Commit graph

10622 commits

Author SHA1 Message Date
Greg Becker
f5bb93c75b tutorial basics section: fix gcc install version (#10298) 2019-01-09 17:37:37 -06:00
Satish Balay
8ca674a574 petsc: fix petsc+debug to not reset COPTFLAGS - i.e use configure defaults '-g' (#10296) 2019-01-09 17:36:28 -06:00
Daryl W. Grunau
d1bb9caba4 eospac version bump to 6.4.0beta.4 (#10294) 2019-01-09 15:57:05 -06:00
Mark W. Krentel
1b991f9385 elfutils: option to install elf.h header file (#10185)
* elfutils: option to install elf.h header file

Add variant 'elfh' (default False) to install the elf.h header file to
the include directory.  This provides access to a newer version of
elf.h and allows an elf application to build with the same elf.h that
libelf.so was built with.

Add version 0.175.

* Drop the variant 'elfh' and always install elf.h instead.
2019-01-09 14:40:15 -06:00
Eric
b4dc73bed4 py-pyyaml: Add version 3.13 (#10293) 2019-01-09 13:39:34 -06:00
Simon Flood
0b2314bbc4 R: add version 3.5.2 (#10292) 2019-01-09 12:19:58 -06:00
Andreas Baumbach
730c629b09 New package: git-fat-git (#10266)
* new package: git-fat

* backport of rsync -> older versions no longer available

Change-Id: I3a41f17df0f88ca11e08ea6fd2f2d381435e0f09

* fix legal stuff and use new git attribute

Change-Id: Ice156dfe8ad4137a861f7b2938ee92f4024142be

* use date as version number rather than hash

Change-Id: Ib537659e368f69124895306d6a6ac0c5e36061a7

* only use the date once

Change-Id: I2592fa28aaa53fed949ddc82959d712ff3f6f752
2019-01-09 09:07:12 -06:00
marvinbernhardt
7571787a3a gromacs: added simd and rdtscp variants + version 2019 (#9931) 2019-01-09 10:39:05 +01:00
Axel Huebl
efe3e905a3 OpenMPI: Add Development Version (#10257)
Add the development version of OpenMPI from the git repo
in `master`.
2019-01-08 20:48:55 -06:00
sknigh
e3a2c94d60 Updated fish to 3.0.0 (#10286) 2019-01-08 20:47:52 -06:00
Owen Solberg
c48b0a13b9 bug fix: copy permissions when staging (#10285)
Fixes #10284

#10152 replaced shutil.move with llnl's copy and copy_tree for
resources. This did not copy permissions so led to later failures
if an executable was copied (e.g. a configure script). This uses
install/install_tree instead, which preserve permissions.
2019-01-08 17:56:16 -08:00
Srinath Vadlamani
4fdd3b6794 Armcompiler (#9840)
* Initial compiler support

* added arm.py

* Changed licence to Arm suggested header

* Changed licence to the same as clang.py
Main author of file is Nick Forrington <Nick.Forrington@arm.com>
Minor changes by Srinath Vadlamani <srinath.vadlamani@arm.com>

* compilers: add arm compiler detection to Spack

- added arm.py with support for detecting `armclang` and `armflang`

Co-authored-by: Srinath Vadlamani <srinath.vadlamani@arm.com>

* Changed to using get get_compiler_version

* linking to general cc for arm compiler

* For arm compiler add CFLAGS to use compiler-rt rtlib.

* Escape for special characters in rexep

* Cleaned up for Flake8 to pass.

* libcompiler-rt should be part of the LDFLAGS not CFLAGS

* fixed m4 when using clang to used LDFLAGS.  Fixed comments for arm.py to display compiler --version output with # NOAQ for flakes pass.

* added arm compilers

* proper linked names
2019-01-08 16:31:25 -08:00
Owen Solberg
ee64db4764 r-ape: new versions (#10258)
* updated versions for r-ape

* added type=('build', 'run') to r dependency
2019-01-08 18:15:03 -06:00
Owen Solberg
aa20724519 r-cowplot: new versions, more specific dependencies (#10259)
* updated versions for r-cowplot

* depends_on: added type=('build', 'run') to r, and added r-scales
2019-01-08 18:14:50 -06:00
Owen Solberg
7a816b9a66 r-data-table: new versions (#10260)
* updated versions for r-data-table

* added type=('build', 'run') to r dependency
2019-01-08 18:14:34 -06:00
Owen Solberg
2bd054adff r-dbplyr: new versions (#10262)
* added new versions, and tightened up depends_on() specs

* added type=('build', 'run') to r dependency
2019-01-08 18:14:19 -06:00
thelfer
d3caad4cd7 New package: MGIS (#10273)
* 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)

* Add support for the MFrontGenericInterfaceSupport project (MGIS)

