Commit graph

8444 commits

Author SHA1 Message Date
lingnanyuan
384b8f43a2 r-rmarkdown: Update version to 1.7 (#6506)
* r-rmarkdown: Update version to 1.7

* r-rmarkdown: add version constraints.
2018-01-10 23:12:35 -06:00
Massimiliano Culpo
a4c4739626 Travis: upload the coverage data as part of the script (#6877)
According to Travis docs the exit code of after_success doesn't affect
the build result. Instead, uploading the coverage data as the last step
of the script will cause the job to fail if the command exits with
non-zero.

https://docs.travis-ci.com/user/customizing-the-build/#Breaking-the-Build
2018-01-10 20:41:19 -06:00
snehring
d07b83237d discovardenovo: adding new package (#6888) 2018-01-10 20:40:41 -06:00
Adam J. Stewart
d7920ab4f3
Keep track of source and versions for external libraries (#6803)
* Keep track of source and versions for external libraries

* Note source of more obscure libraries

* We aren't upgrading jsonschema after all

* Add note on modifications made to pytest
2018-01-10 19:14:19 -06:00
Adam J. Stewart
57c71aea89
Update to pytest 3.2.5 (#6801)
* Update to pytest 3.2.5

* Get pytest to pass Python 2.6 compatibility checks
2018-01-10 17:41:50 -06:00
Adam J. Stewart
10ee7d6d81
Add suggestion to Contribution Guide to activate flake8 (#6886) 2018-01-10 13:02:33 -06:00
jkelling
da01c8a541 package libharu: Add build deps (#6883)
... libtool,autoconf,automake
2018-01-10 12:28:32 -06:00
stefanosoffia
8a7525064d Updated i3 dependencies. (#6885) 2018-01-10 11:02:07 -06:00
Massimiliano Culpo
596d463714 Travis: use --concurrency=multiprocessing only on build tests (#6872)
On a local workstation, it seems that tracking multiple processes during
coverage may result in malformed coverage reports for unit tests and not
for build tests.

Given that multiple processes make a difference in coverage mainly for
build tests, try to disable the tracking for unit tests to see if we get
more stable coverage results.
2018-01-10 10:14:17 -06:00
Adam J. Stewart
d17a10c6ac
Update to the latest version of jinja2 (#6790) 2018-01-10 10:06:04 -06:00
Adam J. Stewart
4fdf08e51c
Update to py 1.4.34 (#6789)
* Update to the latest version of py

* Revert back to py 1.4.34
2018-01-10 10:05:39 -06:00
Adam J. Stewart
e4c0ed8540
Add unit tests for spack versions command (#6774)
* Add unit tests for spack versions command

* Fix bug in web spidering for Python 2.6
2018-01-10 10:04:47 -06:00
Adam J. Stewart
2f0dd02c10
Update to the latest version of six (#6787) 2018-01-10 10:04:07 -06:00
Adam J. Stewart
cab34d7d3b
Fix bug in placeholder spack cd command and add unit tests (#6776) 2018-01-10 10:03:45 -06:00
Adam J. Stewart
db42d080f7
Geant4: fix qt dependency (#6828) 2018-01-10 09:48:15 -06:00
Adam J. Stewart
ab4e20a49c
Older versions of libiconv don't work with newer versions of GCC (#6829) 2018-01-10 09:47:33 -06:00
Levi Baber
c1117f0593 opa-psm2: new package (#6874)
* opa-psm2: new package

* opa-psm2: installs now. think the module file needs work

* opa-psm2: module file seems good now

* opa-psm2: remove fixme

* opa-psm2: flake8 fixes

* opa-psm2: removing unnecessary make in install phase
2018-01-10 09:45:34 -06:00
健美猫
b733ce1e5f bcftools is a AutotoolsPackage. (#6881) 2018-01-10 09:45:05 -06:00
Geoffrey Oxberry
77a29f09f9 emacs: on darwin, do not build Cocoa app (#6882)
Building emacs on darwin throws an error when trying to build an Emacs
app in the nextstep/Emacs.app path of the build tree. For now, disable
building this app.

