Commit graph

10015 commits

Author SHA1 Message Date
Michael Kuhn
e31b997162 icu4c: Update to 60.1 (#6295)
Previous versions try to include xlocale.h, which fails on glibc >= 2.26.
2017-11-14 09:21:35 -07:00
Yifan Zhu
a8f9182ef3 r-forcats: created new package (#6291) 2017-11-14 09:21:21 -07:00
Michael Kuhn
93bca2f3a2 libbson, libmongoc: Update to 1.8.1 (#6290) 2017-11-14 09:21:05 -07:00
Eric
137a9e64ac trimgalore: add version 0.4.5 (#6288) 2017-11-14 09:20:20 -07:00
Yifan Zhu
392e25b7e6 r-mnormt: created new package (#6287) 2017-11-14 09:20:06 -07:00
Yifan Zhu
05eb287ed9 r-bindr: created new package (#6285) 2017-11-14 09:19:49 -07:00
Yifan Zhu
c042644b53 r-glue: created new package (#6283) 2017-11-13 16:25:52 -07:00
Douglas Duckworth
c7d2b4dbd6 relion 2.1 - update variant defaults (#6201)
Default precision should be double for CPU. Generally users also want
to use GPUs so the +cuda variant is now also enabled by default.
2017-11-13 12:29:43 -08:00
Massimiliano Culpo
2d6cccdc53 Added an issue template for Github (#6205)
The MD file has been added in the root folder, as CONTRIBUTING.md
2017-11-13 10:51:53 -07:00
Christoph Junghans
bde727e187
mpibash: move to autotools (#6253) 2017-11-13 10:48:31 -07:00
Christoph Junghans
02335fa849
ucx: initial commit (#6265) 2017-11-13 10:47:58 -07:00
Eric
306aca812d ont-albacore: add version 2.1.2 (#6278) 2017-11-13 10:47:40 -07:00
Todd Gamblin
9c93c4a42b
Update tutorial slide links. (#6276) 2017-11-13 07:52:43 -07:00
Todd Gamblin
fffcd77662
Allow types and 'any' in variant definitions. (#4524)
- Previously variant values had to be a tuple or a callable predicate.

- This allows 'any' as shorthand for `lambda x: True` and type objects
  as shorthand for "any value of this type".

- Makes variant definitions more readable, keeps lambdas out of
  packages for common cases.
2017-11-13 00:22:59 -07:00
becker33
9b80f2fd38 basics tutorial: output updated (#6267)
* basics tutorial: output updated through gcc

* finished update for basics tutorial

* missed two lines

* doc error fix
2017-11-13 00:12:23 -07:00
Todd Gamblin
24d636eb30
Updates to build systems tutorial (#6273)
* Get rid of period in command

* formatting

* fix header

* Change GNU Make to Make

* Add variants
2017-11-13 00:11:55 -07:00
Mario Melara
2f1cbb5caa Add build systems tutorial for SC17 (#6125)
* First draft for SC17 build systems portion

Added tutorial_buildsystems.rst file as well as example files under
the tutorial/ directory.

* Remove floating `

* Add requested changes, and examples of subclasses

Added in the requested changes to the documentation. Also added in
information about the subclasses and the defaults that they provide.
Also fixed some phrasing issues, formatting and punctuation.

* Flake8 fixes and new files for classes

Made flake8 fixes to pass tests and also added files to demonstrate code
in the classes.

* Minor edits

Edits in formatting and made some sentence changes

* Flake8 fixes

More flake8 fixes

* Flake8 fix

* Change section order on tutorial and minor edits

Placed the section at the appropriate section for the tutorial and then
added some minor edits that were requested.

* Add requested changes and more details

Added more details to Cmake, Makefile and Python Packages.

