08 08:30:23 -05:00
Amjad Kotobi
c76ab4d8fe
R: url-version custom, release 4 (#16962) 
* R: url-version custom, release 4

* r: pcre condition
 2020-06-08 08:28:21 -05:00
iarspider
3ea65818e1
Add py-storm@0.23 and update URL (#16991) 
* Add py-storm@0.23 and update URL

* Update package.py
 2020-06-08 14:09:48 +02:00
Justin S
d9738f569d
ltr-retriever: new package at v2.8.7 (#16832) 
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
 2020-06-08 08:07:34 +02:00
Greg Becker
bd1a0a9ad4
view remove: directly check whether specs own files before removing from view (#16955) 
Bugfix for hardlinks and copies
 2020-06-08 06:43:52 +02:00
Mark W. Krentel
763760cfe0
hpcviewer, ibm-java: updates versions (#16987) 
hpcviewer: added v2020.05.
ibm-java:  added v8.0.6.10.
 2020-06-08 06:15:37 +02:00
iarspider
664c32efb4
py-ipykernel: added v5.1.1 (#16988) 2020-06-08 06:11:24 +02:00
Toyohisa Kameyama
b00f97f7cc
boost: Don't use pre-compiled headers for Fujitsu compiler (#16914) 
* boost: Dopn't use pre compile header.

* move %fj.
 2020-06-07 09:39:53 -05:00
John Jolly
33923320a8
rose: Add build dependencies for flex and bison (#16981) 2020-06-07 09:36:14 -05:00
Sinan
a2c6f6a703
py-gast: add version 0.3.3 (#16945) 
* py-gast: add version 0.3.3

* add python version constraints

Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
 2020-06-07 09:33:03 -05:00
iarspider
6498b752d1
Add rpy2@3.0.4 (#16924) 
* Add rpy2@3.0.4

* Style fixes

* Update package.py

* Proper Python version requirement
 2020-06-06 16:33:34 -05:00
Toyohisa Kameyama
7bc44fa165
ffr: fix mpi programs to use mpi compiler wrapper. (#16948) 2020-06-06 16:30:43 -05:00
vvolkl
8f291c7e95
[prmon] add package (#16949) 2020-06-06 16:29:42 -05:00
Michael Kuhn
ad2dd4be01
mongo-c-driver: Add 1.16.2 (#16956) 
This also updates libbson to the corresponding version and adds a few
missing older versions.
 2020-06-06 16:18:48 -05:00
Matthieu Dorier
543f9f91d4
added CTRE package (#16964) 2020-06-06 16:14:40 -05:00
John Jolly
46a751081d
gcc: Fix error 'size of array is negative' (#16969) 
gcc 9.3.0 and glibc 2.31 (found in the base install of Ubuntu 20.04)
cause the gcc package to error during build with the error:

    "size of array 'assertion_failed__####' is negative"

Previous to this fix, the error was resolved for v8.1.0 <= gcc <= v9.2.0
via two patches.

This fix backports those patches for v5.3.0 <= gcc <= v7.4.0

Potentially these patches need to be backported to versions of gcc
before v5.3.0, but other compile issues need to be resolved for earlier
versions of gcc first.

Fixes #16968
 2020-06-06 16:14:11 -05:00
Tom Payerle
885808cc13
intel-tbb: Fix for #16938 add custom libs method (#16972) 
* intel-tbb: Fix for #16938 add custom libs method

Override the libs method to look for libraries of form libtbb*
(instead of inherited which looks for libintel-tbb*)

* Fixing pre-existing flake8 issues
 2020-06-06 16:12:46 -05:00
darmac
c835b93109
Add new package: py-louie (#16983) 2020-06-06 16:02:15 -05:00
darmac
77fbdff8a2
Add new package: lxc (#16984) 2020-06-06 16:00:59 -05:00
Sinan
36f9550178
py-mysqlclient: relax dependency constraint, add new versions (#16985) 
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
 2020-06-06 16:00:29 -05:00
Sinan
73d13461b1
ensure xla is turned off (#16974) 
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
 2020-06-06 15:51:19 -05:00
Sinan
7b6e1ae9d3
py-astunparse: add version 1.6.3 (#16946) 
Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
 2020-06-06 15:50:16 -05:00
darmac
c5ac168f31
protobuf: support aarch64 @2.5.0 (#16862) 
* protobuf: support aarch64 @2.5.0

