Commit graph

3193 commits

Author SHA1 Message Date
Elizabeth Fischer
b27f4e3aeb py-matplotlib: Add variants for optional dependencies. (#2008) 2016-10-12 14:55:38 -07:00
Elizabeth Fischer
67ef6df4db Made optional CGAL dependencies optional. (#2006)
* Made optional CGAL dependencies optional.

* cgal: Added note explaining that the CORE library is not the same as core CGAL functionality.

* Bug fix and flake8

* flake8
2016-10-12 13:02:06 -07:00
Ben Boeckel
b369be65d7 Mock up Xcode devdir to make Qt5 work on Mac OS X (#1832)
* build_environment: allow compilers to set up an environment

* clang: mock up a toolchain directory for xcode

Some projects ignore CC and CXX flags and instead use xcode to find the
toolchain. Clang on Apple should set up the environment properly.
Arguably, every compiler could do this on Apple, but let's see how this
works out just for AppleClang for now.

The Documentation directory is ~1.7G and the excluded platforms add up
to about 7G. Ignoring swift saves another 500M. The resulting Xcode.app
copy is in the 2G range.

* compiler: set member variables early

This is required so that later methods can query things such as the
version of the compiler.

* compiler: support finding the real path of the compiler

On Apple, the /usr/bin compilers are actually wrapping tools themselves
which query xcrun for the currently selected Xcode installation. Pierce
this veil and get the real, full path the to underlying compilers
instead.

* icu4c: install with rpath

On macOS, icu installs with a library ID of the library name. Enabling
rpath makes its ID its full installed path which lets Qt5 link against
it successfully.

* qt: no -no-gtkstyle flag on Qt5 on macOS
2016-10-12 09:58:12 -07:00
Todd Gamblin
488e1bab2c Make insecure option work with curl AND git. (#1786) 2016-10-11 23:13:40 -07:00
Elizabeth Fischer
a6f85f51d0 patchelf: Add version (#1540)
* patchelf: Add version

* flake8

* Removed unnecessary url_for_version() function.

* Restored old URL
2016-10-11 23:11:25 -07:00
Denis Davydov
025b914079 oce: fix for Sierra (#1934) 2016-10-11 23:10:51 -07:00
gmatteo
949766d92e Abinit: Added package(s) (#1995)
* First version of Abinit package

* Ignore *.swp files

* Add libxc, etsf_io packages

* AtomPaw package

* Make Abinit depend on mpi@2: and external version of libxc, netcdf, hdf5, etsf_io

* etsf_io: install Fortran modules in prefix.include

* Remove etsf_io from abinit requirements

* Add libxc2.2.1 (required by Abinit and atompaw)

* Cleanup

* Run make check

* Cleanup

* Use ld_flags instead of hard-coded libs, fix pep8, add copyright

* Put scalapack before lapackblas
2016-10-11 15:22:46 -07:00
Joseph Ciurej
37d125b890 Update Package : ExodusII (#1504)
* Added support for the 'maxdims' and 'maxvars' flags for 'NetCDF'.

* Added the '+mpi' variant and improved dependencies for 'exodusii'.
Improved the 'exodusii' package so that it's less reliant on patches.

* Added better type checking to variant values in the 'netcdf' package.

* Corrected the required CMake version for the 'exodusii' package.

* Fixed the dependencies of the '+mpi' variant of the 'exodusii' package.
2016-10-11 14:53:02 -07:00
Adam J. Stewart
6dc8bbcb3a Package all of Xorg/X11/XCB (#1740)
* Updates to Mesa and other Xorg packages

* Add packages for all Xorg Protocol extensions

* Add packages for first half of Xorg libraries

* Add packages for remaining Xorg libraries

* Add packages for all Xorg utilities

* Add packages for Xorg documentation tools

* Add build deps to Xorg protocol headers

* Add packages for XCB

* Add build deps to Xorg libraries

* Add build deps to Xorg utilities

* Add packages for Xorg fonts and font-related utilities

* Change font deptype from build to default

I wasn't sure which deptype was appropriate at first since none of
the packages are actually linked together. I initially chose the
build deptype for this reason. However, the font packages don't
install into their own prefix. They install into font-config. If
font-config is a build dependency, that means you can uninstall it
without uninstalling the font packages, which wouldn't make sense
since they install into font-config. So I switched them back to
the default deptype.

* Minor formatting changes to ncview

* Add half-way done xorg-server package

* Add packages for Xorg test suites, not yet tested!

* Add packages for Xorg data

* Add first quarter of Xorg apps

* Add more packages for Xorg apps

* Add dependencies to mesa

* Remove comments from mesa package

* Flake8

* Add more packages for Xorg apps

* Add more packages for Xorg apps

* Add more packages for Xorg apps

* Add more packages for Xorg apps

* Add more packages for Xorg apps

* Add package for Sublime Text

* Add packages for remaining Xorg apps

* Revisit testing packages, add missing dependencies

* Add dependencies, clean up FIXMEs
2016-10-11 09:42:20 -07:00
alalazo
c7a5dd36e2 qa : flake8 issues 2016-10-11 16:30:06 +02:00
alalazo
ab995df777 Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases_rebase
Conflicts:
	lib/spack/spack/build_environment.py
	lib/spack/spack/cmd/install.py
	lib/spack/spack/cmd/setup.py
	lib/spack/spack/package.py
	var/spack/repos/builtin/packages/gmp/package.py
	var/spack/repos/builtin/packages/hdf5/package.py
2016-10-11 16:28:08 +02:00
Denis Davydov
4d939802ae hypre: fix blas/lapack for MKL (#1993) 2016-10-11 06:48:16 -07:00
Todd Gamblin
1dff309a3f Merge pull request #1989 from KineticTheory/cray_compile_wrappers
On Cray machines, use the Cray compile wrappers instead of MPI wrappers.
2016-10-11 06:46:29 -07:00
Adam J. Stewart
aa079dbdf1 Add variant to MPICH to enable ROMIO support (#1944) 2016-10-11 02:16:01 -07:00
Denis Davydov
49aed3969c tethex: add a new package (#1991) 2016-10-11 02:13:25 -07:00
Adam J. Stewart
5988b3a222 More specific dependency versions, wrap make check (#1962) 2016-10-11 01:36:40 -07:00
Sergey Kosukhin
7fd639d6fc Update libjpeg-turbo: added new version and removed redundant dependency. (#1897) 2016-10-11 01:32:05 -07:00
Denis Davydov
6c250ab486 pango: add missing dependency (#1958) 2016-10-11 01:19:44 -07:00
Denis Davydov
907546b55e libcerf: fix for modern clang (#1959) 2016-10-11 01:19:12 -07:00
scheibelp
9e7f53a35a [WIP] Use boost system layout by default (#1955)
Use boost system layout by default
2016-10-11 01:17:26 -07:00
Erik Schnetter
f555b8110d Charm++: Ignore compiler warnings while configuring (#1981) 2016-10-11 00:45:01 -07:00
Kelly Thompson
1891ce3545 Trilinos: Use more flexible option for locating the BLAS library directory. (#1987)
+ This change fixes a problem that manifests when trilinos is built against a
  MKL installation defined as an external package. In this scenario, the MKL
  libraries are found one directory deeper than for the case where spack
  provides MKL. The extra directory is a platform name like 'intel64'.
+ The changes in this PR were recommended by contributor @davydden. I
  implemented and tested with intel@16.0.3. These changes fix the issue I
  reported. I did not attempt building trilinos against other BLAS
  implementations.
+ fixes #1923
2016-10-11 00:42:59 -07:00
Pramod Kumbhar
afd5d6b5cd hpx5 version update (#1967) 2016-10-11 00:36:31 -07:00
Geoffrey Oxberry
9a05ffea27 Mfem 3.2 (#1202)
* mfem: add tarball extension

Add tarball extension as a result of a feature added in PR#1926, which
fixes earlier issues in this PR (PR#1202). Prior to adding this feature,
Spack would not autodetect the extension of the tarball downloaded from
the redirected, shorted Google URL, requiring a messy hack. This hack
worked for mfem version 3.1, but led to errors when adding mfem version
3.2 because the files downloaded from Google did not contain the package
name, version number, or extension. Adding the extension enables Spack
to rename the tarball downloaded from Google to a sensible name that is
compatible with its filename parsing algorithms so that Spack "does the
right thing" (detects that the file is a GZipped tarball, decompresses
it, runs GNU Make) in fetching and staging the package.

* mfem: add linkage to KLU & BTF

Add linkage to the KLU & BTF solvers, which are now enabled in MFEM for
versions 3.2 and later.

* mfem: Add superlu-dist variant

Add linkage to SuperLU_DIST, which is a new linear solver interface for
MFEM versions 3.2 and later.

* mfem: add netcdf variant for cubit mesh support

Add NetCDF variant for MFEM versions 3.2 and later; installing the
NetCDF interfaces enables CUBIT mesh support.
2016-10-11 00:33:26 -07:00
Kelly (KT) Thompson
3553c8b9e9 On Cray machines, use the Cray compile wrappers instead of MPI wrappers.
+ Cray compile wrappers are MPI wrappers.
+ Packages that need to be compiled with MPI compile wrappers normally use
  'mpicc', 'mpic++' and 'mpif90' provided by the MPI vendor. However, when using
  cray-mpich as the MPI vendor, the compile wrappers 'CC', 'cc' and 'ftn' must
  be used.
+ In this scenario, the mpich package is hijacked by specifying cray-mpich as an
  external package under the 'mpich:' section of packages.yaml. For example:

  packages:
    mpich:
      modules:
        mpich@7.4.2%intel@16.0.3 arch=cray-CNL-haswell: cray-mpich/7.4.2
      buildable: False
    all:
      providers:
        mpi: [mpich]

+ This change allows packages like parmetis to be built using the Cray compile
  wrappers. For example: 'spack install parmetis%intel@16.0.3 ^mpich@7.4.2 os=CNL'
+ This commit relies on the existence of the environment variable CRAYPE_VERSION
  to determine if the current machine is running a Cray environment. This check is
  insufficient, but I'm not sure how to improve this logic.
+ Fixes #1827
2016-10-10 19:10:26 -06:00
Kelly Thompson
29fc9cd22c Update package to use MPI compile wrappers as specified in MPI package. (#1985)
+ Previouly, these strings were hard coded to 'mpicc', 'mpic++', and 'mpifort'.
2016-10-10 15:33:00 -07:00
Denis Davydov
c2ca8693e9 fix blas-lapack in scipy and numpy (#1949)
* fix blas-lapack in scipy and numpy

* py-numpy: do not set rpath on macOS

* py-scipy: do not set Blas/Lapack. This appears to be picked up from py-numpy

* py-numpy: don't write rpath= in Sierra only

* py-numpy: add a link to build notes
2016-10-10 12:38:44 -07:00
Erik Schnetter
377ac68690 Correct Charm++ install procedure (#1957)
Charm++ only creates symbolic links instead of copying files. Correct this.
2016-10-10 09:13:20 -07:00
Jean-Paul Pelteret
d3daa829f0 Added symengine and associated packages (#1885)
Symengine and associated packages
2016-10-07 22:45:24 -07:00
Todd Gamblin
dbc864c9db Restore default RPATH settings but allow packages to limit to immediate deps. (#1954)
- Some packages (netcdf) NEED RPATHs for transitive deps.
- Others (dealii) will exceed OS limits when the DAG is too large.
2016-10-06 15:57:23 -07:00
Denis Davydov
9683e0df07 atlas: add 3.10.3 (#1952) 2016-10-06 15:23:18 -07:00
Joseph Ciurej
82fcc5e1de Feature Proposal : Make All Python Extensions User Configuration Independent (#1435)
* Updated all Python extension packages to use 'setup_py' on install.

* Fixed a few minor style issues with the updated Python packages.
2016-10-06 14:43:49 -07:00
Sergey Kosukhin
ebef9628a3 Update gmp: fixed an issue with intel compiler. (#1898) 2016-10-06 12:49:03 -07:00
Jay
6e9353f1a8 Updated nettle to have m4 as an immediate dependency (#1946)
* Updated nettle to have m4 as an immediate dependency to match new PATH
construction logic which only includes immediate dependencies.

* Update package.py
2016-10-06 11:50:50 -07:00
James Wynne III
7dc11472bf Sqlite ppc64le configure build guess fix (#1684)
* Added check for ppc64le because configure cant guess the build type for rhel on ppc64le

Expand/clarify description of dependency types

Refactored getting the arch so that its less verbose

* Fixed flake8 issues
2016-10-06 02:48:05 -07:00
Sergey Kosukhin
92ca6d6423 Update pixman: mmx is disabled only for MacOS. (#1896) 2016-10-06 02:43:34 -07:00
Sergey Kosukhin
4cce23ea89 Update libtiff: updated homepage and fetch urls. (#1895)
* Update libtiff: updated homepage and fetch urls.

* Update libtiff: new version 4.0.6.
2016-10-06 02:43:23 -07:00
Elizabeth Fischer
264604df3e cgal: build out of source. (#1918)
* cgal: build out of source.

* Simplify cmake out-of-source.
2016-10-06 02:36:27 -07:00
Jeffrey Salmond
a648dc6b33 add python options to vtk package (#1931) 2016-10-06 02:29:25 -07:00
Elizabeth Fischer
2966f174ae mumps: Add alternate download location (in comments) (#1919) 2016-10-05 23:15:38 -07:00
Adam J. Stewart
6ee020cea4 Add package for CONVERGE CFD (#1905) 2016-10-05 10:37:50 -07:00
Adam J. Stewart
95b07c365c Add latest versions, resolve variant resolution bug (#1909) 2016-10-05 10:37:35 -07:00
Elizabeth Fischer
42c69b3809 everytrace: New package (#1543)
* everytrace: New package

Everytrace ensures that stack trace is obtained every time a program exits, for whatever reason.

* everytrace: Change CMake to build dependency

* Renamed to everytrace-example, flake8 and copyright issues.

* flake8

* Missing type=build
2016-10-05 10:03:05 -07:00
Adam J. Stewart
d5e5e4ed1a Add missing dependencies for Flake8 (#1883)
* Warn user if flake8 can't find setuptools

* Add missing dependencies of flake8

* Updates to py-autopep8, make packages activateable

* Check for presence of setuptools for Sphinx too

* Fix bug in order of commands
2016-10-05 10:00:31 -07:00
Elizabeth Fischer
42a60b2434 Added copyright and build deps specification; should be ready to merge. 2016-10-05 12:14:08 -04:00
Axel Huebl
ac3e21f8d4 PNGwriter, libSplash: Add master version (#1744)
* PNGwriter, libSplash: Add `master` version

* PNGwriter, libSplash: Add `dev` versions

Can be used for now, `develop` is currently discouraged.
2016-10-05 06:46:20 -07:00
Denis Davydov
4e5d340665 boost: set 1.61 as preffered until 1.62 is fixed (#1908) 2016-10-05 05:16:06 -07:00
alalazo
7a26c60dbd Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases_rebase
Conflicts:
	lib/spack/spack/cmd/setup.py
	lib/spack/spack/package.py
	var/spack/repos/builtin/packages/gmp/package.py
2016-10-05 09:33:59 +02:00
Pramod Kumbhar
9daafc32f1 Packages for Darshan I/O performance characterization tool from ANL (#1900) 2016-10-04 14:40:35 -07:00
Adam J. Stewart
7806fded3e Update documentation URL after switch to readthedocs (#1901) 2016-10-04 11:47:25 -07:00
Sergey Kosukhin
1d981ebd50 A set of tools used in climate modeling and numerical weather prediction. (#1317)
* Update grib-api: switched to cmake building system.

