summaryrefslogtreecommitdiff
AgeCommit message (Collapse)AuthorFilesLines
2017-10-02patch: add workdir option (#5501)Christoph Junghans3-11/+46
* patch: add working_dir option * added documentation
2017-10-02mrtrix3: new package (#5568)Audrey Thoma1-0/+62
* mrtrix3: new package * specifying conflict dependency ve
2017-10-02r-a4reporting: new package. (#5575)lingnanyuan1-0/+37
2017-10-02r-locfit: created new package (#5572)Yifan Zhu1-0/+37
2017-10-02Added support for BML+mpi variant (#5563)Robert Pavel1-1/+14
* Added support for BML+mpi variant Added support for BML+mpi variant. Currently restricted to master (develop) branch pending release of next bml tag * Update package.py Removing redundant statement * Update package.py Added explicit disabling of MPI when not requested
2017-10-02Added Spackage for YAJL (#5566)Robert Pavel1-0/+35
Added spackage for YAJL
2017-10-02linkphase3: new package (#5493)Audrey Thoma1-0/+41
* linkphase3: new package * adding ifort option * Update package.py
2017-10-02hisat2: new package (#5488)Audrey Thoma1-0/+63
2017-10-02CUDA 9.0.176 (#5562)Axel Huebl1-0/+2
The first stable release of CUDA 9, v9.0.176, is out. This adds its installer and checksum.
2017-09-30Port CTest's log scraping logic to Spack (#5561)Todd Gamblin4-62/+387
- This steals the magic regular expressions that CTest uses to parse log files and addds them to Spack. See here: https://github.com/Kitware/CMake/blob/master/Source/CTest/cmCTestBuildHandler.cxx These are BSD licensed, so the port is in `externa/ctest_log_parser.py` - We currently use these to do better filtering of errors from build output. Plan is to use them to generate good CDash output.
2017-09-30Add testing for spack blame; refactor llnl.util testsTodd Gamblin7-23/+106
2017-09-30Add 'spack blame' command: shows contributors to packagesTodd Gamblin6-25/+280
`spack blame` prints out the contributors to a package. By modification time: ``` $ spack blame --time llvm LAST_COMMIT LINES % AUTHOR EMAIL 3 days ago 2 0.6 Andrey Prokopenko <andrey.prok@gmail.com> 3 weeks ago 125 34.7 Massimiliano Culpo <massimiliano.culpo@epfl.ch> 3 weeks ago 3 0.8 Peter Scheibel <scheibel1@llnl.gov> 2 months ago 21 5.8 Adam J. Stewart <ajstewart426@gmail.com> 2 months ago 1 0.3 Gregory Becker <becker33@llnl.gov> 3 months ago 116 32.2 Todd Gamblin <tgamblin@llnl.gov> 5 months ago 2 0.6 Jimmy Tang <jcftang@gmail.com> 5 months ago 6 1.7 Jean-Paul Pelteret <jppelteret@gmail.com> 7 months ago 65 18.1 Tom Scogland <tscogland@llnl.gov> 11 months ago 13 3.6 Kelly (KT) Thompson <kgt@lanl.gov> a year ago 1 0.3 Scott Pakin <pakin@lanl.gov> a year ago 3 0.8 Erik Schnetter <schnetter@gmail.com> 3 years ago 2 0.6 David Beckingsale <davidbeckingsale@gmail.com> 3 days ago 360 100.0 ``` Or by percent contribution: ``` $ spack blame --percent llvm LAST_COMMIT LINES % AUTHOR EMAIL 3 weeks ago 125 34.7 Massimiliano Culpo <massimiliano.culpo@epfl.ch> 3 months ago 116 32.2 Todd Gamblin <tgamblin@llnl.gov> 7 months ago 65 18.1 Tom Scogland <tscogland@llnl.gov> 2 months ago 21 5.8 Adam J. Stewart <ajstewart426@gmail.com> 11 months ago 13 3.6 Kelly (KT) Thompson <kgt@lanl.gov> 5 months ago 6 1.7 Jean-Paul Pelteret <jppelteret@gmail.com> 3 weeks ago 3 0.8 Peter Scheibel <scheibel1@llnl.gov> a year ago 3 0.8 Erik Schnetter <schnetter@gmail.com> 3 years ago 2 0.6 David Beckingsale <davidbeckingsale@gmail.com> 3 days ago 2 0.6 Andrey Prokopenko <andrey.prok@gmail.com> 5 months ago 2 0.6 Jimmy Tang <jcftang@gmail.com> 2 months ago 1 0.3 Gregory Becker <becker33@llnl.gov> a year ago 1 0.3 Scott Pakin <pakin@lanl.gov> 3 days ago 360 100.0 ```
2017-09-30Typo: file -> directory (#5560)George Hartzell1-1/+1
Mirrors are directories (that use `file://` URLS, not files.
2017-09-30Documentation for dependency patching.Todd Gamblin3-23/+189
2017-09-30Patches are hashed with specs, and can be associated with dependencies.Todd Gamblin26-197/+754
- A package can depend on a special patched version of its dependencies. - The `Spec` YAML (and therefore the hash) now includes the sha256 of the patch in the `Spec` YAML, which changes its hash. - The special patched version will be built separately from a "vanilla" version of the same package. - This allows packages to maintain patches on their dependencies without affecting either the dependency package or its dependents. This could previously be accomplished with special variants, but having to add variants means the hash of the dependency changes frequently when it really doesn't need to. This commit allows the hash to change *just* for dependencies that need patches. - Patching dependencies shouldn't be the common case, but some packages (qmcpack, hpctoolkit, openspeedshop) do this kind of thing and it makes the code structure mirror maintenance responsibilities. - Note that this commit means that adding or changing a patch on a package will change its hash. This is probably what *should* happen, but we haven't done it so far. - Only applies to `patch()` directives; `package.py` files (and their `patch()` functions) are not hashed, but we'd like to do that in the future. - The interface looks like this: `depends_on()` can optionally take a patch directive or a list of them: depends_on(<spec>, patches=patch(..., when=<cond>), when=<cond>) # or depends_on(<spec>, patches=[patch(..., when=<cond>), patch(..., when=<cond>)], when=<cond>) - Previously, the `patch()` directive only took an `md5` parameter. Now it only takes a `sha256` parameter. We restrict this because we want to be consistent about which hash is used in the `Spec`. - A side effect of hashing patches is that *compressed* patches fetched from URLs now need *two* checksums: one for the downloaded archive and one for the content of the patch itself. Patches fetched uncompressed only need a checksum for the patch. Rationale: - we include the content of the *patch* in the spec hash, as that is the checksum we can do consistently for patches included in Spack's source and patches fetched remotely, both compressed and uncompressed. - we *still* need the patch of the downloaded archive, because we want to verify the download *before* handing it off to tar, unzip, or another decompressor. Not doing so is a security risk and leaves users exposed to any arbitrary code execution vulnerabilities in compression tools.
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
generated by cgit v1.2.3-70-g09d2 (git 2.46.0) at 2024-09-13 18:25:39 +0000