Commit graph

8119 commits

Author SHA1 Message Date
becker33
feb4f1b387
separate stdout and stderr for module loading (#6713) 2017-12-21 16:27:52 -08:00
Levi Baber
f2e061debf Feature/fasttree (#6227)
* fasttree: new package

* fasttree: better version handling

* fixing line length for flake8
2017-12-20 19:10:24 -08:00
Patrick Gartung
e5d6f28b4e binary caching: handle files misidentified as needing relocation (#6679)
* Only specify a file as needing relocation if it contains the spack
  root as a text string (this constraint also applies to binaries)
* Don't fail if there is an error retrieving RPATH information from a
  binary (even if it is specified as requiring relocation)
2017-12-20 18:21:41 -08:00
becker33
28d8784ab9 Compiler flag handlers (#6415)
This adds the ability for packages to apply compiler flags in one of
three ways: by injecting them into the compiler wrapper calls (the
default in this PR and previously the only automated choice);
exporting environment variable definitions for variables with
corresponding names (e.g. CPPFLAGS=...); providing them as arguments
to the build system (e.g. configure).

When applying compiler flags using build system arguments, a package
must implement the 'flags_to_build_system_args" function. This is
provided for CMake and autotools packages, so for packages which
subclass those build systems, they need only update their flag
handler method specify which compiler flags should be specified as
arguments to the build system.

Convenience methods are provided to specify that all flags be applied
in one of the 3 available ways, so a custom implementation is only
required if more than one method of applying compiler flags is
needed.

This also removes redundant build system definitions from tutorial
examples
2017-12-20 15:40:38 -08:00
Mark Olesen
ef2e51571d ENH: better handling of mpich for openfoam packages
- define MPICH_SKIP_MPICXX, link libmpich instead of libmpi
  (as per disussion in PR #4990)

ENH: more flexible editing/patching of openfoam env files

CONFIG: comment out requirement for openmpi+thread_multiple

- was originally slated for the 1712 release and beyond, but there are
  reportedly unstable version/network combinations.
  Leave as comment for future reference, since it may be arise again.

STYLE: renamed openfoam-site.patch as 1706-site.patch (and reformatted)

- to preserve against impending changes in the layout of
  config.{csh,sh}/settings
2017-12-20 11:32:33 -08:00
Mark Olesen
235c3c1025 ENH: improved openfoam module creation (issue #4942)
- post-install module settings for openfoam-com and foam-extend.
2017-12-20 11:32:33 -08:00
Eric
6ea4614dbd picard: Add version 2.17.0 (#6729) 2017-12-20 13:28:37 +01:00
Denis Davydov
ea5f8c7382 octave: add optim and struct packages (#6733) 2017-12-20 13:27:50 +01:00
Gregory Lee
241ea77229 sqlite package: apply B0 patch to additional versions (#6728) 2017-12-19 11:06:39 -08:00
Denis Davydov
0ef741d291 slepc: add 3.8.2 (#6724) 2017-12-19 15:40:30 +01:00
Denis Davydov
e462d39afe intel-tbb: add 2018.2 (#6725) 2017-12-19 15:39:42 +01:00
Denis Davydov
98f220b304 hypre: add 2.13.0 (#6726) 2017-12-19 15:39:27 +01:00
Denis Davydov
599094abbd suite-sparse: add 5.1.0 (#6727) 2017-12-19 15:39:12 +01:00
Jack Morrison
720ad57bcd Added GDB verison 8.0 (#6704) 2017-12-19 09:54:18 +01:00
peetsv
d0a10edb67 nextflow: adding version 0.21.0 (#6722) 2017-12-19 09:07:33 +01:00
Peter Doak
d4c84be91b Emacs: added gnutls variant (tested on Centos 7) (#6711) 2017-12-19 08:36:54 +01:00
Denis Davydov
69f959ec0b gmsh: add 3.0.6 (#6718) 2017-12-19 08:31:23 +01:00
junkudo
d69d692203 CoinHSL : Prevent CoinHSL from building in parallel (#6715)
CoinHSL does not seem to be able to be built in parallel. This commit forces serial compilation.
2017-12-19 08:30:39 +01:00
Denis Davydov
548c225d45 dealii: add GMSH, add CMAKE_FIND_APPBUNDLE to CMakePackage (#6723)
* dealii: add GMSH dependency

* CMakePackage: add CMAKE_FIND_APPBUNDLE to prevent picking up binaries from /Applications
2017-12-19 08:28:55 +01:00
peetsv
e8de22ce46 lftp: adding version 4.6.4 (#6721) 2017-12-19 08:19:33 +01:00
Mark Olesen
b3e9192d18 openfoam-org: new version (#6686)
Add new version with a patch.
2017-12-18 19:47:49 -08:00
peetsv
f7a5a27138 IGV: new package (#6710) 2017-12-18 19:37:09 -08:00
Massimiliano Culpo
0192455885 spack install: make restaging the default (#6465)
Fixes #5940

This PR changes the option '--restage' of 'spack install' to
'--dont-restage', inverting its meaning and the default behavior
of the command.
2017-12-18 18:50:02 -08:00
Benedikt Riedel
36fa574779 globus-toolkit: add version and openssl dependency (#6617) 2017-12-18 15:23:56 -08:00
Douglas Duckworth
d3519af7de relion - added new stable version 2.1 (#6706) 2017-12-18 10:38:20 -08:00
healther
0cff0fba73 fix post install method for py3 in mercurial (#6497)
* fix post install method for py3 in mercurial

* Update package.py

* Update package.py

* use print_str instead of manual print detection

* Update package.py

* use only depends_on

* Update package.py

* Update package.py

State py3 compatibility for @4.3: according to setup.py from the 4.3.tar.gz from pypi
2017-12-17 12:00:58 -06:00
Sergey Kosukhin
576ef5e2b3 Package 'cdo': get rid of unnecessary dependency on MPI C++ library. (#6632) 2017-12-16 19:48:56 -07:00
nshtg
2a639097b0 Add new package signify (#6645)
OpenBSD tool to sign and verify signatures on files.