* Update harfbuzz: added pkg-config dependency.

* Update pango: added pkg-config dependency.

* Add libemos package.

* Add Magics (from ECMWF) package.

* Revert "Variant for building cdo without mpi (#1638)":
CDO does not use MPI.

This reverts commit 079d063c6d.

* Update CDO package: full featured implementation.

* Update magics: added python as build dependency.

* Update cdo: added disabling configuration options.
2016-10-04 09:29:22 -07:00
Ivo Jimenez
d36028cff4 Adds mpip package (#1886) 2016-10-04 01:30:52 -07:00
Ivo Jimenez
2c701d372e Adds lulesh package (#1887) 2016-10-04 01:28:23 -07:00
Pramod Kumbhar
e546d6246f Spack package for HPCToolkit (#1892)
* Spack package for HPCToolkit (performance analysis tool)

* Correction for PR comments, make flake8 happy

* update note / comments
2016-10-04 01:02:50 -07:00
Massimiliano Culpo
50fcade81b cp2k : added support for libint, fixed compilation issues on elpa (#1889) 2016-10-03 08:25:36 -07:00
Geoffrey Oxberry
df79ba0dcf gcc: fix darwin dispatch/object.h header issue (#1518)
Fixes #1203. Apple ships headers in Yosemite (and possibly earlier) that
are gcc-incompatible, but compile fine with clang. The fix is to copy
the offending system header from /usr/include/${REST_OF_HEADER_PATH} to
${GCC_PREFIX}/include/${REST_OF_HEADER_PATH} and replace the non-gcc-
compatible features with gcc-compatible equivalents.

See https://github.com/hashdist/hashstack/pull/771/files for
inspiration, and
http://hamelot.io/programming/osx-gcc-dispatch_block_t-has-not-been-declared-invalid-typedef/
for a description of the header issue.
2016-10-02 18:54:43 -07:00
Nicolas Richart
16f99bd0b2 Adding latest version of fenics (#1528)
* Adding last version of fenics and making trilinos not ambiguous on hdf5

* forcing fenics to ignore hdf5 cxx

* Adding deptypes and correcting the hdf5 patch

* flake8 corrections

* cleaning some useless code
2016-10-02 18:51:34 -07:00
Kelly Thompson
621a4d637d Provide newer versions of llvm (3.8.1, 3.9.0) (#1765)
* Provide new versions of llvm.

+ Provide file list and md5 hashes for 3.8.1 and 3.9.0.
+ Clean up indentation for the 'releases' data structure to improve
  consistency.

* Adding a block of code to the 'resources' structure for cfe.

* Merge cfe and clang resources into single entity.
2016-10-02 18:50:42 -07:00
Alfredo Adolfo Gimenez
1ea9582218 Added hadoop, spark, and variant spark+hadoop (#1833)
* Added hadoop, spark, and variant spark+hadoop

* Docstrings, dependency types, urls, copyright

* Flake8 fixes, link dependency for hadoop

* Build type for spark, env problem setting JAVA_HOME
2016-10-02 18:49:30 -07:00
Erik Schnetter
b22956bab2 git: Don't link against -lrt on Darwin (#1877)
There is no librt on Darwin, and it's not necessary either.
2016-10-02 18:37:45 -07:00
Erik Schnetter
28b48f3e1a Update PAPI to 5.5.0 (#1878) 2016-10-02 18:37:26 -07:00
Erik Schnetter
b2ff9dbcd4 Update tmux to 2.3.0 (#1879) 2016-10-02 18:37:17 -07:00
Kelly Thompson
051c5dbc27 New package: libquo (#1880)
* New package: libquo

libquo is a high-level, easy to use programming interface tailored specifically
for MPI/MPI+X codes that may benefit from evolving process binding policies
during their execution. QUO allows for arbitrary process binding policies to
be enacted and reverted during the execution of an MPI/MPI+X application as
different computational phases are entered and exited, respectively.

https://github.com/losalamos/libquo

* Remove use of 'which' and fix style non-conformance.
2016-10-02 18:36:48 -07:00
Bruno Turcksin
e854e053e4 Add boost 1.62.0 (#1882) 2016-10-02 18:36:31 -07:00
Jean-Paul Pelteret
c86d4c8920 Added bash-completion package (#951) 2016-10-02 17:50:39 -07:00
Pramod Kumbhar
4b34ba1035 pdt url change to download full installer tarball (#1881) 2016-09-30 14:31:28 -07:00
Pramod Kumbhar
6c627dbac9 Add cube variant for building GUI component with qt, parallel built supported (#1525) 2016-09-29 15:37:35 -04:00
Pramod Kumbhar
6ec46ca802 updated to latest available package and fixed installation issue (old packages are no longer available for download) (#1523) 2016-09-29 15:37:07 -04:00
Mitchell Devlin
86cad961e5 added libxstream (#1454) 2016-09-29 15:36:37 -04:00
Adam J. Stewart
deb1cb4805 Add libint package (#1264)
* Add libint package

* Add Intel optimization flags recommended by CP2K

* Add new version and Intel compiler optimization flags for libxc

* Add older version of libint

* Libint depends on GMP C++ library
2016-09-29 15:35:10 -04:00
Robert D. French
a77b48f491 Library for manipulating grib1 and grib2 files (#1736)
Pro tips from @adamjstewart:
* line too long in package description
* name it grib-api instead of grib_api
* depend on netcdf without reference to unnecessary constraints
2016-09-28 17:02:29 -04:00
Elizabeth Fischer
3352889d73 py-pil: Protect against building with Python3. (#1868)
* py-pil: Does not build with Python3.

* Set py-pillow to be the default pil provider

* Update package.py

* Change to comments requested by adamjstewart

* Remove version constraint from extends(), avoid a Spack bug.
2016-09-28 16:51:41 -04:00
Erik Schnetter
4040792501 Update Qthreads to 1.11 (#1863) 2016-09-28 15:22:02 -04:00
Todd Gamblin
295742e2b5 Fixes #1860. Subversion builds sequentially due to race. 2016-09-28 15:18:52 -04:00
Robert D. French
fea0a74bec vim8 is out! (#1753)
* depends on ncurses for 8.0 or higher
2016-09-28 15:17:15 -04:00
Adam J. Stewart
66c2ac0bc9 Tell Mercurial where to find CA certs (#1873) 2016-09-28 14:58:51 -04:00
Adam J. Stewart
9b575dd976 Various updates to scipy and numpy (#1856) 2016-09-27 10:56:24 -04:00
Michael Kuhn
00b3aa77ae Update cdo to 1.7.2 (#1858) 2016-09-27 10:56:04 -04:00
Erik Schnetter
88af9f783d Make PETSc build on Darwin (#1835)
Don't set cpp when building on Darwin.
2016-09-26 10:38:02 -07:00
Erik Schnetter
3282eaea8d Update OpenSSL (#1853) 2016-09-26 10:37:40 -07:00
Denis Davydov
1e10309ff7 some fixes to blas/lapack usage in packages (#1852)
* atlas: fix unit test

* openblas: remove symlinks; use lapack_libs.ld_flags in the test

* mkl: fix openmp variant of blas/lapack libs

* intel-parallel-studio: fix openmp variant of blas/lapack libs

* netlib-scalapack: fix blas/lapack for multilib case (e.g. mkl)

* arpack-ng: fix blas/lapack for multilib case (e.g. mkl)

* petsc: explicitly specify blas/lapack

* minor

* cantera: fix blas/lapack usage

* ipopt: fix blas/lapack usage

* netlib-lapack: fix external blas usage

* mfem: fix lapack/blas usage

* superlu-mt: fix blas usage

* flake8 fixes
2016-09-26 10:37:23 -07:00
Todd Gamblin
cb36aadaf6 Fix doc bugs, widen columns in the package list 2016-09-23 18:07:33 -07:00
Patrick Gartung
ec91152a36 a few package used in HEP including ROOT6 2016-09-23 18:07:22 -07:00
Adam J. Stewart
64194a823a Remove duplicate ICU package (#1837)
* Remove duplicate ICU package

* Ignore deleted files during flake8 tests

* Rename Boost ICU variant
2016-09-23 14:16:59 -07:00
Denis Davydov
6ef6428331 m4: fix compilation on Sierra with GCC (#1844)
* m4: fix compilation on Sierra with GCC

* m4: check macOS version
2016-09-23 13:38:29 -07:00
Bruno Turcksin
98d54182d3 Add Trilinos 12.8.1 (#1843) 2016-09-23 13:36:21 -07:00
Erik Schnetter
73ec2a27d0 Don't require git for Julia @0.5: (#1834) 2016-09-23 13:35:12 -07:00
Erik Schnetter
8147a09489 Update jemalloc to 4.2.1 (#1839) 2016-09-23 13:32:57 -07:00
Robert D. French
3d282b9239 Add libmesh, needed for some FEM applications (#1846) 2016-09-23 13:26:27 -07:00
Denis Davydov
df5e151049 hypre: fix a bug with blas/lapack names (#1841) 2016-09-23 10:06:18 -07:00
Erik Schnetter
c0ebbc97c9 Update OpenSSL (#1836)
This is a security update with priority "HIGH".
2016-09-23 08:21:15 -07:00
Denis Davydov
462a4a1353 boost: fix a bug which broke it on macOS with clang+gfortran (#1816)
* dealii: add missing python dependency

* boost: fix a bug which  broke it on macOS with clang+gfortran

Boost was using gcc compiler instead of clang++, which lead to
cryptic Undefined symbols linking errors for boost::python::objects::function_object()
when building other packages against boost+python.

* boost: add exceptions for intel

* boost: use spack_cxx
2016-09-22 13:47:22 -07:00
Adam J. Stewart
a638b62ab1 Updates to CGAL and ICU4C packages (#1828) 2016-09-22 11:50:50 -07:00
Elizabeth Fischer
64c3b11478 suitesparse: Added +fpic (for linking with shared libraries) (#1542) 2016-09-22 11:03:49 -07:00
Erik Schnetter
7ad6c35627 New package "charm" for the Charm++ parallel programming framework (#1766) 2016-09-22 00:48:00 -07:00
Massimiliano Culpo
d848559f70 Reworking of lapack_shared_libs and similar properties (#1682)
* Turned <provider>_libs into an iterable

Modifications :
- added class LibraryList + unit tests
- added convenience functions `find_libraries` and `dedupe`
- modifed non Intel blas/lapack providers
- modified packages using blas_shared_libs and similar functions

* atlas : added pthread variant

* intel packages : added lapack_libs and blas_libs

* find_library_path : removed unused function

* PR review : fixed last issues

* LibraryList : added test on __add__ return type

* LibraryList : added __radd__ fixed unit tests

fix : failing unit tests due to missing `self`

* cp2k and dependecies : fixed blas-lapack related statements in package.py
2016-09-21 12:27:59 -07:00
Todd Gamblin
6b6f868f2a Flake8 fixes. 2016-09-21 04:35:15 -07:00
Todd Gamblin
786ab114b7 Merge branch 'qt-osx' of git://github.com/mathstuf/spack into mathstuf-qt-osx 2016-09-21 04:32:03 -07:00
George Hartzell
51d869493a Add package for bedtools2 (#1572)
Add package for bedtools2, with support for v2.25.0 and v2.26.0.
2016-09-21 04:23:03 -07:00
George Hartzell
db0baaafe3 Add package for bamtools (#1571)
bamtools provides a C++ API & command-line toolkit for working with BAM
data.
2016-09-21 04:22:55 -07:00
Mayeul d'Avezac
3d1c92e22c Update espresso recipe to track change in spack internals (#1734) 2016-09-21 04:18:35 -07:00
Adam J. Stewart
cf925ddc97 Add missing build dependencies to hdf package (#1812) 2016-09-21 04:16:57 -07:00
Kelly Thompson
3d3614e522 Update to allow netlib-scalapack to build against netlib-lapack. (#1539) 2016-09-21 04:10:30 -07:00
Glenn Johnson
c1284a9046 Stop python from linking with system ncurses (#1672)
Python will look to link with libncursesw in preference to libncurses. Since
ncurses in spack is built without suffixes there is no libncursesw and
python will link to the system libncursesw for _curses.so and
_curses_panel.so, as well as libpanelw for _curses_panel.so.

This PR introduces a patch that simple removes the check for ncursesw in
setup.py and therefore sets `curses_library` to `ncurses`.
2016-09-21 04:02:28 -07:00
Glenn Johnson
851b58248d Build pkg-config files for ncurses (#1673) 2016-09-21 04:02:07 -07:00
Glenn Johnson
73012ec4c8 Rework libgd package (#1679)
* Added missing libtiff dependency
* added dependency on fontconfig
* Added version 2.2.3
* use autotools rather than cmake

The cmake build was not producing a complete install.
* There was no versioning of the installed libraries.
* gdlib-config was missing
* pkgconfig directory was missing

These problems do not happen when built with autotools.
2016-09-21 01:56:20 -07:00
Todd Gamblin
ae6252ca5f Merge branch 'efischer/160914-FixBinutils226Question' of git://github.com/citibeth/spack into bugfix/efischer-160914-FixBinutils226Question 2016-09-21 01:45:38 -07:00
Axel Huebl
d3e04b3daf Close #1683 Apply ADIOS 1.10.0 Patch (HDF5 1.10+) (#1699)
* Close #1683 Apply ADIOS 1.10.0 Patch

Also correct version dependencies and comments.

* Clean Up ADIOS

- add develop
- simplify HDF5 options (parallel only)
- remove optional netCDF (not fully v4)
2016-09-21 00:55:54 -07:00
Massimiliano Culpo
3254d2f8f9 cp2k : added dependencies (#1724)
* wannier90 : added package (#24)

* wannier90 : added package

* cp2k : added dependency on wannier90

* elpa : updated package, added cp2k dependency (#26)

Conflicts:
	var/spack/repos/builtin/packages/elpa/package.py
2016-09-21 00:53:06 -07:00
Alfredo Adolfo Gimenez
02307cf7ce Set JAVA_HOME on module load and on dependent installs. (#1716)
* Set JAVA_HOME on module load and on dependent installs.

* Include environment setup from dependencies in dependee module (#1714)
2016-09-21 00:52:09 -07:00
Massimiliano Culpo
1cc48bf7d7 grackle : added package (#1725)
Modifications :

* grackle : added package
* grackle : added version 2.2
2016-09-21 00:51:49 -07:00
Erik Schnetter
3c7ea3000a Wrap yt package (#1751)
yt is a python package for analyzing and visualizing volumetric, multi-resolution data from astrophysical simulations, radio telescopes, and a burgeoning interdisciplinary community.
2016-09-21 00:37:46 -07:00
Sergey Kosukhin
746495896c Qt library: added variant to enable/disable compilation of examples (#1763) 2016-09-21 00:25:14 -07:00
Patrick Gartung
e6dc448f18 Compiling python with gnu c++ on macos fails with toolboxglue enabled. 2016-09-20 23:34:15 -07:00
Gregory L. Lee
25ee9456f5 added STAT release 3.0.0 2016-09-20 16:09:31 -07:00
Erik Schnetter
ef1f441424 Julia: Add version 0.5.0 (#1809) 2016-09-20 12:40:58 -07:00
Adam J. Stewart
db483e77e4 Remove url_for_version as it breaks spack info (#1503) 2016-09-20 10:17:51 -07:00
Joseph Ciurej
7f9e89eb53 Update Package: Git-LFS (#1769)
* Fixed a few small bugs in the 'git-lfs' install script.

