Commit graph

13151 commits

Author SHA1 Message Date
Nicholas Sly
d79d11b6d4 Removed github repository and develop version from dataspaces package as it is no longer present/accessible. (#13740) 2019-11-14 16:20:13 -06:00
xfzhao
11e65661ac update vsearch (#13736) 2019-11-14 16:17:02 -06:00
Massimiliano Culpo
7e84fe966c hwloc: added 'master' version pointing at the HEAD of the master branch (#13731) 2019-11-14 12:06:07 -06:00
Sinan
00bf299e46 new package Qscintilla (with python bindings via py-pyqt ) (#12793)
* qscintilla_with_python_bindings_disabled

* pyqt5 with variant +qsci to compile qscintilla python bindings

* fix a dyn linking issue for Qsci python module

* fix a bug

* fix bug: use sip provided by py-pyqt5

* fix typo

* tidy up, make designer

* tidy up

* fix designer build issue, set env for designer plugin

* tidy up

* tidy up

* minor improvements

* improve style

* build Qscintilla python bindings here

* make qsci config option variant dependent

* get rid of commented out code

* improvements: add resource for qscintilla, improve config_args

* flake8: spaces, blank lines etc

* flake8: fix long lines

* Update var/spack/repos/builtin/packages/py-pyqt4/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt4/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt4/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/qscintilla/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* dont install source tree under prefix

* remove duplicate line

* use os.path.join instead of +

* separate build and run environment setups

* flake8

* Update var/spack/repos/builtin/packages/py-pyqt5/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt5/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt5/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* fix rsrc path

* use python_include_dir

* use "with working_dir"

* Update var/spack/repos/builtin/packages/py-pyqt4/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt5/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt5/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt5/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/qscintilla/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt4/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pyqt4/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* flake8
2019-11-14 12:01:49 -06:00
Matthias Maiterth
ab2b3f30a5 package/geopm: Added versions 1.0.0 and 1.1.0 (#13721)
* package/geopm: Added versions 1.0.0 and 1.1.0

Added changes for 1.1.0 and 1.0.0 in this patch.
Patch for 1.0.0 was previously not merged.
variant for hwloc removed since that is not a dependency since 0.5.1 and
variant('hwloc', when=:0.5.1 is not supported afaik.
made depends_on versions more explicit.

* package/geopm: removed 1.0.0 release candidates 1 and 2.
2019-11-14 12:01:03 -06:00
Hector Martinez-Seara
cd04538bb9 Adding final bug-releases for the gromacs-2016 and -2018 and Plumed (#13715)
* Adding final bug-releases for the gromacs-2016 and -2018

* Added newer versions of plumed and libmatheval not a dependency >v2.5

* plumed package: chamge name git branch to master
2019-11-14 12:00:36 -06:00
Seth R. Johnson
b8916ecc08 Fix libbsd on Intel compilers (#13720)
Libbsd assumes GCC-defined compiler macros:
```
In file included from nlist.c(44):
local-elf.h(238): catastrophic error: #error directive: Unknown ELF machine type
  #error Unknown ELF machine type
   ^
```
The `__amd64__` and `__x86_64__` macros should be equivalent, but the
latter is defined by intel.
2019-11-14 11:59:46 -06:00
Peter Scheibel
3f861e18b0 symlink relativization: determine target relative to the link directory (#13710)
when making a package relative, relocate links relative to link directory

rather than the full link path (which includes the file name) because `os.path.relpath` expects a directory.
2019-11-13 17:51:57 -08:00
sknigh
045e9c905f Added "file" package and added missing depenency to VIM (#13705)
* Added "file" package and added missing depenency to Vim

* added which and grep

* Added gzip

* added missing dependency to gmake
2019-11-13 18:12:10 -06:00
David Böhme
1ed8de8757 Add Caliper v2.2.0 and v2.1.1 (#13723)
* Add Caliper v2.2.0 and v2.1.1

* Add conflict for adiak when for versions <2.2

* Trim trailing whitespace
2019-11-13 18:11:09 -06:00
Greg Becker
43b0356e14 Allow binary relocation of strings in relative binaries (#13725)
Binaries with relative RPATHS currently do not relocate strings
hard-coded in binaries

This PR extends the best-effort relocation of strings hard-coded
in binaries to those whose RPATHs have been relativized.
2019-11-13 16:03:35 -08:00
G-Ragghianti
dc36b4737d Papi components (#13706)
* Added support for papi components.

