Commit graph

14551 commits

Author SHA1 Message Date
iarspider
95fcd9ac13
superchic: added new package (#21463)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-02-03 15:29:52 +01:00
sameershende
d5d1cb09ad
Updated TAU v2.30.1. (#21453) 2021-02-02 15:21:30 -08:00
mic84
e2294ea0b0
amrex: new version 21.02 (#21426) 2021-02-02 14:49:51 -08:00
iarspider
4691177bbf
New package: apfel (#21440) 2021-02-02 14:42:07 -08:00
Axel Huebl
d8ba71993c
openPMD-api: 0.13.2 (#21450) 2021-02-02 14:25:18 -08:00
Andrew-Dunning-NNL
09190c0876
py-bash-kernel: new package (#21441)
* py-bash-kernel: new package

* py-bash-kernel: remove git bash kernel dependency
2021-02-02 15:42:08 -06:00
Bryan Herman
182ab78940
add py-python-fsutil recipe (#21449) 2021-02-02 15:41:21 -06:00
Mark W. Krentel
040204c261
intel-xed: add patch to 12.0.1 to fix segfault (#21436)
Fix segfault due to uninitialized data when trying to decode some cases of data that aren't a valid instruction.
2021-02-02 12:40:24 -08:00
bryanherman
d048048911
py-nbsphinx: new package (#21444)
* added py-nbsphinx package

* added a comment about nbsphinx use
2021-02-02 11:24:28 -06:00
Andrew-Dunning-NNL
959df6bb12
py-grandalf: new recipe (#21348)
* py-grandalf: new recipe

* py-grandalf: add runtime dependency

* py-grandalf: add runtime dependency)
2021-02-02 11:22:36 -06:00
Andrew-Dunning-NNL
59a54905ea
py-dictdiffer: fix offline dependencies (#21345)
* py-dictdiffer: fix offline dependencies

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-02-02 11:21:58 -06:00
Andrew-Dunning-NNL
8b6c468cdf
py-ftfy: new recipe (#21333)
* py-ftfy: new recipe

* py-ftfy: depend on python>3.5
2021-02-02 11:19:02 -06:00
Andrew-Dunning-NNL
71309f75b2
py-dulwich: new recipe (#21330)
* py-dulwich: new recipe

* py-dulwhich: add python dependency

* py-dulwich: fix flake8 whitespace
2021-02-02 11:15:34 -06:00
Andrew-Dunning-NNL
49b3ab684e
py-flatten-dict: new recipe (#21329)
* py-flatten-dict: new recipe

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

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

* py-flatten-dict: fix dependencies

* py-flatten-dict: fix dependency

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-02-02 11:14:12 -06:00
apreifsteck
df0cc9ee02
OSU mvapich2 GDR 2.3.5 package.py update (#21270)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: NOWLAB PACKAGER <mvapich-help@cse.ohio-state.edu>
2021-02-01 18:48:16 -08:00
Sergei Shudler
8f2acc3123
mfem: Add e4s testsuite-inspired smoke test (#21228) 2021-02-01 17:49:20 -08:00
Desmond Orton
71b12e9b27
New R Package Pegas@0.14 (#21359) 2021-02-01 16:42:44 -08:00
Desmond Orton
6cc23e6137
New Feature r-quickplot (#21430) 2021-02-01 18:02:14 -06:00
iarspider
eac95c866a
FastJet: add optional patch to make random generator thread-local (#21395) 2021-02-01 11:18:04 -08:00
Phil Carns
03fce1f0c9
replace margo pkg with updated mochi-margo pkg (#20273) 2021-02-01 12:38:02 -06:00
iarspider
586ff05af1
New package: frontier-client (#21405) 2021-02-01 10:23:56 -08:00
iarspider
5add6c4e03
New package: unigen (#21338) 2021-02-01 10:21:02 -08:00
Ryan Mast
5cb8d1894b
libgcrypt: add versions up to 1.9.1 (#21401) 2021-02-01 10:11:51 -08:00
Jose E. Roman
4523cce791
SLEPc: add v3.14.2 (#21422) 2021-02-01 09:42:13 -08:00
Adam J. Stewart
1d636bed6a
R: add maintainer(s) (#21119)
* R: add maintainer(s)