* Fixed formatting and minor edits

* Fix doc build error
2017-11-12 23:24:18 -07:00
Adam J. Stewart
9db7eaade8 Last minute edits to the Configuration Tutorial (#6271) 2017-11-12 23:14:44 -07:00
becker33
b77acd0896 Add configuration tutorial for SC17 (#6141) 2017-11-12 20:12:57 -07:00
Matthew LeGendre
265c30b943 Update packaging tutorial (#6270)
* Allow types and 'any' in variant definitions.

- Previously variant values had to be a tuple or a callable predicate.

- This allows 'any' as shorthand for `lambda x: True` and type objects
  as shorthand for "any value of this type".

- Makes variant definitions more readable, keeps lambdas out of
  packages for common cases.

* Update packaging tutorial

* Fix bad file reference in packaging tutorial
2017-11-12 20:09:12 -07:00
becker33
b09341d861 binary packages: do post install hooks (#6269) 2017-11-12 17:57:10 -07:00
Massimiliano Culpo
1ab703448d SC17: advanced packaging tutorial (#6148)
* First draft of the advanced packaging tutorial

* advanced packaging tutorial: improved phrasing

Thanks Denis and Hartzell!

* Fixed typos + reworded a couple of sentences
2017-11-12 00:27:57 -08:00
Massimiliano Culpo
fe889124eb SC17: reworked module file tutorial section (#5657)
* Reworked module file tutorial section

First draft for the SC17 update. This includes:

 - adding an introduction on module files + Spack's module
   generation blueprints
 - adding a set-up section and provide a docker image for easy set-up
 - updating all the relevant snippets
 - extending a bit some of the concepts that were already touched

* Added reference to #5582 + committed Dockerfiles

Also fixed a couple of typos spotted by Denis.

* module file tutorial: added section on template customization

* module file tutorial: fixed minor typos + rephrased a sentence

* module file tutorial: made explicit that Docker image comes with software

* module file tutorial: improved phrasing and layout.

Thanks Hartzell!

* module file tutorial: added vim and nano to editors

* module file tutorial: fixed typo

* Fixed typos

Thanks Adam!

* module file tutorial: updated Dockerfile + minor changes in introduction
2017-11-12 00:27:20 -08:00
becker33
1008975bc0 Don't include build-only dependencies in build cache hash (#6262) 2017-11-11 20:54:17 -08:00
Satish Balay
6fd92e4257 petsc: update to version 3.8.2 (#6244)
Includes pkgconfig fix [for mfem static build failure]
2017-11-11 07:16:03 -07:00
Brian Homerding
19f8940c01 Nekbone: Installing data files for example runs (#6243)
* Nekbone: Installing data files for example runs

* Typo Fix
2017-11-10 19:59:33 -07:00
Sergey Kosukhin
263126bc5d Create symlink for 'swig' binary after installation. (#6240) 2017-11-10 19:50:11 -07:00
Aaron Fisher
af06ea0e74 Fixed mfem mpi build issue. (#6254)
* Fixed mfem mpi build issue.

* Fixed a non-mpi build issue and switched to the latest official MFEM release.
2017-11-10 19:49:17 -07:00
Yifan Zhu
e38f31e773 feature/r-reprex: new package (#6257) 2017-11-10 19:47:21 -07:00
Cyrus Harrison
b079e1dbd5 add alpine ascent (#6224)
* add ascent package and and deps

* proper use of site_packages_dir prop

* flake8

* add maitain, small updates

* flake8

* flake8

* fixs for docstrings for sphinx
2017-11-10 17:00:47 -08:00
scheibelp
8c458a856f
Group flags and values separated by space (#6169)
Fixes #6154

For compiler options which set values using the syntax "-flag value"
(with a space between the flag and the flag's value) the flag and
value were treated as separate and reordered. This updates Spack's
logic to treat the flag and value as a single unit, even if there is
a space between them. It assumes that all flags are prefixed with
"-" and that all flag values are not.
2017-11-10 16:33:50 -08:00
becker33
917d021997 Add version 1.04 (#6259) 2017-11-10 15:52:48 -08:00
becker33
a7b817b494 elfutils: add --no-as-needed flag for library ordering issue (#6256)
* add --no-as-needed flag for library ordering issue libelf

