Commit graph

10622 commits

Author SHA1 Message Date
Neil Flood
451bfbd1ab py-pynio: new package (#10074)
* py-pynio: new package

* Major re-working to add some of the optional dependencies, and make it conform to the approach described in the pynio setup.py comments. Much of it turned out to be too complicated, and I have added some notes in comments to explain this to future adventurers.

* Added variants for the hdf5 and gdal dependencies, which do seem to be genuinely optional. Also added absolute dependencies for jpeg and zlib, which setup.py says it wants, but were being found as the os-installed versions.

* Added descriptions for the new variants, and moved them to above the dependencies
2018-12-23 09:50:41 -06:00
Jim Galarowicz
93d9139ff6 Add missing module env variable setting causing OSS to fail. (#10182) 2018-12-22 17:24:44 -06:00
Justin Stanley
90dce26db9 r-corhmm: new package at 1.22 (#9859) 2018-12-22 19:09:20 +01:00
Satish Balay
fad4ecc90b
petsc-3.10.3: syncs with superlu-dist-6.1. (#10166) 2018-12-22 10:40:08 -06:00
Levi Baber
ec2c5e5b0d gpgme: new package (#10174) 2018-12-21 12:17:45 -06:00
Jordan Ogas
b1944d4cbf add charliecloud 0.9.6 (#10176) 2018-12-21 12:17:33 -06:00
Matthias Wolf
a3ecdf1f41 py-numba: fix py-llvmlite version (#10175) 2018-12-21 11:34:32 -06:00
George Hartzell
7f095cee48 Add libiconv variant to glib (#10165)
Enable explicitly building glib with or without libiconv.

Heads up: if you build with ~iconv but there is something else in the
spec that includes libiconv then glib will *still* automagically
discover it and the build will fail.
2018-12-21 11:33:28 -06:00
Elsa Gonsiorowski, PhD
74a5d92f07 Remove /nfs/tmp2 from default build_stage locations (#10170)
* Remove /nfs/tmp2 from default configuration
* /nfs/tmp2 is going away from LC... and doesn’t exist for the rest of the world.
* update documentation to remove /nfs/tmp2 as well
2018-12-21 02:03:54 -08:00
Daryl W. Grunau
36ab7be406 R3D spackage (#10164)
* r3d spackage

* address Adam's review comments

* fix flake8: too many blank lines
2018-12-20 17:23:38 -06:00
Sajid Ali
e57ddda4cc update h5py to 2.9.0 (#10169)
* 	modified:   var/spack/repos/builtin/packages/py-h5py/package.py

* Update package.py

* Update package.py
2018-12-20 17:23:17 -06:00
thelfer
00d84b1978 Update TFEL package (#9995)
* add the tfel package

* fix the tfel package

* fix the tfel package

* fix the tfel package

* Taking Adam J. Steward' remarks into account

* fixes trailing white spaces

* Update description

* Update dependencies following @adamjstewart adices

* Style fixes

* Style fixes

* Add java optional support

* add the maintainers attribute (following @alalazo advice), disable interface not selected (following @adamjstewart advice)

* flake8 fixes

* Fix Cast3M and python-bindings support. Python detection is made compatible with cmake'FindPythonLibs module (at least how it is used in TFEL)

* Style fixes

* Style fixes

* Fix test on python version

* Follow @adamjstewart advices: code is much cleaner and readable

* Small fix

* Small fix

* Add comment

* Small fix in cmake option

* try again (trying to overcome Travis CI unstable build process)
2018-12-20 15:47:24 -06:00
Mark Olesen
7ded7fdbda OpenFOAM-v1812 - new version (#10167) 2018-12-20 13:18:51 -06:00
Omar Padron
60298787e4 Fix docker builds (#9805)
* move docker test logic to share/spack/qa
* update Dockerfile for archlinux
2018-12-20 11:17:46 -08:00
Omar Padron
56cb691fcc fix multiple issues with the docker images (#9718)
- fixed an issue where some undesirable parts of
   the spack source tree were being copied into
   the image context.