* Fixed a bug in the '(go|go-bootstrap)@1.4.2+test' install scripts.

* Fixing a minor style issue in the 'git-lfs' install script.
2016-09-20 10:08:25 -07:00
Erik Schnetter
00bac8f294 PETSc: Explicitly point to cpp when configuring (#1807)
I encountered an HPC system where PETSc's configure stage does not find a valid `cpp` (C preprocessor). Explicitly pointing to Spack's `cpp` wrapper resolves the problem.
2016-09-20 10:05:57 -07:00
Adam J. Stewart
f180d748be Remove lingering boilerplate FIXMEs (#1756) 2016-09-20 08:01:55 -07:00
Joseph Ciurej
2cbae1d691 Update Package: Metis (#1783)
* Fixed a bug that was causing post-install METIS tests to fail.

* Improved the patching procedure used in the 'metis' install script.

* Enabled patch skipping for the 'metis' and 'parmetis' packages.

* Fixed some minor style issues in the 'parmetis' package.

* Improved the 'metis' test fix and added 'run_tests' support.
2016-09-20 02:48:31 -07:00
Robert D. French
5c11fe88df Add UberFTP utility (#1780) 2016-09-20 02:47:10 -07:00
Denis Davydov
1565a643bd dealii: add 8.4.2 (#1782) 2016-09-20 02:46:57 -07:00
Bruno Turcksin
20fcd3f1dd Add Python support to gdb. (#1790) 2016-09-20 02:46:30 -07:00
Joseph Ciurej
e73a7c80bf Update Package : Zoltan (#1793)
* Refactored and reorganized the 'zoltan' install script.

* Fixed a few bugs with the '+mpi' and '+fortan' variants of 'zoltan'.

* Reintroduced and improved the '+shared' variant for the 'zoltan' package.

* Improved compatibility with different MPI providers for 'zoltan'.
2016-09-20 02:46:13 -07:00
Tom Merrick
d71f8dcab5 samtools could not find the ncurses library (#1785) 2016-09-20 02:27:19 -07:00
Massimiliano Culpo
ea446c0f0e lmod : added support for the creation of hierarchical lua module files (#1723)
Includes :
- treatment of a generic hierarchy (i.e. lapack + mpi + compiler)
- possibility to specify which compilers are to be considered Core
- correct treatment of the 'family' directive
- unit tests for most new features
2016-09-20 02:26:25 -07:00
Erik Schnetter
bd6aac3102 Update Julia to 0.4.7 (#1805) 2016-09-20 02:16:25 -07:00
Erik Schnetter
bddb15ef4c Make VisIt build again (#1762)
- add new version 2.10.3
- explicitly require hdf5 variant ~mpi, since we don't know how to build with mpicc
- explicitly disable glew since it may not be installed
2016-09-20 02:15:58 -07:00
Erik Schnetter
70424b511e Work around cmake problems in VTK (#1761)
The cmake scripts can't handle the semicolons in gcc's version output. Filter them out before detecting the version.
2016-09-20 02:15:37 -07:00
Erik Schnetter
2a558e9d7a Tighten HDF5 version requirements for Silo (#1760) 2016-09-20 02:14:55 -07:00
Erik Schnetter
8426b65592 Make cmake @2.8 build again (#1759) 2016-09-20 02:14:37 -07:00
Erik Schnetter
140f1773cf Update hwloc to 1.11.4 (#1752) 2016-09-20 02:14:17 -07:00
Erik Schnetter
682ac5194e Declare py-beautifulsoup4's dependency on py-setuptools (#1748) 2016-09-20 02:14:06 -07:00
Erik Schnetter
48c87da07b Update curl to 7.50.3 (#1747)
* Update curl to 7.50.2
* Update curl to 7.50.3
2016-09-20 02:13:54 -07:00
Erik Schnetter
bbdc429db3 Update OpenMPI to 2.0.1 (#1721) 2016-09-20 02:13:40 -07:00
Erik Schnetter
2e490050f6 Update OpenBLAS to 0.2.19 (#1702) 2016-09-20 02:13:25 -07:00
Erik Schnetter
ebde2a101e Reorder versions in openssl (#1601) 2016-09-20 02:13:14 -07:00
Erik Schnetter
ee2ddaa7cc Update mbedtls to 2.3.0 (#1600) 2016-09-20 02:13:03 -07:00
Erik Schnetter
6848752fed Update cereal to 1.2.1 (#1599) 2016-09-20 02:12:52 -07:00
Erik Schnetter
dfad4a0abc Update binutils to 2.27 (#1598) 2016-09-20 02:12:40 -07:00
Michael Kuhn
7fd44a983d Update mvapich2 to 2.2 (#1775) 2016-09-15 10:42:57 +08:00
Elizabeth Fischer
2a823fbdfd [RtM] Added py-proj/package.py (RtM = Ready to Merge) (#717)
* Added py-proj package

* Added bug-fix patched version to the package.

* Removed dependency of py-proj on proj.

* py-proj: Added missing dependency

* py-proj: Removed versions from forked repos, now that necessary bug fixes have been merged into the main repo.

* Update package.py

Added a blank line that Travis wanted.

* 1. Added copyright
2. Used setup_py
3. Added type='build' for dependencies.
2016-09-15 10:35:57 +08:00
Elizabeth Fischer
a954d0976a Put back full-length URL. 2016-09-14 16:52:33 -04:00
Elizabeth Fischer
595ec7e034 Bug fix capturing which packages work with which binutils. 2016-09-14 16:50:17 -04:00
Elizabeth Fischer
4a1df7e0b2 Resolved issues of py-pillow, py-scipy and binutils dependencies. Resolves #1506
py-pillow: Remove version dependency on binutils@2.25.  In tests, it works just fine with binutils@2.26.

Fixed flake8 issues.
2016-09-14 10:56:08 -04:00
Erik Schnetter
1d09d1a4e2 Update netlib-lapack to 3.6.1 (#1597) 2016-09-09 13:50:37 -07:00
Erik Schnetter
567d67fae2 Add libiconv dependency for git (#1468)
Also remove "--without-pcre" flag that git does not understand any more.
2016-09-09 12:57:49 -07:00
Erik Schnetter
8249108cc6 Qthreads: Switch back to using tarball to get released version (#1739)
* Qthreads: Switch back to using tarball for download

* Don't require autotools any more

* Re-enable autotools

* Remove autotools again

* Use .tar.bz tarball; remove outdated code
2016-09-09 06:56:11 -07:00
Erik Schnetter
e06a0271a4 New package h5hut (#1737)
* New package h5hut -- High-Performance I/O Library for Particle-based Simulations

* Set up MPI compilers

* Add version 1.8.12 to HDF5

* Correct Sphinx error
2016-09-08 13:27:47 -07:00
Erik Schnetter
ff7c0335ff Declare fontconfig dependency on pkg-config (#1686) 2016-09-08 12:15:42 -07:00
Todd Gamblin
3d3d65f3f7 Merge pull request #1553 from adamjstewart/fixes/netcdf-hdf5
Fix NetCDF/HDF5 dependency resolution problems
2016-09-08 11:58:46 -07:00
Adam J. Stewart
0586b388df Add latest version of libpng, ncview depends on libpng (#1502)
* Add latest version of libpng

* ncview depends on libpng
2016-09-08 09:02:10 -07:00
Ben Boeckel
77611913c6 qt: only pass -qt-xcb on non-OS X 2016-09-06 16:53:38 -04:00
Ben Boeckel
112122bc28 qt: progress on qt5.5 on osx
Qt5.5 searches for the SDK itself and just ignores environment variables
like CC and CXX, skipping the spack wrappers.
2016-09-06 16:01:16 -04:00
Ben Boeckel
fca26c0b79 qt: make -no-phonon specific to qt4 2016-09-06 16:00:22 -04:00
Ben Boeckel
67462ca65a qt: fix pcre header conflict in javascriptcore 2016-09-06 16:00:21 -04:00
Ben Boeckel
4687860885 qt: force the 10.9 SDK on macos
The 10.11 SDK fails to configure.
2016-09-06 16:00:21 -04:00
Ben Boeckel
a05a6456d5 glib: build on macos 2016-09-06 16:00:21 -04:00
Ben Boeckel
b810a113af pixman: disable mmx 2016-09-06 16:00:21 -04:00
Ben Boeckel
3df1eeccb9 qt: setup the sdk and platform arguments 2016-09-06 16:00:21 -04:00
Ben Boeckel
71c357e485 qt: support building with 10.10+ SDKs 2016-09-06 16:00:21 -04:00
Ben Boeckel
aa9faceb03 qt: disable phonon support 2016-09-06 16:00:21 -04:00
Ben Boeckel
6075abfbdb qt: depend on icu4c 2016-09-06 16:00:21 -04:00
Ben Boeckel
a9bfd88248 qt: depend on OpenSSL
OS X doesn't come with an OpenSSL supported by Qt4.
2016-09-06 16:00:21 -04:00
Ben Boeckel
4c566617f7 qt: make libxcb a conditional dependency
OS X doesn't have X (usually).
2016-09-06 16:00:21 -04:00
Ben Boeckel
5ba1144515 qt: create a dbus variant 2016-09-06 16:00:20 -04:00
Ben Boeckel
4b471ecc6e qt: support detecting newer SDK paths 2016-09-06 15:59:46 -04:00
Robert D. French
ccfbfcc890 ITS XML Translation Tool (#1728) 2016-09-06 06:56:13 -07:00
Jeffrey Salmond
26d45bc106 fontconfig: add --disable-docs to configure (#1729) 2016-09-06 06:55:58 -07:00
Kelly Thompson
f0192edf0d For OpenMPI v 2+, add a configure option to provide C++ bindings. (#1730)
+ Starting with version 2.0, OpenMPI no longer provides C++ bindings by default
  (libmpi_cxx.so). Add a configure option to instruct the build to also build
  and install libmpi_cxx.so.
+ This MPI feature is needed by at least one spack package (moab).
2016-09-06 06:55:37 -07:00
alalazo
d39b666913 plumed : avoid linking with libgslcblas 2016-09-06 11:21:26 +02:00
alalazo
47f6a6d3cf Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases_rebase
Conflicts:
	lib/spack/spack/build_environment.py
	lib/spack/spack/package.py
	var/spack/repos/builtin/packages/astyle/package.py
	var/spack/repos/builtin/packages/lzo/package.py
	var/spack/repos/builtin/packages/openjpeg/package.py
	var/spack/repos/builtin/packages/swiftsim/package.py
2016-09-04 10:12:52 +02:00
Massimiliano Culpo
497bbb3ae3 added package : pexsi (#1550)
* pexsi : added package
* cp2k : added pexsi (works for gcc+openmpi with and without plumed)
2016-09-03 08:13:47 -07:00
becker33
fa310c825d Merge pull request #1704 from eschnett/eschnett/libiconf-gets
Make libiconv work with C11
2016-09-02 16:46:40 -07:00
becker33
6de191a926 Merge pull request #1708 from robertdfrench/globus-toolkit
Globus Toolkit
2016-09-02 15:31:34 -07:00
becker33
ea6143402f Merge pull request #1715 from alfredo-gimenez/bugfix/vim
Fix vim package.
2016-09-02 14:59:14 -07:00
Alfredo Gimenez
19102559f0 Add sbt (scala build tool) package 2016-09-02 14:15:20 -07:00
Alfredo Gimenez
817c120b1c Fix vim package 2016-09-02 14:09:46 -07:00
Erik Schnetter
d78d18c4bd Update OpenMPI description (#1705) 2016-09-02 10:57:35 -07:00
Jeffrey Salmond
5146c64dfc Fixes for the ImageMagick package. (#1709)
* add pango dependency

* add new package ghostscript-fonts & add to ImageMagick as dependency

also tell ImageMagick's configure where the font dir is!

* refactor to fix flake8

* add homepage to ghostscript-fonts

* use install_tree

* remove unneeded import
2016-09-02 10:41:35 -07:00
Erik Schnetter
c7bb523c8f Declare qthreads dependency on automake (#1711) 2016-09-02 10:34:07 -07:00
Robert.French
d876d9b778 Globus Toolkit 2016-09-02 16:04:26 +00:00
Erik Schnetter
9ceb3f6b49 Add two famous old versions of autoconf
These old versions are often used because their immediate successors are incompatible in some way.
2016-09-02 11:23:33 -04:00
Erik Schnetter
0bd63ce8be Make libiconv work with C11
C11 does not provide gets() any more, so we cannot reference it
2016-09-02 10:53:59 -04:00
Todd Gamblin
8d755c010d Merge pull request #1658 from LLNL/features/git-lfs
Add git-lfs package.
2016-09-01 11:58:18 -07:00
Erik Schnetter
932cd6fa19 Switch lzo download from https to http
lzo's download server does not present a valid certificate, so that downloads via https are failing. Spack's MD5 checksum still ensure a safe download.

