Commit graph

10336 commits

Author SHA1 Message Date
Christoph Junghans
a785e302cc
portage: needs to be linked against lapack:c (#15259) 2020-02-27 20:23:45 -06:00
Jean-Paul Pelteret
7217592c24 Fix Trilinos 12.18.1 build when using Apple Clang 8.0.0 2020-02-27 18:22:09 -08:00
Jean-Paul Pelteret
7fc908e0e1 Update package: Trilinos + Mesquite 2020-02-27 18:22:09 -08:00
Robert Blake
b88c66cb52
Adding an option to build the C api for Umpire. (#15238)
* Adding an option to build the C api for Umpire.

This is useful if you need to link to a C code and you're using
a compiler suite that doesn't support fortran.

* Also updating the versions while I'm here.

* Adding conflict: Fortran requires C.

To ease transition and confusion, default to C-bindings being
present.  This shouldn't hurt anyone who is upgrading an existing
installation.
2020-02-27 20:17:55 -06:00
Glenn Johnson
4d5e75d825
new package: py-auxlib (#15221) 2020-02-27 20:12:32 -06:00
Mark W. Krentel
fc20b352e7 hpcviewer: add version 2020.02 2020-02-27 15:40:55 -08:00
Roberto Di Remigio
d083c17242
New package: XCFun (#15199) 2020-02-27 15:40:21 -08:00
Michael Kuhn
f580b340f8 Add new timeout fetch_option
This allows packages to override the global connect_timeout.
2020-02-27 10:52:52 -08:00
Michael Kuhn
b7cfd05ef7 Generalize curl_options into fetch_options
This allows us to support higher-level concepts such as 'cookie' and
'timeout' without users having to specify curl options.
2020-02-27 10:52:52 -08:00
Sheng Di
ffb9591dc9
release sz 2.1.8.3 (#15250) 2020-02-27 12:25:06 -06:00
Glenn Johnson
167c75842a
new package: py-cnvkit and py-pomegranate (#15222)
The py-pomegranate package is a dependency of py-cnvkit
2020-02-27 12:06:19 -06:00
Glenn Johnson
c34ed6e6b5
new package: py-pycifrw (#15224) 2020-02-27 11:55:10 -06:00
Glenn Johnson
2d0ae0deb2
new package: py-pycosat (#15225) 2020-02-27 11:53:30 -06:00
Glenn Johnson
130a77f322
New packages: py-pymc3 and py-arviz (#15226)
This PR adds py-pymc3 and py-arviz as a dependency.
2020-02-27 11:51:15 -06:00
Paul
0d2f8e314b
Added go 1.14 (#15249) 2020-02-27 11:42:48 -06:00
Kai Torben Ohlhus
b37d7b8ed7
arpack-ng: ILP64 support (#15103)
Details about ILP64 support: `INTERFACE64=1` are described on the [ARPACK-NG GitHub website](https://github.com/opencollab/arpack-ng).
2020-02-27 07:19:24 +01:00
Anthony Scemama
9c194b22dc
f77-zmq: add version 4.3.2 (#15204)
Version 4.3.1 only works with Python3. Version 4.3.2 also works
with Python2. These constraints were not listed before and are added
by this commit.
2020-02-26 19:05:46 -08:00
Andreas Baumbach
f1a12966b0
py-git-review: add version 1.28 (#15203) 2020-02-26 19:02:51 -08:00
Luca Carrogu
350235ba71
AWS ParallelCluster: add version 2.6.0 (#15240) 2020-02-26 19:02:24 -08:00
genric
9a1a346999
h5py: add version 2.10.0 (#15205)
Also add dependency on py-cached-property
2020-02-26 19:01:22 -08:00
Kevin Huck
ebd248b27e
SQLite shouldn't be enabled by default for TAU package (#15228)
Also Adding conflict for SQLite and ADIOS2 for older TAU releases
2020-02-26 17:14:09 -06:00
Seth R. Johnson
578e8031ce
Default to +termlib for ncurses for LLVM (#15039)
LLVM is the only package that explicitly sets the "termlib" variant
of ncurses and it specifies +termlib. ncurses defaults to ~termlib;
if a package depends on LLVM and ncurses, there is a concretizer bug
that incorrectly detects a constraint conflict (see #267). Setting
+termlib as the default is a stopgap measure to avoid this conflict.

If other packages were to explicitly request ~termlib in the future,
the same issue would come up again (and could not be resolved by
adjusting the default of "termlib").