 - added a workaround for a tty ioctl warning on
   ubuntu

 - adjusted how the main images are built so that
   `RUN spack ...` works automatically for child
   images that base themselves on them.
2018-12-20 11:11:55 -08:00
Zack Galbreath
b90f619037 Performance improvements for CDash reporter
* Record build output as an array of lines rather than concatenating to a
  single large string.
* Use string.find to avoid running re.search on every line of output.
2018-12-20 09:23:08 -08:00
Zack Galbreath
6355ee208c Include accurate build time in CDash report 2018-12-20 09:23:08 -08:00
Zack Galbreath
8d0872083c Report current git commit of Spack to CDash
When using the CDash reporter, upload a Update.xml file that
indicates the hash of Spack's current git commit.
2018-12-20 09:23:08 -08:00
Scott Wittenburg
7217b4a4b9 Make sure to urlencode cdash submit parameters 2018-12-20 09:23:08 -08:00
Zack Galbreath
aed9a532c6 Get buildId from CDash at submit time
Pass extra data when submitting to CDash.  If CDash responds with a buildId,
construct and display helpful URL that links to the uploaded report.
2018-12-20 09:23:08 -08:00
Zack Galbreath
738d2bd77a Allow more customization for CDash reporter
Add new command line arguments to `spack install` that allow users
to set the build name, site name, and track in their CDash report.
2018-12-20 09:23:08 -08:00
Zack Galbreath
0bae6626a4 Avoid UnboundLocalError
Make sure cdash_phase is defined before referring to it.
2018-12-20 09:23:08 -08:00
jthies
9110c727bb packages/phist: add maintainer (#10162) 2018-12-20 13:23:35 +01:00
Greg Sjaardema
93c491f729 CGNS: Allow use of git branch versions (#10156)
* CGNS: Allow use of git branch versions

Add ability to use git `master` and `develop` branches of the CGNS library.  The `seacas` package sometimes needs to use the `master` or `develop` branch due to some new changes to the parallel I/O implementation in CGNS which has not yet been released.

* CGNS: Reorder to put newest version on top

Based on review comments, place newest version (develop) first in list.
2018-12-19 20:02:24 -06:00
Todd Gamblin
207c37759c env: all commands that disambiguate specs should be env-aware
- some commands were missed in the rollout of spack environments

- this makes all commands that need to disambiguate specs restrict the
  disambiguation to installed packages in the active environment, as
  users would expect
2018-12-19 17:49:51 -08:00
Mark W. Krentel
84b33523ec dyninst: patch to build dyninst with older gcc (#10160)
* dyninst: patch to build dyninst with older gcc

Add 'v9.3.2-auto.patch'.  This patch changes some 'auto t: type' usage
to the older but equivalent 'type.begin()'.  This allows building
dyninst 9.3.2 with gcc 4.4 which doesn't support the newer syntax.
This patch is harmless with newer gcc.

* Fix typo in patch.  (My bad for sloppy cut-and-paste.)

* Restrict the patch to gcc 4.7 and earlier.  gcc 4.8 supports the newer
usage and thus doesn't need the patch.
2018-12-19 17:24:43 -08:00
Michael Kuhn
84c547cf6e sqlite: add 3.26.0 (#10138) 2018-12-19 17:07:03 -06:00
Owen Solberg
6b1b9031ea updated checksum for kallisto (#10158) 2018-12-19 17:06:33 -06:00
Michael Kuhn
67ab73d381 fetch_strategy: improve GitFetchStrategy (#10153)
Currently, only the Git repsository's URL shows up in the `spack info`
output, which makes it hard to distinguish different versions:
```
Safe versions:
    develop    [git] https://github.com/LLNL/H5Z-ZFP.git
    0.8.0      [git] https://github.com/LLNL/H5Z-ZFP.git
    0.7.0      [git] https://github.com/LLNL/H5Z-ZFP.git
```

