Commit graph

11596 commits

Author SHA1 Message Date
Levi Baber
829bbd7884 r-emmli: new package (#11557) 2019-05-26 20:43:22 -05:00
Olaf Mersmann
af2de9eb2a Update GnuPG and associated packages (#11564)
* libassuan: Update to v2.5.3

* gnupg: Update to v2.2.15

* libgpg-error: Update to v1.36

* libgcrypt: Update to v1.8.4
2019-05-26 20:41:37 -05:00
Axel Huebl
86b2156921 New Package: sl (#11565)
Add the sl program.
2019-05-26 20:40:55 -05:00
Todd Gamblin
d6f2ff1426 link_tree: add option to merge link trees with relative targets
- previous version of link trees would only do absolute symlinks

- this version can do relative links using merge(relative=True)
2019-05-26 18:23:44 -07:00
Todd Gamblin
f32843528e docs: make docs build relocatable for localized builds
- make all Spack paths relative to a `_spack_root` symlink, so that we
  can easily relocate the docs build *outside* lib/spack/docs

- set some useful defaults for gettext translation variables in conf.py

- update `relativeinclude` and other references to the spack root in the
  RST files to use _spack_root
2019-05-26 18:23:44 -07:00
Todd Gamblin
8bf1bd4637 docs: remove legacy import for Sphinx 1.7 2019-05-26 18:23:44 -07:00
Todd Gamblin
e1c5d1378b docs: match ReadTheDocs; use -W (warnings as errors) with Sphinx 2019-05-26 18:23:44 -07:00
Todd Gamblin
3340d586c4 commands: add --update option to spack list
- Add a `--update FILE` option to `spack list`
- Output is written to the file only if any package is newer than the file
- Simplify the code in docs/conf.py using this new option
2019-05-26 18:23:44 -07:00
Todd Gamblin
6380f1917a commands: Add --header and --update options to spack commands
The Spack documentation currently hard-codes some functionality in
`conf.py`, which makes the doc build less "pluggable" for things like
localized doc builds.

In particular, we unconditionally generate an index of commands and a
package list as part of the docs, but those should really only be done if
things are not up to date.

This commit does the following:

- Add `--header` option to `spack commands` so that it can do the work of
  prepending text to its output.

- Add `--update FILE` option to `spack commands` that makes it generate a
  new command index *only* if FILE is out of date w.r.t. commands in the
  Spack source.

- Simplify code in `conf.py` to use these options and only update the
  command index when needed.
2019-05-26 18:23:44 -07:00
Todd Gamblin
43aaf8c404 docs: Use HDF5 as the example package for spack graph 2019-05-26 18:23:44 -07:00
Satish Balay
727089c4ef
xsdk@0.4.0: update dealii defaults wrt changes in a973ab475 (#11562)
wrt xsdk@develop - ginkgo requires openmp - so disable until we can add openmp dependencies consistantly
2019-05-26 10:43:06 -05:00
Mark W. Krentel
7c32a4c399 mbedtls: add pic variant (#11558)
Add variant 'pic' for including in shared libraries.

Add build dependency on perl.  Compiling mbedtls runs several perl
scripts.

Add versions 2.7.10 and 2.16.1, the heads of the two main stable
branches.
2019-05-24 21:50:13 -05:00
Stephen Hudson
bb09bdedc6 Update libensemble to v0.5.0 (#11544) 2019-05-24 15:11:56 -05:00
健美猞猁
137cad2915 Add nettle@3.4.1 (#11547) 2019-05-24 15:08:02 -05:00
Massimiliano Culpo
c291866b9a build env: simplify handling of parallel jobs (#11524)
This PR implements several refactors requested in #11373, specifically:

- Config scopes are used to handle builtin defaults, command line overrides 
  and package overrides (`parallel=False`)
- `Package.make_jobs` attribute has been removed; `make_jobs` remains
  as a module-scope variable in the build environment.
- The use of the argument `-j` has been rationalized across commands
  - move '-j'/'--jobs' argument into `spack.cmd.common.arguments`
- Add unit tests to check that setting parallel jobs works as expected
  - add new test to ensure that build job setting is isolated to each build
- Fix packages that used `Package.make_jobs` (i.e. `bazel`)
2019-05-24 11:45:22 -07:00
Massimiliano Culpo
1bd4521f72 Updated lmod (to version 8.1.5) and associated dependencies (#11552)
Lmod version 8.1.5
Lua version 5.3.5
Lua Filesystem 1.7.0.2