* Add maintainer to base class
2021-02-01 11:33:33 -06:00
Andrew-Dunning-NNL
f781403615
py-colored-traceback: new package (#21423) 2021-02-01 11:14:00 -06:00
eugeneswalker
0b58499d7a
llvm: "master" branch is now "main" branch (#21411) 2021-02-01 08:32:36 -06:00
iarspider
af988fc32d
sqlite: add v3.32.03 (#21417) 2021-02-01 15:04:19 +01:00
Tomoki, Karatsu
6feb697b62
abinit: fix build with Fujitsu compilers (#21213) 2021-02-01 15:03:03 +01:00
iarspider
260706c186
coin3d: depend on gl/glu (virtual packages), not on opengl/openglu (#21419) 2021-02-01 15:01:05 +01:00
Tomoyasu Nojiri
c279983c10
cgdb: add a few build dependencies (#20927) 2021-02-01 15:00:52 +01:00
Jean-Paul Pelteret
a04e0d2525
Add package: py-beancount (#21274)
* Add package: py-beancount

* Fixes
2021-01-31 12:29:29 -06:00
darmac
f7929aaeb1
chrony: add missing dependency (#21403) 2021-01-31 12:21:23 -05:00
Jean-Paul Pelteret
6ac3d98f4c
Add package: py-flask-babel (#21272) 2021-01-31 10:50:16 -06:00
Jean-Paul Pelteret
6c03c9996a
Add package: py-markdown2 (#21273) 2021-01-31 10:49:49 -06:00
Adam J. Stewart
c950f4a4ff
py-numpy: add v1.20.0 (#21409) 2021-01-31 06:28:21 +01:00
Toyohisa Kameyama
c175c05af9
quantum-expresso: fix for Fujitsu compiler (#21368) 2021-01-29 17:36:58 -08:00
Harmen Stoppels
371247c14a
Fix https://github.com/spack/spack/pull/21391#issuecomment-769961025 (#21397) 2021-01-29 17:21:56 -08:00
Massimiliano Culpo
13ac7198d3
clingo: added a package with option for bootstrapping clingo (#20652)
* clingo/clingo-bootstrap: added a package with option for bootstrapping clingo

package builds in Release mode
uses GCC options to link libstdc++ and libgcc statically

* clingo-bootstrap: apple-clang options to bootstrap statically on darwin

* clingo: fix the path of the Python interpreter

In case multiple Python versions are in the same prefix
(e.g. when clingo is built against an external Python),
it may happen that the Python used by CMake does not
match the corresponding node in the current spec.

This is fixed here by defining "Python_EXECUTABLE"
properly as a hint to CMake.

* clingo: the commit for "spack" version has been updated.
2021-01-29 12:22:57 -08:00
Robert Underwood
0611036abd
doxygen: add support for external detection (#20642) 2021-01-29 21:05:48 +01:00
Peter Lindstrom
0f82fa5151
zfp: several package improvements (#21244)
- add variants for build targets, language bindings, backends
- ensure selected variants are compatible with zfp version
- point to GitHub (not LLNL) tar balls
- add dependencies
- update link to homepage
- add maintainers

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-01-29 17:51:30 +01:00
albestro
47c85059fb
it seems like there was a bug in the version of APEX that we set by default in 1.5.x (#21391) 2021-01-29 16:51:28 +01:00
a-saitoh-fj
9761c13878
dssp: added smoke tests (#21366) 2021-01-29 10:29:42 +01:00
Tomoyasu Nojiri
e3a0c48599
py-cheetah: restrict valid python interpreter to 2.7.X, add v2.4.4 (#21363) 2021-01-29 09:43:43 +01:00
Tomoyasu Nojiri
7b6c99655c
py-cheetah3: add new package at v3.2.6 (#21387) 2021-01-29 09:41:32 +01:00
Tomoyasu Nojiri
bc639fe60b
wtdbg2: enable build for aarch64 (#21390)
Use sse2neon to maintain the same API calls for aarch64
2021-01-29 09:37:00 +01:00
Tomoyasu Nojiri
b18479a2bd
swarm: add v3.0.0 (#21389) 2021-01-29 09:18:41 +01:00
Adam J. Stewart
519ba5590c
py-graphviz: add v0.8.4 (#21383) 2021-01-28 18:25:07 -08:00
Cyrus Harrison
57c23b964a
add new package: bloaty (#21355) 2021-01-28 16:44:07 -08:00
Dan Lipsa
5a9da90d07
Use utf8 for latex build. (#21360)
Patch provided by @Billae

