Commit Graph

23416 Commits

Author SHA1 Message Date
Glenn Johnson
6df1b509fa repeatmasker: update and fix package (#22785)
- version 4.0.7 was not building
- version 4.0.9 was not setting search correctly due to an extra "return"
  in config
- added version 4.1.2-p1
- new version needs py-h5py
- new version does not need utf8 patch
- url format changed
2021-04-06 08:35:51 +02:00
Glenn Johnson
a4f19853b8 hmmer: add v3.3.2 (#22787) 2021-04-06 08:26:22 +02:00
Andrew W Elble
b924440f79 exabayes: add v1.5.1 (#22789) 2021-04-06 08:11:48 +02:00
Adam J. Stewart
3336fff229 Remove erroneous warnings about quotes for from_source_file (#22767) 2021-04-06 07:13:54 +02:00
Axel Huebl
c1cf643780 libfabric: add v1.12.1 (#22790)
Add latest patch release to fix build issues with unconditional
usage of `infiniband/ib.h`
2021-04-06 07:06:01 +02:00
Valentin Volkl
1908e6834d qt: backport build issue fix on 5.14 due to isystem (#22772) 2021-04-04 09:55:42 -04:00
Cameron Stanavige
bfb3b55414 rankstr: add v0.0.3 (#22763) 2021-04-03 21:11:37 +02:00
Jen Herting
3a36ca4b36 New package: r-anytime (#22624)
Co-authored-by: Alex C Leute <aclrc@rit.edu>
2021-04-02 21:09:50 -05:00
Jen Herting
b51363e0ac New package: r-pheatmap (#22617)
Co-authored-by: Alex C Leute <aclrc@rit.edu>
2021-04-02 20:57:09 -05:00
Jen Herting
0d4e0b8198 New package: r-amelia (#22623)
Co-authored-by: Alex C Leute <aclrc@rit.edu>
2021-04-02 20:54:29 -05:00
Zack Galbreath
7cc2db1b4e Check against a list of known-broken specs in ci generate (#22690)
* Strip leading slash from S3 key in url_exists()

* Check against a list of known-broken specs in `ci generate`
2021-04-02 17:40:47 -06:00
Harmen Stoppels
69d123a1a0 Document unzip (#22723) 2021-04-02 20:56:24 +00:00
Desmond Orton
76b54816cf New package py-gffutils (#22552) 2021-04-02 22:33:20 +02:00
Axel Huebl
2dbaf23fca Ascent: CUDA ~shared (#22760)
Add a conflict for CUDA and shared libraries in Ascent.
The new concretizer will automatically change the default for
Ascent in that case. Until then, dependencies like WarpX need
to hint the `~shared` wish explicitly.
2021-04-02 12:16:27 -07:00
Axel Huebl
5a75f7e0d6 WarpX: 21.04 (#22740)
Update WarpX: add first tagged version.
2021-04-02 14:37:56 -04:00
Robert Mijakovic
d978d72e19 py-wheel: new version (#22751)
Co-authored-by: Robert Mijakovic <robert.mijakovic@lrz.de>
2021-04-02 09:56:16 -05:00
iarspider
9f90659aa7 igprof: new package (#22666) 2021-04-02 15:41:58 +02:00
darmac
d528ff6e5a sandbox: add build dependency on gawk (#22748) 2021-04-02 14:45:05 +02:00
Thilina Rathnayake
bbaf6e05d2 nekRS: new package (#22519)
This initial package recipe uses a custom-built wrapper to drive an internal CMake file. Since nekRS also includes built-in copies of several dependencies such as BLAS and HYPRE, it cannot be linked with other such dependencies. However, to work with the `ceed` metapackage, we cannot add `^blas` conflicts to nekRS.

See https://github.com/spack/spack/pull/22519 for discussion.
2021-04-02 07:50:31 -04:00
Todd Gamblin
0d387678b7 concretizer: improve display of optimization criteria (#22433)
By default, clingo doesn't show any optimization criteria (maximized or
minimized sums) if the set they aggregate is empty. Per the clingo
mailing list, we can get around that by adding, e.g.:

```
 #minimize{ 0@2 : #true }.
```

for the 2nd criterion. This forces clingo to print out the criterion but
does not affect the optimization.