Setting +termlib on ncurses moves some symbols into a separate
"libtinfo". Not all packages may be able to detect libtinfo properly
so may require an update; vim, samtools, and libedit have been
updated to use ncurses+termlib (in the case of libedit, the only
necessary action was to add a newer version where the build system
was updated to check libtinfo).
2020-02-26 11:27:12 -08:00
Anthony Scemama
1c227db7a9
Basis set exchange command-line tool (#15126)
* Flake8 OK

* Update var/spack/repos/builtin/packages/py-basis-set-exchange/package.py

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

* Update var/spack/repos/builtin/packages/py-basis-set-exchange/package.py

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

* Added missing dependencies proposed by @adamjstewart

* Without py-versioneer

* Added py-versioneer

* Python2 for bse

* Python build error

* Update var/spack/repos/builtin/packages/py-basis-set-exchange/package.py

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

* Removed py-versioneer, according to @adamjstewart

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-26 07:27:02 -06:00
Kai Torben Ohlhus
8d8925c725
qrupdate: ILP64 support (#15104)
- When compiling qrupdate with `FFLAGS=-fdefault-integer-8` it can be perfectly used for larger problem dimensions.
- Improved the readability of the file with the added rules.
2020-02-25 10:36:54 +01:00
Kevin Huck
21afb13be6
Adding ADIOS2 and SQLite3 output support to TAU. Also fixing MPI include and library paths. (#15189)
Setup package to use MPI the way Spack recommends, and remove extra iowrapper option from configure
Making flake happy
2020-02-24 22:33:05 -06:00
OliverPerks
5c68caeb1e
Update of OpenFOAM package.py (#15190) 2020-02-24 22:28:13 -06:00
Kai Torben Ohlhus
4a0b7c9d20
suite-sparse: add version 5.7.1 (#15195)
Release notes: https://github.com/DrTimothyAldenDavis/SuiteSparse/releases/tag/v5.7.1

Version 5.7.0 was an incomplete release.
2020-02-24 22:22:00 -06:00
ktsai7
9b3f5f3890
update flecsi and legion package.py (#15159)
* update flecsi and legion package.py

* comment out a conflict

* update to use extend
2020-02-24 13:22:25 -06:00
darmac
b1e097b035
add new package : agrep (#15165)
* add new package : agrep

* agrep: move binary to bin/
2020-02-24 08:00:34 -06:00
Anthony Scemama
48d6da3b6e
Added extra versions of OCaml (#15177)
* Aded extra versions for OCaml

* Added maintainer
2020-02-24 07:59:59 -06:00
Robert Underwood
79dcf835b2
sz: update to version 2.1.8.1 (#15154)
The newer versions of SZ now uses CMake to build.
2020-02-24 07:55:39 -06:00
Glenn Johnson
c2e1319f2d
Update py-bx-python package (#15175)
* Update py-bx-python package

- add update to py-bx-python
- switch to pypi downloads
- set dependencies

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

I had initially pulled version 0.8.6 and then updated that to 0.8.8 but missed the change in the python specs between those two versions.

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

* Fix version 0.7.4

- set dependency on python2
- add dependency on py-python-lzo
- add py-python-lzo package
- set py-numpy dependency to correspond to latest version that works
  with python2

* Add constraint for py-six dependency

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

Ah, I had that `when` clause in and then took it out as it did not seem to be needed. I guess it is always better to be more explicit.

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

* Remove py-numpy constraint

Let the concretizer catch the conflict with python2 and py-numpy
versions.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-24 07:54:08 -06:00
Glenn Johnson
6615fbccbc
Update py-rseqc package (#15176)
This PR depends on #15175
- add updated version
- set depedencies
2020-02-23 22:15:47 -06:00
darmac
edca0e9da2
add new package : batctl (#15160)
* add new package : batctl

* batctl: move binary to bin/
2020-02-23 22:08:03 -06:00
darmac
fd3c08e925
add new package : bubblewrap (#15162)
* add new package : bubblewrap

* bubblewrap: remove some comment in package.py
2020-02-23 22:07:39 -06:00
Michael Kuhn
a5461f5cba
py-setproctitle: Add new package (#15170) 2020-02-23 12:46:22 -06:00
iarspider
fd60977613
Separate HepMC2 and HepMC3 build recipes; Python3 support for HepMC3 (#15147)
* Fixes & additional variant(s) for HepMC3

* Syntax

* Restore recipe for HepMC2

* Remove FIXME

* Update package.py

* Apply suggestions from code review

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-23 12:07:00 -06:00
Seth R. Johnson
b927e3799f
Fix silex build (#15172)
* Mark silo+silex as requiring QT4