* Restored sha256 hashes to package files.
2019-11-13 15:49:06 -06:00
Justin S
a2ef7896b7 rnaz: new package at 2.1 (#13707) 2019-11-13 15:48:06 -06:00
thelfer
ff9b03edc3 Fix mgis package dependency on boost/numpy (#13717) 2019-11-13 15:35:09 -06:00
William F Godoy
d6274e1a1d Docs update for deprecated spack sha256 (#13701)
* Docs update for deprecated `spack sha256`

* Added macOS shasum

* Update lib/spack/docs/packaging_guide.rst

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-13 15:21:27 -06:00
Sinan
9ae4f42ab5 new package: sfcgal (#12624)
* new package: sfcgal

* improve meta information

* add variant and optional dependencies

* add cmake options for building with viewer

* improve dependency type

* improve viewer variant

* improve viewer variant

* specify dependency versions

* add ref

* remove depricated variant
2019-11-13 15:19:43 -06:00
Hari Subramoni
1a6bba1632 Update MVAPICH2 package for 2.3.2 release (#13236)
* Update MVAPICH2 package for 2.3.2 release
Update default build from psm to mrail

* Update different provides for older versions based on feedback from Todd Gamblin

* Simplify rule so one rule covers 2.1 and 2.2

* Add support for disabling rpath based on feedback from Dr. Shende

* Add colon based on comment

* Address review comment by Adam Stewart

* Add declaration of the wrapperpath variant.
    - Thanks to Massimiliano Culpo for the comment
2019-11-13 15:18:35 -06:00
Satish Balay
4d37db02da superlu_dist: fix build with xl compilers (#13702)
* superlu_dist: fix build with xl compilers

* fix link error  ../SRC/libsuperlu_dist.so.6.1.1: undefined reference to `ztrtri_'

* Fixed the ordering of the spec on the xl-611 patch.

* fix flake8 error
2019-11-13 15:03:24 -06:00
Chris Green
56de86dda6 root: relax libxml2 requirements when ~python. (#13657)
* Relax libxml2 requirements when ~python.

Per https://github.com/spack/spack/issues/13637#issuecomment-552026561

* Satisfy package_sanity.py::test_prs_update_old_api.
2019-11-12 23:33:47 -08:00
Satish Balay
53b2add34f
strumpack: revert default to ~shared [i.e behavior before this variant was added] as +shared fails on multiple builds (#13703) 2019-11-12 20:22:34 -06:00
Todd Gamblin
da386b560a docs: use nicer looking code blocks in docs (#13708)
- [x] Use higher contrast terminal output font
- [x] Use higher contrast code block background color than default
- [x] Use a noticeable prompt character

See also https://github.com/spack/spack-tutorial/pull/10.
2019-11-12 18:18:41 -08:00
Simon Pintarelli
d0de9f8d9d add new version for py-ranger-fm (formerly py-ranger) (#13681)
- download from pypi, drop 1.7.2
- drop 1.7.2, it is not available from pypi
2019-11-12 12:05:18 -06:00
sknigh
1ae824737e Add missing dependencies to flex. (#13692) 2019-11-12 12:01:15 -06:00
h-denpo
2b6c4245d0 Fixed url. url="https://sourceware.org/pub/libffi/libffi-3.2.1.tar.gz") (#13693) 2019-11-12 11:58:49 -06:00
t-karatsu
ca19fb86c1 damselfly: Add mpi dependency. (#13694) 2019-11-12 11:58:11 -06:00
Adrian Jackson
57aa7ba045 Fixing Fortran MPI compiler reference in mpt package (#13699) 2019-11-12 11:57:07 -06:00
Stephen Hudson
cea7403b67 Update nlopt package to add Python bindings to PYTHONPATH (#13688)
* Update nlopt package to add Python bindings to PYTHONPATH

* Use extends for nlopt/python fix

* nlopt - change develop to master and add python dep qualifiers
2019-11-12 11:46:12 -06:00
Massimiliano Culpo
826e8c6394 athena, mvapich2, spectrum-mpi: use new API to setup environment (#13677)
* athena: updated api call to setup build environment

* mvapich2: updated api call to setup build and run environment

* spectrum-mpi: updated api call to setup build and run environment
2019-11-12 11:44:12 -06:00
Frédéric Simonis
b1965fa913 precice: enable petsc by default (#13696) 2019-11-12 11:40:37 -06:00
Satish Balay
cbfdc85d26
trilinos: add version 12.18.1 with dtk-3.1 (#13690) 2019-11-12 07:52:24 -06:00
Satish Balay
9e12b4e95a
sundial: add patch for build failure on cori/theta (#13665) 2019-11-12 07:52:05 -06:00
Daryl W. Grunau
5a9389a528 verify.py: os.path.exists exception handling (#13656) 2019-11-11 17:47:47 -06:00
Simon Pintarelli
e5b38c525e SIRIUS: add new version, add magma support (#13680)
- depends on spfft starting from 6.4.0
- add magma variant
- avoid setting cuda_arch to none
- add python dependencies
- use release as default build type
2019-11-11 16:19:40 -06:00
sknigh
fdb85744e3 added lcov package (#13687) 2019-11-11 15:13:48 -06:00
Adrian Jackson
3eaa790efa Add HPE MPT package (#13616)
* Adding in HMPT package for HPE MPI libraries