Closes #1675.
2016-08-31 12:41:04 -04:00
Adam J. Stewart
1be6267149 Undo changes to trailing triple quotes in docstring 2016-08-30 16:28:55 -05:00
Adam J. Stewart
9b455e9254 Resolve new documentation issues that have cropped up 2016-08-30 15:58:22 -05:00
Adam J. Stewart
a0c8aca3a2 Remove py-mercurial, going with mercurial package instead 2016-08-30 15:35:58 -05:00
Adam J. Stewart
eb56744f4d Fix package docstrings, #1612 2016-08-30 15:29:50 -05:00
Adam J. Stewart
7f9d098c2f Add mercurial package, used as test dependency 2016-08-30 15:21:15 -05:00
Todd Gamblin
7e4c6afd91 Merge pull request #1412 from adamjstewart/features/cmake
Overhaul of CMake package and compression libraries
2016-08-30 12:18:56 -07:00
Todd Gamblin
abd1546d86 Merge pull request #1668 from ax3l/topic-pngwriter
PNGwriter: Add Spack Package
2016-08-30 10:21:27 -07:00
Axel Huebl
d2d2234def
HDF5 Dependency: Rewrite to Union
@adamjstewart
```
think you'll find that if you try running something like:
spack spec libsplash ^hdf5@1.8.15
It will complain that libsplash does not depend on hdf5.
This is a bug in Spack's dependency resolution. A workaround
for this is to tell it to always depend on hdf5.
```

@davydden
```
to expand on @adamjstewart comment, spack will make a union
of dependencies,
i.e. hdf5@1.8.6: + hdf5+mpi = hdf5:1.8.6:+mpi, that's why it works.
```

thank you for the hint!
2016-08-30 17:00:09 +02:00
Axel Huebl
03c4d65af1
PNGwriter: Add Spack Package
Adds a package for
[PNGwriter](https://github.com/pngwriter/pngwriter/),
a simple high-level C++ png API used in scientific projects.

```
PNGwriter is a very easy to use open source graphics library that
uses PNG as its output format. The interface has been designed to be
as simple and intuitive as possible. It supports plotting and reading
pixels in the RGB (red, green, blue), HSV (hue, saturation,
value/brightness) and CMYK (cyan, magenta, yellow, black) colour
spaces, basic shapes, scaling, bilinear interpolation, full TrueType
antialiased and rotated text support, bezier curves, opening existing
PNG images and more.
```

PNGwriter is a dependency for [PIConGPU](http://picongpu.hzdr.de),
an open-source, many-core, fully-relativistic particle-in-cell code
and further software developed at
[Helmholz-Zentrum Dresden - Rossendorf](https://www.hzdr.de).
2016-08-30 12:45:53 +02:00
Axel Huebl
3aaa077c9f
libSplash: Add Spack Package
Adds a package for
[libSplash](https://github.com/ComputationalRadiationPhysics/libSplash),
a high-level library around serial and parallel HDF5 for regular
grids and particle data sets.

```
libSplash aims at developing a HDF5-based I/O library for HPC
simulations. It is created as an easy-to-use frontend for the
standard HDF5 library with support for MPI processes in a cluster
environment. While the standard HDF5 library provides detailed
low-level control, libSplash simplifies tasks commonly found in
large-scale HPC simulations, such as iter- ative computations
and MPI distributed processes.
```

libSplash is a dependency for [PIConGPU](http://picongpu.hzdr.de),
an open-source, many-core, fully-relativistic particle-in-cell
code and further software developed at
[Helmholz-Zentrum Dresden - Rossendorf](https://www.hzdr.de).

libSplash builds in two versions, one without MPI writing
domain-decomposed posix-style HDF5 files per process and one
(default) with MPI and MPI-I/O ("parallel HDF5") support
aggregating into a single file per MPI communicator.

libSplash is used in conjunction with
[openPMD](http://openPMD.org), see also
[github.com/openPMD/](https://github.com/openPMD/).
2016-08-30 12:42:39 +02:00
Todd Gamblin
47bf7ecb2b Merge pull request #1652 from ax3l/topic-updateAdios110
Update ADIOS Package
2016-08-29 22:59:39 -07:00
Elizabeth Fischer
cf11c32720 libpciaccess: Changed libtool to a build dependency. (#1602) 2016-08-29 22:11:27 -07:00
Axel Huebl
0f40175524
Remove Space, Enable Parallel
- remove space before comma
- enable parallel build again (seems to work)
2016-08-30 02:02:48 +02:00
Axel Huebl
ecacce7e07
ADIOS: Use NetCDF Prefix from spec's 2016-08-30 00:51:44 +02:00
Gregory Lee
e32247e53a added qt-creator (#1659) 2016-08-29 15:45:16 -07:00
Axel Huebl
37f489886e
Defaults: MPI=True, Fortran=False
- ADIOS is mainly a parallel I/O library
- a Fortran compiler is non-standard in a minimal install
2016-08-30 00:14:29 +02:00
Axel Huebl
b33777fd2f
RM Outdated Comments, Versions & Code 2016-08-29 23:18:31 +02:00
Axel Huebl
88254a14a7
Always External MXML; type='build'
- always use `mxml` as an external dependency in spack
- declare `build`-only dependencies correctly
2016-08-29 23:01:20 +02:00
Axel Huebl
e1464ece55
ADIOS: disable parallel make 2016-08-29 19:06:22 +02:00
Robert D. French
a21d3d353b New URL scheme for newer (and older) PDTs (#1651) 2016-08-29 10:01:04 -07:00
Axel Huebl
f2eb1c93df
ADIOS: Run Autotools First 2016-08-29 18:42:07 +02:00
Robert D. French
4095eb2196 Ole' GNU nano; Actually ran flake8 (#1649) 2016-08-29 09:21:19 -07:00
Todd Gamblin
57033a62fa Merge pull request #1563 from adamjstewart/features/sphinx
Add all Sphinx dependencies
2016-08-29 09:08:46 -07:00
Axel Huebl
4bd863761a
Update ADIOS Package
This PR updates the ADIOS package.

**Changes:**

- add latest stable release `1.10.0`
- add previous versions (hashes)
- add default license header
- add build options (shamelessly taken from HDF5 package)
- add validation for excisting FC (as in HDF5) and make optional
- handle mxml dependency correctly (not required in 1.10.0+)
- add `CFLAGS=-fPIC` to build shared (python) libs in ADIOS' lib
- remove `-DMPICH_IGNORE_CXX_SEEK` since it is normally not required
- remove `MPICC/CXX?FC` since `--with-mpi` just performs well
- add transforms:
  - `zlib`: useful (optional) default
  - `szip`: optional (compile often broken)
- add transports that are not as performant as the `.bp` format:
  - `hdf5`: non-default
  - `netcdf`: non-default, close #1610
2016-08-29 17:16:15 +02:00
Todd Gamblin
31cab4bae2 Merge pull request #1619 from davydden/pkg/nwchem_macos_fix
nwchem: use basename for CC and FC
2016-08-29 06:51:14 -07:00
Denis Davydov
66ea42f8d7 nwchem: use basename for CC and FC 2016-08-29 15:15:23 +02:00
Todd Gamblin
f5c9a8c2ee Merge pull request #1650 from davydden/pkg/ape_octopus_comments
ape octopus: in-code comments
2016-08-29 06:02:19 -07:00
Denis Davydov
5333a799ea octopus: in-code comments to explain compiler flags 2016-08-29 08:45:28 +02:00
Denis Davydov
90070c317d ape: in-code comments to explain compiler flags 2016-08-29 08:45:15 +02:00
Todd Gamblin
a3f1ae8c4f Merge pull request #1041 from adamjstewart/features/matplotlib
Matplotlib Python package overhaul
2016-08-28 21:22:44 -07:00
Abhinav Bhatele
a9a29d207d add versions 2.2rc2 and 2.1 to the mvapich2 package (#1630) 2016-08-28 20:18:57 -07:00
Erik Schnetter
e119c32a9c Hot-fix for qthreads (#1632)
The download tarball for qthreads vanished. Install it from a git branch instead as temporary work-around.
2016-08-28 20:18:24 -07:00
Jeffrey Salmond
82808f944a New package: opencoarrays (#1633)
* opencoarrays: new package

* opencoarrays: remove tests from install due to (unimportant) failures in some configurations

* opencoarrays: fix flake8 errors
2016-08-28 20:17:22 -07:00
Todd Gamblin
ed365614f4 Add git-lfs package. 2016-08-28 19:27:59 -07:00
Robert D. French
974749aaf6 Provide mpi-less variant for nco (#1643) 2016-08-28 19:15:15 -07:00
Erik Schnetter
6acfcd82b1 Update Julia to 0.5 release branch; install some Julia package as well (#1637)
* Update Julia to 0.5 release branch; install some Julia package as well

* Add comments, correct flake8 error

* Correct flake8 error
2016-08-28 17:46:10 -07:00
Robert D. French
079d063c6d Variant for building cdo without mpi (#1638) 2016-08-28 17:43:54 -07:00
Erik Schnetter
db7c3d2de6 New package for the Mercurial (hg) version control system (#1644)
* New package "mercurial"

* Disable self-checks

The self-checks require subversion, which we don't want to require.
2016-08-28 17:31:15 -07:00
becker33
e73a1a4ec3 Merge pull request #1558 from mcfadden8/mmcfadden-features/gcc-pic-libraries
Added variant to gcc package to install PIC versions of libgfortran and libstdc++
2016-08-25 16:00:00 -07:00
Gregory Lee
77c24d4127 Merge pull request #1379 from LLNL/features/graphlib3
added stat 3.0 beta and added pygtk and dependent packages
2016-08-25 09:14:36 -07:00
Todd Gamblin
8170bcfcdd Merge pull request #1574 from ARCCA/plumed-push
Update plumed package to include optional modules
2016-08-25 02:45:33 -07:00
Andrew Williams
07e0da24c5 Reverted url to point to tarball rather than git tag 2016-08-25 10:21:56 +01:00
Todd Gamblin
22d2786940 Merge pull request #1580 from davydden/pkg/trilinos_url_fix
trilinos: switch to github url; fix missing py-numpy dependency
2016-08-25 02:10:05 -07:00
Kelly (KT) Thompson
2ddaabed25 + Boost: fix recipe for intel compilers.
This is the same patch provided by PR #550, but rebased against the current
develop branch. It also passes the flake8 checks.
2016-08-24 15:57:28 -06:00
Todd Gamblin
93cb2db531 Fix build dependency. 2016-08-24 14:10:12 -07:00
Todd Gamblin
a7e568b1d1 Merge branch 'eschnett/sympol' of git://github.com/eschnett/spack into eschnett-eschnett/sympol 2016-08-24 14:05:05 -07:00
Todd Gamblin
19bbe5e421 Merge pull request #1596 from eschnett/eschnett/git-update
Update git to 2.9.3
2016-08-24 14:03:04 -07:00
Todd Gamblin
86fe78f5f1 Merge pull request #1582 from eschnett/eschnett/gcc-update
Update gcc to @6.2.0
2016-08-24 14:02:54 -07:00
Adam J. Stewart
eace068788 Use self.run_tests for make check 2016-08-24 15:21:23 -05:00
Adam J. Stewart
70bb1f1707 Reduce number of variants, just use system or no-system libs 2016-08-24 14:39:05 -05:00
Todd Gamblin
e6bac6f208 Merge pull request #1613 from eschnett/eschnett/cmake-update
Update cmake to 3.6.1
2016-08-24 08:49:33 -07:00
Todd Gamblin
63859bf113 Merge pull request #1575 from davydden/pkg/nwchem
nwchem: add new package
2016-08-24 08:49:11 -07:00
Todd Gamblin
5cfa74801f Merge pull request #1565 from adamjstewart/features/fftw
Add latest version of fftw
2016-08-24 08:49:00 -07:00
Adam J. Stewart
5970b7a00a Only run tests if explicitly requested 2016-08-24 10:34:20 -05:00
Erik Schnetter
41750ce70d Update cmake to 3.6.1 2016-08-24 10:45:13 -04:00
Denis Davydov
d154f151aa py-cclib: new package 2016-08-24 16:26:35 +02:00
Denis Davydov
6d2d5806b5 nwchem: add python module 2016-08-24 13:40:02 +02:00
Denis Davydov
dae219d5c3 nwchem: add another patch 2016-08-23 22:24:16 +02:00
Denis Davydov
459b6eae11 nwchem: add another patch 2016-08-23 22:15:38 +02:00
Erik Schnetter
3194f2001b Update git to 2.9.3 2016-08-23 15:35:43 -04:00
Erik Schnetter
05f5ba4bf9 Correct flake8 errors 2016-08-23 14:57:29 -04:00
Erik Schnetter
73cae8d9c4 Implement review requests
- use two empty lines before `class`
- change version numbering scheme for packages, use `url_for_version` to make things work
- specify dependency types
- add comment about temporarily moved download location
- update two packages to newer versions
2016-08-23 13:52:28 -04:00
Denis Davydov
52ae0ea055 trilinos: use version.dashed 2016-08-23 18:48:17 +02:00
David Beckingsale
243d516bf0 Ensure RAJA builds out-of-source 2016-08-23 08:18:26 -07:00
Denis Davydov
6500ac80e4 nwchem: fix lapack detection 2016-08-23 16:46:40 +02:00
Erik Schnetter
a2692e4ef5 sympol: Add package 2016-08-23 10:41:08 -04:00
Erik Schnetter
bdc825fc3c cddlib: Point download url to a (more reliable) Fedora server 2016-08-23 09:59:56 -04:00
Erik Schnetter
64d3f87e60 Merge branch 'develop' into eschnett/sympol 2016-08-23 09:45:46 -04:00
Denis Davydov
7eb386e55e nwchem: add patches 2016-08-23 14:52:18 +02:00
Denis Davydov
5da9116c06 nwchem: add scalapack; extra steps for 32bit blas/lapack 2016-08-23 11:55:00 +02:00
Denis Davydov
aca8576de4 trilinos: switch to github url; fix missing py-numpy dependency 2016-08-23 10:50:08 +02:00
Todd Gamblin
e81f3daa28 Merge pull request #1519 from mathstuf/fix-deptypes
Fix deptypes
2016-08-22 21:40:25 -07:00
Erik Schnetter
7b49166f9b Update gcc to @6.2.0
Also add some missing older version.
Update download location to original GNU location.
2016-08-22 20:26:54 -04:00
Denis Davydov
a44beee172 nwchem: add new package 2016-08-23 02:22:44 +02:00
Andrew Williams
65abd279cd Renamed intelmpi as suggested 2016-08-22 13:44:21 +01:00
Andrew Williams
87d15212eb Cleaned branch to only include plumed package 2016-08-22 12:30:17 +01:00
Andrew Williams
226d4f04f3 Spelling tweaks and consistent quoting 2016-08-22 12:09:50 +01:00
Andrew Williams
5661afa315 Passed flake8 tests 2016-08-22 12:03:47 +01:00
Andrew Williams
0c8462723b Found upstream plumed package and modified this one to match 2016-08-22 11:24:03 +01:00
Erik Schnetter
78685addbb hdf5-blosc: Correct download url 2016-08-21 14:39:54 -04:00
Todd Gamblin
55b1182a4c Merge pull request #1554 from eschnett/eschnett/hdf5-blosc
hdf5-blosc: Remove commit id from version specification
2016-08-21 09:44:25 -07:00
Adam J. Stewart
d5903e4612 Flake8 2016-08-19 17:06:34 -05:00
Adam J. Stewart
f0f2c6c486 Add latest version of fftw 2016-08-19 17:05:14 -05:00
Gregory L. Lee
a177b9be8a updated stat 3.0.0b url 2016-08-19 13:11:21 -07:00
Adam J. Stewart
835b8f246e py-sphinx requires py-setuptools during runtime 2016-08-19 14:20:31 -05:00
Adam J. Stewart
d7873b5319 Swap lowercase for uppercase in URL 2016-08-19 14:00:50 -05:00
Adam J. Stewart
c1af0d3806 Fix binary conflicts during sphinx activation 2016-08-19 13:54:22 -05:00
Adam J. Stewart
d4e3699510 Add all Sphinx dependencies 2016-08-19 13:44:00 -05:00
Erik Schnetter
466da3afcc Remove commented-out outdated commit id 2016-08-19 11:52:40 -04:00
Andrew Williams
90e5ccd98c Cleaned up commented out code in intelmpi package 2016-08-19 15:01:46 +01:00
Andrew Williams
13f636ec68 Added required arguments to get plumed to build with intelmpi 2016-08-19 15:00:21 +01:00
Adam J. Stewart
28537ae7b7 Workaround until variant forwarding works properly 2016-08-18 14:40:21 -05:00
Stephen Herbein
3445a781eb py-cffi: set LDSHARED env so that rpath is set
py-cffi's .so was being built without the rpath being set.  distutils
looks at the LDSHARED for which compiler to use to build the final .so.
Since it was not set, distutils fell back to the system provided
compiler.  Setting it forces the shared library to be compiled with the
spack compiler (meaning that the rpath is set correctly).
2016-08-18 11:32:19 -07:00
Andrew Williams
6641f42417 Not compiling due to mpi error. Also getting this error from the command line so could be separate issue. Otherwise package definition first draft complete. 2016-08-18 13:19:36 +01:00
Erik Schnetter
296212d78d hdf5-blosc: Remove commit id from version specification
The respective commit seems to have vanished.
Now using the master branch without specifying a particular commit.
2016-08-17 16:36:33 -04:00
Adam J. Stewart
4d12c5455a Fix NetCDF/HDF5 dependency resolution problems 2016-08-17 13:03:56 -05:00
Marty McFadden
f4ec99ecb4 Added +piclibs variant for building PIC versions of libgfortran.a and libstdc++.a 2016-08-17 09:28:21 -07:00
Andrew Williams
b99e945e6d Added variants and dependencies to plumed but I'm getting an error when trying to resolve mpi to a valid virtual package 2016-08-17 15:43:59 +01:00
Elizabeth Fischer
a733e7e303 py-pathspec: New package
Related to Python unit testing.
2016-08-17 00:34:33 -04:00
becker33
7f57405eac Merge pull request #1531 from davydden/pkg/ape
ape: add new package
2016-08-16 10:52:27 -07:00
becker33
e8afbfbce7 Merge pull request #1530 from davydden/pkg/octopus
octopus: new package
2016-08-16 10:49:41 -07:00
Denis Davydov
5dcc0f7802 ape: add new package 2016-08-16 19:42:32 +02:00
Denis Davydov
9509c10064 octopus: new package 2016-08-16 19:38:38 +02:00
Gregory L. Lee
f182590aae added pkg-config to build deps of cairo and pixman 2016-08-15 15:17:53 -07:00
Gregory L. Lee
54ef9443d3 fix atk url_for_version 2016-08-15 13:51:54 -07:00
Gregory L. Lee
74dd7a36b5 allow parallel build of stat 2016-08-15 13:51:54 -07:00
Gregory L. Lee
749a4e78c7 gobject-introspection requires glib version 2.48.1 2016-08-15 13:51:54 -07:00
Gregory L. Lee
3df208efc0 stat and dependences package updates 2016-08-15 13:51:53 -07:00
Gregory L. Lee
69931996bf added dyninst patches for stat+dysect 2016-08-15 13:51:53 -07:00
Gregory L. Lee
f9cb21e886 flake 8 fixes for dyninst 2016-08-15 13:51:53 -07:00
Gregory L. Lee
0074ecd6fa dyninst package use spec.satisfies instead of @when 2016-08-15 13:51:52 -07:00
Gregory L. Lee
8b94937609 flake 8 fixes for stat and dependents
flake 8 fixes for dyninst