Turned tcl to a link dependency so that Lmod's configure can find it.
2019-05-24 12:45:52 -05:00
Adam J. Stewart
6212e0d9b2
Add latest version of py-cython (#11494)
* Add latest version of py-cython

* Fix cython unit tests
2019-05-23 20:01:45 -05:00
Todd Gamblin
ab21b3d194 docs: truncate spack list output in basic usage
`spack list` output is very long and takes up a lot of space in the docs.
Truncate it to just 10 lines and link to the package list page.
2019-05-23 12:40:01 -07:00
Hans Pabst
d6cf3b6718 LIBXSMM 1.12.1 (#11538) 2019-05-23 10:16:32 -05:00
Jon Rood
4c465d2602 Add cppcheck version 1.87. (#11536) 2019-05-22 18:52:48 -05:00
Jon Rood
e57edebb50 Add CMake 3.14.3 and 3.14.4. (#11534) 2019-05-22 15:46:52 -05:00
Omar Padron
a37efefd3d
package vtk - improve gl handling (#11530)
* package vtk - improve gl handling

* package vtk - minor cleanup
2019-05-22 12:04:29 -04:00
Dustin Wheeler
c2e087c411 Fix typo in openmpi@2.1.6 libmpi.so comment. (#11529) 2019-05-22 10:37:33 -05:00
t-karatsu
1e9bb8c512 Add Fujitsu compiler to Spack. (#11287)
* Add Fujitsu compiler to Spack.

* Fixes for flake8

* Chenges location of FCC to subdirectory called case-insensitive

* Add compiler tests for Fujitsu compiler

* Modify the logic of taking compiler version for new version of Fujitsu compiler
2019-05-21 20:31:14 -05:00
Denis Davydov
a973ab4751 dealii: add 9.1.0 (#11527) 2019-05-21 16:23:03 -05:00
Levi Baber
b13665d065 py-htseq: new version (#11525) 2019-05-21 12:08:31 -05:00
Elizabeth Fischer
a45c4ef33d Add version (#10594) 2019-05-21 10:03:50 -04:00
Michael Kuhn
1f828ce5b8 Update scorep and friends (#11523) 2019-05-21 12:28:12 +02:00
Denis Davydov
5d6461b895 dealii: fix symengine constraints (#11517)
disable symengine constraints due to limitations of Spack
2019-05-21 07:38:58 +02:00
Chuck Atkins
a34142ed30
mesa: Patch missing gl symbols in OSMesa (#11518) 2019-05-20 22:41:41 -04:00
Glenn Johnson
d1ea5ba2cd OpenMPI: update behavior for fabrics/schedulers=auto (#11431)
* When fabrics=auto or schedulers=auto, the intent is to defer to the
  OpenMPI configure and let it determine and use what it finds
  available on the system. The current behavior for 'with_or_without'
  in the case of 'auto' explicitly disables all possible values.
  This updates the logic to call 'with_or_without' only when the
  value of fabrics/schedulers is not 'auto'.
* To allow explicitly disabling all fabrics/schedulers, each of these
  variants has added support for 'none' (which is also the default
  value).
* Add a conflict for the loadleveler scheduler for openmpi-3 and
  above as it is no longer a valid configure option.
2019-05-20 17:52:17 -07:00
Adam J. Stewart
e2065fad72 Make flake8 check spack script as well as .py files (#11513)
* Make flake8 check bin/spack
2019-05-20 13:39:25 -07:00
Mario Melara
4d71117080 Get Cray OS version from PrgEnv-cray (#10774)
The regex used for finding the Cray OS version from the PrgEnv-cray
module was not exact and was at times pulling the version from other
PrgEnv modules. This updates the regular expression to be more exact.
2019-05-20 11:06:02 -07:00
Andrew Gaspar
2168c08ac5 Update optional-lite and span-lite to use CMakePackage (#11407)
* Update optional-lite and span-lite to use CMakePackage

These packages only have CMake installs on their most recent versions.
Therefore, we overload all of the CMake stages to fallback to the old
versions (no-op for most, copytree for install), and use CMakePackage on
the new versions.