This change adds additional information as shown when cloning a Git
repository:
```
Safe versions:
    develop    [git] https://github.com/LLNL/H5Z-ZFP.git on branch master
    0.8.0      [git] https://github.com/LLNL/H5Z-ZFP.git at commit af165c4
    0.7.0      [git] https://github.com/LLNL/H5Z-ZFP.git at commit 58ac811
```
2018-12-19 14:33:58 -08:00
jthies
5f3d9a4076 phist tag 1.7.5 was moved (#10155) 2018-12-19 13:36:49 -06:00
sknigh
5adec7e491 Updated Dakota to 6.9 (#10157)
* Updated Dakota to 6.9

* Change comment wording
2018-12-19 13:03:14 -06:00
Adam J. Stewart
adfbe71b1b
Add python bindings to libxslt (#10149) 2018-12-19 11:39:19 -06:00
Adam J. Stewart
654360d2ad
Add missing libiconv dependency to libxml2 (#10148) 2018-12-19 11:38:14 -06:00
Adam J. Stewart
0fcca9f422
Add list_url to docbook-xml (#10146) 2018-12-19 11:37:54 -06:00
Adam J. Stewart
e19e176e67
Add latest version of docbook-xsl (#10147) 2018-12-19 11:37:35 -06:00
Adam J. Stewart
ed0ca18c3c
Restrict patch to oldest version of libbsd (#10145) 2018-12-19 11:37:11 -06:00
Satish Balay
c1e562f333
PETSc: add version 3.10.3 (#10154) 2018-12-19 10:46:02 -06:00
Neil Flood
a6e2f1a96a mapserver: new package (#10067) 2018-12-19 10:04:25 +01:00
Massimiliano Culpo
e057500009
Added labels in github issue templates (#10128) 2018-12-19 09:56:26 +01:00
Adam J. Stewart
c1a99bf8ec
Add additional info to MesonPackage docs (#10133)
* Add additional info to MesonPackage docs

* No Pygments lexer for Meson code, default to none
2018-12-18 21:51:42 -06:00
Elsa Gonsiorowski, PhD
b091fcdb8e fix for mpifileutils package (#10142)
* proper include & linking of libarchive

* due to linux headers, mfu can't build on mac

* hard code deps in configure line

rather than relying on pkg-config

* +xattr during config

* must also link the lib

* find mfu.h

* long lines
2018-12-18 21:51:24 -06:00
Dave
b27f81ac00 WarpX: Added dependency on fftw when +psatd (#10144) 2018-12-18 20:11:08 -06:00
Matthias Wolf
22d9938560 flatbuffers: add 1.10.0 (#10137)
Also unpin the version from the arrow package.
2018-12-18 10:53:02 -06:00
Adam J. Stewart
f8c650b9c4 Add pdf variant to cairo (#10135) 2018-12-18 16:39:36 +01:00
Justin Stanley
59d7854b89 clp: add build_directory, remove old hack (#10112)
* clp: add build_directory, remove old hack

* clp: use spack-build for building
2018-12-18 08:36:40 -06:00
Adam J. Stewart
d4b5fc141c
Add latest version of libxkbcommon (#10134) 2018-12-17 19:27:58 -06:00
Alberto Chiusole
a41571a1b6 Add variant to ecflow to choose whether to use static boost libraries. (#9933)
When this variant is set, it requires boost to be built with the +pic variant.
2018-12-17 19:23:53 -06:00
David Hows
c70ea22c6f Add thread count variant to atlas (#9999)
* Add thread count variant

Atlas automatically configures itself and optimizes to run with a fixed number of threads. This can be overridden during compile by setting a flag and atlas will tune itself to use the specified number, rather than all system CPUs. 

Default value is the existing logic, autoconfigure.

* Fix Linting

* Another lint for longline
2018-12-17 19:12:00 -06:00
Jannek Squar
09d2df690a Add spack package for saga-gis (#10018)
* Add spack package for saga-gis

* Adjusted license header

* Adjust saga-gis package, added fixme comments

* Removed version constraint

* Fixed fixme comment
2018-12-17 19:10:50 -06:00
Matthias Diener
776f99a414 git: add version 2.20.1 (#10130) 2018-12-17 17:36:57 -06:00