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2017-09-30add spack flake8 exception for long checksumsTodd Gamblin1-2/+2
2017-09-30Clean up exceptions and function names in directives.Todd Gamblin1-41/+23
- Functions returned by directives were all called `_execute`, which made reading stack traces hard because you couldn't tell what directive a frame came from. - renamed them all to `_execute_<directive>` - Exceptions in directives were only really used in one or two places -- get rid of the boilerplate init functions and let the callsite specify the message.
2017-09-30Consolidate some web-spidering commands in spack.util.webTodd Gamblin6-116/+118
- move `spack.cmd.checksum.get_checksums` to `spack.util.web.spider_checksums` - move `spack.error.NoNetworkError` to `spack.util.web.NoNetworkError` since it is only used there.
2017-09-30Disable duplicate cross-reference warnings in Sphinx.Todd Gamblin1-0/+14
2017-09-30Refactor Package dependency metadataTodd Gamblin14-123/+217
- Previously, dependencies and dependency_types were stored as separate dicts on Package. - This means a package can only depend on another in one specific way, which is usually but not always true. - Prior code unioned dependency types statically across dependencies on the same package. - New code stores dependency relationships as their own object, with a spec constraint and a set of dependency types per relationship. - Dependency types are now more precise - There is now room to add more information to dependency relationships. - New Dependency class lives in dependency.py, along with deptype definitions that used to live in spack.spec. Move deptype definitions to spack.dependency
2017-09-30Patch.apply() shouldn't affect working directory of caller.Todd Gamblin1-11/+12
2017-09-30Only print "no patches needed" if there were no patches.Todd Gamblin1-1/+5
2017-09-29Add test deptype (#5132)scheibelp10-13/+182
* Add '--test=all' and '--test=root' options to test either the root or the root and all dependencies. * add a test dependency type that is only used when --test is enabled. * test dependencies are not added to the spec, but they are provided in the test environment.
2017-09-29r-limma: added version 3.32.7 (#5558)Yifan Zhu1-0/+2
2017-09-29Masa requires python if +python. (#5547)Jon Rood1-0/+1
2017-09-29r-a4classif: new package. (#5557)lingnanyuan1-0/+43
2017-09-29r-yaml: Correct url (#5550)lingnanyuan1-1/+1
* pr-quantities: add version & py-numpy conflict (#5307) * r-yaml: Correct url.
2017-09-29r-downloader: created new package (#5556)Yifan Zhu1-0/+42
2017-09-29r-mlinterfaces: new package. (#5555)lingnanyuan1-0/+51
* pr-quantities: add version & py-numpy conflict (#5307) * r-mlinterfaces: Create new package.
2017-09-29r-biomart: created new package (#5554)Yifan Zhu1-0/+49
2017-09-29r-threejs: Correct url. (#5553)lingnanyuan1-1/+1
* pr-quantities: add version & py-numpy conflict (#5307) * r-threejs: Correct url.
2017-09-29Adding new Trilinos version and updating Nalu to utilize it. (#5552)Jon Rood2-3/+6
2017-09-29r-hwriter: new package. (#5549)lingnanyuan1-0/+35
* pr-quantities: add version & py-numpy conflict (#5307) * r-hwriter: Create new package.
2017-09-29r-gbm: new package. (#5548)lingnanyuan1-0/+37
* pr-quantities: add version & py-numpy conflict (#5307) * r-gbm: Create new package.
2017-09-29r-htmlwidgets: Update version to 0.8. (#5551)lingnanyuan1-0/+2
2017-09-29r-a4preproc: Create new package. (#5499)lingnanyuan1-0/+36
2017-09-29modules: specialized configure_options for external packages (#5543)Massimiliano Culpo2-2/+20
closes #5473 Prior to this PR we were not exiting early for external packages, which caused the `configure_options` property of the contexts to fail with e.g. a key error because the DAG gets truncated for them. More importantly Spack configure options don't make any sense for externals. Now we exit early, and leave a message in the module file clarifying that this package has been installed outside of Spack.