flake 8 fixes for dyninst

flake 8 fixes for dyninst
2016-08-15 13:50:39 -07:00
Gregory L. Lee
bd8aab00e4 updated stat and added pygtk and dependent packages 2016-08-15 13:48:58 -07:00
Andrew Williams
27793d97dc temp commit in current state 2016-08-15 16:16:00 +01:00
Ben Boeckel
9ec1c0e18e opencv: make py-numpy a nolink dependency 2016-08-15 10:47:00 -04:00
Ben Boeckel
042666eb7e go: mark git as also being a runtime dependency 2016-08-15 10:46:45 -04:00
Ben Boeckel
826732efec packages: mark builddeps as type='build'
Less sure about these.
2016-08-15 10:46:23 -04:00
Ben Boeckel
eb13cbe9bd r-datatable: fix nolink dependency 2016-08-15 10:46:05 -04:00
Ben Boeckel
0d17d90b29 packages: mark builddeps as type='build' 2016-08-15 10:45:19 -04:00
Andrew Williams
3edfa390f7 Basic package file for plumed and boilerplate for external intel mpi 2016-08-15 11:19:40 +01:00
Adam J. Stewart
bc64990bc6 Replace python('setup.py' with setup_py( 2016-08-12 12:16:48 -05:00
Todd Gamblin
e1c2ea5123 Merge pull request #1342 from adamjstewart/features/cgns
Add CGNS package
2016-08-12 09:19:07 -07:00
Adam J. Stewart
d4377c1293 Add Python 3.5 support, latest version of PySide 2016-08-12 09:59:38 -05:00
Adam J. Stewart
633e540a17 Use GitHub URL for ImageMagick 2016-08-11 14:13:33 -05:00
Adam J. Stewart
f147d64527 Rebase messed up flake8 2016-08-11 11:01:57 -05:00
Adam J. Stewart
04cee45ac9 Skip webengine until webkit support is added 2016-08-11 10:33:43 -05:00
Adam J. Stewart
2b0444b6f4 Latest version of pyside still has problems, add deps 2016-08-11 10:33:43 -05:00
Adam J. Stewart
b6fad65f52 Combine patch for all versions
Patch doesn't work with @when unless you specify a patch for every
version. When running `spack patch` for a version without a patch,
spack thinks that a patch exists, tries to apply it, but it doesn't
exist. Spack gets very confused.
2016-08-11 10:33:43 -05:00
Adam J. Stewart
1363b05e93 Add test dependencies 2016-08-11 10:33:43 -05:00
Adam J. Stewart
5cc76f7d84 Fix patch for py-pyside 1.2.4 2016-08-11 10:33:43 -05:00
Adam J. Stewart
59ce0c7514 Add patch to build qt 4 with GCC 6 2016-08-11 10:33:42 -05:00
Adam J. Stewart
ddf1879bed Remove glib dependency, causes problems with PCRE and JavaScript 2016-08-11 10:33:02 -05:00
Adam J. Stewart
90dd26397c Fix qt patch 2016-08-11 10:33:02 -05:00
Adam J. Stewart
7135299a66 Add latest version of pcre 2016-08-11 10:33:02 -05:00
Adam J. Stewart
ac15d5d619 Add patch for qt gamepad compilation problems 2016-08-11 10:33:01 -05:00
Adam J. Stewart
eac9a5905f Flake8 and url_for_version changes 2016-08-11 10:33:01 -05:00
Adam J. Stewart
80742b2647 Add latest version of qt 2016-08-11 10:30:31 -05:00
Adam J. Stewart
8a0824df09 Update matplotlibrc filtering for GUI backends 2016-08-11 10:28:35 -05:00
Adam J. Stewart
a388871083 Update ImageMagick to latest version 2016-08-11 10:28:35 -05:00
Adam J. Stewart
2b83ea30e7 Re-add ipython support 2016-08-11 10:28:35 -05:00
Adam J. Stewart
f56de63972 Fix cycler dependencies, update qhull version names 2016-08-11 10:28:35 -05:00
Adam J. Stewart
0b8a3ad8ad Flake8 2016-08-11 10:28:34 -05:00
Adam J. Stewart
aa6a6df640 Undo changes to GUI framework 2016-08-11 10:28:34 -05:00
Adam J. Stewart
e905ce16c9 Flake8 2016-08-11 10:28:34 -05:00
Adam J. Stewart
11e595089d Matplotlib overhaul 2016-08-11 10:28:33 -05:00
Adam J. Stewart
b47357d73c Add patch for Intel compilers 2016-08-11 10:22:47 -05:00
Adam J. Stewart
5fc20487e4 Flake8 and formatting changes 2016-08-11 10:22:47 -05:00
Adam J. Stewart
534e1cbf1b Some tests don't pass with Intel compilers 2016-08-11 10:20:08 -05:00
Adam J. Stewart
ee5e20dae3 Add dependencies to libarchive and cmake 2016-08-11 10:17:42 -05:00
Adam J. Stewart
58d7704060 Overhaul of compression libraries 2016-08-11 10:15:13 -05:00
Todd Gamblin
e6a122417a Merge pull request #1491 from eschnett/eschnett/curl
Update curl to 7.50.1
2016-08-11 03:04:07 -07:00
alalazo
f5433477b9 qa : flake8 issues 2016-08-11 09:08:00 +02:00
alalazo
b4b9ebe7d7 Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases
Conflicts:
	lib/spack/llnl/util/tty/log.py
	lib/spack/spack/__init__.py
	lib/spack/spack/cmd/install.py
	lib/spack/spack/cmd/setup.py
	lib/spack/spack/package.py
	var/spack/repos/builtin/packages/blitz/package.py
	var/spack/repos/builtin/packages/gmp/package.py
	var/spack/repos/builtin/packages/qhull/package.py
	var/spack/repos/builtin/packages/szip/package.py
2016-08-11 08:55:20 +02:00
Todd Gamblin
84e331c586 Remove unneeded noqa comments. 2016-08-10 16:33:39 -07:00
Todd Gamblin
240f1fd223 Spack packages now PEP8 compliant. 2016-08-10 16:33:39 -07:00
Erik Schnetter
158deae625 Update curl to 7.50.1 2016-08-10 13:51:57 -04:00
Matt Belhorn
2be065418b Openssl package should not require openssl (https) to obtain source. 2016-08-09 15:57:07 -04:00
alalazo
38dcd6bce9 qa : flake8 issues 2016-08-09 09:54:24 +02:00
alalazo
5362864cc9 plumed : fixed name clash on attribute 2016-08-09 09:24:36 +02:00
Massimiliano Culpo
15d9fb1879 plumed : adding dependents
* cp2k : added plumed
* gromacs : patched pme load balancing
* gromacs : added plumed
2016-08-09 09:23:53 +02:00
becker33
3ea1325620 Merge pull request #1345 from hartzell/feature/add-perl-dependency-to-git
Add depends_on('perl'), depends_on('pcre') to git package
2016-08-08 09:44:50 -07:00
Todd Gamblin
dd30066feb Merge pull request #1449 from hartzell/feature/add-package-for-prank
Add package for prank and supporting tools
2016-08-07 23:43:40 -07:00
Todd Gamblin
e65a8b6a9a Merge pull request #1463 from davydden/pkg/opium
opium: add new package
2016-08-07 15:56:27 -07:00
Todd Gamblin
8121ac2c27 Merge pull request #1464 from hartzell/feature/update-lmod
No need to patch Lmod after 6.4.4
2016-08-07 15:55:16 -07:00
Todd Gamblin
93f5a750cb Merge pull request #1465 from glennpj/pango_url
Add list_url to pango package
2016-08-07 15:55:04 -07:00
Todd Gamblin
281f6f18e1 Merge pull request #1466 from pramodk/develop
PDT should download full installer package
2016-08-07 15:54:50 -07:00
Denis Davydov
db87a9d3ce tar: fix 1.28 on macOS; add 1.29 (#1462) 2016-08-07 15:54:01 -07:00
Adam J. Stewart
d7329d7bc2 Fix erroneously stripped trailing whitespace in patch (#1467) 2016-08-07 15:53:25 -07:00
Pramod Kumbhar
e9edfec0ec PDT should download full installer package pdtoolkit-X.tar.gz (default pdt-X.tar.gz is only for x86 and cray) 2016-08-07 01:14:26 +02:00
Glenn Johnson
2ad21e7070 Add list_url to pango package
Added a `list_url` so the updated pango tar file can be retrieved.
2016-08-06 18:12:47 -05:00
George Hartzell
09d96bef9f No need to patch Lmod after 6.4.4
The Lmod author changed the src so that it uses the tclsh (and shared
libraries) discovered at configure time.  He did it differently that I
did in this patch, but he changes solve our problem too, so...
2016-08-06 17:39:05 -04:00
George Hartzell
9ebbde0e01 Make configure use our gettext library
The configure script needs extra encouragement to link against our
gettext/libintl library.
2016-08-06 16:28:47 -04:00
George Hartzell
1de5817b58 Clean up rebase problems
My rebase duplicated the depends_on('zlib') and dropped the --with-curl
from the configure.

This fixes those.
2016-08-06 16:28:47 -04:00
George Hartzell
f699d7c08e [Whitespace] Gather the depends_on's together. 2016-08-06 16:28:47 -04:00
George Hartzell
152fa33a55 Call configure --with-libpcre=... to use our pcre
An earlier commit claimed that this package depends_on('pcre') but I
didn't fix the call to configure that enabled it.

This fixes that.
2016-08-06 16:28:47 -04:00
George Hartzell
3cf2fd40a8 Enable depends_on('pcre') also
While I have the patient on the operating table, @adamjstewart asked
me to uncomment and test the depends_on('pcre').

Did it and it Works For Me(tm).
2016-08-06 16:28:47 -04:00
George Hartzell
653905e3a2 Add depends_on('perl') to git package
This commit changes the git package to depend_on('perl').  The system
perl is not always sufficient to install git (e.g. a CentOS7 system with
the development tools group installed has perl but not the
ExtUtils::MakeMaker package that git needs) and one can't always update
the system's perl.

This PR depends_on PR #1339, which adds a perl package to spack.
2016-08-06 16:28:47 -04:00
George Hartzell
f800708ef3 Switch to using *std_cmake_args 2016-08-06 16:27:40 -04:00
George Hartzell
6a62a6b693 Flake8 whitespace cleanup 2016-08-06 16:27:40 -04:00
George Hartzell
a07a0ef54b Add Bio++ tool suite and supporting libs
Add the Bio++ suite and its supporting libraries.
2016-08-06 16:27:40 -04:00
George Hartzell
3c81bb44ba Add package for mafft 2016-08-06 16:27:40 -04:00
George Hartzell
e0db1f0268 Add package for exonerate 2016-08-06 16:27:40 -04:00
George Hartzell
9e16902397 Fix name of bpp-suite (missing -...) 2016-08-06 16:27:40 -04:00
George Hartzell
63592096c5 Add package for prank 2016-08-06 16:27:40 -04:00
Denis Davydov
4983ebcf7c opium: add new package 2016-08-06 21:35:52 +02:00
becker33
d3f115933e Merge pull request #1451 from hartzell/feature/add-package-for-fastx_toolkit
Add package for fastx toolkit
2016-08-05 15:09:46 -07:00
becker33
18d155e713 Merge pull request #1452 from hartzell/feature/add-package-for-samtools
Add package for samtools
2016-08-05 15:09:41 -07:00
George Hartzell
a6afaeb974 Remove lingering FIXME commentary 2016-08-05 17:51:24 -04:00
George Hartzell
769408130a Samtools depends on htslib from 1.3.1 onward
Samtools used to (before 1.3.1) include it's own copy of htslib.  Going
forward, it needs to use the standalone htslib.
2016-08-05 17:47:11 -04:00
becker33
8e20a14945 Merge pull request #1453 from hartzell/feature/add-package-for-seqtk
Add package for seqtk
2016-08-05 10:25:19 -07:00
becker33
f403f256ca Merge pull request #1450 from hartzell/feature/add-package-for-bwa
Add package for bwa
2016-08-05 10:21:10 -07:00
becker33
594a6710ed Merge pull request #1442 from suraia/update-scorep-2.0
Update Score-P to 2.0

Most likely this can be generalized to link against older versions of dependencies, but it looks good for now.
2016-08-05 08:57:25 -07:00
George Hartzell
d6dedee6ff Flake8 cleanup 2016-08-04 15:23:04 -04:00
Bruno Turcksin
0c02ee86a7 Add Trilinos 12.6.4 (#1447) 2016-08-04 11:29:10 -07:00
George Hartzell
e12d7aadda Add package for seqtk
Seqtk is a tool for working with fast[aq] files.
2016-08-04 14:18:03 -04:00
George Hartzell
fd11db92e1 Add package for bcftools 2016-08-04 14:18:03 -04:00
George Hartzell
ba0577dc96 Update samtools to support v1.3.1
Update the samtools package to support v1.3.1, which
- now uses configure script; and
- now depends on external htslib package.

The dependency on mpc seems to have been bogus, it's never linked in,
nor is it mentioned in the source tree.  I *do* have a version in
/usr/lib64, but ldd does not sure it being linked in either....