* fix syntax error.
2017-11-10 11:42:37 -08:00
Yifan Zhu
f6ed8d856a xclip: created new package (#6248) 2017-11-10 11:13:00 -07:00
Yifan Zhu
a872dc5927 r-clipr: created new package (#6249) 2017-11-10 11:11:45 -07:00
Todd Gamblin
7dea7aad51
Add a code of conduct to Spack (#6251)
We're adopting the contributor covenant for now.  This isn't something we've needed to use yet, but it is good to have in case we actually do have a problem.
2017-11-09 21:18:58 -08:00
Patrick Gartung
124b5fc296 deal with case where symbolic links are copied (#6178)
* deal with case where symbolic links are copied

* Suggested changes
2017-11-09 14:38:12 -08:00
lingnanyuan
acc3817ffc r-purrr: Create new package. (#6241) 2017-11-09 14:51:30 -07:00
lingnanyuan
65a278c927 r-covr: Create new package. (#6239) 2017-11-09 13:19:53 -07:00
lingnanyuan
e43e29209d r-readxl: Create new package. (#6238) 2017-11-09 13:19:43 -07:00
lingnanyuan
0902f58f3d r-cellranger: Create new package. (#6237) 2017-11-09 13:19:25 -07:00
lingnanyuan
5e0e3092f6 r-rematch: Create new package. (#6236) 2017-11-09 13:19:12 -07:00
Satish Balay
2b07379831 petsc: when hdf5 depends on zlib - petsc+hdf5 should also be configur… (#6189)
* petsc: when hdf5 depends on zlib - petsc+hdf5 should also be configured with zlib

* petsc: fix dependency [of zlib to be on hdf5 - and not on petsc]

* petsc: use the fact that hdf5/package.py has a hard dependency on zlib [so no need to check for this dependency in code]

recommended-by: @davydden

* petsc: change hdf5 dependency to 'hdf5+hl' as petsc configure is looing for -lhdf5_hl

https://github.com/spack/spack/issues/5846
2017-11-09 11:34:59 -08:00
Satish Balay
8d512ce9ae magma: cuda updates [from xsdk-0.3.0 branch] (#6160)
- add gcc dependency per cuda versions
- Fix for cuda-9.0  as it does not support sm20

    nvcc fatal   : Unsupported gpu architecture 'compute_20'
2017-11-09 11:34:40 -08:00
Patrick Gartung
1484a94b1e spack buildcache: symlink and relative RPATH fixes (#6140)
* Skip rewriting files that are links (this also avoids issues with parsing
  the output of the 'file' command for symlinks)
* Fail rather than warn for several gpg signing issues (e.g. if there is no
  key available to sign with)
* Installation with 'buildcache install' only retrieves link and run
  dependencies (this matches 'buildcache create' which only creates tarballs
  of link/run dependencies)
* Don't rewrite RPATHs for a binary if the binary cached package was created
  with relative RPATHs
* Refactor relocate_binary to operate on multiple binaries (given as a
  collection of paths). This was likewise done for relocate_text and
  make_binary_relative
2017-11-09 10:53:34 -08:00
lingnanyuan
ee867db5de r-log4r: Create new package. (#6133) 2017-11-09 10:23:48 -07:00
Simone Bnà
c79a0fbbf2 mesa: fixed url for version (#5818) 2017-11-09 10:16:52 -07:00
Benedikt Riedel
266de67c24 ROOT needs to have a consistent version of binutils, as it is very sensitive to the version of libopcodes. You can't move the code from one system (with the same OS) as another. (#6226) 2017-11-09 06:49:27 -08:00
lingnanyuan
935a6b00d7 r-analysispageserver: Create new package. (#6135) 2017-11-09 07:23:10 -07:00
Levi Baber
74d38b3150 py-dlcpar (#6229)
* py-dlcpar: new package

* py-dlcpar: whitespace
2017-11-09 07:21:56 -07:00