This PR adds directives as above for all of our optimization criteria, as
well as facts with descriptions of each criterion,like this:

```
opt_criterion(2, "number of non-default variants")
```

We use facts in `concretize.lp` rather than hard-coding these in `asp.py`
so that the names can be maintained in the same place as the other
optimization criteria.

The now-displayed weights and the names are used to display optimization
output like this:

```console
(spackle):solver> spack solve --show opt zlib
==> Best of 0 answers.
==> Optimization Criteria:
  Priority  Criterion                                            Value
  1         version weight                                           0
  2         number of non-default variants (roots)                   0
  3         multi-valued variants + preferred providers for roots    0
  4         number of non-default variants (non-roots)               0
  5         number of non-default providers (non-roots)              0
  6         count of non-root multi-valued variants                  0
  7         compiler matches + number of nodes                       1
  8         version badness                                          0
  9         non-preferred compilers                                  0
  10        target matches                                           0
  11        non-preferred targets                                    0

zlib@1.2.11%apple-clang@12.0.0+optimize+pic+shared arch=darwin-catalina-skylake
```

Note that this is all hidden behind a `--show opt` option to `spack
solve`. Optimization weights are no longer shown by default, but you can
at least inspect them and more easily understand what is going on.

- [x] always show optimization criteria in `clingo` output
- [x] add `opt_criterion()` facts for all optimizationc criteria
- [x] make display of opt criteria optional in `spack solve`
- [x] rework how optimization criteria are displayed, and add a `--show opt`
      optiong to `spack solve`
2021-04-02 08:54:49 +00:00
Chris White
45c616529c axom: convert to Cached CMakePackage
This updates axom to use the new CachedCMakePackage superclass.

Co-authored-by: Greg Becker <becker33@llnl.gov>
2021-04-01 20:06:39 -07:00
Greg Becker
fb062428f9 add CachedCMakePackage for using CMake initial config files
CachedCMakePackage is a CMakePackage subclass for using CMake initial
cache. This feature of CMake allows packages to increase reproducibility,
especially between spack builds and manual builds. It also allows
packages to sidestep certain parsing bugs in extremely long cmake
commands, and to avoid system limits on the length of the command line.

Co-authored by: Chris White <white238@llnl.gov>
2021-04-01 20:06:39 -07:00
Todd Gamblin
fc48c63355 Revert "CachedCMakePackage for using *.cmake initial config files (#19316)""
This reverts commit 7daf582357.
2021-04-01 20:06:39 -07:00
Robert Pavel
3f7c111e29 Added ML Suite to ECP Proxy App Suite (#22728) 2021-04-01 17:52:17 -07:00
Shintaro Iwasaki
7e6048fef5 argobots: add Argobots 1.1 and 1.0.1 (#22729) 2021-04-01 18:49:11 -06:00
Jose E. Roman
49b222442f Update SLEPc and slepc4py to version 3.15 (#22714)
Co-authored-by: Satish Balay <balay@mcs.anl.gov>
2021-04-01 17:38:47 -07:00
AMD Toolchain Support
252f42f115 Fix for static library export issue in blis package (#22673) 2021-04-01 16:57:46 -07:00
Amiya Maji
73a4a5d394 gdal package needs to import the 'os' module (#22731)
* 'gdal+java' build needs to import the 'os' module (line 191).

* Make style-check happy.
2021-04-01 17:52:04 -06:00
Michael Kuhn
c89fa98b16 Fix pkgconfig dependencies (#22702)
pkgconfig is the correct virtual provider.
2021-04-01 23:45:01 +00:00
Simon Bolding
9c139bf7a2 mpark-variant: ICC Patch (#22727)
* Add patch for Intel C++ compiler

- On some machines (in particular MacOSX Catalina), the icpc in some way
utilizes the preprocessor of the associated "developer tools" used by
icpc. This leads to, in some cases, a preprocessor claiming support for
__tuple_element_packs, even though icpc (as of version 21.1) can't
actually parse such code. Just use the MPARK_TUPLE_ELEMENT_PACK impl
with __icc until icpc supports it, to avoid issues with developer tools
that are untested.
- The same patch has been PRed against mpark-variant
2021-04-01 23:15:25 +00:00
mic84
2ae7e25501 amrex: new version 21.04 (#22730) 2021-04-01 14:11:14 -07:00
Elizabeth Fischer
82e97124c8 bugfix: compiler wrappers should handle extra spaces between arguments (#22725)
In the face of two consecutive spaces in the command line, the compiler wrapper would skip all remaining arguments, causing problems building py-scipy with Intel compiler. This PR solves the problem.