2017-09-28r-dbi: updated to version 0.7 (#5537)Yifan Zhu1-3/+4
* pr-quantities: add version & py-numpy conflict (#5307) * r-dbi: Create new package. * r-dbi: modified according to flake8 * Update package.py * Update package.py
2017-09-28r-gdata: Update version to 2.18.0 (#5495)lingnanyuan1-1/+3
2017-09-28fixing tag name for development branch (#5496)Mark C. Miller1-1/+1
2017-09-28r-biostrings: created new package (#5498)Yifan Zhu1-0/+41
2017-09-28r-gcrma: created new package (#5500)Yifan Zhu1-0/+42
2017-09-28r-yaqcaffy: created new package (#5538)Yifan Zhu1-0/+38
2017-09-28Add metaphysicl package (#5539)Jon Rood1-0/+38
* Adding package Metaphysicl. * Removing list_url from metaphysical package.
2017-09-28Adding masa package. (#5541)Jon Rood1-0/+65
2017-09-28r-rlang: created new package (#5535)Yifan Zhu1-0/+36
2017-09-28tycho2: initial commit (#5196)Christoph Junghans1-0/+56
2017-09-28Restrict openfoam to using openmpi+thread_multiple (partially resolves ↵Mark Olesen1-0/+4
#5428) (#5479) - latest version requires openmpi+thread_multiple for collated output.
2017-09-28snappy: Build shared library by default (#5534)Michael Kuhn1-0/+14
2017-09-28r-ggvis: Update version to 0.4.3 (#5532)lingnanyuan1-1/+3
* pr-quantities: add version & py-numpy conflict (#5307) * r-ggvis: Update version to 0.4.3 * Update package.py * Update package.py
2017-09-28r-dplyr: Update version to 0.7.3 (#5531)lingnanyuan1-1/+3
* pr-quantities: add version & py-numpy conflict (#5307) * r-dplyr: Update version to 0.7.3 * Update package.py * Update package.py
2017-09-28ncl: Add tcsh dependency (#5195)Michael Kuhn1-0/+19
All ncl scripts hardcode /bin/csh, so fix them up.
2017-09-28tcsh: New package (#5194)Michael Kuhn1-0/+65
The patches are taken from the Fedora package.
2017-09-28r-annaffy: new package. (#5414)lingnanyuan3-0/+116
* r-annaffy: Create New Package. * r-annaffy: Create new package. * r-go-db: Create new package. * r-kegg-db: Create new package. * r-annaffy: Correct indentation. * r-go-db: Correct indentation. * r-kegg-db: Correct format. * r-kegg-db: Correct format. * r-go-db: Correct format. * r-annaffy: Correct format.
2017-09-28fastq-screen: new package (#5431)Audrey Thoma6-0/+228
* fastq-screen: new package * fixing descriptions and previously made packages' old copyright date * added wrong perl package after change
2017-09-28Added hacckernels package (#5533)Brian Homerding1-0/+46
2017-09-28r-r6: Update version to 2.2.2 (#5529)lingnanyuan1-1/+3
* pr-quantities: add version & py-numpy conflict (#5307) * r-r6: Update version to 2.2.2
2017-09-28r-shiny: update version to 1.0.5 (#5530)lingnanyuan1-1/+3
* pr-quantities: add version & py-numpy conflict (#5307) * r-shiny: Update version to 1.0.5
2017-09-28r-htmltools: Update version to 0.3.6 (#5528)lingnanyuan1-1/+3
* pr-quantities: add version & py-numpy conflict (#5307) * r-htmltools: Update version to 0.3.6
2017-09-28r-httpuv: Update version to 1.3.5 (#5527)lingnanyuan1-1/+3
* pr-quantities: add version & py-numpy conflict (#5307) * r-httpuv: Update version to 1.3.5
2017-09-28r-rcpp: Update version to 0.12.13 (#5526)lingnanyuan1-1/+3
* pr-quantities: add version & py-numpy conflict (#5307) * r-rcpp: Update version to 0.12.13 * r-rcpp: Correct url.
2017-09-28Provide a new Perl package 'cloc'. (#5525)Kelly (KT) Thompson1-0/+50
+ Count, or compute differences of, physical lines of source code in the given files (may be archives such as compressed tarballs or zip files) and/or recursively below the given directories.
2017-09-28r-jsonlite: Update version to 1.5 (#5524)lingnanyuan1-1/+3
* pr-quantities: add version & py-numpy conflict (#5307) * r-jsonlite: Update version to 1.5
2017-09-28r-rda: new package. (#5523)lingnanyuan1-0/+35
* pr-quantities: add version & py-numpy conflict (#5307) * r-rda: Create new package.
2017-09-27- build paraview without qt when osmesa is specified. (#5480)Mark Olesen1-0/+4
- new paraview version (5.4.1 from August)
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