* Add new string-view-lite version with CMake install support

* Only override phases for old versions of *-lite packages
2019-05-20 13:04:06 -05:00
Adam J. Stewart
7fe0230492
Add py-kmodes package (#11497) 2019-05-19 14:17:30 -05:00
Adam J. Stewart
5b6445e519
Add latest version of joblib (#11495) 2019-05-19 14:17:03 -05:00
Adam J. Stewart
ac358a1b4d
Add latest version of setuptools (#11493) 2019-05-19 14:16:37 -05:00
David Beckingsale
866b9b5d13 Update Umpire package with new versions (#11441)
* Update Umpire package with new versions

* Fix version ordering
2019-05-18 23:04:12 -05:00
Denis Davydov
a66cc59bb0 trilinos: add variant to disable chaco from seacas (#11482)
* trilinos: add variant to disable chaco from seacas

keep it OFF by default due to the presence of the global symbol "divide"
that can lead to symbol clash with other libraries, for example see
https://github.com/dealii/dealii/issues/8170#issuecomment-492700787

* dealii: add conflict statement for adol-c and Trilinos SEACAS Chaco
2019-05-18 23:01:44 -05:00
Mark W. Krentel
e1bb6821aa dyninst: rework the cmake args for version 10.1 and later (#11484)
* dyninst: rework the cmake args for version 10.1 and later

Add a separate when() case for the cmake args for Dyninst 10.1.0 and
later.  The prereq args have changed enough that this makes things
easier going forward.  (My previous commit 26b9369c was inaccurate and
temporary.)

Dyninst 10.1.0 accepts boost 1.70, but earlier dyninst are restricted
to <= 1.69 (not worth back porting every boost change).

Change all the dyninst versions to 3 digits for clarity and
consistency.

* Add version 10.1.0.
2019-05-18 23:00:48 -05:00
Nichols A. Romero
6ba6c84de5 QMCPACK Update May 2019 (#11492)
* Add QMCPACK 3.7.0

* SOA is now the default.

* Add QMCPACK converter based on QE 6.4
2019-05-18 22:57:52 -05:00
Jean-Paul Pelteret
517212b8a3 Add conflicts in deal.II package between SymEngine and Trilinos variants (#11499) 2019-05-18 22:56:56 -05:00
Adam J. Stewart
6b068a855e
Fix typo in spack executable (#11512) 2019-05-18 21:00:46 -05:00
Owen Solberg
92604ed576 intel-tbb: fix patch for old compilers (#11371)
* added patch for intel-tbb@2019.1: with old compilers

* sparately specify when @:2018 and @2019

the reason we can't say @:2019 is that would include @2019.1 where the
patch doesn't work.

* should be possible to list when constraint as @:2019

According to my reading of ["Version ranges" in the Spack
docs](https://spack.readthedocs.io/en/latest/packaging_guide.html#version-ranges),
this should apply to up to `2019` but not `2019.1:`

* @:2019.0 appears to be necessary to specify 2019 but not 2019.1

* specifying 2019.1 2019.2 2019.3 2019.4 separately and explcitly

* flake8 fixes for long lines.

* add comments to explain why so many different patch directives

* remove blank like for flake8

* revert spec %gcc@4.8.0:4.99999 -> %gcc@4.8.0:
2019-05-18 21:00:32 -05:00
George Hartzell
e592262da8 Typos: funciton, woudl, hm,... (#11511) 2019-05-18 11:39:23 -05:00
Mario Melara
9957093e53 Execute modulecmd in bash shell (#11510)
Adds executable=/bin/bash into Popen. We discovered this bug while
working in a csh/tsch environment. By executing with /bin/bash we ensure
that the module command works.
2019-05-18 01:49:19 +02:00
Justin S
c595883195 r-popvar: new package at 1.2.1 (#11490) 2019-05-17 14:45:21 -05:00
Justin S
cc6f822cb1 smof: new package at 2.13.1 (#11502) 2019-05-17 14:44:35 -05:00
Justin S
c7a28ec1d4 r-bglr: new package at 1.0.8 (#11489) 2019-05-17 14:35:38 -05:00
Justin S
719cd6741d r-rrblup: new package at 4.6 (#11488) 2019-05-17 14:34:33 -05:00