* Add missing readline dependency to silo

* Fix silo QT4 usage and verify silex works on mac

```
-- darwin-mojave-x86_64 / clang@11.0.0-apple --------------------
7gdcud4 silo@4.10.2+fortran~mpi patches=7b5a1dc2a0e358e667088d77e7caa780967fa8ea60be89c44986605df9990abe +pic+shared+silex
pk3wbwd     hdf5@1.10.6~cxx~debug~fortran+hl~mpi+pic+shared+szip~threadsafe
slsy6ko         libszip@2.1.1
xj36ejk         zlib@1.2.11+optimize+pic+shared
u4662xx     libx11@1.6.4
3lpe6j3     qt@4.8.7~dbus~examples~framework freetype=none ~gtk~opengl patches=03f9893882c63a9a9617d9ecab9caf80661c96df13f596a9b24fc4579490144a,a4f37427b34d88df6a6adc16e1e6c805087d4f3a7c658e1797450b0912fcbf5d,f17e0b5fb1f43bccadf7298533eca57294f4acab11ed83b176c61c441f745c19 ~phonon+shared~sql~ssl~tools~webkit
shdhdbh         glib@2.56.3~libmount patches=c325997b72a205ad1638bb3e3ba0e5b73e3d32ce63b2d0d3282f3e3a2ff4663c tracing=none
msyeqht             gettext@0.20.1+bzip2+curses+git~libunistring+libxml2+tar+xz
ysmjykg                 bzip2@1.0.8+shared
w354vrb                 libxml2@2.9.9~python
jg6ekuh                     libiconv@1.16
b7n722h                     xz@5.2.4
zbgxvxi                 ncurses@6.1~symlinks~termlib
2e6sifw                 tar@1.32
7yg7qah             libffi@3.2.1
zg55iyu             pcre@8.43~jit+multibyte+utf
zqrlxlz             perl@5.30.0+cpanm+shared+threads
un7wzvl             python@3.7.4+bz2+ctypes+dbm~debug+libxml2+lzma~nis~optimizations patches=210df3f28cde02a8135b58cc4168e70ab91dbf9097359d05938f1e2843875e57 +pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tix~tkinter~ucs4+uuid+zlib
l4gxq46                 expat@2.2.9~libbsd
3t4dwsv                 gdbm@1.18.1
h2bjtz2                     readline@8.0
ugvknwc                 openssl@1.1.1d+systemcerts
hsmq6ou                 sqlite@3.30.1~column_metadata+fts~functions~rtree
lpfob23         icu4c@65.1 cxxstd=11
lf66vbr         inputproto@2.3.2
afovyhg         libjpeg-turbo@2.0.3
5dgw556         libmng@2.0.3 build_type=RelWithDebInfo
3z4lw2w             lcms@2.9
flleuyu                 libtiff@4.0.10
67tigfp         libpng@1.6.37
```
2020-02-23 10:45:19 -06:00
Seth R. Johnson
629c69d383
Automatically run LLDB codesign script on mac (#15169)
Newer versions of LLVM provide a one-line command to set up LLDB code
signing. Now the build will abort only if this command fails.

https://lldb.llvm.org/resources/build.html#code-signing-on-macos
2020-02-22 13:09:22 -06:00
darmac
0ea6bab984
add new package : brltty (#15161) 2020-02-22 09:02:34 -06:00
darmac
50b5e6b94b
add new package : audit-userspace (#15163) 2020-02-22 09:01:27 -06:00
darmac
1a479b5e9e
add new package : apachetop (#15164) 2020-02-22 09:00:55 -06:00
darmac
3104bfe93e
add new package : advancecomp (#15166) 2020-02-22 08:59:26 -06:00
darmac
f961f64215
add new package : acpid (#15167) 2020-02-22 08:58:54 -06:00
darmac
9f2cee43cf
lighttpd : fix pcre depends (#15168) 2020-02-22 08:58:25 -06:00
Cody Balos
16a9464b5c
sundials: add version 5.1.0 and trilinos variant (#15155)
* sundials: add version 5.1.0 and trilinos variant

* sundials: add version 5.1.0 and trilinos variant
2020-02-21 14:54:27 -06:00
Robert Blake
6764a9464d
Changes necessary to build lbann@develop (#15153)
* Necessary changes to get lbann develop to compile.

* Reformatting for flake8

* More flake8 changes.

* Removing redundant clara dependency.
2020-02-21 14:42:37 -06:00
Erik Schnetter
6d8e0699f4
shtools: New package (#15133)
* shtools: New package

* shtools: Convert to MakefilePackage, use Spack's generic compiler flags

* shtools: Make function location explicit
2020-02-21 14:30:25 -06:00
iarspider
0bc4a778bd
Add extra version of py-jsonschema (#14993)
* Add extra version of py-jsonschema

* Update dependencies

* Update dependencies + flake8

* Add py-pyrsistent package

* Update package.py

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

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

* Update package.py

* Update package.py

* Apply suggestions from code review

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

* Apply suggestions from code review

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-21 14:29:42 -06:00
Erik Schnetter
4a5c64ab6e
amrex: New version 20.02 (#15132) 2020-02-21 12:52:19 -06:00