Commit graph

9831 commits

Author SHA1 Message Date
Levi Baber
059daa2012 r-summarizedexperiment: new version (#9054)
* r-summarizedexperiment: new version

* r-summarizedexperiment: add ending range for r3.4 dep

* r-summarizedexperiment: fix range
2018-09-04 14:34:45 -05:00
Miles Perry
447db2fe8d Feature/py pycogent New-Version (#9095)
* added py-pycogent

* flake8 edits

* added type=('build', 'run') to deps, changed py-matplotlib and mpi4py

* changed python min version to 2.6

* fixed cython to py-cython dep

* fixed mpi4py to py-mpi4py

* fixed py-sqlalchemy

* added 1.5.3 version

* fixed version 1.5.3 install

* changed deps names to reflect convention

* added variants

* changed download URL and added SHA256 hash

* fixed deps

* added github url for 1.5.3

* removed unneeded deps

* doesn't require py-setuptools

* fixed url and added py-setuptools specific to version 1.9

* fixed variant names and changed cython to normal dependency instead of variant

* removed cython dep, failed to build when it was present. Changed variant name 'mpi4py' to 'mpi' and changed sqlalchemy variant name to mpi

* fixed dependencies and added py-pymysql dep

* added setup-environment step

* changed download url for 1.5.3 to pypi

* fixed flake8 issue

* updated

* added changes
2018-09-04 14:34:18 -05:00
Francesco Di Natale
e85f737d1f py-maestrowf: Addition of new releases. (#9135)
* Addition of latest maestrowf releases.

* Addition of filelock to dependencies.

* Addition of when clause to depends_on for filelock and tabulate.

* Correction of the tar url.
2018-09-04 14:33:55 -05:00
Chris Green
dd27662b40 Enable testing in parallel when using CMake. (#8484)
* Add 'extra_env' argument to Executable.__call__: this will be added
  to the environment but does not affect whether the current
  environment is reused. If 'env' is not set, then the current
  environment is copied and the variables from 'extra_env' are added
  to it.
* MakeExecutable can take a 'jobs_env' parameter that specifies the
  name of an environment variable used to set the level of parallelism.
  This is added to 'extra_env' (so does not affect whether the current
  environment is reused).
* CMake-based Spack packages set 'jobs_env' when executing the 'test'
  target for make and ninja (which does not use -j)
2018-09-04 11:37:19 -07:00
Adam J. Stewart
0ca69fef42 Better warning message when fetching non-existent URL 2018-09-03 20:42:01 -07:00
Levi Baber
3c9b0ee2ea r-genomicalignments: new version (#9055)
* r-genomicalignments: new version

* r-genomicalignments: ending range for r3.4 dep

* r-genomicalignments: fix range
2018-09-03 21:04:22 -05:00
Levi Baber
35d87bdf09 r-biomart: new version; (#9058)
* r-biomart: new version;

* r-biomart: ending range for r3.4 dep

* r-biomart: fix version range
2018-09-03 21:03:47 -05:00
Levi Baber
cb9a95fc37 r-deseq2: new version (#9062)
* r-deseq2: new version

* r-deseq2: fix r 3.4 dep range
2018-09-03 21:03:08 -05:00
Hadrien G
930e266a36 New package: AIDA (#9094)
* Trying to package old AIDA

* Document the incompleteness

* Install the jars too
2018-09-03 21:02:06 -05:00
Miles Perry
cb9e8eda8f Feature/py picrust New Package (#9096)
* added py-picrust

* flake8 edits

* fixed boilerplate, added type='build', 'run'

* fixed errors

* added deps

* fixed error

* fixed numpy max version

* fixed future version

* fixed version issues
2018-09-03 20:58:49 -05:00
Neil Flood
ee14d273e5 nlopt: Only support release>=2.5.0, since earlier release tarballs were actually AutoTools, not CMake. (#9110) 2018-09-03 20:56:48 -05:00
Miles Perry
ad8fbe3c7f aperture-photometry: new package (#9119) 2018-09-03 20:52:11 -05:00
Miles Perry
585c69b94c py-pymysql: new package (#9122)
* py-pymysql: new package

* added type build and run
2018-09-03 20:50:39 -05:00
Geoffrey Oxberry
4bdfa19d97 openblas: add @0.3.1, patch CMake export bug in @0.3.1:0.3.2 (#9123)
* openblas@0.3.1:0.3.2: patch CMake export bug

See https://github.com/xianyi/OpenBLAS/pull/1703.