By depending on 'ncurses' I can do away with the need for the patch.
2016-08-04 14:18:03 -04:00
George Hartzell
ef1369c365 Add package for htslib
Htslib was pulled out of samtools and made into a standalone thing.
This commit adds a packag for it, in support of the samtools package.
2016-08-04 14:18:03 -04:00
George Hartzell
e17862c421 Add package for fastx toolkit
Tools for working with FASTA/FASTQ files.
2016-08-04 14:18:02 -04:00
George Hartzell
d5bb2955b1 Add package for libgtextutils
Gordon's Text utils Library, in support of fastx toolkit.
2016-08-04 14:18:02 -04:00
George Hartzell
d4274b32f2 Make flake8 happy (long lines) 2016-08-04 14:18:01 -04:00
Michael Kuhn
d7665a63e3 flake8 fixes 2016-08-04 19:04:48 +02:00
becker33
1ac1cc3d2c Merge pull request #1437 from jgalarowicz/update-xercesc
Update the version of xerces-c, where the developers remove the old v…
2016-08-04 09:00:36 -07:00
becker33
3c6f6fc811 Merge pull request #1438 from jgalarowicz/update-libmonitor
Update libmonitor to use its new github location, it does not exist w…
2016-08-04 08:59:35 -07:00
becker33
cabcdf0ec9 Merge pull request #1443 from davydden/pkg/dealii_python
dealii: add optional python bindings
2016-08-04 08:43:36 -07:00
becker33
fcc8b1d3e4 Merge pull request #1431 from hartzell/feature/add-package-for-unison
Add package for unison (and ocaml)
2016-08-04 08:41:45 -07:00
Denis Davydov
af8741c23c dealii: add optional python bindings 2016-08-04 16:11:14 +02:00
Michael Kuhn
584e5506f2 Update Score-P to 2.0 2016-08-04 14:24:25 +02:00
Todd Gamblin
b7fa2c4e21 Fix #1429: Remove git dep from gettext; break circular dependency.
- It's not really a circular dependency -- git is a run dependency of gettext

- We can revert this change when Spack is smart enough to make git a run
  dependency and build it.
2016-08-03 21:53:53 -07:00
Jim Galarowicz
2e1dbd0697 Fix flake8 errors for: Update libmonitor to use its new github location, it does not exist where the package file now points to. 2016-08-03 21:32:15 -05:00
Jim Galarowicz
e69423a154 Fix flake8 errors for Update the version of xerces-c, where the developers remove the old version, so there is no fallback. 2016-08-03 21:28:56 -05:00
Jim Galarowicz
e68b7d8c63 Update libmonitor to use its new github location, it does not exist where the package file now points to. 2016-08-03 21:08:48 -05:00
Jim Galarowicz
638f779841 Update the version of xerces-c, where the developers remove the old version, so there is no fallback. 2016-08-03 21:04:17 -05:00
George Hartzell
43371c31a2 Flake8 cleanup 2016-08-03 16:51:53 -04:00
Todd Gamblin
dce105d16f Merge pull request #1382 from KineticTheory/gktplus3-deps
GTK+3: Provide updates to package dependencies.
2016-08-03 13:45:18 -07:00
George Hartzell
4acf6d76bf Add package for unison
Add package for unison (the file synchronizer).

Needs the ocaml compiler to build.
2016-08-03 16:41:31 -04:00
George Hartzell
a7bfaa3797 Add package for ocaml compiler
Installs the ocaml compiler.
2016-08-03 16:41:31 -04:00
Kelly (KT) Thompson
7c46a4c0e4 Provide minor updates after code review
+ Always depend on the gettext package. This simplifies the logic and I no
  longer need to 'import sys'
+ Only apply the patch for the older version of glib.
2016-08-03 13:26:02 -06:00
becker33
3e6ebd577f Merge pull request #1378 from LLNL/bugfix/gh-1324-intel-parallel-studio
Bugfix/gh 1324 intel parallel studio
2016-08-03 10:46:40 -07:00
becker33
353726f08f Merge pull request #1156 from adamjstewart/features/py-meep
Add py-meep package and dependencies

Merging to add the gettext support, will submit a separate issue for the LD_LIBRARY_PATH issue with MPI and py-meep
2016-08-03 10:07:05 -07:00
becker33
b9195b415a Merge pull request #1420 from epfl-scitas/packages/plumed
plumed : added package
2016-08-03 08:36:31 -07:00
alalazo
2f1c000f62 qa : flake8 issues 2016-08-03 08:26:58 +02:00
Kelly (KT) Thompson
d7d12aa2dc One more formatting change to make flake8 happy. 2016-08-02 19:05:48 -06:00
becker33
48997cffa1 Merge pull request #1233 from hartzell/add-nextflow
First cut package for nextflow, has issues
2016-08-02 11:52:19 -07:00
Denis Davydov
f90692cf81 arpack-ng: fix blas/lapack libraries 2016-08-02 20:27:34 +02:00
becker33
b5a117c923 Merge pull request #1366 from hartzell/feature/add-package-for-ack
Add package for ack
2016-08-02 10:11:11 -07:00
becker33
1534a115bd Merge pull request #1421 from hartzell/feature/add-package-for-texlive
Add package for texlive
2016-08-02 10:10:43 -07:00
becker33
a03a35565e Merge pull request #1339 from hartzell/features/add-perl
Add perl package
2016-08-02 10:10:04 -07:00
George Hartzell
fa70a837d4 Remove accidentally committed cabal-install bits 2016-08-02 13:00:47 -04:00
becker33
91004158c6 Merge pull request #1243 from davydden/pkg/atlas_urls
atlas: fix urls and shared libs
2016-08-02 09:59:05 -07:00
becker33
3f26bbc8b3 Merge pull request #864 from davydden/kdiff3
kdiff3: initial version of the package
2016-08-02 09:35:00 -07:00
becker33
a3322fab0a Merge pull request #1360 from glennpj/pysetuptoolsdep
Add py-setuptools dependencies to packages
2016-08-02 09:33:40 -07:00
becker33
21158195fb Merge pull request #1354 from paulhopkins/bugfix/preferred_variants_do_not_recognise_-variant
Bugfix/preferred variants do not recognise  -variant
2016-08-02 09:15:06 -07:00
George Hartzell
74a181febc Remove local copy of cpanm installer
This is handled as a resource in the package now.
2016-08-02 12:13:24 -04:00
George Hartzell
4c8672ed1f Add previous versions back into package
Following the advice of @glennpj, added the old versions back into the
packages.

I can install the current packages and the previous packages.
2016-08-02 11:45:16 -04:00
George Hartzell
c77425bb22 Remove useless def unpack
Before I learned that I was stumbling over a real but (#1308), I thought
I needed to arrange for the fetcher to skip the unpack step.

This commit removes the useful `def unpack`.
2016-08-02 11:32:19 -04:00
George Hartzell
a6605d842b Flake8 cleanup. 2016-08-02 11:25:03 -04:00
George Hartzell
f2f5f6c279 Touch up variant comment 2016-08-02 11:18:50 -04:00
George Hartzell
c994565c62 Use "resource" machinery to manage cpanm tarball
Use the resource machinery to fetch/cache/unpack/... the App::cpanminus
tarball.

- this hardcodes the version, I can't figure out how to use a variant to
  hold/set the value and access it in the resource().
- change up the install to use the `with working_dir()` meme.
2016-08-02 11:16:46 -04:00
George Hartzell
1b9becc541 Add the std spack header to perl/package.py
Stole the example header from antlr/package.py, included it at the top
of perl/package.py.
2016-08-02 11:16:46 -04:00
George Hartzell
08ff7b65af Make running perl's tests conditional
Make running perl's tests conditional, one must now specify the
`--run-tests` flag to the `spack install` command in order to run the
tests.

On one system (8 core, 16GB Digital Ocean Droplet), installing without
tests takes 3 minutes, with tests takes 16 minutes.
2016-08-02 11:16:46 -04:00
George Hartzell
4d72e0fb9d Make the cpanm version a variant
Rather than hard-coding the verison of `cpanm` that's [optionally]
installed into the core, make it a variant with a default value of
'1.7042'.

Also discovered that `prefix + 'bin'` is the same as `prefix.bin`, so
embetter that bit of code.
2016-08-02 11:16:46 -04:00
George Hartzell
a5a4525bed Add perl package
Add perl package, based on [work by
justintoo](https://github.com/LLNL/spack/pull/105).  He had too many
things pulled into that pull request, this just adds a perl package.

Support the current releases on the past three minor branches.

Run perl's tests before installing.

Install cpanm into the core (makes building on top of this perl *much*
simpler).  Controlled by a variant.
2016-08-02 11:16:46 -04:00
George Hartzell
949621eb7f Add package for texlive 2016-08-02 11:15:42 -04:00
George Hartzell
857a03c127 Ack should depends_on('perl')
Add a depends_on('perl') and rewrite the script's `#!` line to refer to
that Perl's `perl` executable.
2016-08-02 11:11:05 -04:00
George Hartzell
114da813a3 Remove unnecessary imports.
Now that it's sporting a cleaner install method, these imports are
unnecessary.
2016-08-02 11:11:05 -04:00
George Hartzell
bf467c5df3 Remove override of unpack(self)
I cargo culted that from my *nextflow* package.  I [thought I] needed it
to work around Spack trying to use tar to unpack something that was
neither a tar ball nor unpackable.

This package works fine without it.  In retrospect, the error that I was
seeing in the *nextflow* package was probably this problem #1308.
2016-08-02 11:11:05 -04:00
George Hartzell
6c3623422f Use cleaner mech to install script
Use @adamjstewart's nicer bit of python code in the
install method.
2016-08-02 11:11:05 -04:00
George Hartzell
63121a0c49 Add package for ack
Add a package for [ack](http://beyondgrep.com/install/).  Simply install
the fatpacked script.

It uses '#!/usr/bin/env perl' and it very much not choosy about what
perl it needs.  For now just trust that there's one available, perhaps
someday we can/should uncomment the depends_on('perl').

Follows the methodolgy I used in nextflow.  Has the same
uninstall/install problem that nextflow has, there is an issue in
progress for that: https://github.com/LLNL/spack/issues/1308.

Tested on CentOS7.
2016-08-02 11:11:05 -04:00
George Hartzell
12d1263980 Update several R packages (r-shiny prereqs)
r-jsonlite 0.0.21 -> 1.0
r-mime     0.4    -> 0.5
rcpp       0.12.5 -> 0.12.6

CRAN is funny.  The older versions of these packages are still available
in package specific directories but the current version is not there, so
I don't see any way to make the older versions work.
2016-08-02 11:10:41 -04:00
George Hartzell
6f332c7e4c Fix whitespace, make flake8 happ{y,ier}. 2016-08-02 11:10:12 -04:00
George Hartzell
bfcec69630 Add standard header, use spack helpers
Added the standard header (stolen from R).

Touched up the install to use set_executable rather than doing it
myself.
2016-08-02 11:10:12 -04:00
George Hartzell
4373a2b629 First cut package for nextflow, has issues
This is my first cut at a package to support nextflow.  It's also my
first package.  It works, but has issues.  I'm going to submit a pull
request and get some coaching on how to deal with it.

One issue particular: if I install, then uninstall, then try to install
again (which uses the cached copy of the "distribution file"), it
explodes.
2016-08-02 11:10:12 -04:00
Glenn Johnson
a57d94af03 Fix flake8 issues. 2016-08-02 09:53:57 -05:00
Denis Davydov
a1703bf70d kdiff3: add license block 2016-08-02 16:37:14 +02:00
Gilles Fourestey
dea7bbb4a0 added plumed
* plumed : first version
* plumed : added dependencies and docs
2016-08-02 15:06:46 +02:00
Denis Davydov
565bd5f51e atlas: revert to lapack 3.5.0 2016-08-02 13:52:32 +02:00
Denis Davydov
bef7e2645a atlas: flake8 fixes 2016-08-02 13:52:32 +02:00
Denis Davydov
f6a4a6b00f atlas: add install_test 2016-08-02 13:52:32 +02:00
Denis Davydov
0c0b37800d atlas: set (blas|lapack)_shared_lib 2016-08-02 13:52:32 +02:00
Denis Davydov
4ecf481337 atlas: fix shared libs; set compilers 2016-08-02 13:52:32 +02:00
Denis Davydov
6f7e12d49b atlas: fix urls and use lapack 3.6.0 2016-08-02 13:52:32 +02:00
Denis Davydov
0aa513ad70 libxau: mark pkg-config as build-type dependency 2016-08-02 13:50:46 +02:00
Denis Davydov
450c750214 kdiff3: initial version of the package 2016-08-02 13:49:40 +02:00
Denis Davydov
a4e59c2758 libxau: add missing dependency 2016-08-02 13:49:40 +02:00
Kelly (KT) Thompson
9433e84776 Formatting changes for flake8. 2016-08-01 22:54:51 -06:00
Kelly (KT) Thompson
17f0eb5148 Provide correct download urls and additional dependencies. 2016-08-01 22:10:54 -06:00
ba11f19efc Merge remote-tracking branch 'upstream/develop' into gktplus3-deps 2016-08-01 20:50:28 -06:00
becker33
b892cebe8a Merge pull request #1343 from glennpj/r_unfilter
R extension dependencies with compiler wrapper
2016-08-01 13:51:13 -07:00
becker33
e861e35acf Merge pull request #1234 from mwilliammyers/package-opencv
Update opencv package
2016-08-01 13:44:31 -07:00
becker33
1847aa035d Merge pull request #1348 from glennpj/rcurl
r-curl update and changed remote archive
2016-08-01 13:38:38 -07:00
becker33
94238eebfa Merge pull request #1381 from davydden/pkg/mkl_linux
MKL linux fixes
2016-08-01 13:36:10 -07:00
becker33
dc9fcea989 Merge pull request #1365 from hartzell/feature/add-package-for-tree
Add package for tree
2016-08-01 13:21:09 -07:00
becker33
15514792d5 Merge pull request #1374 from hartzell/bug/fix-jdk-import-of-distutils
Bug: fix jdk package's use of distutils
2016-08-01 13:20:44 -07:00
becker33
851bc506e4 Merge pull request #1367 from adamjstewart/features/pgi
Add latest version of PGI
2016-08-01 13:07:35 -07:00
becker33
932300256c Merge pull request #1413 from mdevlin1/fixes/libxsmm
Fixed libxsmm package
2016-08-01 13:06:05 -07:00
becker33
6361f5c2d4 Merge pull request #1359 from sknigh/libhio
added libhio package
2016-08-01 13:05:29 -07:00
Mitchell Devlin
2d51ea5da4 fixed libxsmm makefile filter 2016-08-01 14:38:16 -05:00
Adam J. Stewart
fed7ba1dab Add latest version of PGI 2016-08-01 13:42:00 -05:00
Adam J. Stewart
ab885a5397 Allow git to depend on gettext now that it works 2016-08-01 13:35:22 -05:00
Adam J. Stewart
4014a29d2b Use proper deptype so that spack activate works 2016-08-01 13:35:22 -05:00
Adam J. Stewart
f5aed63b0b pkg-config should be a build dependency only 2016-08-01 13:35:22 -05:00
Adam J. Stewart
5cac0a528c Fix undefined symbols by building shared libraries 2016-08-01 13:35:22 -05:00
Adam J. Stewart
bdb64c2e39 Tell MEEP where to find libctl 2016-08-01 13:35:22 -05:00
Adam J. Stewart
0903ae0599 Final fixes to get libctl working 2016-08-01 13:35:22 -05:00
Adam J. Stewart
1e3a5d4e26 Final fixes to get guile to build 2016-08-01 13:35:21 -05:00
Adam J. Stewart
6db99a4fe7 Rename gc => bdw-gc, fix libunistring bug 2016-08-01 13:35:21 -05:00
Adam J. Stewart
5b1a882fc2 Update meep's url_for_version 2016-08-01 13:35:21 -05:00
Adam J. Stewart
a2578c21e4 Supply flags to bdist 2016-08-01 13:35:21 -05:00
Adam J. Stewart
8d0758fc4c Allow py-meep to link properly 2016-08-01 13:35:21 -05:00
Adam J. Stewart
880cbb2217 Better testing for MEEP 2016-08-01 13:35:21 -05:00
Adam J. Stewart
3b4820f290 Patch pkg-config and update installs for various packages 2016-08-01 13:35:21 -05:00
Adam J. Stewart
9e05fdf4a1 Bug fixes 2016-08-01 13:35:20 -05:00
Adam J. Stewart
7e53f4328f Add py-meep package and dependencies 2016-08-01 13:35:20 -05:00
George Hartzell
7d303afd64 Address flake8 issue 2016-08-01 13:42:55 -04:00
George Hartzell
1552ed943a Add package for cask
Add a package for cask, the emacs project/dependency management tool.