It's possible to enable building the app also; Homebrew offers options
to this effect, and also adds Mac-specific options for starting the
emacs daemon. However, for the sake of simplicity and getting a
workable up-to-date emacs installation on my machine as quickly as
possible, this commit focuses on a minimal viable modification.
2018-01-10 09:44:35 -06:00
健美猫
ac5b5724c6 Add a new package: unblur. (#6867)
* Add a new package: unblur.

* Add a new package: unblur.

* Add a new package: unblur.

* Add a new package: unblur.

Conflicts:
	var/spack/repos/builtin/packages/unblur/package.py

* Add a new package: unblur.
2018-01-10 09:35:00 -06:00
Adam J. Stewart
ba84630caf Add unit tests for spack arch command (#6775) 2018-01-10 13:53:55 +01:00
Adam J. Stewart
f7bf73a458 Add unit tests for spack graph command (#6778) 2018-01-10 13:52:34 +01:00
Adam J. Stewart
5f6df40f3b Fix bash tab completion for spack install (#6868) 2018-01-10 13:51:04 +01:00
Adam J. Stewart
824e078140 Fix a typo in fetch_strategy error message formatting (#6878) 2018-01-10 13:49:16 +01:00
Adam J. Stewart
8555947e05 Explicitly cast Version to str in openfoam-org (#6880) 2018-01-10 13:48:22 +01:00
Adam J. Stewart
4d4fc8760d Fix tests for git package (#6869) 2018-01-10 13:47:38 +01:00
Yifan Zhu
f498f52a2d casper: new package (#6873)
* casper: create package

* jellyfish: added version 2.2.7

* casper: new package

* casper: depends on jellyfish 2.2.3 or higher

* casper: moved depends_on above install

* casper: updated package.py

* fixing download url for 1.11.1

* casper: set up environment

* casper: add conflicts gcc@7.1.0, cannot install with 7.1.0

* capser: flake8 error corrcted

* casper: create package

* jellyfish: added version 2.2.7

* casper: new package

* casper: depends on jellyfish 2.2.3 or higher

* casper: moved depends_on above install

* casper: updated package.py

* fixing download url for 1.11.1

* casper: set up environment

* casper: add conflicts gcc@7.1.0, cannot install with 7.1.0

* capser: flake8 error corrcted
2018-01-09 22:07:05 -06:00
Eric
15111177a2 prodigal: Create new package (#6870) 2018-01-09 12:57:58 -06:00
健美猫
2dd0749b5f A new package: jbigkit. (#6847)
* A new package: jbigkit.

* A new package: jbigkit.

* Add a new package: jbigkit.
2018-01-09 10:03:31 -06:00
BenBrands
9ef39163d8 changed url for astyle (#6863)
* changed url for astyle

* use SourceForge
2018-01-09 09:40:27 -06:00
George Hartzell
ffa20d2171 [WIP] Fix git gettext/libintl handling (builds on ubuntu) (#6859)
* Fix git on ubuntu, first cut

Spack needs to pass information about where the linker
can find `libintl`.  We're currently using `LDFLAGS` to do so.
The `LDFLAGS` info is pasted into the command line upstream
of the a file (`libgit.a`) that includes unresolved symbols that
need that library.  This fails on Ubuntu, although it seems to
work on CentOS (see #6841).

This change allows git to build on a Ubuntu 16.04.3 droplet.

TODO: test on other platforms...