* refine cmake args

* fix patch name
 2020-06-06 15:47:30 -05:00
Nithin Senthil Kumar
944f0abb36
Update package for MVAPICH2 2.3.4 release (#16960) 
Co-authored-by: senthilkumar.16 <senthilkumar.16@nowlab.cse.ohio-state.edu>
 2020-06-06 12:51:27 +02:00
John Jolly
d755cc8ce9
iegenlib: add build dependencies for automake and libtool (#16980) 2020-06-06 09:55:14 +02:00
Andrew Gaspar
374f1a62e2
py-flake8: add version 2.8.2 (#16959) 
* py-flake8: add version 3.8.2
  * This version depends on different versions of py-pycodestyle
    and py-pyflakes
  * When built for python@:3.7, this depends on the
    py-importlib-metadata backport library
* py-pycodestyle: add version 2.6.0
* py-pyflakes: add version 2.2.0
 2020-06-05 18:25:42 -07:00
Amjad Kotobi
27eb7d9f5f
xrootd: add version 4.12.1 (#16966) 2020-06-05 18:18:00 -07:00
Sinan
a08f3dd505
New package: py-asteval (#16976) 2020-06-05 18:16:13 -07:00
Michael Kuhn
bfa05628cb pkgconf: Add 1.7.3 2020-06-05 18:14:20 -07:00
Christoph Junghans
76abf35813
cajita: got merged in cabana (#16971) 2020-06-05 12:38:07 -06:00
Tomoki, Karatsu
89cc507cf6
cmake: add linker option for VerifyFortranC when using Fujitsu compiler. (#16963) 2020-06-05 13:29:36 +02:00
Tomoki, Karatsu
c3be6d903a
cmake: modify FindMPI.cmake to treat Fujitsu MPI correctly (#16864) 2020-06-05 13:25:02 +02:00
Tomoki, Karatsu
8be7823cc5
suite-sparse: change the condition to add C11 flag. (#16859) 2020-06-05 13:17:41 +02:00
eugeneswalker
92e24950e5
add erlang version 23.0 (#16961) 2020-06-04 22:49:46 -07:00
Andrew Gaspar
0d43e41da0
Rust v1.44.0 (#16957) 
* libgit2 v1.0.1

* Rust 1.44.0

* Fix flake8
 2020-06-04 16:59:14 -05:00
Andrew Gaspar
0a3601a3f1
libgit2 v1.0.1 (#16952) 2020-06-04 16:34:19 -05:00
eugeneswalker
44ec8cc4e4
sz: patch in ctag optionality from robertu94/sz 3637a87f986c (#16953) 2020-06-04 09:16:11 -07:00
eugeneswalker
b64ec7fba4
pass hwloc to configure via useropt; use lib/ or lib64/ as appropriate for libunwind (#16941) 2020-06-04 06:58:33 -07:00
Adam J. Stewart
7617054a5d
Fix obsolete references to wx package (#16944) 2020-06-04 08:05:48 -05:00
Adam J. Stewart
0dd1d1f21a
NumPy: add 1.18.5 (#16943) 2020-06-04 08:05:22 -05:00
iarspider
ad50a02188
Add matplotlib 3.1.0 (#16921) 2020-06-03 22:26:13 -05:00
iarspider
6f4631ee48
Add py-jupyter-core@4.6.1 (#16922) 2020-06-03 22:25:38 -05:00
Seth R. Johnson
104a0c4259
Trilinos: add Stratimikos package (#16925) 
Stratimikos is an optional dependency for our project. It depends on
Thyra, and thyra has subpackages that should be enabled based on
tpetra/epetra/epetraext.
 2020-06-03 22:25:09 -05:00
Mathew Cleveland
02548c56fa
+ Add opppy-0_1_3 (#16926) 
+ Update maintainers for OPPPY package
+ remove "run" requirement for setuptools and sphynx

Co-authored-by: Cleveland <cleveland@lanl.gov>
 2020-06-03 22:16:46 -05:00
iarspider
16e8e434c2
Add pytest@5.3.4 (#16927) 
Dropping atomicwrites dependency: https://github.com/pytest-dev/pytest/issues/6147
 2020-06-03 22:15:01 -05:00
Seth R. Johnson
6f6c243699
mpfr: update hash for 4.0.2 patch (#16937) 2020-06-03 22:11:44 -05:00
Adam J. Stewart
61f61f3cde
py-openpyxl: add 3.0.3 (#16940) 2020-06-03 22:09:58 -05:00
Adam J. Stewart
5a7b555314
IPython: fix setuptools dependency (#16915) 
* IPython: fix setuptools dependency

* Remove extra colon
 2020-06-03 22:09:40 -05:00
Tom Payerle
0fb671a19e
Gnuplot fix 16928 (#16929) 
* gnuplot: Fix for #16928

Dependency for --with-wx flag mistyped (should be wxwidgets)

* Revert "gnuplot: Fix for #16928"

This reverts commit 2b85814e5ccf5c9b2c70c7959994e89c18fdc3d8.