Based on [Homebrew's formula][brew].

[brew]: https://github.com/Homebrew/homebrew-core/blob/master/Formula/cask.rb
2016-08-01 13:41:28 -04:00
George Hartzell
31b7580b76 Fix jdk package's use of distutils
See issue #1364.  @citibeth's fix works fine.
2016-08-01 13:33:27 -04:00
becker33
cc3fc2ba4c Merge pull request #1322 from mdevlin1/feature/libxsmm
Add libxsmm package
2016-08-01 09:56:09 -07:00
Paul Hopkins
cca240c8f9 Add concretize_preferences tests 2016-08-01 16:18:11 +01:00
alalazo
ec09dfe5d1 cp2k : added package 2016-08-01 10:41:33 +02:00
Todd Gamblin
fbbb82259a Merge pull request #1407 from glennpj/r-ncdf4
New package - r-ncdf4
2016-07-31 22:15:52 -07:00
Todd Gamblin
ea11aab71f Merge pull request #1406 from glennpj/r-np
New package - r-np
2016-07-31 22:15:37 -07:00
Todd Gamblin
2042c94a6c Merge pull request #1405 from glennpj/r-survey
New package - r-survey
2016-07-31 22:15:09 -07:00
Todd Gamblin
64be8a80b2 Merge pull request #1404 from glennpj/r-tarifx
New package - r-tarifx
2016-07-31 22:14:56 -07:00
Todd Gamblin
7185fe2876 Merge pull request #1403 from glennpj/r-e1071
New package - r-e1071
2016-07-31 22:14:40 -07:00
Todd Gamblin
0724eba935 Merge pull request #1402 from glennpj/r-plotrix
New package - r-plotrix
2016-07-31 22:14:25 -07:00
Todd Gamblin
441bb83682 Merge pull request #1401 from glennpj/r-gdata
New package - r-gdata
2016-07-31 22:13:50 -07:00
Todd Gamblin
2cffc90284 Merge pull request #1400 from glennpj/r-roxygen2
New package - r-roxygen2
2016-07-31 22:13:16 -07:00
Todd Gamblin
68cedd2599 Merge pull request #1399 from glennpj/r-testthat
New package - r-testthat
2016-07-31 22:12:06 -07:00
Todd Gamblin
d00fd06095 Merge pull request #1398 from glennpj/r-xml
New package - r-xml
2016-07-31 22:11:38 -07:00
Glenn Johnson
8815f0a0b5 New package - r-ncdf4
Interface to Unidata netCDF (version 4 or earlier) format data files.
2016-07-31 17:12:29 -05:00
Glenn Johnson
bfd03db12a New package - r-np
Nonparametric kernel smoothing methods for mixed data types.
2016-07-31 16:18:55 -05:00
Glenn Johnson
f14eb07dc1 New package - r-survey
Analysis of complex survey samples.
2016-07-31 15:50:19 -05:00
Glenn Johnson
a9cc6a7d08 New package - r-tarifx
A collection of various utility and convenience functions.
2016-07-31 15:39:09 -05:00
Glenn Johnson
be2f2e42db New package - r-e1071
Misc functions of the Department of Statistics, Probability Theory Group
(Formerly: E1071), TU Wien.
2016-07-31 15:26:13 -05:00
Glenn Johnson
05e5276aec New package - r-plotrix
Various plotting functions.
2016-07-31 15:15:55 -05:00
Glenn Johnson
dbf799bbf9 New package - r-gdata
Data manipulation tools.
2016-07-31 15:07:40 -05:00
Glenn Johnson
f39e570f36 New package - r-roxygen2
In-source documentation for R.
2016-07-31 14:52:16 -05:00
Glenn Johnson
58a6039c0a New package - r-testthat
A unit testing system for R.
2016-07-31 14:40:46 -05:00
Glenn Johnson
0662b953f0 New package - r-xml
Tools for parsing and generating XML within R and S-Plus.
2016-07-31 14:25:17 -05:00
Glenn Johnson
1b04b8be01 New package - r-datatable
Extension of Data.frame
2016-07-31 14:11:04 -05:00
Todd Gamblin
173a16b38a Merge pull request #1396 from glennpj/r-quantmod
New package - r-quantmod
2016-07-30 20:15:53 -07:00
Todd Gamblin
68ba5377c1 Merge pull request #1395 from glennpj/r-ggmap
New package - r-ggmap and dependencies
2016-07-30 20:14:57 -07:00
Todd Gamblin
253507c0c3 Merge pull request #1394 from glennpj/r-maps
New package - r-maps
2016-07-30 20:14:27 -07:00
Todd Gamblin
7684652ce3 Merge pull request #1393 from glennpj/r-maptools
New package - r-maptools
2016-07-30 20:14:19 -07:00
Todd Gamblin
b12dc34ba7 Merge pull request #1391 from glennpj/r-caret
New package - r-caret
2016-07-30 20:14:09 -07:00
Todd Gamblin
9c31ee8a75 Merge pull request #1390 from glennpj/r-glmnet
New package - r-glmnet
2016-07-30 20:13:50 -07:00
Todd Gamblin
ae5ba2b110 Merge pull request #1389 from glennpj/r-vcd
New package - r-vcd
2016-07-30 20:13:05 -07:00
Todd Gamblin
13499f1655 Merge pull request #1388 from glennpj/r-multcomp
New package - r-multcomp
2016-07-30 20:12:51 -07:00
Todd Gamblin
49e9f365d8 Merge pull request #1387 from glennpj/r-randomforest
New package r-randomforest
2016-07-30 20:12:21 -07:00
Glenn Johnson
41cd861861 New package - r-quantmod
Qualitative Financial modelling framework.
2016-07-30 18:25:43 -05:00
Glenn Johnson
2913aa8d09 New package - r-ggmap and dependencies
Spatial visualization with ggplot2
2016-07-30 18:14:02 -05:00
Glenn Johnson
1bd2def41e New package - r-maps
Draw geographical maps.
2016-07-30 17:34:07 -05:00
Glenn Johnson
386f0e577a New package - r-maptools
Tools for reading and handling spatial objects.
2016-07-30 17:26:31 -05:00
Glenn Johnson
7207ce2a18 New package - r-caret
Classification and Regression Training
2016-07-30 16:53:54 -05:00
Glenn Johnson
20e52e5052 New package - r-glmnet
Lasso and Elastic-Net Regularized Generalized Linear Models
2016-07-30 16:38:00 -05:00
Glenn Johnson
e9944150a5 New package - r-vcd
Visualizing Categorical Data
2016-07-30 16:28:43 -05:00
Glenn Johnson
fc1804974c New package - r-multcomp
Simultaneous Inference in General Parametric Models.
2016-07-30 16:09:57 -05:00
Glenn Johnson
12167e8f37 New package r-randomforest
Breiman and Cutler's Random Forests for Classification and Regression.
2016-07-30 15:39:28 -05:00
Glenn Johnson
8dc26bbcd9 Have R extensions build in parallel.
Set `MAKEFLAGS` so R extensions can be built in parallel if that is set
in spack.
2016-07-30 15:20:14 -05:00
Glenn Johnson
ee7acc6b13 New package r-car
Companion to Applied Regression.
2016-07-30 15:10:25 -05:00
Kelly (KT) Thompson
6c80b15220 GTK+3: Provide updates to package dependencies.
WIP: I started trying to build gtkplus@3.20, but this package has many more
dependencies than v2 and it requires newer versions of existing packages. This
commit provides updates for 5 packages that are required by GTK+3. This is not
the complete set of changes required for GTK+3.

atk  - move default version from 2.14 -> 2.20.
glib - move default version from 2.42 -> 2.49
     - v2.49 requires pcre+utf as a new dependency.
pcre - if variant +utf is selected, add '--enable-unicode-properties' to the
       configure options.
libepoxy - new package to spack
         - manages OpenGL function pointers.
pango    - move default version from 1.36 -> 1.40
2016-07-29 09:05:44 -06:00
Denis Davydov
aad5a4c4b3 mkl: flake8 fixes; minor docu update 2016-07-29 14:12:07 +02:00
Denis Davydov
b6ce0e6f0e trilinos: make sure hdf5 is picked up from Spack 2016-07-29 13:11:12 +02:00
Denis Davydov
943896e237 trilinos: fix lapack lib dir 2016-07-29 13:09:34 +02:00
Denis Davydov
8ee4df8101 hypre: minor cleanup related to blas/lapack 2016-07-29 11:37:19 +02:00
Denis Davydov
572f1cd427 mkl: symlink libs to prefix.lib 2016-07-29 11:36:37 +02:00
Todd Gamblin
e04662f84f Merge pull request #1344 from LLNL/bugfix/py-nose-nosetests
do not ignore nosetests script in py-nose
2016-07-28 10:19:13 -07:00
becker33
5caaa2cd75 Merge pull request #1331 from adamjstewart/fixes/mvapich2
MVAPICH2 depends on libpciaccess
2016-07-28 09:52:51 -07:00
becker33
3759f62cba Merge pull request #1235 from davydden/pkg/p4est_run_tests
p4est: use run_tests instead of a variant
2016-07-27 18:36:36 -07:00
George Hartzell
f855cf6bab Add package for tree
Add a package for [tree](http://mama.indstate.edu/users/ice/tree/).

It has a Makefile that hardcodes a prefix and some CFLAGS.  Used
filter_file to:

- set the make variable *prefix* to `prefix`; and
- comment out their CFLAGS, just use ours....

It installs, runs on CentOS7, and uninstalls cleanly.
2016-07-27 11:32:03 -04:00
Todd Gamblin
458deaae5e Merge pull request #1350 from adamjstewart/fixes/openssl
Fix OpenSSL url_for_version
2016-07-27 08:08:00 -07:00
Greg Lee
e4525e57bb intel parallel studio itac fixes 2016-07-25 14:02:15 -07:00
Greg Lee
dba384108b intel parallel studio setup mkl environment 2016-07-25 14:01:49 -07:00
Samuel Knight
a2d4dcc636 Added libhio package 2016-07-25 17:32:03 +00:00
becker33
969e785d94 Merge pull request #1352 from glennpj/r_googlevis
New package - r-googlevis
2016-07-25 10:25:47 -07:00
becker33
5b7ec8de95 Merge pull request #1351 from glennpj/r_htmlwidgets
New packages - R htmlwidgets
2016-07-25 10:25:19 -07:00
Glenn Johnson
eb865b0df2 Add py-setuptools as dependency
With the addition of dependency types and with `py-setuptools` set as
type='build' there are more packages that need to have `py-setuptools`
added as a dependency.

This PR adds that dependency for the following packages:
- py-h5py
- py-networkx
- py-pytables
- py-scikit-image
2016-07-25 11:23:09 -05:00
Glenn Johnson
81cd458c26 r-curl update and chaged remote archive
This updates to the 1.0 version of r-curl. The remote archive directory
name also changed so change that here as well.
2016-07-24 16:48:07 -05:00
Glenn Johnson
27986c9edf New packages - R htmlwidgets 2016-07-24 16:43:35 -05:00
Glenn Johnson
b7bf88c761 New package - r-googlevis 2016-07-24 16:38:36 -05:00
Adam J. Stewart
29278090eb Fix OpenSSL url_for_version 2016-07-24 15:19:27 -05:00
Glenn Johnson
a8855f48aa Add dependency type tp r- packages
This PR adds the `nolink` dependency type to r- package dependencies.
This is needed due to the new dependency types in Spack. A couple of
packages were updated with new versions as well.
2016-07-23 19:43:55 -05:00
Greg Lee
773bca159a do not ignore nosetests script in py-nose 2016-07-22 15:49:36 -07:00
Glenn Johnson
ec9959b152 R extension dependencies with compiler wrapper
This commit introduces a mechanism to insure that R package dependencies
are built with the Spack compiler wrapper. A copy of Makeconf is made
before `filter_compilers` is called. This is then pointed to by the
R_MAKEVARS_SITE environment variable set up in
`setup_dependent_environment`. With this the normal compilers are used
outside of spack and the spack wrapper compilers are used inside of
spack.

This commit also standardizes on the `join_path` call. It also sets the
commented build command to reflect what is actually used with the newer
string formatting.
2016-07-22 17:05:01 -05:00
Adam J. Stewart
1be486c90a Add CGNS package 2016-07-22 17:02:45 -05:00
Todd Gamblin
395c616a48 Merge pull request #950 from xjrc/packages/python
Enhancement Proposal: Make Python Spack Installs Ignore User Configuration
2016-07-22 13:56:19 -07:00
Joseph Ciurej
fa92f58167 Adding temporary script that fixes all Python extensions w/ 'setup_py'. 2016-07-22 11:17:19 -07:00
Joseph Ciurej
ac2e0962ce Improved the build flag construction code in the python install method. 2016-07-22 11:12:02 -07:00
Joseph Ciurej
fb2d2303d6 Fixed a bug that was causing Python installs to be affected by user config. 2016-07-22 11:11:08 -07:00
Todd Gamblin
f5b4664c7c Merge pull request #1336 from glennpj/rcase
Fix alpha case of dependencies for some r-packages
2016-07-22 10:08:14 -07:00
Todd Gamblin
adffba5081 Merge pull request #1230 from hartzell/update-jdk
Add URL and md5 for jdk-8u92.
2016-07-21 22:06:29 -07:00
Glenn Johnson
e083c91d5e Fix alpha case of dependencies.
A while ago I was asked to convert packages to all lowercase. That was
done but some dependencies did not get converted in the specification.
This commit fixes that as well as a couple of urls that need to be made
explicit and a missing dependency on jdk.
2016-07-21 19:58:04 -05:00
Todd Gamblin
ed737cb2a2 Merge pull request #1333 from LLNL/features/no-openssl-pinging
Remove remote website pinging from OpenSSL
2016-07-21 16:46:59 -07:00
Todd Gamblin
488550c2e6 Merge pull request #1334 from hartzell/add-gcc-5.4.0
Update gcc package with info about gcc-5.4.0
2016-07-21 16:37:31 -07:00
Todd Gamblin
8523f75e6c Remove remote website pinging from OpenSSL
- OpenSSL no longer checks remote versions on the openssl site.

