Commit graph

9085 commits

Author SHA1 Message Date
George Hartzell
9af953a4cb Add info for nextflow@v0.25.6 (#5148) 2017-08-18 09:36:02 -05:00
Stephen McDowell
61238baf56 add man-db package and friends (#4844)
* add man-db package and friends

* fix groff, libpipeline, and man-db dependencies

* remove parallel groff altogether, build-only deps
2017-08-18 14:17:25 +02:00
zenln
6d2092e1eb Add a new package for gaussian (#5149)
* Gaussian: Gaussian install

* Adding Patch to spack installed files

* Adding extra environment variables for gaussian at run time

* Adding provides linda

* Adding linda as a provided package

* Shortning vars and fixing flake8 indentation and spacings
2017-08-17 18:33:44 -05:00
Audrey Thoma
cf796ed595 pagit: new package (#5140)
* pagit: new package

* removed unneeded env var
2017-08-17 15:32:30 -05:00
Audrey Thoma
94af7ccb77 new package libfabric (#5146)
* pbmpi: new package

* forgot about libfabric
2017-08-17 15:31:31 -05:00
Audrey Thoma
cb4ede001c pbmpi: new package (#5144) 2017-08-17 11:59:02 -05:00
Axel Huebl
6472c39c2e Docs: Travis-CI Workflow (#5133)
* Docs: Travis-CI Workflow

Add a workflow how to use spack on Travis-CI.

Future Work:

depending if and how we can simplify 5101:
add a multi-compiler, multi-C++-standard, multi-software
build matrix example

* Fix Typos
2017-08-17 11:25:40 -05:00
Audrey Thoma
46d8cb8913 paml: new package (#5142) 2017-08-17 11:21:56 -05:00
Massimiliano Culpo
0f5582cefc Colorize spack info. Adds prominence to preferred version. (#4994)
* Colorize spack info. Adds prominence to preferred version. fixes #2708

This uses 'llnl.util.tty.color' to colorize the output of 'spack info'.
It also displays versions in the order the concretizer would choose
them and shows the preferred in a line on its own and in bold.

* Modified output according to Adam and Denis reviews.

Section titles are not bold + black, but bold + blue. Added a new
section named "Preferred version", which prints the preferred version
in bold characters.

* Further modifications according to Adam and Denis reviews.

After "Homepage:" we now have a single space. Removed newline after each
variant. Preferred version is not in bold fonts anymore. Added a simple
test that just runs the command.
2017-08-17 09:15:57 -07:00
Audrey Thoma
aa21590099 microbiomeutil: new package (#5134)
* microbiomeutil: new package

* got rid of unnecessary self

* oops
2017-08-17 09:19:00 -05:00
Adam J. Stewart
187f4420e2 Add new package for rhash, a cmake dependency (#5120)
* Add new package for rhash, a cmake dependency

* Add missing libuv dependency to cmake
2017-08-17 08:17:45 -05:00
Audrey Thoma
3bb7767839 py-faststructure: new package (#5131) 2017-08-17 07:49:57 -05:00
healther
d65d1269b9 add libiconv dependency to libxslt (#5138)
this is a fix to an installation that failed due to
configure for some reason not finding the libiconv
shipped with glibc, but still trying to link against it
see http://xmlsoft.org/FAQ.html
2017-08-17 07:18:02 -05:00
Massimiliano Culpo
101693d823 Improved error message for unsatisfiable specs (#5113)
* Improved error message for unsatisfiable specs. fixes #5066

This PR improves the error message for unsatisfiable specs by showing in tree format both the spec that cannot satisfy the constraint and the spec that asked for that constraint. After that follows a readable error message.
2017-08-17 08:26:04 +02:00
Massimiliano Culpo
c16a68f517 Relaxed constraints on config.yaml structure (#5115)
This PR allows additional unused properties at the top-level of the config.yaml file. Having these properties permits to use two different versions of Spack, one of which adds a new property, without receiving error messages due to the presence of this new property in a configuration cache stored in the user's home.
2017-08-17 06:37:09 +02:00
Patrick Gartung
1c8bdd7e24 buildcache fixes: index.html & unsigned installs
This fixes a syntax error in the index.html file generated by the
"spack buildcache" command when creating build caches. This also
fixes support for installing unsigned binaries.
2017-08-16 19:03:14 -07:00
sknigh
dd790fdaae add missing dependencies to elfutils (#5135) 2017-08-16 20:46:12 -05:00
Audrey Thoma
4c32b0ad56 tppred: new package (#5091)
* tppred: new package