* Add a bit of useful commentary
2018-01-09 09:40:09 -06:00
Federico Ficarelli
43f98dc0d5 Fix missing dependency in ghostscript (#6866) 2018-01-09 08:43:53 -06:00
Adam J. Stewart
eb42013727 Remove std_cmake_args from VTK definition (#6856) 2018-01-09 08:56:00 +01:00
Eric
697f1061c5 perl-xml-simple: Create new package (#6849)
* perl-xml-simple: Create new package

* perl-xml-simple: fix homepage url
2018-01-08 19:36:04 -06:00
Eric
785389be58 perl-digest-md5: Create new package (#6852) 2018-01-08 19:35:48 -06:00
Eric
c99ad2b4a5 barrnap: Create new package (#6855) 2018-01-08 19:35:31 -06:00
Eric
e72c5ee8a3 perl-swissknife: Create new package (#6851) 2018-01-08 18:46:51 -06:00
Eric
6cf530f28d perl-time-piece: Create new package (#6853) 2018-01-08 18:46:16 -06:00
Eric
8935a0b90b perl-text-unidecode: Create new package (#6854) 2018-01-08 18:45:58 -06:00
Axel Huebl
257d23581c Cleanup: Remove Dbl Brackets (#6848)
Remove unnecessary double brackets in ADIOS2 and gearshifft packages.
2018-01-08 19:42:51 +01:00
Bryce Allen
747dbcb82b fix swift-t packages dependencies (#6530) 2018-01-08 17:25:15 +01:00
Kelly (KT) Thompson
eb66aca9ae Upgrade recipe for parmetis to be a CMakePackage (#6807)
* Upgrade recipe for parmetis to be a CMakePackage

+ Eliminate `install` method (use the one from CMakePackage).
+ Move configure options to new method `cmake_args`
+ Move special install instructions for DarwinOS to a `run_after` method.

* Fix run_after section; Remove variant +debug.
2018-01-08 09:18:42 -06:00
Axel Huebl
298f5562c9 Rmlab: Control PNG (#6846)
Control the find_package of the PNG variant explicitly.
This avoids picking up an "external" PNGwriter install in
case `~png` is picked by changing the default "AUTO" search
to explicit "ON" (required) of "OFF" (ignore if exists).
2018-01-08 09:14:38 -06:00
Adam J. Stewart
ffd435bad7 Add documentation on Codecov (#6842) 2018-01-07 08:28:56 -08:00
Michael Kuron
38fabce2aa Siesta: only apply patch to <4.1 and fix Intel compiler (#6466)
* Siesta: add 3.2 and don't apply patch to 4.1

* siesta: fix bad optimization with Intel compiler

* siesta: Fix download URL

* siesta: build utilities too

* siesta: fix binary name collision

* siesta: Cleanup
2018-01-06 12:03:54 -06:00
Milton Woods
ce0c77c991 Blitz 1.0.1 (#6765)
* blitz: update to version 1.0.1

* blitz: change URL for release tarballs

* blitz: update checksum of @1.0.0 after changing URL
2018-01-06 12:02:41 -06:00
Milton Woods
3c43a2d79c py-psyclone: Parallelisation System for climate models (#6797)
* py-psyclone: Code generation for the PSyKAl framework from the GungHo project

* py-psyclone: add installation tests based on py.test

* py-psyclone: define 'develop' version as latest master branch

* py-psyclone: extract tagged version 1.5.1 from git repo

* py-psyclone: whitespace adjustments for flake8

* py-psyclone: use compatible versions of py-fparser

* py-psyclone: use type='test' for selected dependencies
2018-01-06 12:02:13 -06:00
Jon Rood
8813b3fbd3 Updating OpenFAST to use explicit lapack and blas libraries from Spack. (#6824)
* Updating OpenFAST to use explicit lapack and blas libraries from Spack.

* Simplifying openfast blas lib logic and fixes flake8 errors.

* Changing order of blas and lapack libs in openfast package.
2018-01-06 12:01:06 -06:00
Eric
4cd9bdedd7 sailfish: Create new package (#6827)
* sailfish: Create new package

* sailfish: fix tbb dependency

* sailfish: fix dependency type
2018-01-05 15:08:45 -06:00
Eric
ea6ebedd0e py-pybedtools: Create new package (#6487)
* py-pybedtools: Create new package

* py-pybedtools: add py-six requirement

* py-pybedtools: remove py-cython dependency for release version

* py-pybedtools: include minimum version of py-pysam
2018-01-05 15:08:22 -06:00