Commit graph

8784 commits

Author SHA1 Message Date
Veselin Dobrev
3858d4a3a3 [hypre] add the 'headers' property (#7278)
* [hypre] Add the 'headers' property plus a small tweak in the 'libs'
property.

* [hypre] Add fallbacks for searching for '.libs' in 'prefix.lib64' and
in all of 'prefix'.

* [hypre] Fix style.

* [hypre] Use find_headers instead of find + HeaderList.
2018-03-22 19:43:23 -05:00
jthies
2e4378bcd0 added a new package file for PHIST (Pipelined, Hybrid-parallel Iterat… (#7361)
* added a new package file for PHIST (Pipelined, Hybrid-parallel Iterative Solver Toolkit)

* packages/phist: fix some formatting errors (too long lines etc)
and set allowed values for option "outlev"

* packages/phist: fix some more flake8 errors

* add headers  property to netlib-lapack and intel-mkl

* ghost: fix finding cblas header and libs (at least for mkl and netlib-lapack, which provide headers())

* added a new package file for PHIST (Pipelined, Hybrid-parallel Iterative Solver Toolkit)

* packages/phist: fix some formatting errors (too long lines etc)
and set allowed values for option "outlev"

* packages/phist: fix some more flake8 errors

* phist: use headers property to find lapacke include dir

* phist: fix flake8 error

* phist: be more specific about dependencies and update version

* phist: state trilinos minimum version when building with Tpetra kernels

* gmp: add oldish version 5.1.3 with checksum

* phist: get rid of the 'petsc+complex' variant, it can be installed by kernel_lib=petsc ^petsc+complex

* phist: new version

* phist: fix version checksum

* Revert "add headers  property to netlib-lapack and intel-mkl"

This reverts commit d8cb62905ebfb2cba186fd2d736d54a88a49d089.

* Revert "ghost: fix finding cblas header and libs (at least for mkl and netlib-lapack, which provide headers())"

This reverts commit d406a77ed7879c124fbaf1d757d002b9f0771620.

* phist: remove unused function

* phist: reorder package file versions/variants/depends_on/rest

* phist: some minor changes requested by @adamjsteward
2018-03-22 19:42:38 -05:00
Eric
9a3a9860df perl-json: Create new package (#7431) 2018-03-22 19:41:50 -05:00
Adam J. Stewart
666341599c
Add py-cvxopt package (#7527)
* Add py-cvxopt package

* Flake8 fixes
2018-03-22 19:38:46 -05:00
Adam J. Stewart
1f23693877
Fix giflib unit tests on macOS/BSD (#7519)
* Fix giflib unit tests on macOS/BSD

* Unit tests occasionally fail when run in parallel
2018-03-22 19:38:17 -05:00
Adam J. Stewart
f721fb3e4c
Fix error raising during install with Python 3 (#6894)
* Fix error raising during install with Python 3

* Fix env_path too
2018-03-22 19:37:49 -05:00
Adam J. Stewart
32a78eae73
Add latest version of MPFR and patches for older versions (#7545)
* Add latest version of MPFR and patches for older versions

* Fetch and checksum patches instead of storing them

* Fix bug, version attribute was being overridden
2018-03-22 19:37:01 -05:00
Sinan
8d4ef999d7 package/py-pyutilib: create new package (#7555) 2018-03-22 21:49:07 +01:00
Gregory Lee
be3f08d0de llvm+python+lldb depends on py-six for versions 5 and up (#7056) 2018-03-22 15:42:41 -05:00
Massimiliano Culpo
0d7652c508 Used names with __ in class level constructs to avoid rebinding (#7563)
fixes #3129
2018-03-22 15:41:55 -05:00
Adam J. Stewart
06e1fdb237 Add latest version of MPC (#7546) 2018-03-22 21:10:58 +01:00
Adam J. Stewart
9c0fb6ccee Add latest version of ISL (#7547) 2018-03-22 21:09:43 +01:00
Sinan
5e7fc91d8a add versions 1.9.6 1.9.7 (#7562) 2018-03-22 21:07:34 +01:00
Massimiliano Culpo
5655895865 Record installation date and time in DB (#7334)
* Added installation date and time to the database

Information on the date and time of installation of a spec is recorded
into the database. The information is retained on reindexing.

* Expose the possibility to query for installation date

The DB can now be queried for specs that have been installed in a given
time window. This query possibility is exposed to command line via two
new options of the `find` command.

