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2017-05-18add mpi support to meme (#4265)Douglas Duckworth1-0/+11
* added openmpi support to meme * openmpi is a link dependency which leverages r_path * openmpi support now the default - meme does not have configure argument for mpi - if it's found then it's used * added serial option and set mpi to not be default * modified meme
2017-05-18Add old version of ROOT 5 (#4288)Adam J. Stewart1-0/+1
2017-05-18Fix spec['python'].home (#4228)Adam J. Stewart1-0/+2
2017-05-18Add mpi support to R (#4286)Tom Merrick2-0/+93
2017-05-18Add the gnupg package and missing dependencies. Update versions of ex… (#4281)Patrick Gartung6-2/+171
* Add the gnupg package and missing dependencies. Update versions of existing dependencies. * this ended up in the wrong repo * put versions back, remove uneeded function * OK ;) * autopep8 * typo on npth line * whitespace
2017-05-18Add a new package for Open Babel (#4256)Adam J. Stewart3-0/+169
* Add a new package for Open Babel * Add post-installation tests, stolen from the fine folks at Homebrew * Add patch to fix Python 3.6 support * Add a more complete patch to get Python 3.6 support working * Add patch to convert tabs to spaces in test script testpdbformat.py contains mixed tabs and spaces causing the unit tests to fail. With this patch, all tests pass with flying colors.
2017-05-17benchmark: New package for the Google Benchmark library (#4194)Erik Schnetter1-0/+36
* benchmark: New package * benchmark: Remove empty function
2017-05-17Add info for miniconda[23]@4.3.14 (#4263)George Hartzell2-0/+2
2017-05-17Package for bcl2fastq2 (updates libxslt) (#4234)George Hartzell4-2/+131
* Add v1.1.26 and make crypto a variant I need 1.1.26 for bcl2fastq2. I also need to build it without crypto support. * Initial support for bcl2fastq2 * Clean up commentary, messages, names No substantial changes intended, just cleanup. * fix flake8 and extra import * The masked grammarian strikes again... * Be normal (messages don't end in periods) * When +crypto, add --with-crypto Add `--with-crypto` to configure args when user hasn't explicitly set `~crypto`. * self.spec.satisfies is unsatisfying, in is in instead See #4135, self.spec.satisfies has issues. @adamjstewart suggests simply using in.
2017-05-17Move doc dependencies to requirements.txt for readthedocs (#4280)Todd Gamblin2-2/+6
* Move doc dependencies to requirements.txt for readthedocs * Move sphinx to doc requirements.
2017-05-17Add a new package for sphinxcontrib-programoutput (#4267)Adam J. Stewart1-0/+41
2017-05-17Add latest version of matplotlib (#4279)Adam J. Stewart1-1/+2
2017-05-17Add latest version of Sphinx (#4264)Adam J. Stewart15-52/+185
* Add latest version of Sphinx * Flake8 fix
2017-05-17fix bug with executables setting their own environment. (#4237)Todd Gamblin1-3/+4
2017-05-17Sphinx no longer supports Python 2.6 (#4266)Adam J. Stewart8-303/+6
* Sphinx no longer supports Python 2.6 * Update vendored sphinxcontrib.programoutput from 0.9.0 to 0.10.0 * Documentation cannot be built in parallel * Let Travis install programoutput for us * Remove vendored sphinxcontrib-programoutput Recent updates to the sphinx package prevent the vendored version from being found in sys.path. We don't vendor sphinx, so it doesn't make sense to vendor sphinxcontrib-programoutput either.