* Fixed compiler wrapper in the face of extra spaces between arguments

Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
2021-04-01 18:39:06 +00:00
Daniel Arndt
cf1b8dd72b xSDK: add ArborX (#22619) 2021-04-01 11:59:05 -05:00
iarspider
1e70ee38a2 New version of OpenLoops (#22240)
New version of OpenLoops; new list of processes; update lcg process collection
Add script to scrape openloops website for process list
2021-04-01 17:06:03 +02:00
Nick Forrington
e22b2ff5c9 arm-forge: cleanup and upgrade to forge v21.0 (#22015)
Backwards incompatible cleanup to target single-tarball-per-arch builds
going forwards.

* Replace per-distro versions with new per-arch builds, and add
  url_for_version to avoid specifying per tarball.
* Customise environment setup to avoid adding lib to LD_LIBRARY_PATH.
* Update homepage and licensing URLs.
* Avoid shell interpretation when running textinstall.sh.
* Added NickRF as maintainer.
2021-04-01 15:47:32 +02:00
iarspider
034211f993 Extra environment variables for Qt (#22717) 2021-04-01 12:40:56 +00:00
Chris Richardson
5ed00560cd Fenicsx package updates for basix install (#22679)
Co-authored-by: Garth N. Wells <gnw20@cam.ac.uk>
2021-04-01 14:35:01 +02:00
Robert Mijakovic
efaa2c160f py-cython: new version (#22712)
Co-authored-by: Robert Mijakovic <robert.mijakovic@lrz.de>
2021-04-01 14:28:12 +02:00
William Downs
db87f62aa5 gchp: add version 13.0.1 and remove release candidate (#22572) 2021-04-01 14:07:13 +02:00
Rémi Lacroix
67f182bb6d MUMPS: Various improvements to the package (#22575)
Use `conflicts` directive whenever possible.
This allows failing early when conflicting variants are used.

Do not silently ignore `+parmetis` variant when `~metis`.
Instead throw an error during concretization.

Simplify the "Makefile.inc" generation.
This will make easier to add new variants in the future.
2021-04-01 14:06:22 +02:00
Michael Kuhn
4a059aad17 libfabric: add 1.12.0 (#22694) 2021-04-01 06:01:19 -06:00
Michael Kuhn
76424c1a91 sqlite: add 3.35.3 (#22697) 2021-04-01 13:57:20 +02:00
Michael Kuhn
2556490cb0 leveldb: add 1.23 (#22695) 2021-04-01 13:56:25 +02:00
Michael Kuhn
5a10c6f822 glib: add 2.66.8 (#22691) 2021-04-01 13:44:09 +02:00
Amiya Maji
09dcb16a70 qt: restrict patch to 5.12.7 (#22705) 2021-04-01 04:38:06 +00:00
Michael Kuhn
bfece29858 pkgconf: add 1.7.4 (#22696) 2021-03-31 21:37:02 -07:00
Michael Kuhn
f7d7cbfacf readline: add 8.1 (#22698) 2021-03-31 21:36:40 -07:00
Michael Kuhn
487ea02044 tar: add 1.34 (#22700) 2021-03-31 21:36:20 -07:00
Michael Kuhn
2922068fdc curl: add 7.76.0 (#22693) 2021-03-31 21:36:01 -07:00
Anthony J. Zukaitis
1c084cd4dd Added version patch for 1.4.0 tag on mpark-variant (#22496)
* Added version patch for 1.4.0 tag on mpark-variant

Redirected urls to git and github tags.

* Updated to commit hashes

* Update var/spack/repos/builtin/packages/mpark-variant/package.py

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* Update var/spack/repos/builtin/packages/mpark-variant/package.py

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* Update var/spack/repos/builtin/packages/mpark-variant/package.py

Co-authored-by: Anthony J Zukaitis <zukaitis@lanl.gov>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-03-31 22:35:00 -06:00