* fixed url_for_version

* fixed version spec on dependency

* removing unneeded dependency
2017-08-16 17:48:50 -07:00
Audrey Thoma
d423f85fed dialign-tx: new package (#5126)
* dialign-tx: new package

* utilizing build_directory variable

* forgot one
2017-08-16 17:36:29 -07:00
Audrey Thoma
3a55d45497 discovar: new package (#5129) 2017-08-16 17:35:04 -07:00
Audrey Thoma
6a2cfedc7a gapcloser: new package (#5130) 2017-08-16 17:34:43 -07:00
Adam J. Stewart
af02774b3e Add tab completion & update docs for buildcache
This adds tab completion and fixes some formatting issues in the
documentation for the "spack buildcache" command.
2017-08-16 13:58:09 -07:00
Audrey Thoma
dc3526c7f1 py-misopy: new package (#5119)
* py-misopy: new package

* waiting for link to be fixed

* got correct url and checksum

* specifying dependency version requirements
2017-08-16 14:53:43 -05:00
healther
b547e6a273 Add package rtags (#5111)
* Add package rtags

* fixed license

* transform to cmakepackage and add dependencies

* add dependencies and patch for rtags

* flake8 fix

* clean up dependencies
2017-08-16 13:14:54 -05:00
Cesare Cugnasco
ffaa0b7eee Adding Thrift versions 0.10.0 and 0.9.3 (#5117)
* Adding Thrift version 0.10.0 and 0.9.3

Hi, I've added the versions 0.10.0 and 0.9.3

* fixed  flake8 errors
2017-08-16 13:14:37 -05:00
Audrey Thoma
b12fd4e831 phylip: new package (#5121) 2017-08-16 13:13:38 -05:00
Audrey Thoma
7aa81afa68 preseq: new package (#5122) 2017-08-16 13:13:18 -05:00
Adam J. Stewart
11b3ce27b7 Add better generator support to CMakePackage (#4988)
* Add better generator support to CMakePackage

* List valid CMake generators on error
2017-08-16 12:25:37 -05:00
Adam J. Stewart
db657d938d Refactor IntelInstaller into IntelPackage base class (#4300)
* Refactor IntelInstaller into IntelPackage base class

* Move license attributes from __init__ to class-level

* Flake8 fixes: remove unused imports

* Fix logic that writes the silent.cfg file

* More specific version numbers for Intel MPI

* Rework logic that selects components to install

* Final changes necessary to get intel package working

* Various updates to intel-parallel-studio

* Add latest version of every Intel package

* Add environment variables for Intel packages

* Update env vars for intel package

* Finalize components for intel-parallel-studio package

Adds a +tbb variant to intel-parallel-studio.
The tbb package was renamed to intel-tbb.
Now both intel-tbb and intel-parallel-studio+tbb
provide tbb.

* Overhaul environment variables set by intel-parallel-studio

* Point dependent packages to the correct MPI wrappers

* Never default to intel-parallel-studio

* Gather env vars by sourcing setup scripts

* Use mpiicc instead of mpicc when using Intel compiler

* Undo change to ARCH

* Add changes from intel-mpi to intel-parallel-studio

* Add comment explaining mpicc vs mpiicc

* Prepend env vars containing 'PATH' or separators

* Flake8 fix

* Fix bugs in from_sourcing_file

* Indentation fix

* Prepend, not set if contains separator

* Fix license symlinking broken by changes to intel-parallel-studio

* Use comments instead of docstrings to document attributes

* Flake8 fixes

* Use a set instead of a list to prevent duplicate components

* Fix MKL and MPI library linking directories

* Remove +all variant from intel-parallel-studio

* It is not possible to build with MKL, GCC, and OpenMP at this time

* Found a workaround for locating GCC libraries

* Typos and variable names

* Fix initialization of empty LibraryList
2017-08-16 12:21:07 -05:00
Audrey Thoma
ad8c60239f mpiblast: new package (#5106) 2017-08-16 10:48:39 -05:00
Michael Kuhn
3a0e9f29e6 scorep: Fix build with GCC 7 (#5107) 2017-08-16 10:48:20 -05:00
Michael Kuhn
95915b81d0 otf2: Add 2.1 (#5108) 2017-08-16 10:48:02 -05:00
Adam J. Stewart
2f9b0f6dd6 Fix future import in hdf5-blosc (#5010) 2017-08-16 10:34:52 -05:00
healther
f6a452d3ad Add package rr (#5105)
* Add package rr