* Extended docstring for Database._add

* Use timestamps since the epoch instead of formatted date in the DB

* Allow 'pretty date' formats from command line

* Substituted kwargs with explicit arguments

* Simplified regex for pretty date strings. Added unit tests.
2018-03-22 11:07:27 -07:00
Massimiliano Culpo
6699ba8769 Recover the old patching order for packages. (#7558)
fixes #7543

This is very likely an hot-fix, while a more permanent solution is
needed. See this comment for more insight:

 https://github.com/spack/spack/pull/7193#discussion_r176448831

on the problem.
2018-03-22 10:09:43 -07:00
Levi Baber
c8a8079c34 meme: fix errors (#6736)
* meme: added perl-xml-parser dependency, resolved issue. still need to fix ghostscript or image-magick, conversion not working.

* meme: fixed issue with libxslt/libxml2 conflict, and added imagemagick support

* meme: removing libxslt/libxml2 dependency lines

* meme: configure args

* meme: separating configure args

* meme: removing a comment, and hoping for travis to rebuild. site seems back up.

* meme: make image-magick optional

* meme: add comment referencing PR

* meme: bah flake8
2018-03-22 12:06:24 -05:00
Federico Ficarelli
9280eba214 tcl-tclxml: new package (#7557) 2018-03-22 07:36:59 -05:00
Adam J. Stewart
aa84ddffed
Add latest version of eigen (#7530)
* Add latest version of eigen

* Fix bug in ptscotch detection
2018-03-22 07:25:26 -05:00
Federico Ficarelli
e71681458b tcl-tcllib: new package (#7481) 2018-03-22 06:35:37 +01:00
becker33
f8657e3fd9 Propagate architecture information during concretization (#7412)
This updates architecture concretization to

* Search for the nearest parent in the DAG for architecture information
  rather than defaulting to the root of the DAG
* Propagate architecture settings transitively, such that if for
  example the target is set at the root of the dag it will set the
  same target on indirect dependencies (assuming no intermediate
  dependency specifies a separate target). Previously this occurred
  in general but under some conditions did not, for example if an
  intermediate dependency specified some subset of architecture
  properties.
2018-03-21 18:14:01 -07:00
Veselin Dobrev
6f0472ea87 [MUMPS] Remove the injection of rpath_args through the inject_libs
variable. This should happen automatically through the Spack compiler
wrapper.
2018-03-21 17:55:04 -07:00
Michael Sternberg
726c7e0f06 Opt avx (#7486)
* Promote to Autotools for simplicity; broaden Intel CPU opt targeting from SSE4.2 to AVX2

* make Intel CPU opt targeting same as in ../libxc

* flake8 W291

* use canonical means to pass (ahem) the test phase, h/t @adamjstewart

* revert f25d598 (unrelated merge)

* re-merge
2018-03-21 19:53:19 -05:00
Leonhard Reichenbach
973a131dac Add latest versions of bazel (#7542)
* Add latest versions of bazel

* Added java as dependency to run bazel
2018-03-21 19:52:28 -05:00
Eric Müller
f5afc98cc2 libXi requires pkgconfig and fixesproto (#7480) 2018-03-21 19:51:58 -05:00
Levi Baber
b0ecd0fd0b py-pybedtools: fix hash for 0.6.9 (#7492) 2018-03-21 19:51:34 -05:00
Levi Baber
383c2aa2d6 Singularity: new version (#7551)
* singularity: new version

* singularity: hash
2018-03-21 19:50:53 -05:00
Eric
81dcd1b33a perl-module-implementation: Create new package (#7549) 2018-03-21 17:16:24 -05:00
Julien Adam
a81ebfc2ba New Package: jchronoss (#7207)
* New Package: jchronoss

* jchronoss: Fix flake8 errors

* jchronoss: Fix according to recommendations

* jchronoss: Remove FIXME

* jchronoss: Fix another flake8 error
2018-03-21 16:56:20 -05:00
lingnanyuan
a2b885d0ba r-dirichletmultinomial: Create new package. (#7227)
* r-dirichletmultinomial: Create new package.

* Change description.

* Change description.
2018-03-21 16:55:35 -05:00
scheibelp
6548f2db5c Enable creation of mirrors for systems with different compilers (#5153)
* Create mirror for system with different compilers

Spack concretizes the spec provided by the user in
"spack mirror create" to ensure downloading the right
dependencies. Under normal circumstances concretization
requires that the chosen compiler exists on the system,
but this is not required when creating download mirrors
for other systems, so this requirement is removed in that
case.

