Commit graph

14324 commits

Author SHA1 Message Date
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
Michael Kuhn
7325c20794 config: Add a new option connect_timeout
connect_timeout can be used to increase the time Spack waits for the
server to answer. This can be used to work around slow connections or
servers.

Fixes #14700
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
Adam J. Stewart
6153eea2c2
CudaPackage: add support for Tesla K80 and older CUDA (#15031)
* CudaPackage: add support for Tesla K80 and older CUDA

* Flake8 fixes

* Fix cuda_arch when no arch is set

* Fine-tune cuda_arch=37,50 supported CUDA versions

* CUDA 6.5+ supports SM_37

* Add @svenevs as a maintainer
2020-02-27 12:16:20 -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
TZ
d6d095a868
Docs: "spack env" is in the meantime called "spack build-env" (#15233) 2020-02-27 09:13:09 +01:00
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
Tamara Dahlgren
ed15adbb9e
bugfix: Add dependents when initializing spec from yaml (#15220)
The new build process, introduced in #13100 , relies on a spec's dependents in addition to their dependencies. Loading a spec from a yaml file was not initializing the dependents.

- [x] populate dependents when loading from yaml
2020-02-26 18:49:29 -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
Seth R. Johnson
6c445a2c0f
Uniquify suffixes added to module names (#14920) 2020-02-26 18:03:28 +01:00
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
Glenn Johnson
a568db00b8
A few edits for the Basic Usage Doc page (#15215)
This PR corrects a few minor things and adds a note about colorized
output.
2020-02-26 10:03:03 +01:00
Patrick Gartung
ae87828520
buildcache cmd: add explicit message with default output dir for buildcaches. (#15090)
* Make -d directory a required option. Print messages about where buildcaches will be written.

* Add mutually exclusive required options

* spack commands --update-completion

* Apply @opadron's patch

* Update share/spack/spack-completion.bash

* Incorporate @opadron's suggestions
2020-02-25 17:49:25 -06:00
Omar Padron
00090f8f97
add --only option to buildcache create cmd (#14921)
* add --only option to buildcache create cmd

replaces the --no-deps option
2020-02-25 17:32:20 -05:00
Omar Padron
8d750db9de
remove catch-all exception handling in buildcache command (#15185)
* remove catch-all exception handling in buildcache command

* fix test
2020-02-25 14:10:50 -06:00
Patrick Gartung
676eb56ab2
Buildcache cmd: add install -o/--otherarch option for installing macOS buildcaches on linux (#15192)
* Buildcache command: add install option -o/--otherarch
This will allow matching specs from other archs, for example
installing macOS buildcaches on linux hosts.

* spack commands --update-completion
2020-02-25 11:01:59 -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
Michael Kuhn
45306206c7
docs: Fix tiny typo (#15181) 2020-02-24 10:58:21 -06:00
Michael Kuhn
94acd8f235
cmd/load: Fix usage output (#15180)
args.specs is a list, which results in output like this:
```
eval `spack load --sh ['libxml2', 'xz']`
```

We want this instead:
```
eval `spack load --sh libxml2 xz`
```
2020-02-24 09:46:41 -06:00
Michael Kuhn
a38eb70e30
modules: store configure args during build (#11084)
This change stores packages' configure arguments during build and makes
use of them while refreshing module files. This fixes problems such as in
#10716.
2020-02-24 15:34:57 +01:00
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
Todd Gamblin
5aa1739bfa Merge branch 'releases/v0.14' into develop 2020-02-23 17:32:12 -08:00
Todd Gamblin
97d46dc36f update CHANGELOG.md for 0.14.0 2020-02-23 17:08:15 -08:00
Todd Gamblin
388960f044 version bump: 0.14.0 2020-02-23 17:08:15 -08:00
Michael Kuhn
a5461f5cba
py-setproctitle: Add new package (#15170) 2020-02-23 12:46:22 -06:00
Michael Kuhn
b935d88282
create: Mention that python dependency does not have to be added (#15173)
A generic python dependency is already added implicitly by the
PythonPackage class.
2020-02-23 10:22:50 -08:00
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