Avoid the following error:
  File "/home/danlipsa/projects/spack/lib/spack/llnl/util/tty/log.py", line 768, in _writer_daemon
    line = _retry(in_pipe.readline)()
  File "/home/danlipsa/projects/spack/lib/spack/llnl/util/tty/log.py", line 830, in wrapped
    return function(*args, **kwargs)
  File "/usr/lib/python3.8/codecs.py", line 322, in decode
    (result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x97 in position 220: invalid start byte
2021-01-28 15:58:55 -05:00
Massimiliano Culpo
f523ea8c4e
perl: add v5.32.1 (#21375)
Make it such that BigSur is seen as 10.16 rather than 11.1, since the latter causes troubles with Perl configuration
2021-01-28 21:54:28 +01:00
Desmond Orton
b095dfb44b
New Package r-fpCompare@0.2.3 (#21380) 2021-01-28 14:29:57 -06:00
iarspider
f28026c040
pacparser: new package at v1.3.7 (#21372)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-01-28 20:42:53 +01:00
Tomoyasu Nojiri
6ae8d5c380
openmx: Fix for aarch64 (#21367) 2021-01-28 10:20:18 -08:00
Ali Ahmed
b6d52fa466
New package: libpulsar (#21369) 2021-01-28 10:12:12 -08:00
Adam J. Stewart
aa15246280
py-matplotlib: add v3.3.4 (#21378) 2021-01-28 10:09:17 -08:00
bryanherman
ff8ef48806
New package: py-pytest-doctestplus (#21335)
* added package py-pytest-doctestplus

* setuptools required for run
2021-01-28 11:00:03 -06:00
bryanherman
ff0a92e6a8
New package: py-pytest-openfiles (#21339)
* added package py-pytest-openfiles

* remove wheel dep
2021-01-28 10:59:35 -06:00
bryanherman
bf33fe4805
openmc: add v0.11.0, v0.12.0 (#21349)
Also added new variants to fine tune the build
2021-01-28 17:04:34 +01:00
iarspider
9baecd0d78
umesimd: add new package (#21370) 2021-01-28 16:22:21 +01:00
Sergey Kosukhin
d577b6fcdf
autoconf: fix v2.70 and patching procedure of bin/autom4te.in (#21255)
This PR adds:

1.  A patch that fixes a bug in version 2.70 
    (will be fixed upstream in the next release: https://savannah.gnu.org/support/?110396).
2. A fix for the way we patch shebang in bin/autom4te.in. 

For 2, we need to keep the original modification timestamp of the file. 
Otherwise, we either get an empty man page for autom4te (versions 2.69 and before)
or a failure at the build time (versions 2.70 and after). 

The difference has to do with the update of the missing script: https://git.savannah.gnu.org/cgit/automake.git/commit/lib/missing?id=a22717dffe37f30ef2ad2c355b68c9b3b5e4b8c7

It will take time until developers of Autotools-based packages adjust their scripts 
to the new version, therefore, 2.69 is marked as preferred.
2021-01-28 11:21:04 +01:00
Adam J. Stewart
5b4d636d73
Clingo: fix missing import (#21364) 2021-01-28 00:38:01 -08:00
Tomoyasu Nojiri
181f921c1a
libpeas: restrict python version range, use pkgconfig virtual dependency (#21313) 2021-01-28 09:31:54 +01:00
Tomoyasu Nojiri
bcb0e80548
fox: add dependency to glu virtual package (#21280) 2021-01-28 09:29:36 +01:00
Jen Herting
0ebefcc92b
New package: py-proglog (#20750)
* [py-proglog] created template