See https://github.com/aperezdc/signify
2017-12-16 19:47:59 -07:00
Eric
7d800a0fc2 breseq: Create new package (#6648) 2017-12-16 19:47:11 -07:00
fpruvost
6c81cf1a78 build lapacke with tmg (#6654) 2017-12-16 19:43:46 -07:00
David Orman
7b8d889d31 bwa: added version 0.7.16a and checksum (#6658) 2017-12-16 19:43:02 -07:00
Jack Morrison
d4cc1ac86b Hadoop: Replace broken url (#6671) 2017-12-16 19:42:03 -07:00
David Böhme
3467c207c8 Caliper update, add version 1.6.0 (#6680) 2017-12-16 19:39:52 -07:00
Eric
dac09dd5fb py-bx-python: Create new package (#6672) 2017-12-16 19:38:59 -07:00
Eric
d08dc0c019 py-tetoolkit: Create new package (#6673) 2017-12-16 19:38:36 -07:00
Eric
d3545ed1b3 py-pandas: add versions 0.19.2 and 0.21.1 (#6687) 2017-12-16 19:38:02 -07:00
Paschalis Korosoglou
a69cfd5f78 Add petsc version 3.8.3 (#6688) 2017-12-16 19:37:35 -07:00
Paschalis Korosoglou
61dbd3182d Add clanguage variant for petsc (#6689) 2017-12-16 19:37:20 -07:00
Eric
87420dccee bedtools2: Add version 2.27.1 (#6693) 2017-12-16 19:36:35 -07:00
peetsv
5d0e7abcc5 MetaSV: adding new package (#6691) 2017-12-16 19:36:11 -07:00
Eric
5539c94e67 PANDAseq: Create new package (#6694) 2017-12-16 19:35:48 -07:00
Eric
554d4045fa DeNovoGear: Create new package (#6699) 2017-12-16 19:34:53 -07:00
lingnanyuan
34cf796b54 mefit: Create new package. (#6700) 2017-12-16 19:34:30 -07:00
Denis Davydov
f78418d8bb moltemplate: add new package (#6702) 2017-12-16 19:33:28 -07:00
David Orman
176b518d4b new package: gatk (#6674) 2017-12-15 11:00:55 -08:00
Jon Rood
7369ba21bf new package: Percept (#6636)
This also adds the 'exception' boost library to the set of default
libraries built by boost.
2017-12-14 18:11:47 -08:00
scheibelp
020ce7735d
Skip collection of compilers which report an empty version (#6684)
Fixes #6200

For compilers that successfully run a version detection script but
don't actually return a version, Spack was keeping track of the
empty version and then failing when attempting to construct a
compiler spec. This skips any attempt to add a compiler entry when
no version is reported (but logs when a compiler fails to report
a version).
2017-12-14 17:54:57 -08:00
Douglas Duckworth
1aed3f7c01 added breakdancer (#6319) 2017-12-14 14:43:32 -07:00
Massimiliano Culpo
6c1fa37e3d
fftw: added version 3.3.7 (#6678) 2017-12-14 21:38:33 +01:00
Mark Olesen
5727054c4a misc fixes, changed to EnvironmentModifications (issue #6501) (#6541)
* Support pruning of vars with Env from_sourcing_file (issue #6501)

- Blacklist string literals or regular expressions of environment
  variables that are to be removed from consideration as being affect
  by the sourcing of the file. Conversely, whitelist modifications
  that should not ignored.  Whitelisted variables have priority over
  blacklisting.
  Eg,

      EnvironmentModifications.from_sourcing_file
      (
          bashrc
          blacklist=['JUNK_ENV', 'OPTIONAL_.*'],
          whitelist=['OPTIONAL_REQUIRED.*']
      )

This modification can be used to eliminate environment variables that
are not generalized for modules (eg, user-specific variables).

* BUG: module prepend-path in wrong order (fixes #6501)

* STYLE: module variables in sorted order (issue #6501)

- looks nicer and also helps when comparing the contents of different
  module files.

* ENH: remove duplicates from env paths when creating modules (issue #6501)

- this makes for a cleaner module environment and helps avoid some
  unnecessary changes to the environment that are only provoked by
  redundancies in the PATH.

  eg,
      before PATH=/usr/bin
      after  PATH=/usr/bin:/usr/bin:/my/application/bin

  should only result in /my/application/bin being added to the PATH
  and not /usr/bin:/my/application/bin

Activate via the 'clean' flag (default: False):

    EnvironmentModifications.from_sourcing_file(bashrc, clean=True,..
2017-12-14 21:24:06 +01:00