* openblas@0.3.1: new version
2018-09-03 20:49:45 -05:00
Abhinav Bhatele
ed657e97fa New package: CODES simulation framework (#9133)
* New package: CODES simulation framework

* CODES: add comments

* CODES: remove -fi from extra autoreconf flags
2018-09-03 20:43:50 -05:00
Edoardo Aprà
187e110ab0 NWChem 6.8.1 (#9140) 2018-09-03 20:36:49 -05:00
rice31
6e7af3362e added version for kull support (#9141) 2018-09-03 20:36:15 -05:00
Timo Heister
89c77051fe aspect: new version (#9146) 2018-09-03 20:35:45 -05:00
Jim Galarowicz
ccd96a2fed Update openspeedshop and cbtf version numbers (#9150)
Update the version numbers and now depend on
the develop version of dyninst because of a
feature in openspeedshop depends on new code
in the dyninst develop tree.  Without dyninst
develop, openspeedshop will not build.
2018-09-03 20:35:25 -05:00
Levi Baber
e3bae8f936 py-matplotlib: incorporate 8532 w/ version range (#9151)
* py-matplotlib: Add patch to fix FreeType library detection

Adds patch to add $CPATH to locations searched for FreeType header file

Patch has been upstreamed:
https://github.com/matplotlib/matplotlib/pull/11457

* py-matplotlib: Add patch to fix FreeType library detection

* Make patch only apply to versin 2.2.2 (as already upstreamed)
* Fix flake8 format issue

* py-matplotlib: add range to freetype patch

* py-matplotlib: whitespace
2018-09-03 20:34:41 -05:00
Adam Moody
801f1a0a7d mpifileutils: add v0.8 (#9152) 2018-09-03 20:34:07 -05:00
Matthias Wolf
4df60caf5b msgpack-c, snappy: explicitly depend on googletest (#9167) 2018-09-03 20:25:17 -05:00
David Wells
734d6306a2 Fix two dependencies with silo. (#9153)
1. I presently get errors of the sort

==> Error: KeyError: 'No spec with name mpi in silo@4.10.2%gcc@8.1.0+fortran+mpi
[...]
$HOME/spack/var/spack/repos/builtin/packages/silo/package.py:84, in configure_args:
         81                'FCFLAGS={0}'.format(self.compiler.pic_flag)]
         82
         83        if '+mpi' in self.spec:
  >>     84            config_args.append('CC=%s' % self.spec['mpi'].mpicc)
         85            config_args.append('CXX=%s' % self.spec['mpi'].mpicxx)
         86            config_args.append('FC=%s' % self.spec['mpi'].mpifc)

without the extra explicit MPI dependency.

2. Silo uses zlib, so we should explicitly depend on it.
2018-09-03 16:43:00 +02:00
Todd Gamblin
940e35059e travis: bring back macOS test in unit test stage 2018-09-03 07:27:21 -07:00
Todd Gamblin
03542f2a07 travis: clean up .travis-ci.yml wrapping and indentation
- fix line wrapping in travis.yml to make parts more legible
- Travis can handle multi-line if statements if you use semicolos.
2018-09-03 07:27:21 -07:00
Todd Gamblin
e58c6e1b73 travis: fix macOS builds, avoid brew autoupdate 2018-09-03 07:27:21 -07:00
Adam J. Stewart
4920f1cff1
Vim: add version 8.1.0338 (#9155) 2018-09-01 08:12:14 -05:00
Adam J. Stewart
c5c3b65c60
GDAL: add version 2.3.1 (#9156) 2018-09-01 07:32:24 -05:00
Cody Balos
e7df911026 SUNDIALS: add new versions, update hashes, and apply clang fix (#9115)
Added SUNDIALS 3.1.2 and 4.0.0-dev.1 versions and relevant dependencies
(3.1.2 requires CMake 2.8.12). Updated all versions to use sha256 hashes.
Addressed issue specific to clang compiler on macOS.
2018-08-31 12:14:15 -07:00
Francesco Di Natale
3d92b975f3 py-filelock: new package (#9136)
* Addition of py-filelock and first page of versions.