* Style fixes

* Package documentation update

* Package documentation update

* Fix a typo thanks to Andreas Baumbach review

* Follow Adam J. Stewart advices

* Fix type
2019-01-08 15:07:47 -06:00
Eric
45882e1b6f usearch: Make installed binary executable (#10269)
* usearch: Make binary executable

* usearch: remove join_path
2019-01-08 14:20:13 -06:00
sknigh
d9c8d2f27b Added bash 5.0 (#10282) 2019-01-08 13:20:30 -06:00
Owen Solberg
0e50ff7339 r-dt: new versions (#10261)
* updated release and checksums, also tightened depends_on()

* remove blank line at end of file

* removing new version 0.5
2019-01-08 13:06:36 -06:00
Owen Solberg
76dd4ca9ae updated versions (#10263) 2019-01-08 13:00:12 -06:00
Owen Solberg
5c4156cd39 updated versions and depends_on() (#10264) 2019-01-08 12:54:55 -06:00
dorier
0a60cae516 added openpa package (#10265) 2019-01-08 12:53:37 -06:00
Eric
6ce6c79beb libzip: Add zlib dependency (#10270)
* libzip: Add zlib dependency

* libzip: Add version limit
2019-01-08 12:49:03 -06:00
Andreas Baumbach
a33d167c72 new version 1.0.1 for py-html5lib (#10278)
Change-Id: I2837dc098fce142b152d2969687d1873e182bbc8
2019-01-08 12:43:33 -06:00
Ross Miller
2934eda311 Check for ARM compiler in addition to clang (#10280)
Add "-rtlib=compiler-rt" to CFLAGS when building with either Clang or
the ARM compiler.

Refs #10279
2019-01-08 12:41:05 -06:00
Eric
dabf4f17d3 salmon: Add version 0.12.0 (#10271) 2019-01-08 14:01:02 +01:00
Michael Kuhn
48db757be1 go: add 1.11.4 (#10272) 2019-01-08 13:57:25 +01:00
Andreas Baumbach
12b52baf7b new package: py-webencodings (#10277)
Change-Id: Icf20035367a34fa88acfef2d3fa3742c3f3901ac
2019-01-08 13:55:41 +01:00
Peter Josef Scheibel
9f79995718 For spec-file-based installs, store the initial spec read from the file as the abstract spec 2019-01-07 20:40:34 -08:00
George Hartzell
b984adb386 bowtie: new versions and %gcc@8.0.0: fix (#10232)
* bowtie: new versions and %gcc@8.0.0: fix

Bowtie development shifted from Sourceforge to GitHub.

This commit adds several versions from GitHub, using the archive
tarballs.  Note that the URL for 1.2.2 tarball is actually an '_p1'
tag....

It leaves the old 1.2 release download info in place.

Versions 1.2.0 and newer come from GitHub (I'm unsure if the 1.2 and
1.2.0 are equivalent).

Include a fix that enables %gcc@8.0.0: from:

  https://github.com/BenLangmead/bowtie/issues/87

But, v1.2.2 has trouble with "newer" gcc's, so it only adds v1.2.2 for
%gcc@6.0.0:.

Feel free to tighten this.  I know that:

- 1.2 -> 1.2.2 work with %gcc@5.5.0;
- 1.2 -> 1.2.1.1 work with %gcc@8.2.0; and
- 1.2.2 fails with %gcc@8.2.0

* Tighten to `conflicts('%gcc@8:', when='@1.2.2')`

* Point 1.2.2 and 1.2.2_p1 at the 1.2.2_p1 tarball
2019-01-07 11:30:59 -06:00
Chad Wood
3b59f70751 doxygen: URL and version hashes updated to project's GitHub home (#10250)
* Update package.py

Doxygen has migrated from a private SVN to GitHub. This PR updates the URLs and adds versioned commit hashes from GitHub. It also includes version 1.8.15 as the latest option.

* Update package.py
2019-01-07 10:38:32 +01:00
Massimiliano Culpo
c4521535e7 Multi-valued variants: better support for combinations (#9481)
This enforces conventions that allow for correct handling of
multi-valued variants where specifying no value is an option,
and adds convenience functionality for specifying multi-valued
variants with conflicting sets of values. This also adds a notion
of "feature values" for variants, which are those that are understood
by the build system (e.g. those that would appear as configure
options). In more detail:

* Add documentation on variants to the packaging guide
* Forbid usage of '' or None as a possible variant value, in
  particular as a default. To indicate choosing no value, the user
  must explicitly define an option like 'none'. Without this,
  multi-valued variants with default set to None were not parsable
  from the command line (Fixes #6314)
* Add "disjoint_sets" function to support the declaration of
  multi-valued variants with conflicting sets of options. For example
  a variant "foo" with possible values "a", "b", and "c" where "c"
  is exclusive of the other values ("foo=a,b" and "foo=c" are
  valid but "foo=a,c" is not).
* Add "any_combination_of" function to support the declaration of
  multi-valued variants where it is valid to choose none of the
  values. This automatically defines "none" as an option (exclusive
  with all other choices); this value does not appear when iterating
  over the variant's values, for example in "with_or_without" (which
  constructs autotools option strings from variant values).
* The "disjoint_sets" and "any_combination_of" methods return an
  object which tracks the possible values. It is also possible to
  indicate that some of these values do not correspond to options
  understood by the package's build system, such that methods like
  "with_or_without" will not define options for those values (this
  occurs automatically for "none")
* Add documentation for usage of new functions for specifying
  multi-valued variants
2019-01-04 19:02:34 -08:00
Michael Kuhn
051057caa3 mvapich2: add missing zlib dependency (#10254) 2019-01-04 20:52:00 -06:00
Elizabeth Fischer
f7b78412b1 Added package osmctools (#10249)
* Added package osmctools

* Simplified

Removed functions that did the same as existing defaults

* flake8
2019-01-04 20:51:44 -06:00
Peter Josef Scheibel
64deda1b0c Add tests for expanding/non-expanding resources 2019-01-04 17:04:28 -08:00
Michael Kuhn
41ef02ee10 stage: fix resources being deleted from local cache (#10152)
Non-expanded resources were being deleted from the cache on account
of two behaviors:

* ResourceStage was moving files rather than copying them, and uses
  "os.path.realpath" to resolve symlinks
* CacheFetchStrategy creates a symlink to a cached resource rather
  than copying it

This alters the first behavior: ResourceStage now copies the file
rather than moving it.
2019-01-04 17:04:28 -08:00
Jimmy Tang
5450303c97 Fix download path, the existing one has been removed from nvidia's site (#10253) 2019-01-04 18:13:11 -06:00
Neil Flood
3477d33751 openssl: add location of system certificates for SUSE Linux (#10242) 2019-01-03 10:02:25 -06:00
Ben Zwick
7d9dbc5fd2 Add missing code block (#10243)
Otherwise the `--` in `--dot` is rendered as a single en-dash.
2019-01-03 09:41:14 -06:00
Michael Kuhn
802dc4a03a patch: split up fetch and clean into separate methods (#10150)
"mirror create" was invoking a package's do_patch method in order to
retrieve and archive URL patches. If a package implements a "patch"
method, this is also called as part of do_patch; this failed when the
package-specific implementation referred to environment variables
that are only available at the time the package is built
(e.g. "spack_cc").

This change introduces fetch and clean methods for patches. They are
no-ops for FilePatch but perform the appropriate actions for
UrlPatch. This allows "mirror create" to invoke do_fetch, which does
not call the package's patch method.
2019-01-02 11:44:50 -08:00
Axel Huebl
63e75c3972 Catch2: v2.5.0 (#10237)
Add the 2.5.0 release of catch2.
2019-01-02 08:59:36 -06:00
Ben Zwick
0c8fd8734d petsc4py: new versions (up to 3.10.0) and update website (#10238) 2019-01-02 08:59:14 -06:00
Ben Zwick
2577a5e686 slepc4py: new versions (up to 3.10.1) and update website (#10239) 2019-01-02 08:58:45 -06:00
Greg Sjaardema
9f40813004 PARALLEL-NETCDF: Update new version and location (#10172)
* PARALLEL-NETCDF: Update new version and location

PnetCDF-1.11.0 is released.

Also, the canonical download area has been changed and they are now using git, so can also provide a develop and master checkout.
One issue is that they changed the name of the tar files, so 1.11.0 needs special handling (and future versions will also).

All checksums at new location match the checksums from the old location.

* Address concerns in review

Added a `url_for_version` function to handle the name change in the tar files at version 1.11.0 and later.  Updated description to match current shown on website.  Updated `homepage` setting since it has recently moved.

* Address issues in second review
2019-01-01 19:55:29 -06:00
Massimiliano Culpo
8540d5390e
Removed an extra comma after a dict literal (#10236)
The extra comma was turning a dict into a tuple, and caused errors
during validation of the schema.
2019-01-02 01:15:15 +01:00
Ben Zwick
aca195367e FEniCS: workaround concretization issue with PETSc (#10235) 2019-01-01 10:39:07 -06:00
George Hartzell
60968a3fbf Add list_url for r-readr, finding old versions (#10231)
r-tidyverse needs r-readr@1.1.1, r-reardr needs a list_url so that it
can find it.
2019-01-01 08:05:53 -06:00
Todd Gamblin
4ecb465a36 README: LLNL release number and SPDX id don't need to be monospaced. 2019-01-01 00:44:28 -08:00
Todd Gamblin
5425a3dad4 flake8: fix flake8 issues with invalid escapes
- in many files, regular strings were used in places where raw strings
  should've been used.

- convert these to raw strings and get rid of new flake8 errors
2019-01-01 00:44:28 -08:00