Douglas Duckworth
47b15feec3
added new package - MotionCor2 ( #6151 )
2017-11-06 11:09:46 -07:00
Denis Davydov
f538b7ac3e
dealii: make sure bundled libs are not used ( #6106 )
2017-11-06 12:38:59 +01:00
Besnard Jean-Baptiste
84c6fea32e
Graphviz : Add a GTS variant ( #6149 )
...
Enable support for the GNU Triangulated Surface Library
- New variant +gts for graphviz
- Optionnal dependency for GTS (already packaged)
2017-11-05 16:55:44 -08:00
Douglas Duckworth
ccc51cea7d
added relion v 2.1 ( #6023 )
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* added relion v 2.1
* relion 2.1 - misssed comma
* relion now pulling from master branch - removed 2.03 - added cuda 8 as dependency given 9 does not yet work with relion per https://github.com/3dem/relion/issues/296
2017-11-05 15:01:21 -08:00
Ben Boeckel
22df09315f
Re-add list_url for all R packages ( #6110 )
...
* r-igraph: find old packages in the archive
Fixes #6104 .
* r-irlba: find old packages in the archive
Fixes #6101 .
* r-lazyeval: find old packages in the archive
Fixes #6102 .
* packages: set list_url for all packages hosted on CRAN
* packages: consistently use the CRAN archive URLs
2017-11-05 13:42:24 -08:00
Adam Moody
2a8c97d440
dtcmp: add v1.1.0 ( #6146 )
2017-11-05 09:25:03 -08:00
Satish Balay
d34d0d6cbc
petsc: update to version 3.8.1 ( #6150 )
...
* petsc: update to version 3.8.1
* petsc: add in conflict between petsc-3.8.0 & mkl
2017-11-05 09:24:42 -08:00
Axel Huebl
5d9dd24daa
ISAAC 1.3.3 ( #6152 )
...
Add a new release of ISAAC.
2017-11-05 09:24:18 -08:00
Todd Gamblin
05fa302655
Replace github.com/llnl/spack with github.com/spack/spack ( #6142 )
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We moved to a new GitHub org! Now make the code and docs reflect that.
2017-11-04 17:08:04 -07:00
vishalkenchan
386e0af089
add rol variant ( #6105 )
2017-11-04 12:14:46 -07:00
Yifan Zhu
9d234c4f8e
r-yapsa: created new package ( #6121 )
2017-11-03 14:21:00 -06:00
Yifan Zhu
fb1160d052
r-keggrest: created new package ( #6120 )
2017-11-03 14:20:36 -06:00
lingnanyuan
3921948b03
r-statmod: Create new package. ( #6119 )
2017-11-03 14:20:14 -06:00
lingnanyuan
b204c7e793
r-deseq: Create new package. ( #6118 )
2017-11-03 14:19:38 -06:00
lingnanyuan
f91c25ddee
r-samr: Create new package. ( #6117 )
2017-11-03 14:19:16 -06:00
lingnanyuan
d54627659a
r-impute: Create new package. ( #6116 )
2017-11-03 14:18:46 -06:00
lingnanyuan
95e290eaf3
r-altcdfenvs: Create new package. ( #6115 )
2017-11-03 14:18:17 -06:00
lingnanyuan
64689bdb01
r-makecdfenv: Create new package. ( #6114 )
2017-11-03 14:17:58 -06:00
lingnanyuan
b614c7970b
r-hypergraph: Create new package. ( #6113 )
2017-11-03 14:17:36 -06:00
Johann Klähn
3fc8a71afb
Fix restaging of resources ( #5681 )
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Part of the resource staging process is to place downloaded/expanded
files in the root stage. This was not happening when a resource stage
was restaged.
2017-11-03 11:29:43 -07:00
Todd Gamblin
12f0725e9f
spack fetch: don't fetch externals. ( #6124 )
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Fixes #6123
spack fetch shouldn't attempt to fetch external deps when invoked
with --dependencies.
2017-11-03 10:15:15 -07:00
Axel Huebl
5a4544ab05
ISAAC 1.3.2 ( #6129 )
...
Add a new release of ISAAC.
2017-11-03 14:58:38 +01:00
Michael Kuhn
bd7d61325f
Configure user for mock Git repository ( #6128 )
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If user.useConfigOnly is set globally and no name or e-mail is
configured, the git_fetch tests fail.
2017-11-02 21:43:28 -07:00
Ben Boeckel
0f896e921f
test_activations: also test perl activations
2017-11-02 18:45:40 -07:00
Peter Scheibel
3a2a0c9ad4
test_activations: test Python's extension logic
2017-11-02 18:45:40 -07:00
Peter Scheibel
dde93c01cf
spec: support a test prefix
...
This is used in tests to test real packages without actually building
and installing them.
2017-11-02 18:45:40 -07:00
Ben Boeckel
be01b2d5f0
aspell: refuse to work with non-global extensions
...
Aspell compiles in the paths it looks for rather than looking relative
to its binary location. There are also no environment variables to
redirect it other than changing the path to the configuration file it
looks at.
2017-11-02 18:45:40 -07:00
Ben Boeckel
a81485cb3f
perl: support extensions in views
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
643a28aac5
python: extensions support for easy-install.pth
2017-11-02 18:45:40 -07:00
Ben Boeckel
d5a3d9d20e
view: test conflicting packages in views
2017-11-02 18:45:40 -07:00
Ben Boeckel
13b669de8e
view: test that extension paths exist
2017-11-02 18:45:40 -07:00
Ben Boeckel
a06c6b0366
filesystem_view: reject packages with activations
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If there are extensions that are globally activated, reject adding them
to a view. Those extensions should not be implicitly activated.
2017-11-02 18:45:40 -07:00
Ben Boeckel
26724688b1
view: test viewing external packages
2017-11-02 18:45:40 -07:00
Ben Boeckel
ea62347c46
view: add a test for extension activation
2017-11-02 18:45:40 -07:00
Ben Boeckel
41dfba0ba1
extension1: add a second version
2017-11-02 18:45:40 -07:00
Ben Boeckel
4511d9d924
extensions: support only showing a subset of information
2017-11-02 18:45:40 -07:00
Ben Boeckel
b7ec870c3b
extensions: support acting on a view
...
This allows extensions to be (de)activated and queried within a view
rather than only acting on the global installation.
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
db529f5b61
view: use the FilesystemView abstraction for creating views
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
af42c24ef5
view: fix some docstrings for arguments
2017-11-02 18:45:40 -07:00
Ben Boeckel
9a39efd966
filesystem_view: do not link external packages
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
538d855e1b
filesystem_view: add a class to handle a view via a Yaml description
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
21dc31a4a1
package: support removing dependencies when deactivating
2017-11-02 18:45:40 -07:00
Ben Boeckel
f50ddeed9f
conftest: mock out spack.store.extensions as well
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
078f85a125
views: support querying view layouts as well
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This abstracts out the layout in use between the global installations
and a specific view.
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
00a893aa79
link_tree: support choosing the link function
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This can be used to make hardlinks rather than symlinks.
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
9024ddcf05
link_tree: support ignoring conflicts
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
20cd82dc56
directory_layout: add a YamlExtensionsLayout class
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This uses a view to query extensions.
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
94c0740a88
link_tree: only remove matching files when unmerging
2017-11-02 18:45:40 -07:00
Oliver Breitwieser
b9e8402104
directory_layout: factor out an ExtensionsLayout class
2017-11-02 18:45:40 -07:00
Ben Boeckel
650ca7db9e
extensions: add an installed_extensions_for method
2017-11-02 18:45:40 -07:00