* [py-proglog] added dependencies

* [py-proglog] fixed pypi url

* [py-proglog] removed fixmes, added homepage and description

* [py-proglog] url -> pypi

* [py-proglog] added dependency on setuptools
2021-01-27 20:59:19 -06:00
Rao Garimella
3dc5ffaf65
Update MSTK version (#21356)
* New interface reconstruction package

* forgot to put in CMake option for Jali

* cleanup whitespace

* fix lines with more than 79 chars

* more long line cleanup

* fix typo WONTON_ENABLE_Kokkos ---> TANGRAM_ENABLE_Kokkos

* New interface reconstruction package

* forgot to put in CMake option for Jali

* cleanup whitespace

* fix lines with more than 79 chars

* more long line cleanup

* fix typo WONTON_ENABLE_Kokkos ---> TANGRAM_ENABLE_Kokkos

* fix bugs in CMake section

* more compact cmake block

* update hash for 1.2.10 and add 1.2.11

* update recipe for Portage 3.0.0

* removing old versions - they won't build with the new recipe and the url specification doesn't work for them

* update version to 3.3.6

Co-authored-by: Rao Garimella <rao@abyzou.lanl.gov>
2021-01-27 20:58:02 -06:00
bryanherman
fe05b16922
New package: py-pytest-benchmark (#21324)
* added pytest-benchmark recipe

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

Added Python2 dependence.

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-01-27 20:57:24 -06:00
bryanherman
d1ce461a81
New package: py-pytest-cpp (#21328)
* added package py-pytest-cpp

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

package is !=5.4.0 use @:5.3.999

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-01-27 20:57:09 -06:00
bryanherman
4efeb39e95
New package: py-pytest-timeout (#21340)
* added package py-pytest-timeout

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

Added Python2.

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-01-27 20:56:52 -06:00
bryanherman
f7a47e4048
New package: py-openmc (#21351)
* added package py-openmc

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

specify branch when using branch names for versions

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

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

use run after fixture to install openmc lib

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

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

Simplify copying openmc library to py-openmc prefix using install

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

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

NumPy should be 1.9+

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

* fix paren missing

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

fixed parens

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

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

use v0.11.0 in URL

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-01-27 20:56:35 -06:00
eugeneswalker
74fbad4742
autoconf: add version 2.70 (#21362) 2021-01-27 17:59:03 -08:00
Stephen Herbein
71375b3446
flux: update to latest releases (#21306) 2021-01-27 17:56:45 -08:00
bryanherman
cc28bcddd1
fix cpio for intel@18 (#21322) 2021-01-27 17:48:26 -08:00
Harmen Stoppels
3172fc3681
Add conflict for mpich 3.4.x for clang <= 7" (#21326) 2021-01-27 17:45:38 -08:00
Michael Kuhn
f9fef22ce8
rdma-core: add 33.1 (#21361) 2021-01-27 17:31:01 -08:00
Greg Becker
0d521d56ec
openmpi find external fixup (#21354) 2021-01-27 15:27:17 -08:00
Desmond Orton
18b3688cd1
Package/spades (#21227)
Co-authored-by: codeandkey <jtst@iastate.edu>
2021-01-27 23:28:37 +01:00
bryanherman
71bac42357
added gawk version 5.1.0 (#21342) 2021-01-27 13:48:53 -08:00
Christoph Junghans
6b63441281
libecpint: initial add (#21353)
* libecpint: initial add