- Spack is used on systems that aren't connected to the internet, and
  this check is probably in the wrong place and affects too many
  commands.  We can work on figuring out a better, more configurable
  place to put a check like this.
2016-07-21 16:35:20 -07:00
George Hartzell
4efe022165 Update with info about gcc-5.4.0 2016-07-21 15:36:22 -04:00
Mitchell Devlin
796308ed85 edit 2016-07-21 13:39:27 -05:00
George Hartzell
4c105895ab Fix flake8 violations 2016-07-21 14:24:51 -04:00
George Hartzell
9523e50732 Fix shebang line in tcl scripts
Lmod's configure script goes to the trouble of finding
tclsh.  This change uses that info to rewrite the #! lines
in the tcl scripts so that they call the tclsh that the
configure script discovered.

It needs to massage the existing shebang lines into something
that the sed statement in the makefile can manipulate and
it needs to add the path_to_tclsh info into the set of sed
statements.

Checked with versions 6.4.1 and 6.3.7 (the checksum for 6.0.1 is
incorrect, a fix for another time).
2016-07-21 13:58:16 -04:00
George Hartzell
52f0249c61 tcl is actually a runtime dependency.
lmod uses tclsh at runtime, so adjust the depends_on accordingly
(thanks @davydden!).
2016-07-21 13:51:03 -04:00
George Hartzell
a27cb639d8 The lmod package should depend_on('tcl')
The lmod package needs a tclsh.  Up until now it just assumed
that one was available on the system.

This change adds a depends_on('tcl') to the lmod package.

The tcl package installs a tclsh script with an embedded version
number (e.g. tclsh8.6) but the lmod configuration looks for tclsh.
This change extends the tcl package to symlink tclshX.Y to tclsh in
the tcl package bin directory.
2016-07-21 13:51:03 -04:00
Adam J. Stewart
cf8f14780f MVAPICH2 depends on libpciaccess 2016-07-21 11:13:17 -05:00
Glenn Johnson
ead1b93f75 MPI related changes
- Redid the code for setting the itac symlink for the cluster edition.
- Removed the *PATH variables for MPI to avoid a conflict with other MPI
  environment modules.
- Added missing test for `+all` when checking variants.
2016-07-20 20:03:05 -05:00
Glenn Johnson
0be4c7dfbd Changes as discussed in PR review
- removed unneeded entry for `debugger/gdb/intel64_mic`
- set `+mpi` directory name to impi
2016-07-20 20:03:05 -05:00
Glenn Johnson
5e5e36a659 Fix flake8 errors. 2016-07-20 19:54:35 -05:00
Glenn Johnson
16f67b5bb1 Setup environment for Intel Parallel Studio
Set up the environment for the Intel compilers and tools. This commit
does the following:

- Unset variables that were incorrect from the auto guess prefix
  inspections.
- Add a RemovePath environment_modifications_formats for dotkit.
- Set the module environment variables appropriate for the different
  variants.
- Change the component logic so that the '+all' variant works. It was
  getting split by letter and leaving COMPONENTS empty.
- Added a variant checking function.
- Added NONRPM_DB_DIR to the silent.cfg so that the product database
  goes to the installation directory.
- With the product database in prefix the code to remove the product
  database file from the home directory is no longer needed and was
  removed.
- Reformat the 'tools' variant description.

There are probably more variables needed for the '+tools' for the
'professional' product version but I do not have access to that.
2016-07-20 19:54:35 -05:00
mwilliammyers
b8444aa518 Merge remote-tracking branch 'upstream/develop' into package-opencv
* upstream/develop: (126 commits)
  Fix indent/flake8 error.
  openexr : Add new package
  Set environment variables
  Added gnu packages datamash, parallel, and screen
  added package as argument to setup_platform_environment
  ilmbase : Add new IlmBase package
  Documented linker default
  fixed flake errors
  removed commented-out code
  Set default link type to dynamic on cray. Includes hooks for platform-based environment changes
  fixed flake errors
  fixed flake errors
  Improved cray_xc detection bug fix
  Improved cray_xc detection
  remove FIXMEs
  Ensure that per-4.4.1 NetCDF doesn't use HDF5 1.10
  Re-ignore licenses directory
  Add "default" configuration scope.
  Draft CDO
  Make frontend OS on Cray machines a proper linux distro.
  ...
2016-07-20 18:34:53 -06:00
mwilliammyers
a09bebcaea opencv : Add section comments 2016-07-20 18:19:59 -06:00
mwilliammyers
a9541997ae opencv : Reorder depends_on statements 2016-07-20 18:19:03 -06:00
mwilliammyers
bd02892f7b opencv : Use dso_suffix for python lib 2016-07-20 18:10:10 -06:00
mwilliammyers
ea9fa81ba5 opencv : Fix python include dir for cmake 2016-07-20 18:10:09 -06:00
mwilliammyers
670157b364 opencv : Add zlib cmake support 2016-07-20 18:10:09 -06:00
mwilliammyers
e5ae48a9da opencv : Add jasper cmake support 2016-07-20 18:10:09 -06:00
mwilliammyers
47514d07b1 opencv : Use dso_suffix 2016-07-20 18:10:08 -06:00
mwilliammyers
f2e8f27c15 opencv : Add libpng cmake support 2016-07-20 18:10:08 -06:00
mwilliammyers
fc79b104f0 opencv : Add libjpeg-turbo cmake support 2016-07-20 18:10:07 -06:00
mwilliammyers
97143768c8 opencv : Add libtiff cmake support 2016-07-20 18:10:07 -06:00
mwilliammyers
d3b97227a1 opencv : Add optional jdk dependency 2016-07-20 18:10:07 -06:00
mwilliammyers
da2b695f93 opencv : Fix lib finding for python 2016-07-20 17:25:05 -06:00
mwilliammyers
10c285a774 opencv : Use string.format() 2016-07-20 17:25:01 -06:00
mwilliammyers
0654ee6a10 opencv : Fix style inconsistencies 2016-07-20 17:24:55 -06:00
mwilliammyers
8cf03c209f opencv : Make extending python optional 2016-07-20 17:24:50 -06:00
mwilliammyers
c588ce9648 opencv : Improve cmake detecting python 2016-07-20 17:24:46 -06:00
mwilliammyers
3fac2dcc41 opencv : Fix cmake not disabling gtk 2016-07-20 17:24:40 -06:00
mwilliammyers
0080ffcf9f opencv : Use in operator 2016-07-20 17:24:35 -06:00
mwilliammyers
ce902bf27a opencv : Minor style changes 2016-07-20 17:24:30 -06:00
mwilliammyers
2cde6aaabd opencv : Add GUI support 2016-07-20 17:24:26 -06:00
mwilliammyers
578ddea418 opencv : Fix pep8 style issues 2016-07-20 17:24:21 -06:00
mwilliammyers
cf0f5756f5 opencv : Fix python extensions issues 2016-07-20 17:24:13 -06:00
mwilliammyers
9e1d26e973 opencv : Add CUDA extensions 2016-07-20 17:23:46 -06:00
Todd Gamblin
e389afedaa Merge pull request #1323 from glennpj/rlib
Set environment variables for R
2016-07-20 15:43:26 -07:00
Todd Gamblin
b9c79824a2 Merge pull request #1313 from sknigh/gnu-tools
Added packages for GNU tools screen, datamash, and parallel
2016-07-20 15:38:55 -07:00
Todd Gamblin
0777d3a5ba Merge pull request #1326 from mwilliammyers/package-openexr
openexr : Add new package
2016-07-20 15:35:36 -07:00
Mitchell Devlin
2344ffd0c7 add libxsmm package 2016-07-20 16:36:31 -05:00
Glenn Johnson
0c75174ec3 Fix indent/flake8 error. 2016-07-20 15:56:20 -05:00
mwilliammyers
e973adf84b openexr : Add new package 2016-07-20 14:49:03 -06:00
Glenn Johnson
f9137f606f Set environment variables
This commit adds `setup_environment` to export the libraries and
headers.

Fixes #1314.
2016-07-20 15:37:31 -05:00
Todd Gamblin
d8acd41ba1 Merge pull request #1321 from mwilliammyers/package-ilmbase
ilmbase : Add new IlmBase package
2016-07-20 13:13:21 -07:00
Todd Gamblin
8efbec3c0b Merge pull request #1292 from eschnett/eschnett/hdf5-default-1.10
Make newest HDF5 release the default version
2016-07-20 12:57:45 -07:00
Todd Gamblin
4c7c9f4ff5 Merge pull request #1303 from adamjstewart/features/armadillo
Updates to Armadillo package
2016-07-20 12:56:41 -07:00
Samuel Knight
24c14ff7a8 Added gnu packages datamash, parallel, and screen 2016-07-20 19:53:14 +00:00
mwilliammyers
c9f4e8ce5a ilmbase : Add new IlmBase package 2016-07-20 13:13:47 -06:00
alalazo
40cb314638 Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases
Conflicts:
	lib/spack/spack/package.py
2016-07-20 21:02:19 +02:00
Todd Gamblin
4434f482c0 remove FIXMEs 2016-07-20 09:48:54 -07:00
Todd Gamblin
3def8ef60e Merge branch 'cdo' of https://github.com/robertdfrench/spack into robertdfrench-cdo 2016-07-20 09:48:01 -07:00
Todd Gamblin
20584ab084 Merge pull request #1302 from robertdfrench/adios-url
Get adios from github, not NCCS
2016-07-20 09:47:23 -07:00
Todd Gamblin
7c28338d60 Merge pull request #1301 from robertdfrench/silver-searcher
Silver Searcher 0.32 is out
2016-07-20 09:47:12 -07:00
Todd Gamblin
17a63c9646 Merge pull request #1284 from eschnett/eschnett/py-h5py.2
Declare dependency of "py-h5py +mpi" on "py-mpi4py"
2016-07-20 09:45:54 -07:00
Todd Gamblin
7f20678969 Merge pull request #1291 from eschnett/eschnett/netcdf-4.4.1
Update NetCDF to version 4.4.1
2016-07-20 09:34:14 -07:00
Erik Schnetter
69e36c9821 Ensure that per-4.4.1 NetCDF doesn't use HDF5 1.10 2016-07-20 11:25:46 -04:00
Robert D. French
6b0fb476ab Draft CDO 2016-07-19 15:57:55 -07:00
Robert D. French
1c9cf668a1 Silver Search 0.32 is out
PEP8 Love + Re-adding v0.30.0
2016-07-19 10:48:53 -07:00
Adam J. Stewart
8034536054 Fix shared object suffix for macOS 2016-07-19 12:37:34 -05:00
Adam J. Stewart
afa4cdc2d8 Updates to Armadillo package 2016-07-19 12:33:04 -05:00
Robert D. French
25e765baae Download Adios from Github
Get adios from github, not NCCS

Use correct hash, thanks Ben
2016-07-19 10:31:59 -07:00
Todd Gamblin
a64a2e72cf Merge pull request #1226 from adamjstewart/features/tkinter
Add Tkinter support for Python
2016-07-19 09:41:12 -07:00
Todd Gamblin
4ad29b6c9b Merge pull request #1262 from davydden/pkg/suite_sparse_fix_blas
suite-sparse: enable TBB and fix Blas/Lapack libs
2016-07-19 09:18:42 -07:00
Erik Schnetter
71684cb071 Flex requires m4 2016-07-18 23:04:20 -04:00
Erik Schnetter
4dec06e4f4 Make HDF5 1.10 the default version
Apply this only after NetCDF 4.4.1 is supported.
2016-07-18 20:14:44 -04:00
Erik Schnetter
94df1b801a Update NetCDF to version 4.4.1
This version supports HDF5 1.10 in a backward-compatible manner.
2016-07-18 20:11:32 -04:00
Todd Gamblin
7555c3d949 Merge pull request #1204 from goxberry/cmake-3.6.0
cmake@3.6.0
2016-07-18 16:53:17 -07:00
Todd Gamblin
25a9181a1b Merge pull request #1287 from mwilliammyers/package-jasper
jasper: Add new jasper package
2016-07-18 15:43:18 -07:00
mwilliammyers
02340062b4 package - jasper - Add new jasper package 2016-07-18 16:17:07 -06:00
Todd Gamblin
607813d5ce setuptools is a build dependency in numpy. 2016-07-18 14:13:14 -07:00
Erik Schnetter
67fade5b1e Declare dependency of "py-h5py +mpi" on "py-mpi4py" 2016-07-18 17:08:56 -04:00
Todd Gamblin
a9ed2296a1 Merge pull request #1282 from eschnett/eschnett/py-numpy
py-numpy: Add py-setuptools dependencies
2016-07-18 13:58:17 -07:00
Todd Gamblin
fa0bbb57ea Merge pull request #1270 from davydden/pkg/mumps_scalapack_fix_blas
Pkg/mumps scalapack fix blas
2016-07-18 13:57:26 -07:00
Erik Schnetter
49cd6f6269 py-numpy: Add py-setuptools dependencies
Closes #1281.
2016-07-18 16:01:48 -04:00
Todd Gamblin
089189afaf Merge pull request #1238 from davydden/pkg/mkl_update
mkl: add provide blas/lapack
2016-07-18 11:52:30 -07:00
Adam J. Stewart
ea425a101a Flake8 and new tk version 2016-07-18 07:51:08 -05:00
Adam J. Stewart
583232ea52 Build Python with Tkinter support 2016-07-18 07:51:08 -05:00
Todd Gamblin
b3789a4693 Merge pull request #1269 from davydden/pkg/hypre_trilinos_blas
Pkg/hypre trilinos blas
2016-07-18 03:06:37 -07:00
Denis Davydov
2e4966c854 netlib-scalapack: use dso_suffix 2016-07-18 10:11:18 +02:00
alalazo
6c00a13ed5 Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases
Conflicts:
	var/spack/repos/builtin/packages/swiftsim/package.py
2016-07-18 08:49:24 +02:00
Todd Gamblin
c898b9db04 Merge pull request #1188 from epfl-scitas/packages/py-numpy
RPATH for blas in py numpy
2016-07-17 21:20:39 -07:00
Todd Gamblin
28ce08b9e2 Merge pull request #1258 from eschnett/eschnett/openmpi-2.0.0
Update to OpenMPI 2.0.0
2016-07-17 21:01:21 -07:00
Denis Davydov
1bd3a702c9 mumps: flake8 fixes 2016-07-16 15:14:06 +02:00
Denis Davydov
561748a063 netlib-scalapack: flake8 fixes 2016-07-16 08:03:54 +02:00
Denis Davydov
9ea4f80f15 flake8 fixes 2016-07-16 07:58:51 +02:00
Denis Davydov
0752eccfa5 mumps: don't hardcode blas name; remove unused depends_on(lapack) 2016-07-16 07:38:42 +02:00
Denis Davydov
6175ce7559 netlib-scalapack: make sure Spack's Lapack is used 2016-07-16 07:37:38 +02:00
Denis Davydov
987fb137f9 trilinos: don't hardcode blas/lapack names 2016-07-16 07:31:38 +02:00