* Addition of setup.py patch for setuptools.

* flake8 failure fixes.

* Reduced url declaration to a single line.

* Correction to py-filelock to use distutils.
2018-08-31 11:21:55 -07:00
Geoffrey Oxberry
d54a91fd2b openblas@0.3.3: new version (#9143) 2018-08-31 11:14:37 -07:00
rice31
20a914374e libpng package: add version (#9142) 2018-08-31 10:26:13 -07:00
Levi Baber
535b09d811 singularity: new version 2018-08-31 08:47:24 -07:00
Michael Sternberg
d95fdc8441 Update instructions to initialize Spack-global license files (#8991)
* Suggest adding contents before the explanatory comment to avoid
  issue #6534
* Mention that the license file may not need to be edited
2018-08-29 22:04:14 -07:00
Michael Sternberg
a86f22d755 Intel prefixes (#7469)
Consolidate prefix calculation logic for intel packages into the
IntelPackage class.

Add documentation on installing Intel packages with Spack an
(alternatively) adding them as external packages in Spack.
2018-08-29 21:09:34 -07:00
Mark W. Krentel
e860307c31 binutils: add variant 'nls' for native language support (#9124)
Add variant 'nls' for native language support with default True.
The default inside binutils was always on, but this gives a way of
turning it off, if desired.

Adjust the dependencies.  Flex is never used for a one-time build.
Bison and m4 should not be needed, except that prior to rev 2.30, gold
did not include its generated files, so bison is needed when +gold.

Drop configure option --enable-interwork.  This option does not exist.
2018-08-29 20:32:41 -07:00
Adam J. Stewart
1383834d15
Add MDB driver support to GDAL (#8614) 2018-08-29 12:35:56 -05:00
Andreas Baumbach
1e0c337fe9 New package: NEST Simulator (#9092) 2018-08-29 13:30:29 -04:00
Abhinav Bhatele
23f89ccc0b ROSS package: fix build error and add v7.0.0 (#9128) 2018-08-29 13:13:50 -04:00
Andreas Baumbach
5aded248a5 spack view suggests -I option for merge conflict (#9035) 2018-08-29 13:10:55 -04:00
Andrew Gaspar
ebf21d1d87 Adds a package for optional-lite header-only library (#9117) 2018-08-29 18:14:59 +02:00
Christoph Junghans
5de47da740
flecsi: fix build (#9129) 2018-08-29 09:23:02 -06:00
Andrew Gaspar
f540b2ca1b Adds a package for span-lite header-only library (#9118) 2018-08-29 11:01:35 +02:00
Geoffrey Oxberry
eeaa924a6f hdf5@1.10.3: new version (#9121) 2018-08-29 10:58:24 +02:00
Geoffrey Oxberry
c7a8b47e74 ipopt@3.12.10: new version (#9120) 2018-08-29 10:58:05 +02:00
Massimiliano Culpo
cf807f6fd1
New package: channelflow (#9111) 2018-08-29 10:54:34 +02:00
Douglas Duckworth
1a7e9e58d0 added star 2.6.1a (#9103) 2018-08-29 07:34:04 +02:00
Michael Kuhn
3d7457edde go: Update to 1.11 (#9101) 2018-08-29 07:00:40 +02:00
Andrew Gaspar
168c6d9428 Add string-view-lite package for header only library (#9125) 2018-08-29 06:54:20 +02:00
Christoph Junghans
cefc1069e6 gasnet:version bump (#9127) 2018-08-29 06:48:52 +02:00