* Add test for disabling compiler existence check

* Update compiler existence checking logic

* improve test for disabling compiler existence check
2018-03-21 14:55:26 -07:00
Eric
88fb67768d py-python-levenshtein: Create new package (#7426)
* py-python-levenshtein: Create new package

* py-python-levenshtein: fix flake8 errors

* py-python-levenshtein: Use pypi.io per packaging guide
2018-03-21 16:54:51 -05:00
Eric
08f3ebf859 perl-cairo: Create new package (#7432)
* perl-cairo: Create new package

* perl-cairo: Add cairo dependency
2018-03-21 16:54:25 -05:00
Levi Baber
5e8370e093 bamutil: needs zlib (#7444) 2018-03-21 16:53:55 -05:00
Sinan
6c23b82d6b package/JAGS: new version (4.3) (#7456)
* package/JAGS: new version (4.3)

* fix typo

fix typo
2018-03-21 16:53:11 -05:00
Levi Baber
720a4854c2 pandaseq: needs bzip and libtool as link (#7465) 2018-03-21 16:52:46 -05:00
Jon Rood
de52c175de Using self.prefix in Trilinos to avoid global name prefix undefined bug (#7478)
* Using self.prefix in Trilinos to avoid global name prefix undefined bug during module refreshing.

* Fixing flake8 errors.
2018-03-21 16:52:08 -05:00
Howard Pritchard
f59a447f71 Open MPI: add 2.1.3 (#7535)
note the libmpi.so itself didn't have changes, only other
components of the package had updates.

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2018-03-21 16:49:31 -05:00
Denis Davydov
75c9083139 suite-sparse: add cmake dependency (#7538) 2018-03-21 16:49:01 -05:00
健美猫
71055a8ef4 Generate spack docset for Dash. (#6981) 2018-03-21 16:37:26 -05:00
Gregory Lee
7504e9997d make py-setuptools a run-time-only dep for py-basemap and patch pytho… (#6989)
* make py-setuptools a run-time-only dep for py-basemap and patch python package to only apply setuptools flag for build deps

* py-qtconsole does not require setuptools
2018-03-21 16:34:27 -05:00
Yifan Zhu
55f4bbb111 snphylo: new package (#7045)
* pushing partially done recipe for snphylo

* r-snphylo: try

* phylip: added version 3.697

* snphylo: updated package.py

* snphylo: flake8 error fixed
2018-03-21 16:21:55 -05:00
scheibelp
e8a0637606 Support MD5 with a warning when OpenSSL is compiled in FIPS mode (#7531)
* This allows Spack to work with MD5 hashes on machines with openssl in FIPS mode.
* We are still using MD5 for validation in many places, and a later PR will replace all uses of MD5 with SHA256.
* This is a quick fix until that happens.
2018-03-21 14:11:54 -07:00
Geoffrey Oxberry
6127b02324 elfutils: document conflict with clang (#7096) 2018-03-21 16:00:49 -05:00
Mark W. Krentel
154401de76 intel-xed: new package (#7106)
* intel-xed: new package

The Intel X86 Encoder Decoder library for encoding and decoding
x86 machine instructions.

* intel-xed: style fixes for flake8.

* intel-xed: better style fix

* intel-xed: update to version 2018.02.14, add PYTHONPATH for
building with python 3, cleanup the opt flag.
2018-03-21 14:39:06 -05:00
lpoirel
9d2fce4544 scotch%intel: remove restrict (#7148)
The restrict compilation option with icc causes deadlock when multithreading is used. This issue has already been reported to the Scotch development team, but for current versions it is more reliable not to use the restrict compilation option.
2018-03-21 14:22:50 -05:00
Geoffrey Oxberry
935cc30c17 librom: new package (#7180)
* libtool: actually do symlinking correctly on darwin

Version 4 of the libtool/darwin debacle:

AutotoolsPackage hardcodes libtool & libtoolize into the autoreconf
stage, so the commands `libtool` and `libtoolize` MUST be present, and
shimming in glibtoolize into AutotoolsPackage when sys.platfrom ==
'darwin' does not work.

join_path(spec['libtool'].prefix.bin, 'libtool') still shadows system
BSD libtool (in apple-cctools, see PR #7177), but this shadowing could
be okay, depending on the combination of dependent specs.

* librom: new package
2018-03-21 14:16:36 -05:00
Eric
e07ed2ab97 py-backports-functools-lru-cache: add version 1.5 (#7206)
* py-backports-functools-lru-cache: add version 1.5

* py-backports-functools-lru-cache: fix conflicts
2018-03-21 14:09:55 -05:00
Jon Rood
3d7930a379 Adding unzip package. (#7446)
* Adding unzip package.

* Removing bzip2 dependency in unzip and raising an error when on Cray.

* Fixing error.

* Using conflicts statement for Cray detection in unzip package.
2018-03-21 13:59:39 -05:00
lingnanyuan
011d407132 Xorg-server: Add dependencies and fix installation. (#7220)
* xorg-server: Add several dependencies.

* libepoxy: Add dependendies mesa and meson.

* mesa: Add dependencies for hwrender.

* mesa: undo some changes.
2018-03-21 13:53:26 -05:00
Eric Müller
647c4a1507 py-py{gobject,gtk} require pkgconfig for build (#7380) 2018-03-21 13:22:08 -05:00