* flake8
2021-01-27 14:19:48 -07:00
Rémi Lacroix
5ef2daaa4a
ELPA: Switch to HTTPS links. (#21352) 2021-01-27 22:06:44 +01:00
Andrew-Dunning-NNL
895c8b33d9
py-dpath: new recipe (#21331) 2021-01-27 14:46:40 -06:00
bryanherman
68a144eaa3
added package py-pytest-flakes (#21337) 2021-01-27 14:38:30 -06:00
Andrew-Dunning-NNL
52c32047ad
py-mailchecker: new recipe (#21346) 2021-01-27 14:33:23 -06:00
Andrew-Dunning-NNL
54f163f7dc
py-jsonpath-ng: new recipe (#21347) 2021-01-27 14:23:20 -06:00
Brian Van Essen
3cbc35dbdd
LBANN: add support for building with OneDNN. (#21305) 2021-01-27 21:11:31 +01:00
Brian Van Essen
aac3699748
OneDNN: add versions up to v2.1-rc (#21304) 2021-01-27 21:10:16 +01:00
Rao Garimella
f2c98a8537
portage: added v3.0.0, deleted old versions (#21293)
old versions won't build with the new recipe and the url 
specification doesn't work for them

Co-authored-by: Rao Garimella <rao@abyzou.lanl.gov>
2021-01-27 20:13:22 +01:00
Ben Morgan
5667759bf5
vecgeom: add v1.1.9 release (#21341) 2021-01-27 19:50:31 +01:00
Sergey Kosukhin
3cc5b7adc7
Python extensions: consistently set LDSHARED to get Spack RPATHs (#21149)
Python extensions use CC and LDSHARED from the sysconfig module to
build. When Spack installs Python, it replaces the Spack compiler
wrappers in these values with the underlying compilers (since these
wrappers are not useful outside of the context of running Spack).
In order to use the Spack compiler wrappers when building Python
extensions with Spack, Spack sets the LDSHARED environment variable
when running `Python.setup_py` (which overrides sysconfig). However,
many Python extensions use an alternative method to build (namely
PythonPackage.setup_py), which meant that LDSHARED was not set (and
RPATHs were not inserted for dependencies).

This commit makes the following changes:

* Sets LDSHARED in the environment: this applies to all commands
  executed during the build, rather than for a single command
  invocation
* Updates the logic to set LDSHARED: this replaces the compiler
  executable in LDSHARED with the Spack compiler wrapper. This
  means that for some externally-built instances of Python,
  Spack will now switch to using the Spack wrappers when building
  extensions. The behavior is expected to be the same for Spack-
  built instances of Python.
* Performs similar modifications for LDCXXSHARED (to ensure RPATHs
  are included for C++ codes)
2021-01-27 10:20:36 -08:00
William Downs
6ba2e3ee5d
gchp: added new package (#21310)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-01-27 18:02:55 +01:00
Luca Heltai
8a7487773b
dealii: added support for simplices, updated sundials (#20621) 2021-01-27 17:02:15 +01:00
bryanherman
c52e95d681
cxxtest: added new package (#21323) 2021-01-27 16:26:26 +01:00
bryanherman
fbdc8b65b1
mesa: add dependency on zlib (#21325)
When installing mesa in an offline environment, mesa tries to download zlib.
2021-01-27 15:19:03 +01:00
Baptiste Jonglez
0efe54f722
mxnet: Fix python lib installation (#21298) 2021-01-27 07:53:09 -06:00
Ben Morgan
561557d2f5
py-h5py: add build dependency on py-wheel (#21320)
h5py requires wheel at build time from version 3.0.0, based on
the project's pyproject.toml.
2021-01-27 08:43:21 -05:00
Brian Van Essen
b8b432c3aa
lbann: add support for building just the LBANN core library (#21235)
Variants to disable vision libraries and NumPy support.
2021-01-27 13:42:49 +01:00
bryanherman
cbdf87cd28
boost: restrict lower bound of ranges for two patches (#21321) 2021-01-27 13:28:29 +01:00
Mohan
4977dcfe9b
knem: added a patch for v1.1.4 (#21312)
Co-authored-by: amd-toolchain-support <toolchainsupport@amd.com>
2021-01-27 13:27:10 +01:00
Brian Spilner
258bfff1da
cdo: add v1.9.10 (#21315) 2021-01-27 11:32:49 +01:00
takanori-ihara
e83cce313b
fujitsu-ssl2: remove mentions of libfj90rt2.a (#21308) 2021-01-27 11:32:23 +01:00