* Updating copyright dates

* Renaming HPE MPI package

* Fixing error in package file

* Tidying up defintions and linting

* liniting

* Adding in library setup so packages that want to manually add mpi libraries can do so (i.e. npb)

* Linting

* Linting

* Investigating old API errors

* Investigating api errors

* Investigating api errors

* Investigating api errors

* Investigating api errors

* Investigating api errors: adding back in functions to see when the build fails

* Investigating api errors: adding back in functions to see when the build fails

* Investigating api errors: adding back in functions to see when the build fails

* Investigating api errors: adding back in functions to see when the build fails

* Investigating api errors: adding back in functions to see when the build fails

* Linting

* Linting

* Fixing

* Fixing
2019-11-11 13:22:20 -06:00
Adam J. Stewart
dc51d676a2
cuDNN: add new versions (#13668)
* cuDNN: add new versions

* cuDNN 9.0 can build against CUDA 9.1

* Undo version format change
2019-11-11 12:53:26 -06:00
Adam J. Stewart
03fb2d61c6
Add new version of Intel MKL-DNN (#13669)
* Add new version of Intel MKL-DNN

* Get OpenMP build working

* lomp is also needed for linking

* http -> https

* Add myself as maintainer
2019-11-11 12:52:53 -06:00
Adam J. Stewart
38da69346c
py-scikit-learn: update OpenMP flag (#13683) 2019-11-11 12:52:30 -06:00
Brian Spilner
3eb19b142f new CDO release 1.9.8 (#13674) 2019-11-11 12:52:06 -06:00
Pieter Ghysels
6fc3e73f8d Update ButterflyPACK and STRUMPACK (#13661)
* Add new strumpack version (3.2.0), with new
dependency on ButterflyPACK.

* add ButterflyPACK version 1.1.0

* Add strumpack version 3.3.0, add dependency on ButterflyPACK 1.1.0

* Sort ButterflyPACk versions from newest to oldest

* Add a shared variant for STRUMPACK

* Also allow possible newer versions of ButterflyPACK
2019-11-11 12:24:13 -06:00
Phil Carns
4934448065 pmdk: fix x86_64 arch check (#13676) 2019-11-11 15:46:44 +01:00
Adam J. Stewart
bd9907809e environments: don't try to modify run-env if a spec is not installed (#13589)
Fixes #13529
Fixes #13509
2019-11-11 13:02:36 +01:00
Adam J. Stewart
e10f8fe531 py-numpy: added version 1.17.4 (#13670) 2019-11-11 11:26:21 +01:00
Adam J. Stewart
901da240f3 CMake: added version 3.13.5 (#13671) 2019-11-11 11:25:50 +01:00
Axel Huebl
86202a5ad0 nlohmann-json 3.7.2 (#13672)
Add the latest bugfix release.
2019-11-11 11:23:50 +01:00
Adam J. Stewart
60070759a0
Improve spack checksum formatting (#13666)
* Improve spack checksum formatting

* Add colon

* Fix Python 2 bug
2019-11-10 16:47:56 -06:00
Adam J. Stewart
1ca91d728a
Update default PyTorch variants (#13667) 2019-11-10 16:46:04 -06:00
Adam J. Stewart
ff330631ed
Add py-scipy 1.3.2 (#13663) 2019-11-09 19:41:44 -06:00
Adam J. Stewart
834a8be933
Add grass 7.8.1 (#13664) 2019-11-09 19:41:29 -06:00
Kelly (KT) Thompson
550e9907f5 New Package: py-pyside2 (#13647)
* New Package: py-pyside2

https://wiki.qt.io/Qt_for_Python

The Qt for Python project aims to provide a complete port of the PySide module
to Qt 5. The development started on GitHub in May 2015. The project managed to
port Pyside to Qt 5.3, 5.4 & 5.5. During April 2016 The Qt Company decided to
properly support the por

* Address review comments:

+ Add a variant for `+doc` and only depned on some packages if this variant is
  active.
+ Enable building the tests if requested.
+ Correct registered required verions for python and qt.

* Remove dead code, fix depends_on command args.

* fix one more flake8 issue.

* One more fix to  arguments and change  version name to .
2019-11-09 18:22:30 -06:00