* Flake8 fixes

* fix flake8 no2

* add future dependency stub, add hw dependency and clean up

* add missing self
2017-08-16 10:29:02 -05:00
healther
dbdf38f617 Add package PyPytestXdist and dependencies (#5095)
* Add py-pytest-xdist

* fixed licenses

* attempt to fix flake8

* added missing build dependency
2017-08-16 10:26:39 -05:00
healther
480764de5c Add package py-pybind11 (#5096)
* py-pybind11 package was missing

* fixed license file

* attempt to fix flake8

* use python3 compatible python detection
2017-08-16 08:29:54 -05:00
Audrey Thoma
619e298b8d cdhit: new package (#5085) 2017-08-16 07:05:16 +02:00
Gregory Lee
450b19b6e0 fix reference to spec in apex package (#5076)
* fix reference to spec in apex package

* fixed md5 sums for ompt-openmp and apex packages
2017-08-15 17:17:02 -05:00
Brian Van Essen
7b51791625 Openblas clang fix (#5065)
* Added a package for the MDAnalysis toolkit.

* Openblas now builds with clang when using 0.2.20

* Fixed flake8 error

* Added a guard to fail for openblas+openmp when on OSX systems

* Changed the guard to look for Apple's build of clang and to improve
the error messages.

* Removed blank line.
2017-08-15 16:57:11 -05:00
healther
8df9f9e1f4 Fix ffmpeg (add missing yasm dependency) (#5087) 2017-08-15 16:54:39 -05:00
Michael Kuhn
256cd68b27 nco: Add patch to fix invalid conversion from char to char* (#5102)
This patch is needed to be able to build nco with GCC 7.
2017-08-15 16:53:22 -05:00
Michael Kuhn
8d4dec7430 ncview: Fix download URL (#5103) 2017-08-15 16:52:34 -05:00
healther
b52e549758 add version 0.2.10 to py-lazyarray (#5093) 2017-08-15 12:15:00 +02:00
Michael Kuhn
43a634ca80 gcc: Add 7.2.0 (#5098) 2017-08-15 12:14:07 +02:00
Mark C. Miller
5712fbfeb0 Use correct variant syntax to build zfp (#5099)
`h5z-zfp` now  builds zfp with correct bit stream word size; the syntax of the variant declaration did not work in previous versions of spack but does now
2017-08-15 12:10:09 +02:00
healther
b229b739de add older versions to package folly (#5088) 2017-08-15 12:01:33 +02:00
Patrick Gartung
ab56c742ca Create, install and relocate tarballs of installed packages
Adds the "buildcache" command to spack. The buildcache command is
used to create gpg signatures for archives of installed spack
packages; the signatures and archives are placed together in a
directory that can be added to a spack mirror. A user can retrieve
the archives from a mirror and verify their integrity using the
buildcache command. It is often the case that the user's Spack
instance is located in a different path compared to the Spack
instance used to generate the package archive and signature, so
this includes logic to relocate the RPATHs generated by Spack.
2017-08-14 14:32:27 -07:00
Massimiliano Culpo
5184edb15f Added a custom action for --clean and --dirty. (#5081)
The action `CleanOrDirtyAction` has been added. It sets the default
value for `dest` to `spack.dirty`, and changes it according to the flags
passed via command line. Added unit tests to check that the arguments
are parsed correctly. Removed lines in `PackageBase` that were setting
the default value of dirty according to what was in the configuration.
2017-08-14 11:29:18 -07:00
scheibelp
4d9ef49b49 Decode process stream only for python3
Popen.communicate outputs a str object for python2 and a bytes
object for python3. This updates the Executable.__call__ function
to call .decode on the output of Popen.communicate only for python3.
This ensures that Executable.__call__ returns a str for python2 and
python3.
2017-08-14 11:23:03 -07:00
Brian Van Essen
3cce3e3ce4 Opencv update (#5079)
* Added a package for the MDAnalysis toolkit.

* Added version 3.3.0
2017-08-11 23:46:39 -05:00