* gnuplot: Fix for #16928

Dependency spec for --with-wx flag mistyped (should be wxwidgets, not
wx)
 2020-06-03 22:08:07 -05:00
shanedsnyder
748be57790
update darshan-runtime & darshan-util versions (#16934) 
* update darshan-runtime & darshan-util versions

includes up through the current release, 3.2.1

* remove pre-releases, not needed in spack
 2020-06-03 18:05:46 -07:00
eugeneswalker
0086c47546
patch lambda capture issue for @1.1906.1, fixed in upstream faodel@master (#16935) 2020-06-03 11:38:27 -07:00
Greg Becker
3347ef2de4
Feature: add option to create view by copying/relocating files (#16480) 
* add subcommand `spack view copy/relocate`

* update bash completions

* add copy/relocate commands to view tests

* allow copied views to be removed
 2020-06-03 09:45:13 -07:00
dmorone
600e2cfc4f
amber: updated dependency constraint on cuda (#16919) 
Fix message 'amber requires cuda version :10.1.243, but spec asked for 10.2.89'
 2020-06-03 13:17:36 +02:00
Amjad Kotobi
eed82a19be
openssh: added v8.3p1 and v8.1p1 (#16917) 2020-06-03 11:28:42 +02:00
Amjad Kotobi
417eb3c5b1
git: added v2.27.0 (#16918) 2020-06-03 11:24:08 +02:00
Justin S
5604c8d91a
mummer4: new package at 4.0.0-beta2 (#16907) 2020-06-02 22:09:39 -05:00
Robert Blake
0e71e8716a
Add new package: sbml (#16898) 
* Adding a module for sbml.

* Adding support for all the languages.

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

Co-authored-by: Greg Becker <becker33@llnl.gov>

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

Co-authored-by: Greg Becker <becker33@llnl.gov>

Co-authored-by: Robert Blake <rob.c.blake.3@gmail.com>
Co-authored-by: Greg Becker <becker33@llnl.gov>
 2020-06-02 17:54:50 -07:00
Adam J. Stewart
7f086af05e
Ruby: add warning about Avira antivirus (#16882) 2020-06-02 15:05:50 -07:00
Toyohisa Kameyama
76142124d2
alsa-lib: Add new version and python dependency. (#16905) 
Add version 1.2.2.
Add conditional python dependency.
Add patch for 1.1.4.1 and python.
 2020-06-02 14:23:14 -07:00
Justin S
5d37439a7b
gmap-gsnap: add 2020-06-01 (#16906) 2020-06-02 14:21:00 -07:00
Chuck Atkins
5ace804dc2
Bump ADIOS to 2.6.0 (#16908) 2020-06-02 14:15:23 -07:00
iarspider
9a17d48455
Add ipython 7.5.0 (#16801) 
* Add ipython 7.5.0

* Update dependencies

* Update package.py
 2020-06-02 15:09:35 -05:00
takanori-ihara
b60ab6eefd
ruby: fixed build with Fujitsu compilers (#16889) 2020-06-02 11:07:48 +02:00
Xavier Delaruelle
c7851f896c
environment-modules: added v4.5.1 (#16896) 2020-06-02 11:06:02 +02:00
Greg Becker
2795414a80
Fix satisfaction checks for excluding variants from matrices (#16893) 
Because of the way abstract variants are implemented, the following 
spec matrix does not work as intended:
```
matrix:
- [foo]
- [bar=a, bar=b]
exclude:
- bar=a
```
because abstract variants always satisfy any variant of the same
name, regardless of values.

This PR converts abstract variants to whatever their appropriate 
type is before running satisfaction checks for the excludes clause 
in a matrix.

fixes #16841
 2020-06-02 11:02:28 +02:00
takanori-ihara
0875c6a5d0
py-grpcio: fixed build with Fujitsu compilers (#16900) 2020-06-02 10:55:55 +02:00
Axel Huebl
6aa0e9944e
ccache: added v3.7.9 (#16902) 
Add the latest CCache release. Fixes issues with `-x cu` that are
not present in the last checksummed release. This fixes workflows
with CMake.
 2020-06-02 10:53:12 +02:00
Sinan
7f2db5c5b0
qt: add conflict for old gcc (#16904) 
Co-authored-by: Sinan81 <Sinan81@github>
 2020-06-02 10:51:35 +02:00
Michael Kuhn
6035b32748
go: added v1.14.4 and v1.13.12 (#16903) 2020-06-02 10:48:35 +02:00
Jonathon Anderson
feda2a3073
openmpi: add opa-psm2 dependency (#16873) 
Also document with_or_without and enable_or_disable, (which are used
to configure the opa-psm2 dependency).
 2020-06-01 15:33:24 -07:00