2017-05-16Sphinx no longer ignores first argument (#4243)Adam J. Stewart1-1/+1
* Sphinx no longer ignores first argument * Duplicate first argument for maximum compatibility
2017-05-16Update checksum for latest version of cudnn (#4254)Adam J. Stewart1-1/+1
2017-05-16added meme package (#4257)Douglas Duckworth1-0/+43
* added albacore package as well as dependency py-ont-fast5-api * added py-cutadapt and dependency py-xopen * made more changes to albacore and cutadapt as well as dependencies * made changes again per @adamjstewart * fixed by python n00b errors i think * fixed? * tw=79 * made changes to py-ont-fast5-api ont-albacore * removed bad characters * albacore requires setuptools as build and run dependency * added vmd * added back albacore * removed vmd package * added meme software * libz is only needed as link depedency for meme * added libxml2 libxslt libgcrypt as link dependencies
2017-05-15albacore requires setuptools as build and run requirement (#4255)Adam J. Stewart1-7/+7
2017-05-15Add missing dependency to glib package (#4253)Adam J. Stewart1-0/+14
2017-05-15Add latest version of util-linux (#4252)Adam J. Stewart1-1/+2
2017-05-15Remove need for autoreconf in glib package (#4240)Adam J. Stewart2-19/+11
2017-05-14mesa-glu: provides libGLU, the OpenGL utility library from SGI (#4244)Milton Woods1-0/+37
2017-05-14harfbuzz: add latest version (1.4.6) (#4245)Milton Woods1-0/+1
2017-05-14ncurses: build "normal" libs, not just "wide-char" libs, for ncurses@6: (#4246)Milton Woods1-1/+2
2017-05-12espressopp: always depends on py-numpy (#4207)Christoph Junghans1-2/+1
Ref espressopp/espressopp#161
2017-05-12albacore and cutadapt again (#4219)Douglas Duckworth4-0/+174
* added albacore package as well as dependency py-ont-fast5-api * added py-cutadapt and dependency py-xopen * made more changes to albacore and cutadapt as well as dependencies * made changes again per @adamjstewart * fixed by python n00b errors i think * fixed? * tw=79 * made changes to py-ont-fast5-api ont-albacore * removed bad characters
2017-05-12LIBXSMM 1.8.1 (#4235)Hans Pabst1-1/+2
* Included LIBXSMM 1.8 into the list of available versions. * LIBXSMM 1.8.1
2017-05-12Convert pixman to AutotoolsPackage (#4231)Adam J. Stewart1-12/+10
2017-05-12Add helpful error message for uncompressed downloads (#4205)Adam J. Stewart1-6/+26
2017-05-12Add SymEngine release 0.3.0 (#4227)Jean-Paul Pelteret1-0/+1
2017-05-12Python cdat-lite package (#4208)Milton Woods1-0/+42
* py-cdat-lite: a python package for managing and analysing climate science data * py-cdat-lite: depends on py-numpy * py-cdat-lite: flake8 compliance * py-cdat-lite: provide a generic URL where multiple versions are listed * py-cdat-lite: restrict python versions; python required at run-time * py-cdat-lite: use URL under pypi.io for consistency with other packages * py-cdat-lite: add run-time dependency on py-numpy
2017-05-12Add pdt support to scorep (#4198)Michael Kuhn2-1/+17
Add pdt dependency to scorep
2017-05-11Download udunits from FTP server (#4218)Adam J. Stewart1-31/+4
2017-05-11Add latest version of eigen (#4224)Adam J. Stewart1-20/+11
2017-05-11Fix typo in PythonPackage documentation (#4221)Adam J. Stewart1-1/+1
2017-05-11Fix metis list_url (#4222)Adam J. Stewart1-1/+1
2017-05-11Flann package (#3966)Stephen McDowell1-0/+141
* Initial attempt at flann packaging. Python2 somehow works. Python3 does not. Still debugging their obscure setup.py configuration. * Flann good enough. Python3 broken but close. Flake8 checks in place. Unsure about CMAKE_BUILD_TYPE and default spack behavior. * spack uses RelWithDebInfo as default build type. * builds py2/3, but direct site-packages install * prefix working, empty python install dir * flann package +python installs correctly * str format {0} instead of {} * potential doctest fix * consistency of build env with PythonPackage * fix python again, test deptype todo, build type * potentially enable matlab, untested
2017-05-11Force suite-sparse to use Spack's compiler wrappers (#4220)Adam J. Stewart1-4/+3
2017-05-11Add patch to fix missing MODULESHOME in profile (#4214)Adam J. Stewart2-12/+40
2017-05-11filesystem.py: fixed bug introduced in #3367 (scrambled order in output) (#4156)Massimiliano Culpo19-7/+95
PR #3367 inadvertently changed the semantics of _find_recursive and _find_non_recursive so that the returned list are not ordered as the input search list. This commit restores the original semantic, and adds tests to verify it.
2017-05-11Update NAG checksum, add F77 and FC (#4196)Adam J. Stewart1-1/+5
2017-05-10Open MPI: add 2.1.1 to the list (#4204)Howard Pritchard1-1/+2
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2017-05-10Add nemesistcpib fabrics variant (#4197)Michael Kuhn1-1/+4
2017-05-10updating git (#4200)Suzanne Parete-Koon1-0/+5
2017-05-10Edits to get setup-env.csh working better (#4044)Matthew Thompson1-3/+9
* Edits to get setup-env.csh working better. Autosets the sys_type a la setup-env.sh * More stealing from bash setup script for module roots * Add error message if SPACK_ROOT isn't set * Remove _sp_lmod_root per Adam J Stewart
2017-05-10cosmomc: Enable Python bindings (#4169)Erik Schnetter1-4/+13
* cosmomc: Enable Python bindings * cosmomc: Make python dependency optional
2017-05-10hdf5: Correct spelling (#4172)Erik Schnetter1-3/+3
* hdf5: Correct spelling * hdf5: avoid trailing spaces
2017-05-10highfive: New package; this is a C++ wrapper for the HDF5 library (#4173)Erik Schnetter1-0/+52
* highfive: New package; this is a C++ wrapper for the HDF5 library The C++ wrapper that is shipped with the HDF5 library has several shortcomings. The highfive library seems to avoid these. * highfive: Make MPI variant default to true
2017-05-10Add latest version of PGI compilers (#4186)Adam J. Stewart1-5/+6
* Add latest version of PGI compilers * Prepend, don't overwrite
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